Oge-coge installation

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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
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