Difference between revisions of "Oge-coge installation"
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− | Create new mysql database | + | ==Create new mysql database== |
*Create new CoGe Database | *Create new CoGe Database | ||
− | create database | + | create database coge |
+ | |||
+ | *Initialize new coge database | ||
+ | |||
+ | mysql -u root -pXXXXXXXX coge < cogetable.sql | ||
+ | |||
+ | |||
+ | ==Deploy new CoGe Web-site== | ||
+ | *Retrieve code-base from SVN (need to update this to a new repository) | ||
+ | *coge.iplantc.org's ssh runs on port 1657. | ||
+ | *Add the following line to your subversion/config file (under the tunnels directive): | ||
+ | |||
+ | [tunnels] | ||
+ | sshtunnel = ssh -p 1657 | ||
+ | |||
+ | *Next, get the CoGE-web repo | ||
+ | svn co svn+sshtunnel://coge.iplantcollaborative.org/storage/SVN.d/CoGe-web | ||
+ | |||
+ | |||
+ | *make directories where files go and give write persmission | ||
+ | |||
+ | mkdir tmp; | ||
+ | chmod 777 tmp/; | ||
+ | |||
+ | cd data/; | ||
+ | mkdir image_cache; | ||
+ | chmod 777 image_cache/; | ||
+ | mkdir genomic_sequence; | ||
+ | chmod 777 genomic_sequence/; | ||
+ | mkdir diags; | ||
+ | chmod 777 diags/; | ||
+ | mkdir bed; | ||
+ | chmod 777 bed/; | ||
+ | mkdir fasta; | ||
+ | chmod 777 fasta/; | ||
+ | mkdir blast/db; | ||
+ | chmod 777 blast/db/; | ||
+ | |||
+ | *configure httpd.conf | ||
+ | |||
+ | sudo vi /etc/httpd/conf/httpd.conf | ||
+ | |||
+ | ScriptAlias /ocoge/ "/var/www/html/ocoge/" | ||
+ | Alias /ocoge "/var/www/html/ocoge" | ||
+ | <Directory "/var/www/html/ocoge"> | ||
+ | # PerlInitHandler Apache2::Reload | ||
+ | Options Includes Indexes ExecCGI FollowSymLinks | ||
+ | AllowOverride None | ||
+ | SetEnv HOME "/var/www/html/ocoge/" | ||
+ | Order allow,deny | ||
+ | Allow from all | ||
+ | </Directory> | ||
+ | |||
+ | *Configure coge.conf file | ||
+ | |||
+ | ##This is a configuration file for CoGe. | ||
+ | ##Key Value pairs: | ||
+ | ##<NAME> <PATH> | ||
+ | |||
+ | #database configuration | ||
+ | DBNAME coge | ||
+ | DBHOST localhost | ||
+ | DBPORT 3306 | ||
+ | DBUSER coge_web | ||
+ | DBPASS ****** | ||
+ | |||
+ | #web cookie name | ||
+ | COOKIE_NAME cogec | ||
+ | |||
+ | #basedir for coge | ||
+ | COGEDIR /var/www/html/ocoge | ||
+ | |||
+ | #bin dir for coge's programs | ||
+ | BINDIR /var/www/html/ocoge/bin/ | ||
+ | |||
+ | #data dir for coge's programs | ||
+ | DATADIR /var/www/html/ocoge/data/ | ||
+ | |||
+ | #dir for pair-wise whole genome comparisons (e.g. SynMap) | ||
+ | DIAGSDIR /var/www/html/ocoge/data/diags/ | ||
+ | |||
+ | #fasta dir | ||
+ | FASTADIR /var/www/html/ocoge/data/fasta/ | ||
+ | |||
+ | #TMPL dir for CoGe's web page templates | ||
+ | TMPLDIR /var/www/html/ocoge/tmpl/ | ||
+ | |||
+ | #temp dir for coge | ||
+ | TEMPDIR /var/www/html/ocoge/tmp/ | ||
+ | |||
+ | #Base URL for web-site | ||
+ | URL /ocoge/ | ||
+ | |||
+ | #URL for temp directory | ||
+ | TEMPURL /ocoge/tmp/ | ||
+ | |||
+ | #blast style scoring matrix dirs | ||
+ | BLASTMATRIX /var/www/html/ocoge/data/blast/matrix/ | ||
+ | |||
+ | #blastable DB | ||
+ | BLASTDB /var/www/html/ocoge/data/blast/db/ | ||
+ | |||
+ | #lastable DB | ||
+ | LASTDB /var/www/html/ocoge/data/last/db/ | ||
+ | |||
+ | #directory for bed files | ||
+ | BEDDIR /var/www/html/ocoge/data/bed/ | ||
+ | |||
+ | #servername for links | ||
+ | #SERVER http://coge.iplantcollaborative.org/CoGe/ | ||
+ | SERVER http://sma.genome.arizona.edu/ocoge/ | ||
+ | |||
+ | #directory for caching genome browser images | ||
+ | IMAGE_CACHE /var/www/html/ocoge/data/image_cache/ | ||
+ | |||
+ | #maximum number of processor to use for multi-CPU systems | ||
+ | MAX_PROC 15 | ||
+ | COGE_BLAST_MAX_PROC 8 | ||
+ | |||
+ | #True Type Font | ||
+ | FONT /usr/local/lib/perl5/site_perl/5.12.4/CoGe/fonts/arial.ttf | ||
+ | |||
+ | #various programs | ||
+ | BL2SEQ /home/genome/linux/bin/bl2seq | ||
+ | BLASTZ /opt/blastz-source/blastz | ||
+ | LASTZ /opt/lastz-distrib-1.02.00/src/lastz | ||
+ | MULTI_LASTZ /var/www/html/ocoge/bin/blastz_wrapper/blastz.py | ||
+ | LAST_PATH /var/www/html/ocoge/bin/last_wrapper/ | ||
+ | MULTI_LAST /var/www/html/ocoge/bin/last_wrapper/last.py | ||
+ | #BLAST 2.2.23+ | ||
+ | BLAST /home/genome/linux/bin/blastall | ||
+ | TBLASTN /usr/bin/tblastn | ||
+ | BLASTN /usr/bin/blastn | ||
+ | BLASTP /usr/bin/blastp | ||
+ | TBLASTX /usr/bin/tblastx | ||
+ | |||
+ | FORMATDB /home/genome/linux/bin/formatdb | ||
+ | LAGAN /var/www/html/ocoge/bin/lagan-64bit/lagan.pl | ||
+ | LAGANDIR /var/www/html/ocoge/bin/lagan-64bit/ | ||
+ | CHAOS /var/www/html/ocoge/bin/lagan-64bit/chaos | ||
+ | GENOMETHREADER /var/www/html/ocoge/bin/gth | ||
+ | DIALIGN /var/www/html/ocoge/bin/dialign2_dir/dialign2-2_coge | ||
+ | DIALIGN2 /var/www/html/ocoge/bin/dialign2_dir/dialign2-2_coge | ||
+ | DIALIGN2_DIR /var/www/html/ocoge/bin/dialign2_dir/ | ||
+ | HISTOGRAM /var/www/html/ocoge/bin/histogram.pl | ||
+ | KS_HISTOGRAM /var/www/html/ocoge/bin/ks_histogram.pl | ||
+ | PYTHON /usr/bin/python | ||
+ | DAG_TOOL /var/www/html/ocoge/bin/SynMap/dag_tools.py | ||
+ | BLAST2BED /var/www/html/ocoge/bin/SynMap/blast2bed.pl | ||
+ | TANDEM_FINDER /var/www/html/ocoge/bin/dagchainer/tandems.py | ||
+ | DAGCHAINER /var/www/html/ocoge/bin/dagchainer_bp/dag_chainer.py | ||
+ | EVALUE_ADJUST /var/www/html/ocoge/bin/dagchainer_bp/dagtools/evalue_adjust.py | ||
+ | FIND_NEARBY /var/www/html/ocoge/bin/dagchainer_bp/dagtools/find_nearby.py | ||
+ | QUOTA_ALIGN /var/www/html/ocoge/bin/quota-alignment/quota_align.py | ||
+ | CLUSTER_UTILS /var/www/html/ocoge/bin/quota-alignment/cluster_utils.py | ||
+ | BLAST2RAW /var/www/html/ocoge/bin/quota-alignment/scripts/blast_to_raw.py | ||
+ | SYNTENY_SCORE /var/www/html/ocoge/bin/quota-alignment/scripts/synteny_score.py | ||
+ | DOTPLOT /var/www/html/ocoge/bin/dotplot.pl | ||
+ | SVG_DOTPLOT /var/www/html/ocoge/bin/SynMap/dotplot.py | ||
+ | NWALIGN /opt/nwalign-0.3.1/nwalign | ||
+ | CODEML /var/www/html/ocoge/bin/codeml/codeml-coge | ||
+ | CODEMLCTL /var/www/html/ocoge/bin/codeml/codeml.ctl | ||
+ | CONVERT_BLAST /var/www/html/ocoge/bin/convert_long_blast_to_short_blast_names.pl | ||
+ | DATASETGROUP2BED /var/www/html/ocoge/bin/dataset_group_2_bed.pl | ||
+ | ARAGORN /usr/local/bin/aragorn | ||
+ | CLUSTALW /home/genome/linux/bin/clustalw | ||
+ | GZIP /bin/gzip | ||
+ | GUNZIP /bin/gunzip | ||
+ | TAR /bin/tar | ||
+ | |||
+ | #MotifView | ||
+ | |||
+ | MOTIF_FILE /opt/apache/CoGe/bin/MotifView/motif_hash_dump | ||
+ | |||
+ | #stuff for Mauve and whole genome alignments | ||
+ | MAUVE /opt/apache/CoGe/bin/GenomeAlign/progressiveMauve-muscleMatrix | ||
+ | COGE_MAUVE /opt/apache/CoGe/bin/GenomeAlign/mauve_alignment.pl | ||
+ | MAUVE_MATRIX /opt/apache/CoGe/data/blast/matrix/nt/Mauve-Matrix-GenomeAlign | ||
+ | #newicktops is part of njplot package | ||
+ | NEWICKTOPS /usr/bin/newicktops | ||
+ | #convert is from ImageMagic | ||
+ | CONVERT /usr/bin/convert | ||
+ | #from graphviz | ||
+ | DOT | ||
+ | NEATO | ||
+ | |||
+ | |||
+ | ==Installing Cogex== | ||
+ | |||
+ | Contains the libraries for connecting to the CoGe Database | ||
+ | Contains the accessory scripts for managing data in the CoGe Database | ||
+ | svn co svn+sshtunnel://coge.iplantcollaborative.org/storage/SVN.d/CoGeX | ||
+ | |||
+ | Put it under /usr/local/lib/perl5/site_perl/5.12.4/ | ||
+ | |||
+ | |||
+ | ==Checking available modules on the system:== | ||
+ | instmodsh | ||
+ | |||
+ | |||
+ | |||
+ | ==Required perl modules:== | ||
+ | JSON/XS.pm -> perl-JSON-XS.x86_64 | ||
+ | common/sense.pm-> perl-common-sense.x86_64 | ||
+ | CGI/Ajax.pm -> perl-CGI.x86_64 | ||
+ | CGI/Ajax.pm-> perl-CGI-Ajax.noarch | ||
+ | CoGe/Accessory/LogUser.pm | ||
+ | CoGe/Accessory/Web.pm | ||
+ | CoGeX.pm | ||
+ | Image/Size.pm -> perl-Image-Size.noarch | ||
+ | CoGe/Graphics.pm | ||
+ | CNS/Expression/Graphics/Var_Means_Tree.pm | ||
+ | AuthCAS.pm | ||
+ | Sort/Versions.pm | ||
+ | DBIxProfiler.pm | ||
+ | |||
+ | |||
+ | ==Check where the perl modules are installed :== | ||
+ | |||
+ | sudo rpm -qal perl-CGI-Ajax | ||
+ | or | ||
+ | instmodsh | ||
+ | or | ||
+ | rpm -qa | grep "perl" | ||
+ | |||
+ | |||
+ | |||
+ | ==To find the port number of the database :== | ||
+ | nmap localhost |
Latest revision as of 10:52, 30 July 2012
Contents
Create new mysql database
- Create new CoGe Database
create database coge
- Initialize new coge database
mysql -u root -pXXXXXXXX coge < cogetable.sql
Deploy new CoGe Web-site
- Retrieve code-base from SVN (need to update this to a new repository)
- coge.iplantc.org's ssh runs on port 1657.
- Add the following line to your subversion/config file (under the tunnels directive):
[tunnels] sshtunnel = ssh -p 1657
- Next, get the CoGE-web repo
svn co svn+sshtunnel://coge.iplantcollaborative.org/storage/SVN.d/CoGe-web
- make directories where files go and give write persmission
mkdir tmp; chmod 777 tmp/;
cd data/; mkdir image_cache; chmod 777 image_cache/; mkdir genomic_sequence; chmod 777 genomic_sequence/; mkdir diags; chmod 777 diags/; mkdir bed; chmod 777 bed/; mkdir fasta; chmod 777 fasta/; mkdir blast/db; chmod 777 blast/db/;
- configure httpd.conf
sudo vi /etc/httpd/conf/httpd.conf
ScriptAlias /ocoge/ "/var/www/html/ocoge/" Alias /ocoge "/var/www/html/ocoge" <Directory "/var/www/html/ocoge"> # PerlInitHandler Apache2::Reload Options Includes Indexes ExecCGI FollowSymLinks AllowOverride None SetEnv HOME "/var/www/html/ocoge/" Order allow,deny Allow from all </Directory>
- Configure coge.conf file
##This is a configuration file for CoGe. ##Key Value pairs: ##<NAME> <PATH>
#database configuration DBNAME coge DBHOST localhost DBPORT 3306 DBUSER coge_web DBPASS ******
#web cookie name COOKIE_NAME cogec
#basedir for coge COGEDIR /var/www/html/ocoge
#bin dir for coge's programs BINDIR /var/www/html/ocoge/bin/
#data dir for coge's programs DATADIR /var/www/html/ocoge/data/
#dir for pair-wise whole genome comparisons (e.g. SynMap) DIAGSDIR /var/www/html/ocoge/data/diags/
#fasta dir FASTADIR /var/www/html/ocoge/data/fasta/
#TMPL dir for CoGe's web page templates TMPLDIR /var/www/html/ocoge/tmpl/
#temp dir for coge TEMPDIR /var/www/html/ocoge/tmp/
#Base URL for web-site URL /ocoge/
#URL for temp directory TEMPURL /ocoge/tmp/
#blast style scoring matrix dirs BLASTMATRIX /var/www/html/ocoge/data/blast/matrix/
#blastable DB BLASTDB /var/www/html/ocoge/data/blast/db/
#lastable DB LASTDB /var/www/html/ocoge/data/last/db/
#directory for bed files BEDDIR /var/www/html/ocoge/data/bed/
#servername for links #SERVER http://coge.iplantcollaborative.org/CoGe/ SERVER http://sma.genome.arizona.edu/ocoge/
#directory for caching genome browser images IMAGE_CACHE /var/www/html/ocoge/data/image_cache/
#maximum number of processor to use for multi-CPU systems MAX_PROC 15 COGE_BLAST_MAX_PROC 8
#True Type Font FONT /usr/local/lib/perl5/site_perl/5.12.4/CoGe/fonts/arial.ttf
#various programs BL2SEQ /home/genome/linux/bin/bl2seq BLASTZ /opt/blastz-source/blastz LASTZ /opt/lastz-distrib-1.02.00/src/lastz MULTI_LASTZ /var/www/html/ocoge/bin/blastz_wrapper/blastz.py LAST_PATH /var/www/html/ocoge/bin/last_wrapper/ MULTI_LAST /var/www/html/ocoge/bin/last_wrapper/last.py #BLAST 2.2.23+ BLAST /home/genome/linux/bin/blastall TBLASTN /usr/bin/tblastn BLASTN /usr/bin/blastn BLASTP /usr/bin/blastp TBLASTX /usr/bin/tblastx
FORMATDB /home/genome/linux/bin/formatdb LAGAN /var/www/html/ocoge/bin/lagan-64bit/lagan.pl LAGANDIR /var/www/html/ocoge/bin/lagan-64bit/ CHAOS /var/www/html/ocoge/bin/lagan-64bit/chaos GENOMETHREADER /var/www/html/ocoge/bin/gth DIALIGN /var/www/html/ocoge/bin/dialign2_dir/dialign2-2_coge DIALIGN2 /var/www/html/ocoge/bin/dialign2_dir/dialign2-2_coge DIALIGN2_DIR /var/www/html/ocoge/bin/dialign2_dir/ HISTOGRAM /var/www/html/ocoge/bin/histogram.pl KS_HISTOGRAM /var/www/html/ocoge/bin/ks_histogram.pl PYTHON /usr/bin/python DAG_TOOL /var/www/html/ocoge/bin/SynMap/dag_tools.py BLAST2BED /var/www/html/ocoge/bin/SynMap/blast2bed.pl TANDEM_FINDER /var/www/html/ocoge/bin/dagchainer/tandems.py DAGCHAINER /var/www/html/ocoge/bin/dagchainer_bp/dag_chainer.py EVALUE_ADJUST /var/www/html/ocoge/bin/dagchainer_bp/dagtools/evalue_adjust.py FIND_NEARBY /var/www/html/ocoge/bin/dagchainer_bp/dagtools/find_nearby.py QUOTA_ALIGN /var/www/html/ocoge/bin/quota-alignment/quota_align.py CLUSTER_UTILS /var/www/html/ocoge/bin/quota-alignment/cluster_utils.py BLAST2RAW /var/www/html/ocoge/bin/quota-alignment/scripts/blast_to_raw.py SYNTENY_SCORE /var/www/html/ocoge/bin/quota-alignment/scripts/synteny_score.py DOTPLOT /var/www/html/ocoge/bin/dotplot.pl SVG_DOTPLOT /var/www/html/ocoge/bin/SynMap/dotplot.py NWALIGN /opt/nwalign-0.3.1/nwalign CODEML /var/www/html/ocoge/bin/codeml/codeml-coge CODEMLCTL /var/www/html/ocoge/bin/codeml/codeml.ctl CONVERT_BLAST /var/www/html/ocoge/bin/convert_long_blast_to_short_blast_names.pl DATASETGROUP2BED /var/www/html/ocoge/bin/dataset_group_2_bed.pl ARAGORN /usr/local/bin/aragorn CLUSTALW /home/genome/linux/bin/clustalw GZIP /bin/gzip GUNZIP /bin/gunzip TAR /bin/tar
#MotifView
MOTIF_FILE /opt/apache/CoGe/bin/MotifView/motif_hash_dump
#stuff for Mauve and whole genome alignments MAUVE /opt/apache/CoGe/bin/GenomeAlign/progressiveMauve-muscleMatrix COGE_MAUVE /opt/apache/CoGe/bin/GenomeAlign/mauve_alignment.pl MAUVE_MATRIX /opt/apache/CoGe/data/blast/matrix/nt/Mauve-Matrix-GenomeAlign #newicktops is part of njplot package NEWICKTOPS /usr/bin/newicktops #convert is from ImageMagic CONVERT /usr/bin/convert #from graphviz DOT NEATO
Installing Cogex
Contains the libraries for connecting to the CoGe Database Contains the accessory scripts for managing data in the CoGe Database svn co svn+sshtunnel://coge.iplantcollaborative.org/storage/SVN.d/CoGeX
Put it under /usr/local/lib/perl5/site_perl/5.12.4/
Checking available modules on the system:
instmodsh
Required perl modules:
JSON/XS.pm -> perl-JSON-XS.x86_64 common/sense.pm-> perl-common-sense.x86_64 CGI/Ajax.pm -> perl-CGI.x86_64 CGI/Ajax.pm-> perl-CGI-Ajax.noarch CoGe/Accessory/LogUser.pm CoGe/Accessory/Web.pm CoGeX.pm Image/Size.pm -> perl-Image-Size.noarch CoGe/Graphics.pm CNS/Expression/Graphics/Var_Means_Tree.pm AuthCAS.pm Sort/Versions.pm DBIxProfiler.pm
Check where the perl modules are installed :
sudo rpm -qal perl-CGI-Ajax or instmodsh or rpm -qa | grep "perl"
To find the port number of the database :
nmap localhost