indexing mode

[cpouchon]

• echo ''

• echo ''

• echo 'Processing OrthoSkim program' Processing OrthoSkim program

• echo ''

• mkdir -p /scratch/Charles/testsoft/run_orthoskim/Assembly/Samples

• (( indexing==indexing ))

• echo 'OrthoSkim: indexing of annotation files' OrthoSkim: indexing of annotation files ++ dirname ./OrthoSkim_v0.0.sh

• ./src/MakeParam.py -p /scratch/Charles/testsoft/release/ -o /scratch/Charles/testsoft/runorthoskim/Assembly/ -cfind Traceback (most recent call last): File "./src/MakeParam.py", line 57, in r1path=os.path.dirname(cf)+"/"+fnmatch.filter(os.listdir(os.path.dirname(cf)), '*[0-9]1*_clean.fastq.gz')[0] IndexError: list index out of range

[cpouchon]

modify MakeParams.py to add a condition for sequencing plateform because for fasteris librairies we have _R1 and R2 and no [0-9]1_clean.fastq.gz as for Genoscope librairies

[cpouchon]

modify also to replace ':' by '_'