16416802 16416822 16417005 16417023 16777303 24051999 24052246 24052251 16613377 16449569 24122702 24122703 24122704 24150080 9 2011-03-15 09:42:01.160 2014-01-07 12:52:12.290 16416825 16416830 16417002 16417003 16417021 24052033 24052034 24052272 24052251 16416802 16416802 16613377 24085011 26443795 4 2014-01-03 13:25:40.607 2014-01-07 12:41:18.290 24052252 24052254 24052269 24052246 16416802 16416802 16613377 24085006 26443796 3 2014-01-03 11:20:34.267 2014-01-07 12:42:41.817 24052249 24052271 16678914 2]]> 16678915 DOEMM false global ]]> 16678913 theme.key ]]> 16417005 16416802 16416802 16613377 16449765 3 2011-04-04 09:39:55.810 2011-04-05 17:53:07.663 16417007 16417038 24051999 16416802 16416802 16613377 24084760 31391745 31391746 31391747 31391748 31391749 31391750 31391751 31424513 33 2013-12-20 12:20:37.467 2019-01-16 08:21:29.330 24052001 24052006 24052008 24052010 24052012 24052014 24052016 24052018 24052020 24052022 24052024 24052026 24052028 24052029 24052030 24052032 24052037 24052208 24052210 24052211 24052212 24052230 24052232 24052234 24052236 24052238 24052240 24052242 24052243 24052244 24052245 31326210 16777303 16416802 16416802 16613377 16810070 2 2011-04-26 09:17:06.830 2011-04-26 09:19:00.663 16777304 16973862 16973863 16973864 16973865 16973866 16973867 16973868 16613377 16416801 16416802 16646145 16646146 16646147 16646148 16646149 16646150 16646151 16646152 16646153 16646154 16646155 16646156 16646157 16646158 16646215 19300595 2011-03-15 09:42:01.127 2011-03-15 09:42:01.127 global 16417023 16416802 16416802 16613377 16449783 16516514 8 2011-04-05 13:56:53.087 2011-04-05 14:51:25.410 16417025 16417026 16417028 16417029 16417033 16417034 16417036 16416822 16416802 16416802 16613377 16449588 4 2011-03-15 12:47:20.420 2011-03-15 13:09:47.210 16416823 16416824 16416828 16547847 16547848 16547849 16547850 16547851 16547852 16547853 19300595 16613377 2012-06-18 17:26:46.247 2012-06-18 17:26:46.247 16646146 16613377 2011-03-15 09:42:01.160 2011-03-15 09:42:01.160 16646145 16613377 2011-03-15 09:42:01.157 2011-03-15 09:42:01.157 16646148 16613377 2011-03-15 09:42:01.160 2011-03-15 09:42:01.160 16646147 16613377 2011-03-15 09:42:01.160 2011-03-15 09:42:01.160 16449783 16417023 24122704 16416802 2014-01-07 12:52:12.573 2014-01-07 12:52:12.573 16646157 16613377 2011-03-15 09:42:01.160 2011-03-15 09:42:01.160 16646158 16613377 2011-03-15 09:42:01.160 2011-03-15 09:42:01.160 24122703 16416802 2014-01-07 12:52:12.573 2014-01-07 12:52:12.573 24122702 16416802 2014-01-07 12:52:12.573 2014-01-07 12:52:12.573 16646153 16613377 2011-03-15 09:42:01.160 2011-03-15 09:42:01.160 24052272 24085032 8 2011-03-15 09:42:01.160 2013-12-20 15:13:10.733 16416802 16646154 16613377 2011-03-15 09:42:01.160 2011-03-15 09:42:01.160 24052271 24085031 2 2014-01-03 11:20:34.267 2014-01-03 11:26:20.750 24052246 16646155 16613377 2011-03-15 09:42:01.160 2011-03-15 09:42:01.160 16449765 16417005 16646156 16613377 2011-03-15 09:42:01.160 2011-03-15 09:42:01.160 16646149 16613377 2011-03-15 09:42:01.160 2011-03-15 09:42:01.160 16646150 16613377 2011-03-15 09:42:01.160 2011-03-15 09:42:01.160 16646151 16613377 2011-03-15 09:42:01.160 2011-03-15 09:42:01.160 16646152 16613377 2011-03-15 09:42:01.160 2011-03-15 09:42:01.160 24052269 24085029 3 2014-01-03 13:25:40.607 2014-01-03 15:51:19.650 24052251 16417002 16449762 3 2011-03-15 09:42:01.160 2011-03-15 13:11:57.983 16416802 31424513 1 24051999 2019-01-17 10:53:15.047 2019-01-17 10:53:15.047 24052254 24085014 2 2014-01-03 13:25:40.607 2014-01-03 15:48:05.533 24052251 24052252 24085012 1 2014-01-03 13:25:40.607 2014-01-03 13:25:40.607 24052251 24052245 24085004 31 2013-12-20 12:20:37.467 2013-12-30 21:58:38.140 24051999 24052244 24085003 30 2013-12-20 12:20:37.467 2013-12-30 21:57:46.260 24051999 16810070 16777303 24052243 24085002 29 2013-12-20 12:20:37.467 2013-12-30 21:50:58.763 24051999 24052249 24085009 1 2014-01-03 11:20:34.267 2014-01-03 11:20:34.267 24052246 24052238 24084997 26 2013-12-20 12:20:37.467 2013-12-30 21:33:02.530 24051999 31326210 31358978 32 2013-12-20 12:20:37.467 2013-12-30 22:02:27.617 24051999 24052236 24084995 25 2013-12-20 12:20:37.467 2013-12-30 21:29:22.507 24051999 24052242 24085001 28 2013-12-20 12:20:37.467 2013-12-30 21:49:15.367 24051999 24052240 24084999 27 2013-12-20 12:20:37.467 2013-12-30 21:46:10.183 24051999 24052230 24084989 22 2013-12-20 12:20:37.467 2013-12-30 15:00:27.823 24051999 24052232 24084991 23 2013-12-20 12:20:37.467 2013-12-30 21:19:44.443 24051999 24052234 24084993 24 2013-12-20 12:20:37.467 2013-12-30 21:27:31.443 24051999 16547850 16416822 2011-03-15 12:55:26.660 2011-03-15 12:55:26.660 4847831 1 16547851 16416822 2011-03-15 12:58:01.150 2011-03-15 12:58:01.150 11796506 1 16547852 16416822 2011-03-15 12:59:53.050 2011-03-15 12:59:53.050 696832 1 16547853 16416822 2011-03-15 13:03:14.720 2011-03-15 13:03:14.720 4818754 1 16547847 16416822 2011-03-15 12:55:26.017 2011-03-15 12:55:26.017 2255653 1 16547848 16416822 2011-03-15 12:55:26.123 2011-03-15 12:55:26.123 13677568 1 16547849 16416822 2011-03-15 12:55:26.457 2011-03-15 12:55:26.457 7663104 1 24052212 24084971 21 2013-12-20 12:20:37.467 2013-12-30 14:59:54.777 24051999 24052211 24084970 20 2013-12-20 12:20:37.467 2013-12-30 14:59:17.417 24051999 24052208 24084967 18 2013-12-20 12:20:37.467 2013-12-30 08:26:35.720 24051999 24150080 2 16416802 2014-01-08 15:13:15.023 2014-01-08 15:15:15.020 24052210 24084969 19 2013-12-20 12:20:37.467 2013-12-30 14:10:48.640 24051999 16417036 16449794 7 2011-04-05 13:56:53.087 2011-04-05 14:49:10.843 16417023 16417038 16449796 2 2011-04-04 09:39:55.810 2011-04-04 09:41:20.317 16417005 16973867 16777303 2011-04-26 09:18:16.927 2011-04-26 09:18:16.927 299291 1 16973866 16777303 2011-04-26 09:17:53.380 2011-04-26 09:17:53.380 404033 1 16973868 16777303 2011-04-26 09:18:16.950 2011-04-26 09:18:16.950 2262117 1 16973863 16777303 2011-04-26 09:17:53.280 2011-04-26 09:17:53.280 571294 1 16973862 16777303 2011-04-26 09:17:53.137 2011-04-26 09:17:53.137 698414 1 16973865 16777303 2011-04-26 09:17:53.320 2011-04-26 09:17:53.320 1772813 1 16973864 16777303 2011-04-26 09:17:53.303 2011-04-26 09:17:53.303 225872 1 24084760 ServerName sequenceserver.shore.mbari.org DocumentRoot /usr/local/apache/htdocs AllowOverride All Options FollowSymLinks Indexes MultiViews Order allow,deny Allow from all RailsBaseURI /sequenceserver-dbs RailsBaseURI /sequenceserver-meta RailsBaseURI /dbs RailsBaseURI /meta RailsEnv development {noformat} # Copied sequenceserver gem to additional directories to support multiple databases and symlinks for short names on sequenceserver.shore.mbari.org: {noformat} cd /usr/local/lib/ruby/gems/1.9.1/gems sudo chown mccann . cp -r sequenceserver-0.8.6 sequenceserver-dbs cp -r sequenceserver-0.8.6 sequenceserver-meta ln -s sequenceserver-dbs dbs ln -s sequenceserver-meta meta sudo chown root . sudo chown -R root sequenceserver-dbs sequenceserver-meta {noformat} # Create symlinks in /usr/local/apache/htdocs for web pages to work: {noformat} cd /usr/local/apache/htdocs ln -s /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-dbs/public sequenceserver-dbs ln -s /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-dbs/public dbs ln -s /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-meta/public sequenceserver-meta ln -s /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-meta/public meta {noformat} # Modified /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-dbs/config.ru, adding SequenceServer::App.config_file = ... {noformat} require 'rubygems' require 'bundler/setup' require 'sequenceserver' SequenceServer::App.config_file = '/home/geneadm/conf/sequenceserver-dbs.conf' SequenceServer::App.init run SequenceServer::App {noformat} # Modified /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-meta/config.ru, adding SequenceServer::App.config_file = ... {noformat} require 'rubygems' require 'bundler/setup' require 'sequenceserver' SequenceServer::App.config_file = '/home/geneadm/conf/sequenceserver-meta.conf' SequenceServer::App.init run SequenceServer::App {noformat} See the FAQ on http://www.sequenceserver.com/. We found that the config.ru files need to be owned by root for the servers to work. # Restart httpd and see the sequenceservers at: * http://sequenceserver.shore.mbari.org/dbs * http://sequenceserver.shore.mbari.org/meta h3. UCSC genome-browser - a collection of C cgi-bin programs # As user mccann on nextgen {noformat} sudo yum install mysql sudo yum install mysql-server sudo yum install mysql-devel sudo yum install png-devel sudo /sbin/chkconfig mysql on sudo /sbin/service mysql start {noformat} # Set the mysql root password {noformat} /usr/bin/mysql -u root -p update mysql.user set Password=PASSWORD('xxxx') where User='root'; # See Mike or Rich for the root password {noformat} # As user geneadm on nextgen {noformat} mkdir ~/dev cd ~/dev git clone git://genome-source.cse.ucsc.edu/kent.git cd kent {noformat} # Follow instructions in the README and src/product/README.building.source, briefly: {noformat} export MACHTYPE=x86_64 mkdir -p ~/bin/${MACHTYPE} cd src make libs cd gfServer make cd ../gfClient make cd ../blat make cd ../utils/faToNib make cd ../../hg make cd htdocs make install # Creates web site files in /usr/local/apache {cgi-bin-mccann, htdocs} {noformat} # Setup apache server by creating a /etc/httpd/conf.d/genome-browser.conf file: {noformat} ScriptAlias /cgi-bin/ "/usr/local/apache/cgi-bin-mccann/" ServerName genomebrowser.shore.mbari.org DocumentRoot "/usr/local/apache/htdocs/" Options Includes Indexes FollowSymLinks AllowOverride None Order allow,deny Allow from all XBitHack on AllowOverride None Options None Order allow,deny Allow from all Options MultiViews Indexes AllowOverride None Order allow,deny Allow from all {noformat} # Restart httpd: {noformat} sudo /sbin/service httpd restart {noformat} # and see the server at: * http://genomebrowser.shore.mbari.org/ ]]> 24051999 24052001 24084762 1 2013-12-20 12:20:37.467 2013-12-20 12:20:37.467 24051999 16417003 16449763 4 2011-03-15 09:42:01.160 2011-04-04 09:37:54.073 16416802 16777304 16810071 1 2011-04-26 09:17:06.830 2011-04-26 09:17:06.830 16777303 16417007 16449767 1 2011-04-04 09:39:55.810 2011-04-04 09:39:55.810 16417005 31391749 24051999 2019-01-16 08:21:29.390 2019-01-16 08:21:29.390 24052008 24084769 3 2013-12-20 12:20:37.467 2013-12-20 13:46:59.113 24051999 31391748 24051999 2019-01-16 08:21:29.390 2019-01-16 08:21:29.390 31391751 24051999 2019-01-16 08:21:29.390 2019-01-16 08:21:29.390 24052010 24084771 4 2013-12-20 12:20:37.467 2013-12-20 13:53:40.920 24051999 31391750 24051999 2019-01-16 08:21:29.390 2019-01-16 08:21:29.390 24052006 24084767 2 2013-12-20 12:20:37.467 2013-12-20 12:26:40.913 24051999 16417021 16449781 5 2011-03-15 09:42:01.160 2011-04-04 09:38:08.517 16416802 16417026 16449786 2 2011-04-05 13:56:53.087 2011-04-05 14:16:08.013 16417023 16416801 16613377 16449568 1 2011-03-15 09:42:01.047 2011-03-15 09:42:01.047 16417025 16449785 1 2011-04-05 13:56:53.087 2011-04-05 13:56:53.087 16417023 31391745 24051999 2019-01-16 08:21:29.383 2019-01-16 08:21:29.383 31391746 24051999 2019-01-16 08:21:29.390 2019-01-16 08:21:29.390 31391747 24051999 2019-01-16 08:21:29.390 2019-01-16 08:21:29.390 16417029 16449789 4 2011-04-05 13:56:53.087 2011-04-05 14:26:51.430 16417023 16417028 16449788 3 2011-04-05 13:56:53.087 2011-04-05 14:17:00.647 16417023 16417034 16449792 6 2011-04-05 13:56:53.087 2011-04-05 14:48:08.783 16417023 16417033 16449791 5 2011-04-05 13:56:53.087 2011-04-05 14:27:41.807 16417023 16516514 16417023 2011-04-05 14:51:25.427 2011-04-05 14:51:25.427 24052029 24084790 14 2013-12-20 12:20:37.467 2013-12-20 15:05:48.140 24051999 24052030 24084791 15 2013-12-20 12:20:37.467 2013-12-20 15:07:09.147 24051999 24052028 24084789 13 2013-12-20 12:20:37.467 2013-12-20 15:02:25.440 24051999 24052033 24084794 6 2011-03-15 09:42:01.160 2011-04-05 13:54:04.067 16416802 24052034 24084795 7 2011-03-15 09:42:01.160 2013-12-20 15:12:28.840 16416802 24052032 24084793 16 2013-12-20 12:20:37.467 2013-12-20 15:08:47.037 24051999 24052037 24084798 17 2013-12-20 12:20:37.467 2013-12-20 15:11:02.667 24051999 16449569 , Emily Reistetter , [Shuangchun "Jeremy" Yan] , Jeltje van Baren , Sam Purvine , Charles Ansong  , Stephen Callister , Josh Stuart , Charles Vaske , Mark Diekhans , Zbigniew S Kolber , Feel free to add or edit pages *For powerpoint presentations of our January meeting, see under Children(below)* \\ \\ \\ \\ \\ h3. Protocols and Procedures [Chemostat] [Configuring nextgen to run sequenceserver and genome-browser]]]> 16416802 24052014 24084775 6 2013-12-20 12:20:37.467 2013-12-20 14:07:02.067 24051999 24052012 24084773 5 2013-12-20 12:20:37.467 2013-12-20 13:56:03.057 24051999 24052018 24084779 8 2013-12-20 12:20:37.467 2013-12-20 14:23:55.447 24051999 24052016 24084777 7 2013-12-20 12:20:37.467 2013-12-20 14:16:06.117 24051999 24052022 24084783 10 2013-12-20 12:20:37.467 2013-12-20 14:37:44.900 24051999 24052020 24084781 9 2013-12-20 12:20:37.467 2013-12-20 14:28:39.037 24051999 24052026 24084787 12 2013-12-20 12:20:37.467 2013-12-20 14:51:17.933 24051999 24052024 24084785 11 2013-12-20 12:20:37.467 2013-12-20 14:39:33.783 24051999 16416828 16449592 3 2011-03-15 12:47:20.420 2011-03-15 12:57:37.483 16416822 16449588 16416822 24085011 {noformat} Login to nextgen \\ {noformat} ssh geneadm@nextgen.shore.mbari.org password: {noformat} Add the new track to the database (CCMP1545_v3 or RCC299_v3) {noformat} hgBbiDbLink CCMP1545_v3 /data/genome_browser_data/bigwigs/ {noformat} Tell the browser about the new track {noformat} formatTrack (then follow prompts) {noformat} And restart the browser {noformat} cd /data/genome_browser_data/genomes/trackDb && ./loadTracks.sh {noformat} Your new tracks should now show up under the blue RNASeq bar in the browser. They are hidden by default. Tip for pros: you can access the mysql database as \-ubrowser \-pgenome. This might be useful if you want to remove tracks. To remove tracks from the browser page, edit the pages under \\ {noformat} /data/genome_browser_data/genomes/trackDb/CCMP1545/CCMP1545_v3/trackDb.ra and /data/genome_browser_data/genomes/trackDb/RCC299/RCC299_v3/trackDb.ra {noformat}]]> 24052251 16416830 16449594 2 2011-03-15 09:42:01.160 2011-03-15 13:05:36.180 16416802 26443796 1 24052246 2014-06-20 18:48:15.027 2014-06-20 18:48:15.027 26443795 1 24052251 2014-06-20 18:46:15.067 2014-06-20 18:46:15.067 16646215 16613377 2011-03-15 09:46:25.103 2011-03-15 09:46:25.103 16416823 16449589 1 2011-03-15 12:47:20.420 2011-03-15 12:47:20.420 16416822 16416824 16449590 2 2011-03-15 12:47:20.420 2011-03-15 12:57:07.407 16416822 16416825 16449591 1 2011-03-15 09:42:01.160 2011-03-15 09:42:01.160 16416802 24085006 CCMP2099_1. Sequence IDs can be rather long, so for instance add the sample ID to them: >MMETSP0022C_CCMP2099_1 # Copy the sequences to the /data/meta (for metatranscriptome and metagenome files) or /data/dbs (for everything else) on nextgen.shore.mbari.org. This can be done using ssh from another computer with username geneadm and password {noformat} scp path/to/fasta geneadm@nextgen.shore.mbari.org:/data/meta {noformat} # Login to nextgen and go to the directory with the sequences {noformat} ssh geneadm@nextgen.shore.mbari.org (same password) cd /data/dbs (or meta) {noformat} # Run {noformat} makeblastdb -dbtype nucl -in -title -parse_seqids {noformat} For protein sequences, dbtype is prot # Restart the sequence server with {noformat} sudo /sbin/service httpd restart {noformat} This will ask you for the password again # Log out with {noformat} exit {noformat} To remove databases, simply remove the files created by makeblastdb and restart the server. \\ \\]]> 24052246 16449762 , Emily Reistetter , Jeremy Yan , Jeltje van Baren , Sam Purvine , Charles Ansong  , Stephen Callister , Josh Stuart , Charles Vaske , Mark Diekhans , Zbigniew S Kolber , Feel free to add or edit pages *For powerpoint presentations of our January meeting, see under Children(below)*\\ \\ \\ \\ \\]]> 16417002 16449788 16417028 16449789 16417029 16449792 16417034 16449791 16417033 16449794 16417036 16449781 , Emily Reistetter , [Shuangchun "Jeremy" Yan] , Jeltje van Baren , Sam Purvine , Charles Ansong  , Stephen Callister , Josh Stuart , Charles Vaske , Mark Diekhans , Zbigniew S Kolber , Feel free to add or edit pages *For powerpoint presentations of our January meeting, see under Children(below)*\\ \\ \\ \\ \\]]> 16417021 16449786 16417026 16449785 16417025 16449763 , Emily Reistetter , [[Shuangchun "Jeremy" Yan]] , Jeltje van Baren , Sam Purvine , Charles Ansong  , Stephen Callister , Josh Stuart , Charles Vaske , Mark Diekhans , Zbigniew S Kolber , Feel free to add or edit pages *For powerpoint presentations of our January meeting, see under Children(below)*\\ \\ \\ \\ \\]]> 16417003 16449767 16417007 16810071 16777304 24084969 ServerName nextgen.shore.mbari.org DocumentRoot /usr/local/apache/htdocs AllowOverride All Options FollowSymLinks Indexes MultiViews Order allow,deny Allow from all RailsBaseURI /sequenceserver RailsBaseURI /sequenceserver-dbs RailsBaseURI /sequenceserver-meta RailsEnv development {noformat} # Copied sequenceserver gem to additional directories to support multiple databases: {noformat} cd /usr/local/lib/ruby/gems/1.9.1/gems sudo chown mccann . cp -r sequenceserver-0.8.6 sequenceserver-dbs cp -r sequenceserver-0.8.6 sequenceserver-meta sudo chown root . sudo chown -R root sequenceserver-dbs sequenceserver-meta cd /usr/local/apache/htdocs ln -s /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-0.8.6/public sequenceserver ln -s /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-dbs/public sequenceserver-dbs ln -s /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-meta/public sequenceserver-meta {noformat} # Modified /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-dbs/config.ru and /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-meta/config.ru to point to the proper sequenceserver.conf file that points to the proper database. Setting the SequenceServer::App.config_file = '/absolute/path/to/configuration_file' is described in the FAQ on http://www.sequenceserver.com/. Note that these sequenceserver.conf files are quite different than the /etc/httpd/conf.d/sequenceserver.conf file. We found that the config.ru files need to be owned by root for the servers to work. # Restart httpd and see the sequenceservers at: * http://nextgen.shore.mbari.org/sequenceserver-dbsb * http://nextgen.shore.mbari.org/sequenceserver-meta h3. UCSC genome-browser - a collection of C cgi-bin programs # As user mccann on nextgen {noformat} sudo yum install mysql sudo yum install mysql-server sudo yum install mysql-devel sudo yum install png-devel sudo /sbin/chkconfig mysql on sudo /sbin/service mysql start {noformat} # Set the mysql root password {noformat} /usr/bin/mysql -u root -p update mysql.user set Password=PASSWORD('xxxx') where User='root'; # See Mike or Rich for the root password {noformat} # As user geneadm on nextgen {noformat} mkdir ~/dev cd ~/dev git clone git://genome-source.cse.ucsc.edu/kent.git cd kent {noformat} # Follow instructions in the README and src/product/README.building.source, briefly: {noformat} export MACHTYPE=x86_64 mkdir -p ~/bin/${MACHTYPE} cd src make libs cd gfServer make cd ../gfClient make cd ../blat make cd ../utils/faToNib make cd ../../hg make cd htdocs make install # Creates web site files in /usr/local/apache {cgi-bin-mccann, htdocs} {noformat} # Setup apache server by creating a /etc/httpd/conf.d/genome-browser.conf file: {noformat} ScriptAlias /cgi-bin/ "/usr/local/apache/cgi-bin-mccann/" # Use same DocumentRoot in sequenceserver so that both can run on the same server DocumentRoot "/usr/local/apache/htdocs/" Options Indexes FollowSymLinks AllowOverride None Order allow,deny Allow from all AllowOverride None Options None Order allow,deny Allow from all Options MultiViews Indexes AllowOverride None Order allow,deny Allow from all {noformat} # Restart httpd and see the server at: * http://nextgen.shore.mbari.org/ ]]> 24052210 24084970 ServerName nextgen.shore.mbari.org DocumentRoot /usr/local/apache/htdocs AllowOverride All Options FollowSymLinks Indexes MultiViews Order allow,deny Allow from all RailsBaseURI /sequenceserver RailsBaseURI /sequenceserver-dbs RailsBaseURI /sequenceserver-meta RailsEnv development {noformat} # Copied sequenceserver gem to additional directories to support multiple databases: {noformat} cd /usr/local/lib/ruby/gems/1.9.1/gems sudo chown mccann . cp -r sequenceserver-0.8.6 sequenceserver-dbs cp -r sequenceserver-0.8.6 sequenceserver-meta sudo chown root . sudo chown -R root sequenceserver-dbs sequenceserver-meta cd /usr/local/apache/htdocs ln -s /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-0.8.6/public sequenceserver ln -s /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-dbs/public sequenceserver-dbs ln -s /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-meta/public sequenceserver-meta {noformat} # Modified /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-dbs/config.ru, adding SequenceServer::App.config_file = ... {noformat} require 'rubygems' require 'bundler/setup' require 'sequenceserver' SequenceServer::App.config_file = '/home/geneadm/conf/sequenceserver-dbs.conf' SequenceServer::App.init run SequenceServer::App {noformat} # Modified /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-meta/config.ru, adding SequenceServer::App.config_file = ... {noformat} require 'rubygems' require 'bundler/setup' require 'sequenceserver' SequenceServer::App.config_file = '/home/geneadm/conf/sequenceserver-meta.conf' SequenceServer::App.init run SequenceServer::App {noformat} Seethe FAQ on http://www.sequenceserver.com/. We found that the config.ru files need to be owned by root for the servers to work. # Restart httpd and see the sequenceservers at: * http://nextgen.shore.mbari.org/sequenceserver-dbsb * http://nextgen.shore.mbari.org/sequenceserver-meta h3. UCSC genome-browser - a collection of C cgi-bin programs # As user mccann on nextgen {noformat} sudo yum install mysql sudo yum install mysql-server sudo yum install mysql-devel sudo yum install png-devel sudo /sbin/chkconfig mysql on sudo /sbin/service mysql start {noformat} # Set the mysql root password {noformat} /usr/bin/mysql -u root -p update mysql.user set Password=PASSWORD('xxxx') where User='root'; # See Mike or Rich for the root password {noformat} # As user geneadm on nextgen {noformat} mkdir ~/dev cd ~/dev git clone git://genome-source.cse.ucsc.edu/kent.git cd kent {noformat} # Follow instructions in the README and src/product/README.building.source, briefly: {noformat} export MACHTYPE=x86_64 mkdir -p ~/bin/${MACHTYPE} cd src make libs cd gfServer make cd ../gfClient make cd ../blat make cd ../utils/faToNib make cd ../../hg make cd htdocs make install # Creates web site files in /usr/local/apache {cgi-bin-mccann, htdocs} {noformat} # Setup apache server by creating a /etc/httpd/conf.d/genome-browser.conf file: {noformat} ScriptAlias /cgi-bin/ "/usr/local/apache/cgi-bin-mccann/" # Use same DocumentRoot in sequenceserver so that both can run on the same server DocumentRoot "/usr/local/apache/htdocs/" Options Indexes FollowSymLinks AllowOverride None Order allow,deny Allow from all AllowOverride None Options None Order allow,deny Allow from all Options MultiViews Indexes AllowOverride None Order allow,deny Allow from all {noformat} # Restart httpd and see the server at: * http://nextgen.shore.mbari.org/ ]]> 24052211 24084967 ServerName nextgen.shore.mbari.org DocumentRoot /usr/local/apache/htdocs AllowOverride All Options FollowSymLinks Indexes MultiViews Order allow,deny Allow from all RailsBaseURI /sequenceserver RailsBaseURI /sequenceserver-dbs RailsBaseURI /sequenceserver-meta RailsEnv development {noformat} # Copied sequenceserver gem to additional directories to support multiple databases: {noformat} cd /usr/local/lib/ruby/gems/1.9.1/gems sudo chown mccann . cp -r sequenceserver-0.8.6 sequenceserver-dbs cp -r sequenceserver-0.8.6 sequenceserver-meta sudo chown root . sudo chown -R root sequenceserver-dbs sequenceserver-meta cd /usr/local/apache/htdocs ln -s /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-0.8.6/public sequenceserver ln -s /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-dbs/public sequenceserver-dbs ln -s /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-meta/public sequenceserver-meta {noformat} # Modified /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-dbs/config.ru and /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-meta/config.ru to point to the proper sequenceserver.conf file that points to the proper database. Setting the SequenceServer::App.config_file = '/absolute/path/to/configuration_file' is described in the FAQ on http://www.sequenceserver.com/. Note that these sequenceserver.conf files are quite different than the /etc/httpd/conf.d/sequenceserver.conf file. # Restart httpd and see the sequenceservers at: * http://nextgen.shore.mbari.org/sequenceserver-dbs * http://nextgen.shore.mbari.org/sequenceserver-meta h3. UCSC genome-browser - a collection of C cgi-bin programs # As user mccann on nextgen {noformat} sudo yum install mysql sudo yum install mysql-server sudo yum install mysql-devel sudo yum install png-devel sudo /sbin/chkconfig mysql on sudo /sbin/service mysql start {noformat} # Set the mysql root password {noformat} /usr/bin/mysql -u root -p update mysql.user set Password=PASSWORD('xxxx') where User='root'; # See Mike or Rich for the root password {noformat} # As user geneadm on nextgen {noformat} mkdir ~/dev cd ~/dev git clone git://genome-source.cse.ucsc.edu/kent.git cd kent {noformat} # Follow instructions in the README and src/product/README.building.source, briefly: {noformat} export MACHTYPE=x86_64 mkdir -p ~/bin/${MACHTYPE} cd src make libs cd gfServer make cd ../gfClient make cd ../blat make cd ../utils/faToNib make cd ../../hg make cd htdocs make install # Creates web site files in /usr/local/apache {cgi-bin-mccann, htdocs} {noformat} # Setup apache server by creating a /etc/httpd/conf.d/genome-browser.conf file: {noformat} ScriptAlias /cgi-bin/ "/usr/local/apache/cgi-bin-mccann/" # Use same DocumentRoot in sequenceserver so that both can run on the same server DocumentRoot "/usr/local/apache/htdocs/" Options Indexes FollowSymLinks AllowOverride None Order allow,deny Allow from all AllowOverride None Options None Order allow,deny Allow from all Options MultiViews Indexes AllowOverride None Order allow,deny Allow from all {noformat} # Restart httpd and see the server at: * http://nextgen.shore.mbari.org/ ]]> 24052208 24084971 ServerName nextgen.shore.mbari.org DocumentRoot /usr/local/apache/htdocs AllowOverride All Options FollowSymLinks Indexes MultiViews Order allow,deny Allow from all RailsBaseURI /sequenceserver RailsBaseURI /sequenceserver-dbs RailsBaseURI /sequenceserver-meta RailsEnv development {noformat} # Copied sequenceserver gem to additional directories to support multiple databases: {noformat} cd /usr/local/lib/ruby/gems/1.9.1/gems sudo chown mccann . cp -r sequenceserver-0.8.6 sequenceserver-dbs cp -r sequenceserver-0.8.6 sequenceserver-meta sudo chown root . sudo chown -R root sequenceserver-dbs sequenceserver-meta cd /usr/local/apache/htdocs ln -s /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-0.8.6/public sequenceserver ln -s /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-dbs/public sequenceserver-dbs ln -s /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-meta/public sequenceserver-meta {noformat} # Modified /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-dbs/config.ru, adding SequenceServer::App.config_file = ... {noformat} require 'rubygems' require 'bundler/setup' require 'sequenceserver' SequenceServer::App.config_file = '/home/geneadm/conf/sequenceserver-dbs.conf' SequenceServer::App.init run SequenceServer::App {noformat} # Modified /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-meta/config.ru, adding SequenceServer::App.config_file = ... {noformat} require 'rubygems' require 'bundler/setup' require 'sequenceserver' SequenceServer::App.config_file = '/home/geneadm/conf/sequenceserver-meta.conf' SequenceServer::App.init run SequenceServer::App {noformat} See the FAQ on http://www.sequenceserver.com/. We found that the config.ru files need to be owned by root for the servers to work. # Restart httpd and see the sequenceservers at: * http://nextgen.shore.mbari.org/sequenceserver-dbsb * http://nextgen.shore.mbari.org/sequenceserver-meta h3. UCSC genome-browser - a collection of C cgi-bin programs # As user mccann on nextgen {noformat} sudo yum install mysql sudo yum install mysql-server sudo yum install mysql-devel sudo yum install png-devel sudo /sbin/chkconfig mysql on sudo /sbin/service mysql start {noformat} # Set the mysql root password {noformat} /usr/bin/mysql -u root -p update mysql.user set Password=PASSWORD('xxxx') where User='root'; # See Mike or Rich for the root password {noformat} # As user geneadm on nextgen {noformat} mkdir ~/dev cd ~/dev git clone git://genome-source.cse.ucsc.edu/kent.git cd kent {noformat} # Follow instructions in the README and src/product/README.building.source, briefly: {noformat} export MACHTYPE=x86_64 mkdir -p ~/bin/${MACHTYPE} cd src make libs cd gfServer make cd ../gfClient make cd ../blat make cd ../utils/faToNib make cd ../../hg make cd htdocs make install # Creates web site files in /usr/local/apache {cgi-bin-mccann, htdocs} {noformat} # Setup apache server by creating a /etc/httpd/conf.d/genome-browser.conf file: {noformat} ScriptAlias /cgi-bin/ "/usr/local/apache/cgi-bin-mccann/" # Use same DocumentRoot in sequenceserver so that both can run on the same server DocumentRoot "/usr/local/apache/htdocs/" Options Indexes FollowSymLinks AllowOverride None Order allow,deny Allow from all AllowOverride None Options None Order allow,deny Allow from all Options MultiViews Indexes AllowOverride None Order allow,deny Allow from all {noformat} # Restart httpd and see the server at: * http://nextgen.shore.mbari.org/ ]]> 24052212 24084993 ServerName nextgen.shore.mbari.org DocumentRoot /usr/local/apache/htdocs AllowOverride All Options FollowSymLinks Indexes MultiViews Order allow,deny Allow from all RailsBaseURI /sequenceserver RailsBaseURI /sequenceserver-dbs RailsBaseURI /sequenceserver-meta RailsEnv development {noformat} # Copied sequenceserver gem to additional directories to support multiple databases: {noformat} cd /usr/local/lib/ruby/gems/1.9.1/gems sudo chown mccann . cp -r sequenceserver-0.8.6 sequenceserver-dbs cp -r sequenceserver-0.8.6 sequenceserver-meta sudo chown root . sudo chown -R root sequenceserver-dbs sequenceserver-meta cd /usr/local/apache/htdocs ln -s /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-0.8.6/public sequenceserver ln -s /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-dbs/public sequenceserver-dbs ln -s /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-meta/public sequenceserver-meta {noformat} # Modified /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-dbs/config.ru, adding SequenceServer::App.config_file = ... {noformat} require 'rubygems' require 'bundler/setup' require 'sequenceserver' SequenceServer::App.config_file = '/home/geneadm/conf/sequenceserver-dbs.conf' SequenceServer::App.init run SequenceServer::App {noformat} # Modified /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-meta/config.ru, adding SequenceServer::App.config_file = ... {noformat} require 'rubygems' require 'bundler/setup' require 'sequenceserver' SequenceServer::App.config_file = '/home/geneadm/conf/sequenceserver-meta.conf' SequenceServer::App.init run SequenceServer::App {noformat} See the FAQ on http://www.sequenceserver.com/. We found that the config.ru files need to be owned by root for the servers to work. # Restart httpd and see the sequenceservers at: * http://nextgen.shore.mbari.org/sequenceserver-dbs * http://nextgen.shore.mbari.org/sequenceserver-meta h3. UCSC genome-browser - a collection of C cgi-bin programs # As user mccann on nextgen {noformat} sudo yum install mysql sudo yum install mysql-server sudo yum install mysql-devel sudo yum install png-devel sudo /sbin/chkconfig mysql on sudo /sbin/service mysql start {noformat} # Set the mysql root password {noformat} /usr/bin/mysql -u root -p update mysql.user set Password=PASSWORD('xxxx') where User='root'; # See Mike or Rich for the root password {noformat} # As user geneadm on nextgen {noformat} mkdir ~/dev cd ~/dev git clone git://genome-source.cse.ucsc.edu/kent.git cd kent {noformat} # Follow instructions in the README and src/product/README.building.source, briefly: {noformat} export MACHTYPE=x86_64 mkdir -p ~/bin/${MACHTYPE} cd src make libs cd gfServer make cd ../gfClient make cd ../blat make cd ../utils/faToNib make cd ../../hg make cd htdocs make install # Creates web site files in /usr/local/apache {cgi-bin-mccann, htdocs} {noformat} # Setup apache server by creating a /etc/httpd/conf.d/genome-browser.conf file: {noformat} ScriptAlias /cgi-bin/ "/usr/local/apache/cgi-bin-mccann/" # Use same DocumentRoot in sequenceserver so that both can run on the same server DocumentRoot "/usr/local/apache/htdocs/" Options Indexes FollowSymLinks AllowOverride None Order allow,deny Allow from all AllowOverride None Options None Order allow,deny Allow from all Options MultiViews Indexes AllowOverride None Order allow,deny Allow from all {noformat} # Restart httpd and see the server at: * http://nextgen.shore.mbari.org/ ]]> 24052234 24084991 ServerName nextgen.shore.mbari.org DocumentRoot /usr/local/apache/htdocs AllowOverride All Options FollowSymLinks Indexes MultiViews Order allow,deny Allow from all RailsBaseURI /sequenceserver RailsBaseURI /sequenceserver-dbs RailsBaseURI /sequenceserver-meta RailsEnv development {noformat} # Copied sequenceserver gem to additional directories to support multiple databases: {noformat} cd /usr/local/lib/ruby/gems/1.9.1/gems sudo chown mccann . cp -r sequenceserver-0.8.6 sequenceserver-dbs cp -r sequenceserver-0.8.6 sequenceserver-meta sudo chown root . sudo chown -R root sequenceserver-dbs sequenceserver-meta cd /usr/local/apache/htdocs ln -s /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-0.8.6/public sequenceserver ln -s /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-dbs/public sequenceserver-dbs ln -s /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-meta/public sequenceserver-meta {noformat} # Modified /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-dbs/config.ru, adding SequenceServer::App.config_file = ... {noformat} require 'rubygems' require 'bundler/setup' require 'sequenceserver' SequenceServer::App.config_file = '/home/geneadm/conf/sequenceserver-dbs.conf' SequenceServer::App.init run SequenceServer::App {noformat} # Modified /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-meta/config.ru, adding SequenceServer::App.config_file = ... {noformat} require 'rubygems' require 'bundler/setup' require 'sequenceserver' SequenceServer::App.config_file = '/home/geneadm/conf/sequenceserver-meta.conf' SequenceServer::App.init run SequenceServer::App {noformat} See the FAQ on http://www.sequenceserver.com/. We found that the config.ru files need to be owned by root for the servers to work. # Restart httpd and see the sequenceservers at: * http://nextgen.shore.mbari.org/sequenceserver-dbs * http://nextgen.shore.mbari.org/sequenceserver-meta h3. UCSC genome-browser - a collection of C cgi-bin programs # As user mccann on nextgen {noformat} sudo yum install mysql sudo yum install mysql-server sudo yum install mysql-devel sudo yum install png-devel sudo /sbin/chkconfig mysql on sudo /sbin/service mysql start {noformat} # Set the mysql root password {noformat} /usr/bin/mysql -u root -p update mysql.user set Password=PASSWORD('xxxx') where User='root'; # See Mike or Rich for the root password {noformat} # As user geneadm on nextgen {noformat} mkdir ~/dev cd ~/dev git clone git://genome-source.cse.ucsc.edu/kent.git cd kent {noformat} # Follow instructions in the README and src/product/README.building.source, briefly: {noformat} export MACHTYPE=x86_64 mkdir -p ~/bin/${MACHTYPE} cd src make libs cd gfServer make cd ../gfClient make cd ../blat make cd ../utils/faToNib make cd ../../hg make cd htdocs make install # Creates web site files in /usr/local/apache {cgi-bin-mccann, htdocs} {noformat} # Setup apache server by creating a /etc/httpd/conf.d/genome-browser.conf file: {noformat} ScriptAlias /cgi-bin/ "/usr/local/apache/cgi-bin-mccann/" # Use same DocumentRoot in sequenceserver so that both can run on the same server DocumentRoot "/usr/local/apache/htdocs/" Options Indexes FollowSymLinks AllowOverride None Order allow,deny Allow from all AllowOverride None Options None Order allow,deny Allow from all Options MultiViews Indexes AllowOverride None Order allow,deny Allow from all {noformat} # Restart httpd and see the server at: * http://nextgen.shore.mbari.org/ ]]> 24052232 24084989 ServerName nextgen.shore.mbari.org DocumentRoot /usr/local/apache/htdocs AllowOverride All Options FollowSymLinks Indexes MultiViews Order allow,deny Allow from all RailsBaseURI /sequenceserver RailsBaseURI /sequenceserver-dbs RailsBaseURI /sequenceserver-meta RailsEnv development {noformat} # Copied sequenceserver gem to additional directories to support multiple databases: {noformat} cd /usr/local/lib/ruby/gems/1.9.1/gems sudo chown mccann . cp -r sequenceserver-0.8.6 sequenceserver-dbs cp -r sequenceserver-0.8.6 sequenceserver-meta sudo chown root . sudo chown -R root sequenceserver-dbs sequenceserver-meta cd /usr/local/apache/htdocs ln -s /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-0.8.6/public sequenceserver ln -s /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-dbs/public sequenceserver-dbs ln -s /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-meta/public sequenceserver-meta {noformat} # Modified /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-dbs/config.ru, adding SequenceServer::App.config_file = ... {noformat} require 'rubygems' require 'bundler/setup' require 'sequenceserver' SequenceServer::App.config_file = '/home/geneadm/conf/sequenceserver-dbs.conf' SequenceServer::App.init run SequenceServer::App {noformat} # Modified /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-meta/config.ru, adding SequenceServer::App.config_file = ... {noformat} require 'rubygems' require 'bundler/setup' require 'sequenceserver' SequenceServer::App.config_file = '/home/geneadm/conf/sequenceserver-meta.conf' SequenceServer::App.init run SequenceServer::App {noformat} See the FAQ on http://www.sequenceserver.com/. We found that the config.ru files need to be owned by root for the servers to work. # Restart httpd and see the sequenceservers at: * http://nextgen.shore.mbari.org/sequenceserver-dbs * http://nextgen.shore.mbari.org/sequenceserver-meta h3. UCSC genome-browser - a collection of C cgi-bin programs # As user mccann on nextgen {noformat} sudo yum install mysql sudo yum install mysql-server sudo yum install mysql-devel sudo yum install png-devel sudo /sbin/chkconfig mysql on sudo /sbin/service mysql start {noformat} # Set the mysql root password {noformat} /usr/bin/mysql -u root -p update mysql.user set Password=PASSWORD('xxxx') where User='root'; # See Mike or Rich for the root password {noformat} # As user geneadm on nextgen {noformat} mkdir ~/dev cd ~/dev git clone git://genome-source.cse.ucsc.edu/kent.git cd kent {noformat} # Follow instructions in the README and src/product/README.building.source, briefly: {noformat} export MACHTYPE=x86_64 mkdir -p ~/bin/${MACHTYPE} cd src make libs cd gfServer make cd ../gfClient make cd ../blat make cd ../utils/faToNib make cd ../../hg make cd htdocs make install # Creates web site files in /usr/local/apache {cgi-bin-mccann, htdocs} {noformat} # Setup apache server by creating a /etc/httpd/conf.d/genome-browser.conf file: {noformat} ScriptAlias /cgi-bin/ "/usr/local/apache/cgi-bin-mccann/" # Use same DocumentRoot in sequenceserver so that both can run on the same server DocumentRoot "/usr/local/apache/htdocs/" Options Indexes FollowSymLinks AllowOverride None Order allow,deny Allow from all AllowOverride None Options None Order allow,deny Allow from all Options MultiViews Indexes AllowOverride None Order allow,deny Allow from all {noformat} # Restart httpd and see the server at: * http://nextgen.shore.mbari.org/ ]]> 24052230 24084767 24052006 31358978 ServerName sequenceserver.shore.mbari.org DocumentRoot /usr/local/apache/htdocs AllowOverride All Options FollowSymLinks Indexes MultiViews Order allow,deny Allow from all RailsBaseURI /sequenceserver-dbs RailsBaseURI /sequenceserver-meta RailsBaseURI /dbs RailsBaseURI /meta RailsEnv development {noformat} # Copied sequenceserver gem to additional directories to support multiple databases and symlinks for short names on sequenceserver.shore.mbari.org: {noformat} cd /usr/local/lib/ruby/gems/1.9.1/gems sudo chown mccann . cp -r sequenceserver-0.8.6 sequenceserver-dbs cp -r sequenceserver-0.8.6 sequenceserver-meta ln -s sequenceserver-dbs dbs ln -s sequenceserver-meta meta sudo chown root . sudo chown -R root sequenceserver-dbs sequenceserver-meta {noformat} # Create symlinks in /usr/local/apache/htdocs for web pages to work: {noformat} cd /usr/local/apache/htdocs ln -s /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-dbs/public sequenceserver-dbs ln -s /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-dbs/public dbs ln -s /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-meta/public sequenceserver-meta ln -s /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-meta/public meta {noformat} # Modified /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-dbs/config.ru, adding SequenceServer::App.config_file = ... {noformat} require 'rubygems' require 'bundler/setup' require 'sequenceserver' SequenceServer::App.config_file = '/home/geneadm/conf/sequenceserver-dbs.conf' SequenceServer::App.init run SequenceServer::App {noformat} # Modified /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-meta/config.ru, adding SequenceServer::App.config_file = ... {noformat} require 'rubygems' require 'bundler/setup' require 'sequenceserver' SequenceServer::App.config_file = '/home/geneadm/conf/sequenceserver-meta.conf' SequenceServer::App.init run SequenceServer::App {noformat} See the FAQ on http://www.sequenceserver.com/. We found that the config.ru files need to be owned by root for the servers to work. # Restart httpd and see the sequenceservers at: * http://sequenceserver.shore.mbari.org/dbs * http://sequenceserver.shore.mbari.org/meta h3. UCSC genome-browser - a collection of C cgi-bin programs # As user mccann on nextgen {noformat} sudo yum install mysql sudo yum install mysql-server sudo yum install mysql-devel sudo yum install png-devel sudo /sbin/chkconfig mysql on sudo /sbin/service mysql start {noformat} # Set the mysql root password {noformat} /usr/bin/mysql -u root -p update mysql.user set Password=PASSWORD('xxxx') where User='root'; # See Mike or Rich for the root password {noformat} # As user geneadm on nextgen {noformat} mkdir ~/dev cd ~/dev git clone git://genome-source.cse.ucsc.edu/kent.git cd kent {noformat} # Follow instructions in the README and src/product/README.building.source, briefly: {noformat} export MACHTYPE=x86_64 mkdir -p ~/bin/${MACHTYPE} cd src make libs cd gfServer make cd ../gfClient make cd ../blat make cd ../utils/faToNib make cd ../../hg make cd htdocs make install # Creates web site files in /usr/local/apache {cgi-bin-mccann, htdocs} {noformat} # Setup apache server by creating a /etc/httpd/conf.d/genome-browser.conf file: {noformat} ScriptAlias /cgi-bin/ "/usr/local/apache/cgi-bin-mccann/" ServerName genomebrowser.shore.mbari.org DocumentRoot "/usr/local/apache/htdocs/" Options Includes Indexes FollowSymLinks AllowOverride None Order allow,deny Allow from all XBitHack on AllowOverride None Options None Order allow,deny Allow from all Options MultiViews Indexes AllowOverride None Order allow,deny Allow from all {noformat} # Restart httpd and see the server at: * http://genomebrowser.shore.mbari.org/ ]]> 31326210 24084769 24052008 24084762 24052001 24084781 ServerName nextgen.shore.mbari.org DocumentRoot /usr/local/apache/htdocs AllowOverride All Options FollowSymLinks Indexes MultiViews Order allow,deny Allow from all RailsBaseURI /sequenceserver RailsBaseURI /sequenceserver-dbs RailsBaseURI /sequenceserver-meta RailsEnv development {noformat} # Copied sequenceserver gem to additional directories to support multiple databases: {noformat} cd /usr/local/lib/ruby/gems/1.9.1/gems sudo chown mccann . cp -r sequenceserver-0.8.6 sequenceserver-dbs cp -r sequenceserver-0.8.6 sequenceserver-meta sudo chown root . sudo chown -R root sequenceserver-dbs sequenceserver-meta cd /usr/local/apache/htdocs ln -s /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-0.8.6/public sequenceserver ln -s /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-dbs/public sequenceserver-dbs ln -s /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-meta/public sequenceserver-meta {noformat} # Modified /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-dbs/config.ru and /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-meta/config.ru to point to the proper sequenceserver.conf file that points to the proper database. (Setting the SequenceServer::App.config_file = '/absolute/path/to/configuration_file' is described in the FAQ on http://www.sequenceserver.com/) # Restart httpd and see the sequenceservers at: * http://nextgen.shore.mbari.org/sequenceserver-dbs * http://nextgen.shore.mbari.org/sequenceserver-meta h3. UCSC genome-browser - a collection of C cgi-bin programs # As user mccann on nextgen {noformat} sudo yum install mysql sudo yum install mysql-server sudo yum install mysql-devel sudo yum install png-devel sudo /sbin/chkconfig mysql on sudo /sbin/service mysql start {noformat} # Set the mysql root password {noformat} /usr/bin/mysql -u root -p update mysql.user set Password=PASSWORD('xxxx') where User='root'; # See Mike or Rich for the root password {noformat} # As user geneadm on nextgen {noformat} mkdir ~/dev cd ~/dev git clone git://genome-source.cse.ucsc.edu/kent.git {noformat}]]> 24052020 24084779 ServerName nextgen.shore.mbari.org DocumentRoot /usr/local/apache/htdocs AllowOverride All Options FollowSymLinks Indexes MultiViews Order allow,deny Allow from all RailsBaseURI /sequenceserver RailsBaseURI /sequenceserver-dbs RailsBaseURI /sequenceserver-meta RailsEnv development {noformat} # Copied sequenceserver gem to additional directories to support multiple databases: {noformat} cd /usr/local/lib/ruby/gems/1.9.1/gems sudo chown mccann . cp -r sequenceserver-0.8.6 sequenceserver-dbs cp -r sequenceserver-0.8.6 sequenceserver-meta sudo chown root . sudo chown -R root sequenceserver-dbs sequenceserver-meta cd /usr/local/apache/htdocs ln -s /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-0.8.6/public sequenceserver ln -s /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-dbs/public sequenceserver-dbs ln -s /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-meta/public sequenceserver-meta {noformat} # Modified /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-dbs/config.ru and /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-meta/config.ru to point to the proper sequenceserver.conf file that points to the proper database. (Setting the SequenceServer::App.config_file = '/absolute/path/to/configuration_file' is described in the FAQ on http://www.sequenceserver.com/) # Restart httpd and see the sequenceservers at: * http://nextgen.shore.mbari.org/sequenceserver-dbs * http://nextgen.shore.mbari.org/sequenceserver-meta h3. UCSC genome-browser - a collection of C cgi-bin programs # As user mccann on nextgen {noformat} sudo yum install mysql sudo yum install mysql-server sudo yum install mysql-devel sudo yum install png-devel sudo /sbin/chkconfig mysql on sudo /sbin/service mysql start {noformat} # As user geneadm on nextgen {noformat} mkdir ~/dev cd ~/dev git clone git://genome-source.cse.ucsc.edu/kent.git {noformat}]]> 24052018 24084785 ServerName nextgen.shore.mbari.org DocumentRoot /usr/local/apache/htdocs AllowOverride All Options FollowSymLinks Indexes MultiViews Order allow,deny Allow from all RailsBaseURI /sequenceserver RailsBaseURI /sequenceserver-dbs RailsBaseURI /sequenceserver-meta RailsEnv development {noformat} # Copied sequenceserver gem to additional directories to support multiple databases: {noformat} cd /usr/local/lib/ruby/gems/1.9.1/gems sudo chown mccann . cp -r sequenceserver-0.8.6 sequenceserver-dbs cp -r sequenceserver-0.8.6 sequenceserver-meta sudo chown root . sudo chown -R root sequenceserver-dbs sequenceserver-meta cd /usr/local/apache/htdocs ln -s /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-0.8.6/public sequenceserver ln -s /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-dbs/public sequenceserver-dbs ln -s /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-meta/public sequenceserver-meta {noformat} # Modified /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-dbs/config.ru and /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-meta/config.ru to point to the proper sequenceserver.conf file that points to the proper database. (Setting the SequenceServer::App.config_file = '/absolute/path/to/configuration_file' is described in the FAQ on http://www.sequenceserver.com/) # Restart httpd and see the sequenceservers at: * http://nextgen.shore.mbari.org/sequenceserver-dbs * http://nextgen.shore.mbari.org/sequenceserver-meta h3. UCSC genome-browser - a collection of C cgi-bin programs # As user mccann on nextgen {noformat} sudo yum install mysql sudo yum install mysql-server sudo yum install mysql-devel sudo yum install png-devel sudo /sbin/chkconfig mysql on sudo /sbin/service mysql start {noformat} # Set the mysql root password {noformat} /usr/bin/mysql -u root -p update mysql.user set Password=PASSWORD('xxxx') where User='root'; # See Mike or Rich for the root password {noformat} # As user geneadm on nextgen {noformat} mkdir ~/dev cd ~/dev git clone git://genome-source.cse.ucsc.edu/kent.git cd kent {noformat} # Follow instructions in the README, briefly: {noformat} export MACHTYPE=x86_64 mkdir -p ~/bin/${MACHTYPE} cd src make libs {noformat} ]]> 24052024 24084783 ServerName nextgen.shore.mbari.org DocumentRoot /usr/local/apache/htdocs AllowOverride All Options FollowSymLinks Indexes MultiViews Order allow,deny Allow from all RailsBaseURI /sequenceserver RailsBaseURI /sequenceserver-dbs RailsBaseURI /sequenceserver-meta RailsEnv development {noformat} # Copied sequenceserver gem to additional directories to support multiple databases: {noformat} cd /usr/local/lib/ruby/gems/1.9.1/gems sudo chown mccann . cp -r sequenceserver-0.8.6 sequenceserver-dbs cp -r sequenceserver-0.8.6 sequenceserver-meta sudo chown root . sudo chown -R root sequenceserver-dbs sequenceserver-meta cd /usr/local/apache/htdocs ln -s /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-0.8.6/public sequenceserver ln -s /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-dbs/public sequenceserver-dbs ln -s /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-meta/public sequenceserver-meta {noformat} # Modified /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-dbs/config.ru and /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-meta/config.ru to point to the proper sequenceserver.conf file that points to the proper database. (Setting the SequenceServer::App.config_file = '/absolute/path/to/configuration_file' is described in the FAQ on http://www.sequenceserver.com/) # Restart httpd and see the sequenceservers at: * http://nextgen.shore.mbari.org/sequenceserver-dbs * http://nextgen.shore.mbari.org/sequenceserver-meta h3. UCSC genome-browser - a collection of C cgi-bin programs # As user mccann on nextgen {noformat} sudo yum install mysql sudo yum install mysql-server sudo yum install mysql-devel sudo yum install png-devel sudo /sbin/chkconfig mysql on sudo /sbin/service mysql start {noformat} # Set the mysql root password {noformat} /usr/bin/mysql -u root -p update mysql.user set Password=PASSWORD('xxxx') where User='root'; # See Mike or Rich for the root password {noformat} # As user geneadm on nextgen {noformat} mkdir ~/dev cd ~/dev git clone git://genome-source.cse.ucsc.edu/kent.git cd kent {noformat} # Follow instructions in the README, briefly: {noformat} mkdir -p ~/bin/x86_64 cd src make libs {noformat} ]]> 24052022 24084773 24052012 24084771 24052010 24084777 ServerName nextgen.shore.mbari.org DocumentRoot /usr/local/apache/htdocs AllowOverride All Options FollowSymLinks Indexes MultiViews Order allow,deny Allow from all RailsBaseURI /sequenceserver RailsBaseURI /sequenceserver-dbs RailsBaseURI /sequenceserver-meta RailsEnv development {noformat} # Copied sequenceserver gem to additional directories to support multiple databases: {noformat} cd /usr/local/lib/ruby/gems/1.9.1/gems sudo chown mccann . cp -r sequenceserver-0.8.6 sequenceserver-dbs cp -r sequenceserver-0.8.6 sequenceserver-meta sudo chown root . sudo chown -R root sequenceserver-dbs sequenceserver-meta cd /usr/local/apache/htdocs ln -s /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-0.8.6/public sequenceserver ln -s /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-dbs/public sequenceserver-dbs ln -s /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-meta/public sequenceserver-meta {noformat} # Modified /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-dbs/config.ru and /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-meta/config.ru to point to the proper sequenceserver.conf file that points to the proper database. (Setting the SequenceServer::App.config_file = '/absolute/path/to/configuration_file' is described in the FAQ on http://www.sequenceserver.com/) ]]> 24052016 24084775 ServerName nextgen.shore.mbari.org DocumentRoot /usr/local/apache/htdocs AllowOverride All Options FollowSymLinks Indexes MultiViews Order allow,deny Allow from all RailsBaseURI /sequenceserver RailsBaseURI /sequenceserver-dbs RailsBaseURI /sequenceserver-meta RailsEnv development {noformat} ]]> 24052014 24084798 ServerName nextgen.shore.mbari.org DocumentRoot /usr/local/apache/htdocs AllowOverride All Options FollowSymLinks Indexes MultiViews Order allow,deny Allow from all RailsBaseURI /sequenceserver RailsBaseURI /sequenceserver-dbs RailsBaseURI /sequenceserver-meta RailsEnv development {noformat} # Copied sequenceserver gem to additional directories to support multiple databases: {noformat} cd /usr/local/lib/ruby/gems/1.9.1/gems sudo chown mccann . cp -r sequenceserver-0.8.6 sequenceserver-dbs cp -r sequenceserver-0.8.6 sequenceserver-meta sudo chown root . sudo chown -R root sequenceserver-dbs sequenceserver-meta cd /usr/local/apache/htdocs ln -s /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-0.8.6/public sequenceserver ln -s /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-dbs/public sequenceserver-dbs ln -s /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-meta/public sequenceserver-meta {noformat} # Modified /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-dbs/config.ru and /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-meta/config.ru to point to the proper sequenceserver.conf file that points to the proper database. Setting the SequenceServer::App.config_file = '/absolute/path/to/configuration_file' is described in the FAQ on http://www.sequenceserver.com/. Note that these sequenceserver.conf files are quite different than the /etc/httpd/conf.d/sequenceserver.conf file. # Restart httpd and see the sequenceservers at: * http://nextgen.shore.mbari.org/sequenceserver-dbs * http://nextgen.shore.mbari.org/sequenceserver-meta h3. UCSC genome-browser - a collection of C cgi-bin programs # As user mccann on nextgen {noformat} sudo yum install mysql sudo yum install mysql-server sudo yum install mysql-devel sudo yum install png-devel sudo /sbin/chkconfig mysql on sudo /sbin/service mysql start {noformat} # Set the mysql root password {noformat} /usr/bin/mysql -u root -p update mysql.user set Password=PASSWORD('xxxx') where User='root'; # See Mike or Rich for the root password {noformat} # As user geneadm on nextgen {noformat} mkdir ~/dev cd ~/dev git clone git://genome-source.cse.ucsc.edu/kent.git cd kent {noformat} # Follow instructions in the README and src/product/README.building.source, briefly: {noformat} export MACHTYPE=x86_64 mkdir -p ~/bin/${MACHTYPE} cd src make libs cd gfServer make cd ../gfClient make cd ../blat make cd ../utils/faToNib make cd ../../hg make cd htdocs make install # Creates web site files in /usr/local/apache {cgi-bin-mccann, htdocs} {noformat} # Setup apache server by creating a /etc/httpd/conf.d/genome-browser.conf file: {noformat} ScriptAlias /cgi-bin/ "/usr/local/apache/cgi-bin-mccann/" # Use same DocumentRoot in sequenceserver so that both can run on the same server DocumentRoot "/usr/local/apache/htdocs/" Options Indexes FollowSymLinks AllowOverride None Order allow,deny Allow from all AllowOverride None Options None Order allow,deny Allow from all Options MultiViews Indexes AllowOverride None Order allow,deny Allow from all {noformat} # Restart httpd and see the server at: * http://nextgen.shore.mbari.org/ ]]> 24052037 24084795 , Emily Reistetter , [Shuangchun "Jeremy" Yan] , Jeltje van Baren , Sam Purvine , Charles Ansong  , Stephen Callister , Josh Stuart , Charles Vaske , Mark Diekhans , Zbigniew S Kolber , Feel free to add or edit pages *For powerpoint presentations of our January meeting, see under Children(below)*\\ \\ \\ \\ \\ h3. Protocols and Procedures [Configuring nextgen to run sequenceserver and genome-browser|DOEMM:Configuring nextgen to run sequenceserver and genome-browser] [Chemostat]]]> 24052034 24084789 ServerName nextgen.shore.mbari.org DocumentRoot /usr/local/apache/htdocs AllowOverride All Options FollowSymLinks Indexes MultiViews Order allow,deny Allow from all RailsBaseURI /sequenceserver RailsBaseURI /sequenceserver-dbs RailsBaseURI /sequenceserver-meta RailsEnv development {noformat} # Copied sequenceserver gem to additional directories to support multiple databases: {noformat} cd /usr/local/lib/ruby/gems/1.9.1/gems sudo chown mccann . cp -r sequenceserver-0.8.6 sequenceserver-dbs cp -r sequenceserver-0.8.6 sequenceserver-meta sudo chown root . sudo chown -R root sequenceserver-dbs sequenceserver-meta cd /usr/local/apache/htdocs ln -s /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-0.8.6/public sequenceserver ln -s /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-dbs/public sequenceserver-dbs ln -s /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-meta/public sequenceserver-meta {noformat} # Modified /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-dbs/config.ru and /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-meta/config.ru to point to the proper sequenceserver.conf file that points to the proper database. (Setting the SequenceServer::App.config_file = '/absolute/path/to/configuration_file' is described in the FAQ on http://www.sequenceserver.com/) # Restart httpd and see the sequenceservers at: * http://nextgen.shore.mbari.org/sequenceserver-dbs * http://nextgen.shore.mbari.org/sequenceserver-meta h3. UCSC genome-browser - a collection of C cgi-bin programs # As user mccann on nextgen {noformat} sudo yum install mysql sudo yum install mysql-server sudo yum install mysql-devel sudo yum install png-devel sudo /sbin/chkconfig mysql on sudo /sbin/service mysql start {noformat} # Set the mysql root password {noformat} /usr/bin/mysql -u root -p update mysql.user set Password=PASSWORD('xxxx') where User='root'; # See Mike or Rich for the root password {noformat} # As user geneadm on nextgen {noformat} mkdir ~/dev cd ~/dev git clone git://genome-source.cse.ucsc.edu/kent.git cd kent {noformat} # Follow instructions in the README and src/product/README.building.source, briefly: {noformat} export MACHTYPE=x86_64 mkdir -p ~/bin/${MACHTYPE} cd src make libs cd gfServer make cd ../gfClient make cd ../blat make cd ../utils/faToNib make cd ../../hg make cd htdocs make install # Creates web site files in /usr/local/apache {cgi-bin-mccann, htdocs} {noformat} # Setup apache server by creating a /etc/httpd/conf.d/genome-browser.conf file: {noformat} ScriptAlias /cgi-bin/ "/usr/local/apache/cgi-bin-mccann/" # Use same DocumentRoot in sequenceserver so that both can run on the same server DocumentRoot "/usr/local/apache/htdocs/" Options Indexes FollowSymLinks AllowOverride None Order allow,deny Allow from all AllowOverride None Options None Order allow,deny Allow from all Options MultiViews Indexes AllowOverride None Order allow,deny Allow from all {noformat}]]> 24052028 24084790 ServerName nextgen.shore.mbari.org DocumentRoot /usr/local/apache/htdocs AllowOverride All Options FollowSymLinks Indexes MultiViews Order allow,deny Allow from all RailsBaseURI /sequenceserver RailsBaseURI /sequenceserver-dbs RailsBaseURI /sequenceserver-meta RailsEnv development {noformat} # Copied sequenceserver gem to additional directories to support multiple databases: {noformat} cd /usr/local/lib/ruby/gems/1.9.1/gems sudo chown mccann . cp -r sequenceserver-0.8.6 sequenceserver-dbs cp -r sequenceserver-0.8.6 sequenceserver-meta sudo chown root . sudo chown -R root sequenceserver-dbs sequenceserver-meta cd /usr/local/apache/htdocs ln -s /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-0.8.6/public sequenceserver ln -s /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-dbs/public sequenceserver-dbs ln -s /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-meta/public sequenceserver-meta {noformat} # Modified /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-dbs/config.ru and /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-meta/config.ru to point to the proper sequenceserver.conf file that points to the proper database. (Setting the SequenceServer::App.config_file = '/absolute/path/to/configuration_file' is described in the FAQ on http://www.sequenceserver.com/) # Restart httpd and see the sequenceservers at: * http://nextgen.shore.mbari.org/sequenceserver-dbs * http://nextgen.shore.mbari.org/sequenceserver-meta h3. UCSC genome-browser - a collection of C cgi-bin programs # As user mccann on nextgen {noformat} sudo yum install mysql sudo yum install mysql-server sudo yum install mysql-devel sudo yum install png-devel sudo /sbin/chkconfig mysql on sudo /sbin/service mysql start {noformat} # Set the mysql root password {noformat} /usr/bin/mysql -u root -p update mysql.user set Password=PASSWORD('xxxx') where User='root'; # See Mike or Rich for the root password {noformat} # As user geneadm on nextgen {noformat} mkdir ~/dev cd ~/dev git clone git://genome-source.cse.ucsc.edu/kent.git cd kent {noformat} # Follow instructions in the README and src/product/README.building.source, briefly: {noformat} export MACHTYPE=x86_64 mkdir -p ~/bin/${MACHTYPE} cd src make libs cd gfServer make cd ../gfClient make cd ../blat make cd ../utils/faToNib make cd ../../hg make cd htdocs make install # Creates web site files in /usr/local/apache {cgi-bin-mccann, htdocs} {noformat} # Setup apache server by creating a /etc/httpd/conf.d/genome-browser.conf file: {noformat} ScriptAlias /cgi-bin/ "/usr/local/apache/cgi-bin-mccann/" # Use same DocumentRoot in sequenceserver so that both can run on the same server DocumentRoot "/usr/local/apache/htdocs/" Options Indexes FollowSymLinks AllowOverride None Order allow,deny Allow from all AllowOverride None Options None Order allow,deny Allow from all Options MultiViews Indexes AllowOverride None Order allow,deny Allow from all {noformat} # Restart httpd and see the server at: * http://nextgen.shore.mbari.org/ ]]> 24052029 24084787 ServerName nextgen.shore.mbari.org DocumentRoot /usr/local/apache/htdocs AllowOverride All Options FollowSymLinks Indexes MultiViews Order allow,deny Allow from all RailsBaseURI /sequenceserver RailsBaseURI /sequenceserver-dbs RailsBaseURI /sequenceserver-meta RailsEnv development {noformat} # Copied sequenceserver gem to additional directories to support multiple databases: {noformat} cd /usr/local/lib/ruby/gems/1.9.1/gems sudo chown mccann . cp -r sequenceserver-0.8.6 sequenceserver-dbs cp -r sequenceserver-0.8.6 sequenceserver-meta sudo chown root . sudo chown -R root sequenceserver-dbs sequenceserver-meta cd /usr/local/apache/htdocs ln -s /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-0.8.6/public sequenceserver ln -s /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-dbs/public sequenceserver-dbs ln -s /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-meta/public sequenceserver-meta {noformat} # Modified /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-dbs/config.ru and /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-meta/config.ru to point to the proper sequenceserver.conf file that points to the proper database. (Setting the SequenceServer::App.config_file = '/absolute/path/to/configuration_file' is described in the FAQ on http://www.sequenceserver.com/) # Restart httpd and see the sequenceservers at: * http://nextgen.shore.mbari.org/sequenceserver-dbs * http://nextgen.shore.mbari.org/sequenceserver-meta h3. UCSC genome-browser - a collection of C cgi-bin programs # As user mccann on nextgen {noformat} sudo yum install mysql sudo yum install mysql-server sudo yum install mysql-devel sudo yum install png-devel sudo /sbin/chkconfig mysql on sudo /sbin/service mysql start {noformat} # Set the mysql root password {noformat} /usr/bin/mysql -u root -p update mysql.user set Password=PASSWORD('xxxx') where User='root'; # See Mike or Rich for the root password {noformat} # As user geneadm on nextgen {noformat} mkdir ~/dev cd ~/dev git clone git://genome-source.cse.ucsc.edu/kent.git cd kent {noformat} # Follow instructions in the README and src/product/README.building.source, briefly: {noformat} export MACHTYPE=x86_64 mkdir -p ~/bin/${MACHTYPE} cd src make libs cd gfServer make cd ../gfClient make cd ../blat make cd ../utils/faToNib make cd ../../hg make {noformat} ]]> 24052026 24084793 ServerName nextgen.shore.mbari.org DocumentRoot /usr/local/apache/htdocs AllowOverride All Options FollowSymLinks Indexes MultiViews Order allow,deny Allow from all RailsBaseURI /sequenceserver RailsBaseURI /sequenceserver-dbs RailsBaseURI /sequenceserver-meta RailsEnv development {noformat} # Copied sequenceserver gem to additional directories to support multiple databases: {noformat} cd /usr/local/lib/ruby/gems/1.9.1/gems sudo chown mccann . cp -r sequenceserver-0.8.6 sequenceserver-dbs cp -r sequenceserver-0.8.6 sequenceserver-meta sudo chown root . sudo chown -R root sequenceserver-dbs sequenceserver-meta cd /usr/local/apache/htdocs ln -s /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-0.8.6/public sequenceserver ln -s /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-dbs/public sequenceserver-dbs ln -s /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-meta/public sequenceserver-meta {noformat} # Modified /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-dbs/config.ru and /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-meta/config.ru to point to the proper sequenceserver.conf file that points to the proper database. (Setting the SequenceServer::App.config_file = '/absolute/path/to/configuration_file' is described in the FAQ on http://www.sequenceserver.com/) # Restart httpd and see the sequenceservers at: * http://nextgen.shore.mbari.org/sequenceserver-dbs * http://nextgen.shore.mbari.org/sequenceserver-meta h3. UCSC genome-browser - a collection of C cgi-bin programs # As user mccann on nextgen {noformat} sudo yum install mysql sudo yum install mysql-server sudo yum install mysql-devel sudo yum install png-devel sudo /sbin/chkconfig mysql on sudo /sbin/service mysql start {noformat} # Set the mysql root password {noformat} /usr/bin/mysql -u root -p update mysql.user set Password=PASSWORD('xxxx') where User='root'; # See Mike or Rich for the root password {noformat} # As user geneadm on nextgen {noformat} mkdir ~/dev cd ~/dev git clone git://genome-source.cse.ucsc.edu/kent.git cd kent {noformat} # Follow instructions in the README and src/product/README.building.source, briefly: {noformat} export MACHTYPE=x86_64 mkdir -p ~/bin/${MACHTYPE} cd src make libs cd gfServer make cd ../gfClient make cd ../blat make cd ../utils/faToNib make cd ../../hg make cd htdocs make install # Creates web site files in /usr/local/apache {cgi-bin-mccann, htdocs} {noformat} # Setup apache server by creating a /etc/httpd/conf.d/genome-browser.conf file: {noformat} ScriptAlias /cgi-bin/ "/usr/local/apache/cgi-bin-mccann/" # Use same DocumentRoot in sequenceserver so that both can run on the same server DocumentRoot "/usr/local/apache/htdocs/" Options Indexes FollowSymLinks AllowOverride None Order allow,deny Allow from all AllowOverride None Options None Order allow,deny Allow from all Options MultiViews Indexes AllowOverride None Order allow,deny Allow from all {noformat} # Restart httpd and see the server at: * http://nextgen.shore.mbari.org/ ]]> 24052032 24084794 , Emily Reistetter , [Shuangchun "Jeremy" Yan] , Jeltje van Baren , Sam Purvine , Charles Ansong  , Stephen Callister , Josh Stuart , Charles Vaske , Mark Diekhans , Zbigniew S Kolber , Feel free to add or edit pages *For powerpoint presentations of our January meeting, see under Children(below)*\\ \\ \\ \\ \\ h3. Protocols and Procedures [Chemostat]]]> 24052033 24084791 ServerName nextgen.shore.mbari.org DocumentRoot /usr/local/apache/htdocs AllowOverride All Options FollowSymLinks Indexes MultiViews Order allow,deny Allow from all RailsBaseURI /sequenceserver RailsBaseURI /sequenceserver-dbs RailsBaseURI /sequenceserver-meta RailsEnv development {noformat} # Copied sequenceserver gem to additional directories to support multiple databases: {noformat} cd /usr/local/lib/ruby/gems/1.9.1/gems sudo chown mccann . cp -r sequenceserver-0.8.6 sequenceserver-dbs cp -r sequenceserver-0.8.6 sequenceserver-meta sudo chown root . sudo chown -R root sequenceserver-dbs sequenceserver-meta cd /usr/local/apache/htdocs ln -s /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-0.8.6/public sequenceserver ln -s /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-dbs/public sequenceserver-dbs ln -s /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-meta/public sequenceserver-meta {noformat} # Modified /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-dbs/config.ru and /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-meta/config.ru to point to the proper sequenceserver.conf file that points to the proper database. (Setting the SequenceServer::App.config_file = '/absolute/path/to/configuration_file' is described in the FAQ on http://www.sequenceserver.com/) # Restart httpd and see the sequenceservers at: * http://nextgen.shore.mbari.org/sequenceserver-dbs * http://nextgen.shore.mbari.org/sequenceserver-meta h3. UCSC genome-browser - a collection of C cgi-bin programs # As user mccann on nextgen {noformat} sudo yum install mysql sudo yum install mysql-server sudo yum install mysql-devel sudo yum install png-devel sudo /sbin/chkconfig mysql on sudo /sbin/service mysql start {noformat} # Set the mysql root password {noformat} /usr/bin/mysql -u root -p update mysql.user set Password=PASSWORD('xxxx') where User='root'; # See Mike or Rich for the root password {noformat} # As user geneadm on nextgen {noformat} mkdir ~/dev cd ~/dev git clone git://genome-source.cse.ucsc.edu/kent.git cd kent {noformat} # Follow instructions in the README and src/product/README.building.source, briefly: {noformat} export MACHTYPE=x86_64 mkdir -p ~/bin/${MACHTYPE} cd src make libs cd gfServer make cd ../gfClient make cd ../blat make cd ../utils/faToNib make cd ../../hg make cd htdocs make install # Creates web site files in /usr/local/apache {cgi-bin-mccann, htdocs} {noformat} # Setup apache server by creating a /etc/httpd/conf.d/genome-browser.conf file: {noformat} ScriptAlias /cgi-bin/ "/usr/local/apache/cgi-bin-mccann/" # Use same DocumentRoot in sequenceserver so that both can run on the same server DocumentRoot "/usr/local/apache/htdocs/" Options Indexes FollowSymLinks AllowOverride None Order allow,deny Allow from all AllowOverride None Options None Order allow,deny Allow from all Options MultiViews Indexes AllowOverride None Order allow,deny Allow from all {noformat} # Restart httpd and see the server at: * http://nextgen.shore.mbari.org/ ]]> 24052030 16449796 16417038 16449568 16416801 24085032 , Emily Reistetter , [Shuangchun "Jeremy" Yan] , Jeltje van Baren , Sam Purvine , Charles Ansong  , Stephen Callister , Josh Stuart , Charles Vaske , Mark Diekhans , Zbigniew S Kolber , Feel free to add or edit pages *For powerpoint presentations of our January meeting, see under Children(below)*\\ \\ \\ \\ \\ h3. Protocols and Procedures [Chemostat] [Configuring nextgen to run sequenceserver and genome-browser] ]]> 24052272 24085031 CCMP2099_1. Sequence IDs can be rather long, so for instance add the sample ID to them: >MMETSP0022C_CCMP2099_1 # Copy the sequences to the /data/meta (for metatranscriptome and metagenome files) or /data/dbs (for everything else) on nextgen.shore.mbari.org. This can be done using ssh from another computer with username geneadm and password G3n3s4u\! {noformat} scp path/to/fasta geneadm@nextgen.shore.mbari.org:/data/meta {noformat} # Login to nextgen and go to the directory with the sequences {noformat}ssh geneadm@nextgen.shore.mbari.org (same password) cd /data/dbs (or meta) {noformat} # Run {noformat}makeblastdb -dbtype nucl -in -title -parse_seqids {noformat} For protein sequences, dbtype is prot # Restart the sequence server with {noformat}sudo /sbin/service httpd restart{noformat} This will ask you for the password again # Log out with {noformat}exit{noformat} To remove databases, simply remove the files created by makeblastdb and restart the server. \\ \\]]> 24052271 24085029 /data/genome_browser_data/bigwigs/ {noformat} Tell the browser about the new track {noformat} formatTrack (then follow prompts) {noformat} And restart the browser {noformat} cd /data/genome_browser_data/genomes/trackDb && ./loadTracks.sh {noformat} Your new tracks should now show up under the blue RNASeq bar in the browser. They are hidden by default. Tip for pros: you can access the mysql database as \-ubrowser \-pgenome. This might be useful if you want to remove tracks. To remove tracks from the browser page, edit the pages under\\ {noformat} /data/genome_browser_data/genomes/trackDb/CCMP1545/CCMP1545_v3/trackDb.ra and /data/genome_browser_data/genomes/trackDb/RCC299/RCC299_v3/trackDb.ra {noformat}]]> 24052269 16449591 16416825 16449592 16416828 16449594 , Emily Reistetter , Jeremy Yan , Jeltje van Baren , Sam Purvine , Charles Ansong  , Stephen Callister , Josh Stuart , Charles Vaske , Mark Diekhans , Zbigniew S Kolber , Feel free to add or edit pages]]> 16416830 24085014 /data/genome_browser_data/bigwigs/ {noformat} Tell the browser about the new track {noformat} formatTrack (then follow prompts) {noformat} And restart the browser {noformat} cd /data/genome_browser_data/genomes/trackDb && ./loadTracks.sh {noformat} Your new tracks should now show up under the blue RNASeq bar in the browser. They are hidden by default.]]> 24052254 16449589 16416823 24085012 /data/genome_browser_data/bigwigs/ {noformat} Tell the browser about the new track {noformat} formatTrack (then follow prompts) {noformat} And restart the browser {noformat} cd /data/genome_browser_data/genomes/trackDb && ./loadTracks.sh {noformat}]]> 24052252 16449590 16416824 24085002 ServerName sequenceserver.shore.mbari.org DocumentRoot /usr/local/apache/htdocs AllowOverride All Options FollowSymLinks Indexes MultiViews Order allow,deny Allow from all RailsBaseURI /sequenceserver-dbs RailsBaseURI /sequenceserver-meta RailsBaseURI /dbs RailsBaseURI /meta RailsEnv development {noformat} # Copied sequenceserver gem to additional directories to support multiple databases and symlinks for short names on sequenceserver.shore.mbari.org: {noformat} cd /usr/local/lib/ruby/gems/1.9.1/gems sudo chown mccann . cp -r sequenceserver-0.8.6 sequenceserver-dbs cp -r sequenceserver-0.8.6 sequenceserver-meta ln -s sequenceserver-dbs dbs ln -s sequenceserver-meta meta sudo chown root . sudo chown -R root sequenceserver-dbs sequenceserver-meta {noformat} # Create symlinks in /usr/local/apache/htdocs for web pages to work: {noformat} cd /usr/local/apache/htdocs ln -s /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-dbs/public sequenceserver-dbs ln -s /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-dbs/public dbs ln -s /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-meta/public sequenceserver-meta ln -s /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-meta/public meta {noformat} # Modified /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-dbs/config.ru, adding SequenceServer::App.config_file = ... {noformat} require 'rubygems' require 'bundler/setup' require 'sequenceserver' SequenceServer::App.config_file = '/home/geneadm/conf/sequenceserver-dbs.conf' SequenceServer::App.init run SequenceServer::App {noformat} # Modified /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-meta/config.ru, adding SequenceServer::App.config_file = ... {noformat} require 'rubygems' require 'bundler/setup' require 'sequenceserver' SequenceServer::App.config_file = '/home/geneadm/conf/sequenceserver-meta.conf' SequenceServer::App.init run SequenceServer::App {noformat} See the FAQ on http://www.sequenceserver.com/. We found that the config.ru files need to be owned by root for the servers to work. # Restart httpd and see the sequenceservers at: * http://sequenceserver.shore.mbari.org/dbs * http://sequenceserver.shore.mbari.org/meta h3. UCSC genome-browser - a collection of C cgi-bin programs # As user mccann on nextgen {noformat} sudo yum install mysql sudo yum install mysql-server sudo yum install mysql-devel sudo yum install png-devel sudo /sbin/chkconfig mysql on sudo /sbin/service mysql start {noformat} # Set the mysql root password {noformat} /usr/bin/mysql -u root -p update mysql.user set Password=PASSWORD('xxxx') where User='root'; # See Mike or Rich for the root password {noformat} # As user geneadm on nextgen {noformat} mkdir ~/dev cd ~/dev git clone git://genome-source.cse.ucsc.edu/kent.git cd kent {noformat} # Follow instructions in the README and src/product/README.building.source, briefly: {noformat} export MACHTYPE=x86_64 mkdir -p ~/bin/${MACHTYPE} cd src make libs cd gfServer make cd ../gfClient make cd ../blat make cd ../utils/faToNib make cd ../../hg make cd htdocs make install # Creates web site files in /usr/local/apache {cgi-bin-mccann, htdocs} {noformat} # Setup apache server by creating a /etc/httpd/conf.d/genome-browser.conf file: {noformat} ScriptAlias /cgi-bin/ "/usr/local/apache/cgi-bin-mccann/" ServerName genomebrowser.shore.mbari.org DocumentRoot "/usr/local/apache/htdocs/" Options Includes Indexes FollowSymLinks AllowOverride None Order allow,deny Allow from all XBitHack on AllowOverride None Options None Order allow,deny Allow from all Options MultiViews Indexes AllowOverride None Order allow,deny Allow from all {noformat} # Restart httpd and see the server at: * http://genomebrowser.shore.mbari.org/ ]]> 24052243 24085001 ServerName sequenceserver.shore.mbari.org DocumentRoot /usr/local/apache/htdocs AllowOverride All Options FollowSymLinks Indexes MultiViews Order allow,deny Allow from all RailsBaseURI /sequenceserver-dbs RailsBaseURI /sequenceserver-meta RailsBaseURI /dbs RailsBaseURI /meta RailsEnv development {noformat} # Copied sequenceserver gem to additional directories to support multiple databases and symlinks for short names on sequenceserver.shore.mbari.org: {noformat} cd /usr/local/lib/ruby/gems/1.9.1/gems sudo chown mccann . cp -r sequenceserver-0.8.6 sequenceserver-dbs cp -r sequenceserver-0.8.6 sequenceserver-meta ln -s sequenceserver-dbs dbs ln -s sequenceserver-meta meta sudo chown root . sudo chown -R root sequenceserver-dbs sequenceserver-meta {noformat} # Create symlinks in /usr/local/apache/htdocs for web pages to work: {noformat} cd /usr/local/apache/htdocs ln -s /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-dbs/public sequenceserver-dbs ln -s /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-dbs/public dbs ln -s /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-meta/public sequenceserver-meta ln -s /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-meta/public meta {noformat} # Modified /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-dbs/config.ru, adding SequenceServer::App.config_file = ... {noformat} require 'rubygems' require 'bundler/setup' require 'sequenceserver' SequenceServer::App.config_file = '/home/geneadm/conf/sequenceserver-dbs.conf' SequenceServer::App.init run SequenceServer::App {noformat} # Modified /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-meta/config.ru, adding SequenceServer::App.config_file = ... {noformat} require 'rubygems' require 'bundler/setup' require 'sequenceserver' SequenceServer::App.config_file = '/home/geneadm/conf/sequenceserver-meta.conf' SequenceServer::App.init run SequenceServer::App {noformat} See the FAQ on http://www.sequenceserver.com/. We found that the config.ru files need to be owned by root for the servers to work. # Restart httpd and see the sequenceservers at: * -http://nextgen.shore.mbari.org/sequenceserver-dbs- http://sequenceserver.shore.mbari.org/dbs * -http://nextgen.shore.mbari.org/sequenceserver-meta- http://sequenceserver.shore.mbari.org/meta h3. UCSC genome-browser - a collection of C cgi-bin programs # As user mccann on nextgen {noformat} sudo yum install mysql sudo yum install mysql-server sudo yum install mysql-devel sudo yum install png-devel sudo /sbin/chkconfig mysql on sudo /sbin/service mysql start {noformat} # Set the mysql root password {noformat} /usr/bin/mysql -u root -p update mysql.user set Password=PASSWORD('xxxx') where User='root'; # See Mike or Rich for the root password {noformat} # As user geneadm on nextgen {noformat} mkdir ~/dev cd ~/dev git clone git://genome-source.cse.ucsc.edu/kent.git cd kent {noformat} # Follow instructions in the README and src/product/README.building.source, briefly: {noformat} export MACHTYPE=x86_64 mkdir -p ~/bin/${MACHTYPE} cd src make libs cd gfServer make cd ../gfClient make cd ../blat make cd ../utils/faToNib make cd ../../hg make cd htdocs make install # Creates web site files in /usr/local/apache {cgi-bin-mccann, htdocs} {noformat} # Setup apache server by creating a /etc/httpd/conf.d/genome-browser.conf file: {noformat} ScriptAlias /cgi-bin/ "/usr/local/apache/cgi-bin-mccann/" ServerName genomebrowser.shore.mbari.org DocumentRoot "/usr/local/apache/htdocs/" Options Includes Indexes FollowSymLinks AllowOverride None Order allow,deny Allow from all XBitHack on AllowOverride None Options None Order allow,deny Allow from all Options MultiViews Indexes AllowOverride None Order allow,deny Allow from all {noformat} # Restart httpd and see the server at: * http://nextgen.shore.mbari.org/ ]]> 24052242 24084999 ServerName sequenceserver.shore.mbari.org DocumentRoot /usr/local/apache/htdocs AllowOverride All Options FollowSymLinks Indexes MultiViews Order allow,deny Allow from all RailsBaseURI /sequenceserver-dbs RailsBaseURI /sequenceserver-meta RailsBaseURI /dbs RailsBaseURI /meta RailsEnv development {noformat} # Copied sequenceserver gem to additional directories to support multiple databases: {noformat} cd /usr/local/lib/ruby/gems/1.9.1/gems sudo chown mccann . cp -r sequenceserver-0.8.6 sequenceserver-dbs cp -r sequenceserver-0.8.6 sequenceserver-meta ln -s sequenceserver-dbs dbs ln -s sequenceserver-meta meta sudo chown root . sudo chown -R root sequenceserver-dbs sequenceserver-meta {noformat} # Create symlinks in /usr/local/apache/htdocs for web pages to work: {noformat} cd /usr/local/apache/htdocs ln -s /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-dbs/public sequenceserver-dbs ln -s /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-dbs/public dbs ln -s /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-meta/public sequenceserver-meta ln -s /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-meta/public meta {noformat} # Modified /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-dbs/config.ru, adding SequenceServer::App.config_file = ... {noformat} require 'rubygems' require 'bundler/setup' require 'sequenceserver' SequenceServer::App.config_file = '/home/geneadm/conf/sequenceserver-dbs.conf' SequenceServer::App.init run SequenceServer::App {noformat} # Modified /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-meta/config.ru, adding SequenceServer::App.config_file = ... {noformat} require 'rubygems' require 'bundler/setup' require 'sequenceserver' SequenceServer::App.config_file = '/home/geneadm/conf/sequenceserver-meta.conf' SequenceServer::App.init run SequenceServer::App {noformat} See the FAQ on http://www.sequenceserver.com/. We found that the config.ru files need to be owned by root for the servers to work. # Restart httpd and see the sequenceservers at: * http://nextgen.shore.mbari.org/sequenceserver-dbs * http://nextgen.shore.mbari.org/sequenceserver-meta h3. UCSC genome-browser - a collection of C cgi-bin programs # As user mccann on nextgen {noformat} sudo yum install mysql sudo yum install mysql-server sudo yum install mysql-devel sudo yum install png-devel sudo /sbin/chkconfig mysql on sudo /sbin/service mysql start {noformat} # Set the mysql root password {noformat} /usr/bin/mysql -u root -p update mysql.user set Password=PASSWORD('xxxx') where User='root'; # See Mike or Rich for the root password {noformat} # As user geneadm on nextgen {noformat} mkdir ~/dev cd ~/dev git clone git://genome-source.cse.ucsc.edu/kent.git cd kent {noformat} # Follow instructions in the README and src/product/README.building.source, briefly: {noformat} export MACHTYPE=x86_64 mkdir -p ~/bin/${MACHTYPE} cd src make libs cd gfServer make cd ../gfClient make cd ../blat make cd ../utils/faToNib make cd ../../hg make cd htdocs make install # Creates web site files in /usr/local/apache {cgi-bin-mccann, htdocs} {noformat} # Setup apache server by creating a /etc/httpd/conf.d/genome-browser.conf file: {noformat} ScriptAlias /cgi-bin/ "/usr/local/apache/cgi-bin-mccann/" ServerName genomebrowser.shore.mbari.org DocumentRoot "/usr/local/apache/htdocs/" Options Includes Indexes FollowSymLinks AllowOverride None Order allow,deny Allow from all XBitHack on AllowOverride None Options None Order allow,deny Allow from all Options MultiViews Indexes AllowOverride None Order allow,deny Allow from all {noformat} # Restart httpd and see the server at: * http://nextgen.shore.mbari.org/ ]]> 24052240 24084997 ServerName sequenceserver.shore.mbari.org DocumentRoot /usr/local/apache/htdocs AllowOverride All Options FollowSymLinks Indexes MultiViews Order allow,deny Allow from all RailsBaseURI /sequenceserver-dbs RailsBaseURI /sequenceserver-meta RailsBaseURI /dbs RailsBaseURI /meta RailsEnv development {noformat} # Copied sequenceserver gem to additional directories to support multiple databases: {noformat} cd /usr/local/lib/ruby/gems/1.9.1/gems sudo chown mccann . cp -r sequenceserver-0.8.6 sequenceserver-dbs cp -r sequenceserver-0.8.6 sequenceserver-meta sudo chown root . sudo chown -R root sequenceserver-dbs sequenceserver-meta cd /usr/local/apache/htdocs ln -s /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-0.8.6/public sequenceserver ln -s /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-dbs/public sequenceserver-dbs ln -s /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-meta/public sequenceserver-meta {noformat} # Modified /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-dbs/config.ru, adding SequenceServer::App.config_file = ... {noformat} require 'rubygems' require 'bundler/setup' require 'sequenceserver' SequenceServer::App.config_file = '/home/geneadm/conf/sequenceserver-dbs.conf' SequenceServer::App.init run SequenceServer::App {noformat} # Modified /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-meta/config.ru, adding SequenceServer::App.config_file = ... {noformat} require 'rubygems' require 'bundler/setup' require 'sequenceserver' SequenceServer::App.config_file = '/home/geneadm/conf/sequenceserver-meta.conf' SequenceServer::App.init run SequenceServer::App {noformat} See the FAQ on http://www.sequenceserver.com/. We found that the config.ru files need to be owned by root for the servers to work. # Restart httpd and see the sequenceservers at: * http://nextgen.shore.mbari.org/sequenceserver-dbs * http://nextgen.shore.mbari.org/sequenceserver-meta h3. UCSC genome-browser - a collection of C cgi-bin programs # As user mccann on nextgen {noformat} sudo yum install mysql sudo yum install mysql-server sudo yum install mysql-devel sudo yum install png-devel sudo /sbin/chkconfig mysql on sudo /sbin/service mysql start {noformat} # Set the mysql root password {noformat} /usr/bin/mysql -u root -p update mysql.user set Password=PASSWORD('xxxx') where User='root'; # See Mike or Rich for the root password {noformat} # As user geneadm on nextgen {noformat} mkdir ~/dev cd ~/dev git clone git://genome-source.cse.ucsc.edu/kent.git cd kent {noformat} # Follow instructions in the README and src/product/README.building.source, briefly: {noformat} export MACHTYPE=x86_64 mkdir -p ~/bin/${MACHTYPE} cd src make libs cd gfServer make cd ../gfClient make cd ../blat make cd ../utils/faToNib make cd ../../hg make cd htdocs make install # Creates web site files in /usr/local/apache {cgi-bin-mccann, htdocs} {noformat} # Setup apache server by creating a /etc/httpd/conf.d/genome-browser.conf file: {noformat} ScriptAlias /cgi-bin/ "/usr/local/apache/cgi-bin-mccann/" ServerName genomebrowser.shore.mbari.org DocumentRoot "/usr/local/apache/htdocs/" Options Includes Indexes FollowSymLinks AllowOverride None Order allow,deny Allow from all XBitHack on AllowOverride None Options None Order allow,deny Allow from all Options MultiViews Indexes AllowOverride None Order allow,deny Allow from all {noformat} # Restart httpd and see the server at: * http://nextgen.shore.mbari.org/ ]]> 24052238 24084995 ServerName nextgen.shore.mbari.org DocumentRoot /usr/local/apache/htdocs AllowOverride All Options FollowSymLinks Indexes MultiViews Order allow,deny Allow from all RailsBaseURI /sequenceserver RailsBaseURI /sequenceserver-dbs RailsBaseURI /sequenceserver-meta RailsEnv development {noformat} # Copied sequenceserver gem to additional directories to support multiple databases: {noformat} cd /usr/local/lib/ruby/gems/1.9.1/gems sudo chown mccann . cp -r sequenceserver-0.8.6 sequenceserver-dbs cp -r sequenceserver-0.8.6 sequenceserver-meta sudo chown root . sudo chown -R root sequenceserver-dbs sequenceserver-meta cd /usr/local/apache/htdocs ln -s /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-0.8.6/public sequenceserver ln -s /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-dbs/public sequenceserver-dbs ln -s /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-meta/public sequenceserver-meta {noformat} # Modified /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-dbs/config.ru, adding SequenceServer::App.config_file = ... {noformat} require 'rubygems' require 'bundler/setup' require 'sequenceserver' SequenceServer::App.config_file = '/home/geneadm/conf/sequenceserver-dbs.conf' SequenceServer::App.init run SequenceServer::App {noformat} # Modified /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-meta/config.ru, adding SequenceServer::App.config_file = ... {noformat} require 'rubygems' require 'bundler/setup' require 'sequenceserver' SequenceServer::App.config_file = '/home/geneadm/conf/sequenceserver-meta.conf' SequenceServer::App.init run SequenceServer::App {noformat} See the FAQ on http://www.sequenceserver.com/. We found that the config.ru files need to be owned by root for the servers to work. # Restart httpd and see the sequenceservers at: * http://nextgen.shore.mbari.org/sequenceserver-dbs * http://nextgen.shore.mbari.org/sequenceserver-meta h3. UCSC genome-browser - a collection of C cgi-bin programs # As user mccann on nextgen {noformat} sudo yum install mysql sudo yum install mysql-server sudo yum install mysql-devel sudo yum install png-devel sudo /sbin/chkconfig mysql on sudo /sbin/service mysql start {noformat} # Set the mysql root password {noformat} /usr/bin/mysql -u root -p update mysql.user set Password=PASSWORD('xxxx') where User='root'; # See Mike or Rich for the root password {noformat} # As user geneadm on nextgen {noformat} mkdir ~/dev cd ~/dev git clone git://genome-source.cse.ucsc.edu/kent.git cd kent {noformat} # Follow instructions in the README and src/product/README.building.source, briefly: {noformat} export MACHTYPE=x86_64 mkdir -p ~/bin/${MACHTYPE} cd src make libs cd gfServer make cd ../gfClient make cd ../blat make cd ../utils/faToNib make cd ../../hg make cd htdocs make install # Creates web site files in /usr/local/apache {cgi-bin-mccann, htdocs} {noformat} # Setup apache server by creating a /etc/httpd/conf.d/genome-browser.conf file: {noformat} ScriptAlias /cgi-bin/ "/usr/local/apache/cgi-bin-mccann/" # Use same DocumentRoot in sequenceserver so that both can run on the same server DocumentRoot "/usr/local/apache/htdocs/" Options Indexes FollowSymLinks AllowOverride None Order allow,deny Allow from all AllowOverride None Options None Order allow,deny Allow from all Options MultiViews Indexes AllowOverride None Order allow,deny Allow from all {noformat} # Restart httpd and see the server at: * http://nextgen.shore.mbari.org/ ]]> 24052236 24085009 CCMP2099_1. Sequence IDs can be rather long, so for instance add the sample ID to them: >MMETSP0022C_CCMP2099_1 # Copy the sequences to the /data/meta (for metatranscriptome and metagenome files) or /data/dbs (for everything else) on nextgen.shore.mbari.org. This can be done using ssh from another computer with username geneadm and password G3n3s4u\! # Login to nextgen with ssh geneadm@nextgen.shore.mbari.org (same password), then cd /data/dbs (or meta) to go to the directory with the sequences # Run makeblastdb \-dbtype nucl \-in \-title \-parse_seqids For protein sequences, dbtype is prot # Restart the sequence server with sudo /sbin/service httpd restart This will ask you for the password again # Log out with exit To remove databases, simply remove the files created by makeblastdb and restart the server. \\ \\]]> 24052249 24085004 ServerName sequenceserver.shore.mbari.org DocumentRoot /usr/local/apache/htdocs AllowOverride All Options FollowSymLinks Indexes MultiViews Order allow,deny Allow from all RailsBaseURI /sequenceserver-dbs RailsBaseURI /sequenceserver-meta RailsBaseURI /dbs RailsBaseURI /meta RailsEnv development {noformat} # Copied sequenceserver gem to additional directories to support multiple databases and symlinks for short names on sequenceserver.shore.mbari.org: {noformat} cd /usr/local/lib/ruby/gems/1.9.1/gems sudo chown mccann . cp -r sequenceserver-0.8.6 sequenceserver-dbs cp -r sequenceserver-0.8.6 sequenceserver-meta ln -s sequenceserver-dbs dbs ln -s sequenceserver-meta meta sudo chown root . sudo chown -R root sequenceserver-dbs sequenceserver-meta {noformat} # Create symlinks in /usr/local/apache/htdocs for web pages to work: {noformat} cd /usr/local/apache/htdocs ln -s /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-dbs/public sequenceserver-dbs ln -s /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-dbs/public dbs ln -s /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-meta/public sequenceserver-meta ln -s /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-meta/public meta {noformat} # Modified /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-dbs/config.ru, adding SequenceServer::App.config_file = ... {noformat} require 'rubygems' require 'bundler/setup' require 'sequenceserver' *SequenceServer::App.config_file = '/home/geneadm/conf/sequenceserver-dbs.conf'* SequenceServer::App.init run SequenceServer::App {noformat} # Modified /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-meta/config.ru, adding SequenceServer::App.config_file = ... {noformat} require 'rubygems' require 'bundler/setup' require 'sequenceserver' SequenceServer::App.config_file = '/home/geneadm/conf/sequenceserver-meta.conf' SequenceServer::App.init run SequenceServer::App {noformat} See the FAQ on http://www.sequenceserver.com/. We found that the config.ru files need to be owned by root for the servers to work. # Restart httpd and see the sequenceservers at: * http://sequenceserver.shore.mbari.org/dbs * http://sequenceserver.shore.mbari.org/meta h3. UCSC genome-browser - a collection of C cgi-bin programs # As user mccann on nextgen {noformat} sudo yum install mysql sudo yum install mysql-server sudo yum install mysql-devel sudo yum install png-devel sudo /sbin/chkconfig mysql on sudo /sbin/service mysql start {noformat} # Set the mysql root password {noformat} /usr/bin/mysql -u root -p update mysql.user set Password=PASSWORD('xxxx') where User='root'; # See Mike or Rich for the root password {noformat} # As user geneadm on nextgen {noformat} mkdir ~/dev cd ~/dev git clone git://genome-source.cse.ucsc.edu/kent.git cd kent {noformat} # Follow instructions in the README and src/product/README.building.source, briefly: {noformat} export MACHTYPE=x86_64 mkdir -p ~/bin/${MACHTYPE} cd src make libs cd gfServer make cd ../gfClient make cd ../blat make cd ../utils/faToNib make cd ../../hg make cd htdocs make install # Creates web site files in /usr/local/apache {cgi-bin-mccann, htdocs} {noformat} # Setup apache server by creating a /etc/httpd/conf.d/genome-browser.conf file: {noformat} ScriptAlias /cgi-bin/ "/usr/local/apache/cgi-bin-mccann/" ServerName genomebrowser.shore.mbari.org DocumentRoot "/usr/local/apache/htdocs/" Options Includes Indexes FollowSymLinks AllowOverride None Order allow,deny Allow from all XBitHack on AllowOverride None Options None Order allow,deny Allow from all Options MultiViews Indexes AllowOverride None Order allow,deny Allow from all {noformat} # Restart httpd and see the server at: * http://genomebrowser.shore.mbari.org/ ]]> 24052245 24085003 ServerName sequenceserver.shore.mbari.org DocumentRoot /usr/local/apache/htdocs AllowOverride All Options FollowSymLinks Indexes MultiViews Order allow,deny Allow from all RailsBaseURI /sequenceserver-dbs RailsBaseURI /sequenceserver-meta RailsBaseURI /dbs RailsBaseURI /meta RailsEnv development {noformat} # Copied sequenceserver gem to additional directories to support multiple databases and symlinks for short names on sequenceserver.shore.mbari.org: {noformat} cd /usr/local/lib/ruby/gems/1.9.1/gems sudo chown mccann . cp -r sequenceserver-0.8.6 sequenceserver-dbs cp -r sequenceserver-0.8.6 sequenceserver-meta ln -s sequenceserver-dbs dbs ln -s sequenceserver-meta meta sudo chown root . sudo chown -R root sequenceserver-dbs sequenceserver-meta {noformat} # Create symlinks in /usr/local/apache/htdocs for web pages to work: {noformat} cd /usr/local/apache/htdocs ln -s /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-dbs/public sequenceserver-dbs ln -s /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-dbs/public dbs ln -s /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-meta/public sequenceserver-meta ln -s /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-meta/public meta {noformat} # Modified /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-dbs/config.ru, adding SequenceServer::App.config_file = ... {noformat} require 'rubygems' require 'bundler/setup' require 'sequenceserver' SequenceServer::App.config_file = '/home/geneadm/conf/sequenceserver-dbs.conf' SequenceServer::App.init run SequenceServer::App {noformat} # Modified /usr/local/lib/ruby/gems/1.9.1/gems/sequenceserver-meta/config.ru, adding SequenceServer::App.config_file = ... {noformat} require 'rubygems' require 'bundler/setup' require 'sequenceserver' SequenceServer::App.config_file = '/home/geneadm/conf/sequenceserver-meta.conf' SequenceServer::App.init run SequenceServer::App {noformat} See the FAQ on http://www.sequenceserver.com/. We found that the config.ru files need to be owned by root for the servers to work. # Restart httpd and see the sequenceservers at: * http://sequenceserver.shore.mbari.org/dbs * http://sequenceserver.shore.mbari.org/meta h3. UCSC genome-browser - a collection of C cgi-bin programs # As user mccann on nextgen {noformat} sudo yum install mysql sudo yum install mysql-server sudo yum install mysql-devel sudo yum install png-devel sudo /sbin/chkconfig mysql on sudo /sbin/service mysql start {noformat} # Set the mysql root password {noformat} /usr/bin/mysql -u root -p update mysql.user set Password=PASSWORD('xxxx') where User='root'; # See Mike or Rich for the root password {noformat} # As user geneadm on nextgen {noformat} mkdir ~/dev cd ~/dev git clone git://genome-source.cse.ucsc.edu/kent.git cd kent {noformat} # Follow instructions in the README and src/product/README.building.source, briefly: {noformat} export MACHTYPE=x86_64 mkdir -p ~/bin/${MACHTYPE} cd src make libs cd gfServer make cd ../gfClient make cd ../blat make cd ../utils/faToNib make cd ../../hg make cd htdocs make install # Creates web site files in /usr/local/apache {cgi-bin-mccann, htdocs} {noformat} # Setup apache server by creating a /etc/httpd/conf.d/genome-browser.conf file: {noformat} ScriptAlias /cgi-bin/ "/usr/local/apache/cgi-bin-mccann/" ServerName genomebrowser.shore.mbari.org DocumentRoot "/usr/local/apache/htdocs/" Options Includes Indexes FollowSymLinks AllowOverride None Order allow,deny Allow from all XBitHack on AllowOverride None Options None Order allow,deny Allow from all Options MultiViews Indexes AllowOverride None Order allow,deny Allow from all {noformat} # Restart httpd and see the server at: * http://genomebrowser.shore.mbari.org/ ]]> 24052244 24052246 5 false 0.0 0 0 16417005 5 false 0.0 0 0 24051999 6 false 0.0 0 0 24051999 5 false 0.0 0 0 16777303 5 false 0.0 0 0 16416802 5 false 0.0 0 0 16416822 5 false 0.0 0 0 16416802 6 false 0.0 0 0 16777303 6 false 0.0 0 0 24052246 6 false 0.0 0 0 16417005 6 false 0.0 0 0 16416822 6 false 0.0 0 0 16417023 5 false 0.0 0 0 24052251 5 false 0.0 0 0 16417023 6 false 0.0 0 0 24052251 6 false 0.0 0 0