Purdue University

Commands

• PrepareAllPathsInputs.pl
• RunAllPathsLG
• CacheLibs.pl
• Fasta2Fastb

Module

You can load the modules by:

module load biocontainers
module load allpathslg

Example job

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run Allpathslg on our our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name 
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 24
#SBATCH --job-name=allpathslg
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers allpathslg

PrepareAllPathsInputs.pl \
                       DATA_DIR=data \
                       PLOIDY=1 \
                       IN_GROUPS_CSV=in_groups.csv\
                       IN_LIBS_CSV=in_libs.csv\
                       OVERWRITE=True\

RunAllPathsLG PRE=allpathlg REFERENCE_NAME=test.genome \
              DATA_SUBDIR=data  RUN=myrun TARGETS=standard \
              SUBDIR=test OVERWRITE=True