<commit_before>#!/usr/bin/env python

'''
Created on Jan 10, 2013

@author: <NAME>

Generate PBS scripts for submission to the Ohio Supercomputer Center to 
run the QIIME parallel blast pick OTUs script on multiple input sequence 
data sets.
'''
import argparse
import os.path as osp

PBS_JOB_NAME_SIZE = 15

PBS_SCRIPT = """#PBS -N {job_name}_{job_num}

# Walltime Limit: hh:nn:ss 
#PBS -l walltime={walltime}:00:00 

# Node Specification:
#PBS -l nodes=1:ppn=12

# Keep output
#PBS -j oe

set -x

module load qiime
cd $PBS_O_WORKDIR
cp $HOME/local/oakley/greengenes/gg_12_10_otus/rep_set/97_otus.fasta $TMPDIR
cp {job_num}.fna $TMPDIR
cd $TMPDIR

time parallel_pick_otus_blast.py -i {job_num}.fna -r 97_otus.fasta -O 12 -o bpo.{job_num}

cp -r bpo.{job_num} $PBS_O_WORKDIR
"""

<commit_msg>Updates to the lastest version of greengenes<commit_after>#!/usr/bin/env python

'''
Created on Jan 10, 2013

@author: <NAME>

Generate PBS scripts for submission to the Ohio Supercomputer Center to 
run the QIIME parallel blast pick OTUs script on multiple input sequence 
data sets.
'''
import argparse
import os.path as osp

PBS_JOB_NAME_SIZE = 15

PBS_SCRIPT = """#PBS -N {job_name}_{job_num}

# Walltime Limit: hh:nn:ss 
#PBS -l walltime={walltime}:00:00 

# Node Specification:
#PBS -l nodes=1:ppn=12

# Keep output
#PBS -j oe

module load qiime
cd $PBS_O_WORKDIR
cp $HOME/local/oakley/greengenes/gg_13_8_otus/rep_set/99_otus.fasta $TMPDIR
cp {job_num}.fna $TMPDIR
cd $TMPDIR

time parallel_pick_otus_blast.py -i {job_num}.fna -r 99_otus.fasta -O 12 -o bpo.{job_num}

cp -r bpo.{job_num} $PBS_O_WORKDIR
"""


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