It is mostly development code, bugs and inefficiencies are likely, please report any problems to the gscripts issues page.
cd path/to/gscripts; easy_install .
(NOT pip)
from gscripts.qtools import Submitter
For example, to submit a single line of code to a compute job, you can do:
from gscripts.qtools import Submitter
exon_seqs = '/projects/ps-yeolab/obotvinnik/miso_helpers/hg19/se_exon2.fasta'
mirna_seqs = '/projects/ps-yeolab/genomes/mirbase/release_21/human_mature_17bp.fa'
rnahybrid_results = '/projects/ps-yeolab/obotvinnik/miso_helpers/hg19/se_exon2_RNAhybrid_mirbase_human_mature_17bp.txt'
command = 'RNAhybrid -c -s 3utr_human -q {} -t {} > {}'.format(mirna_seqs, exon_seqs, rnahybrid_results)
sub = Submitter([command], 'RNAhybrid', walltime='120:00:00', write_and_submit=True, nodes=1, ppn=1)Which will write a file called RNAhybrid.sh which has these contents:
#!/bin/bash
#PBS -N RNAhybrid
#PBS -o RNAhybrid.sh.out
#PBS -e RNAhybrid.sh.err
#PBS -V
#PBS -l walltime=120:00:00
#PBS -l nodes=1:ppn=1
#PBS -A yeo-group
#PBS -q home
# Go to the directory from which the script was called
cd $PBS_O_WORKDIR
RNAhybrid -c -s 3utr_human -q /projects/ps-yeolab/genomes/mirbase/release_21/human_mature_17bp.fa -t /projects/ps-yeolab/obotvinnik/miso_helpers/hg19/se_exon2.fasta > /projects/ps-yeolab/obotvinnik/miso_helpers/hg19/se_exon2_RNAhybrid_mirbase_human_mature_17bp.txtfrom gscripts import which