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 will be granted by case and resource.
An example of a shell script sub.sh to run OrthoMCL at the batch queue:
#!/bin/bash
#SBATCH --job-name=j_orthomcl
#SBATCH --partition=batch
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --mem=100gb
#SBATCH --time=120:00:00
#SBATCH --output=log.%j.out
#SBATCH --error=log.%j.err
#SBATCH --mail-type=ALL
#SBATCH --mail-user=username@uga.edu
cd $SLURM_SUBMIT_DIR
ml OrthoMCL/2.0.9-foss-2019b-Perl-5.30.0
orthomclInstallSchema orthomcl.config.username
orthomclLoadBlast orthomcl.config.username similarSequences.txt
The above configure file orthomcl.config.username will be copied to your home directory by the GACRC after a user and a schema are created on GACRC MySQL server.
In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values.
Example to submit to the queue
sbatch sub.sh
Documentation
For more extensive options. More details is at OrthoMcl
ml OrthoMCL/2.0.9-foss-2019b-Perl-5.30.0 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
ml OrthoMCL/2.0.9-foss-2019b-Perl-5.30.0 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
Installation
Source code downloaded from OrthoMcl
System
64-bit Linux