Hard coded Paths

[Sabryr]

bash-4.1$ python main.py
Directory created: /work/databases/bio/mmetsp_new/mmetsp/
Traceback (most recent call last):
File "main.py", line 2, in
import getdata as data
File "/work/databases/bio/mmetsp_new/dib-MMETSP/getdata.py", line 149, in
for datafile in datafiles:
NameError: name 'datafiles' is not defined

[Sabryr]

Some more hardcoded paths leading to errors:
Traceback (most recent call last):
File "main.py", line 3, in
import trim_qc as trim
File "/work/databases/bio/mmetsp_new/dib-MMETSP/trim_qc.py", line 190, in
execute(url_data,datadir)
File "/work/databases/bio/mmetsp_new/dib-MMETSP/trim_qc.py", line 168, in execute
clusterfunc.check_dir(trimdir)
File "/work/databases/bio/mmetsp_new/dib-MMETSP/clusterfunc.py", line 12, in check_dir
os.mkdir(dirname)
OSError: [Errno 2] No such file or directory: '/mnt/scratch/ljcohen/mmetsp/Fragilariopsis_kerguelensis/SRR1296820/trim/'

Due to:
def fix_fasta(trinity_fasta, trinity_dir, sample):
os.chdir(trinity_dir)
trinity_out = trinity_dir + sample + ".Trinity.fixed.fasta"
fix = """
sed 's_|_-_g' {} > {}
""".format(trinity_fasta, trinity_out)
s = subprocess.Popen(fix, shell=True)
print fix
s.wait()
os.chdir("/mnt/home/ljcohen/MMETSP/")
return trinity_out

[Sabryr]

bash-4.1$ grep -Rni "/mnt/scratch/ljcohen/mmetsp/"
assembly_trinity_20140413p1.py:173:basedir = "/mnt/scratch/ljcohen/mmetsp/"
diginorm_mmetsp.py:183:basedir = "/mnt/scratch/ljcohen/mmetsp/"
trim_qc.py:187:datadir="/mnt/scratch/ljcohen/mmetsp/"
Binary file trim_qc.pyc matches

[Sabryr]

More hardcoded paths

java -jar /mnt/home/ljcohen/bin/Trimmomatic-0.33/trimmomatic-0.33.jar PE \
ILLUMINACLIP:/mnt/home/ljcohen/bin/Trimmomatic-0.33/adapters/combined.fa:2:40:15 \
java -jar /mnt/home/ljcohen/bin/Trimmomatic-0.33/trimmomatic-0.33.jar PE \
ILLUMINACLIP:/mnt/home/ljcohen/bin/Trimmomatic-0.33/adapters/combined.fa:2:40:15 \
datadir="/mnt/scratch/ljcohen/mmetsp/"