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/"