Missing script: make_biom.py

[telatin]

Hi,
When executing the test script an error is raised for not finding make_biom.py, supposedly in the scripts directory.

python ../scripts/make_biom.py /tarp-ngs/bit/scripts/16S/mucobiome/working_directory -o raw.biom
python: can't open file '../scripts/make_biom.py': [Errno 2] No such file or directory
Error in job create_biom while creating output file raw.biom.
RuleException:
CalledProcessError in line 108 of /tarp-ngs/bit/scripts/16S/mucobiome/Snakefile:
Command 'python ../scripts/make_biom.py /tarp-ngs/bit/scripts/16S/mucobiome/working_directory -o raw.biom' returned non-zero exit status 2
  File "/tarp-ngs/bit/scripts/16S/mucobiome/Snakefile", line 108, in __rule_create_biom
  File "/home/ubuntu/miniconda3/envs/mucobiome/lib/python3.5/concurrent/futures/thread.py", line 55, in run

Thank you!

[dridk]

I have no idea where the file is .. :(
So I rewrite a new one ( b09e045 ) using numpy, pandas, biom et Bio::SeqIO library.
Tell me if the last commit fix the issue. Then I will create a singularity package to make it run easier.

[telatin]

Many thanks! I’ll check ASAP
Best

[lisaB29]

@telatin did this modification work for you ?

[telatin]

Sorry,
I'm currently moving server for this analysis so I have to wait to have the system fully set up, but definitely interested in testing it again