OrthoMCL-Sapelo2

Category

Bioinformatics

Program On

Sapelo2

Version

2.0.9

Author / Distributor

More details is at OrthoMcl

Description

"OrthoMCL is a genome-scale algorithm for grouping orthologous protein sequences. It provides not only groups shared by two or more species/genomes, but also groups representing species-specific gene expansion families. So it serves as an important utility for automated eukaryotic genome annotation."

More details is at OrthoMcl

Running Program

Also refer to Running Jobs on Sapelo2

• Version 2.0.9, installed in /apps/eb/OrthoMCL/2.0.9-foss-2019b-Perl-5.30.0

To use this version of OrthoMCL, please first load the module with

module load OrthoMCL/2.0.9-foss-2019b-Perl-5.30.0

Please note, OrthoMCL uses mysql as back-end database, please contact us about mysql information before use OrthoMCL on Sapelo2. Please email us once job is done. Database will be removed from GACRC server upon user's notification. There is limited resource to support mysql applications at GACRC, permission granted by case and resource.

An example of a shell script sub.sh to run OrthoMCL at the batch queue:

#PBS -S /bin/bash
#PBS -N j_orthomcl
#PBS -q batch
#PBS -l nodes=1:ppn=1
#PBS -l walltime=480:00:00
#PBS -l mem=100gb

cd $PBS_O_WORKDIR

module load OrthoMCL/2.0.9-foss-2016b-Perl-5.24.1

orthomclInstallSchema orthomcl.config

time orthomclLoadBlast orthomcl.config similarSequences.txt

A sample of configure file is at /usr/local/apps/eb/OrthoMCL/2.0.9-foss-2016b-Perl-5.24.1/orthomcl.config.gacrc

Example to submit to the queue

qsub  sub.sh

Documentation

For more extensive options. More details is at OrthoMcl

module load OrthoMCL/2.0.9-foss-2016b-Perl-5.24.1
orthomclInstallSchema

Create OrthoMCL schema in an Oracle or Mysql database.

usage: orthomclInstallSchema config_file sql_log_file table_suffix

where:
  config_file : see below
  sql_log_file : optional log of sql executed
  table_suffix : optional string to append to database object names

EXAMPLE: orthomclSoftware/bin/orthomclInstallSchema my_orthomcl_dir/orthomcl.config my_orthomcl_dir/install_schema.log

NOTE: the database login in the config file must have the required database privileges on the tables specified in the config file.

Sample Config File:

dbVendor=oracle  (or mysql)
dbConnectString=dbi:Oracle:orthomcl
dbLogin=my_db_login
dbPassword=my_db_password
oracleIndexTablespace=
similarSequencesTable=SimilarSequences
orthologTable=Ortholog
inParalogTable=InParalog
coOrthologTable=CoOrtholog
interTaxonMatchView=InterTaxonMatch

module load OrthoMCL/2.0.9-foss-2016b-Perl-5.24.1
orthomclLoadBlast --help

Load Blast results into an Oracle or Mysql database.

usage: orthomclLoadBlast config_file similar_seqs_file

where:
  config_file :       see below
  similar_seqs_file : output from orthomclParseBlast 

EXAMPLE: orthomclSoftware/bin/orthomclLoadBlast my_orthomcl_dir/orthomcl.config my_orthomcl_dir/similarSequences.txt

NOTE: the database login in the config file must have update/insert/truncate privileges on the tables specified in the config file.

Sample Config File:

dbVendor=oracle  (or mysql)
dbConnectString=dbi:Oracle:orthomcl
dbLogin=my_db_login
dbPassword=my_db_password
similarSequencesTable=SimilarSequences

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Installation

Source code downloaded from OrthoMcl

System

64-bit Linux