Question: Planemo test - Scripts not found
0
gravatar for Mataivic
23 months ago by
Mataivic0
Roscoff Biology Station
Mataivic0 wrote:

Hello,

I am currently trying to build functionnal tests for a Galaxy tool. My xml wrapper is ready ; it calls one main python script, which then calls many others. I've got this error : except the main script, the scripts used by the tool are not found, yet they are in the same directory of the xml wrapper and the main script.

The error mentions 3 bash scripts. I have no clue about how the others scripts are going, but they are all in python.

Could it be because they are not taken into account into the temporary files of the planemo test ? How do I resolve that ? Maybe by setting the shebang with a #!/usr/bin/env bash instead of #!/usr/bin/bash ?

Here is the error (partially in french, sorry about that) :

status: undefined

problems:

Job in error state.

Job in error state.

command:

python /home/umr7144/abice/vmataigne/Documents/AdaptSearch/adaptsearch-master/galaxy_wrappers/02_Pairwise/03_organize_RBH.py 8 1e-05 /tmp/tmptCRyWo/files/000/dataset_1.dat > /tmp/tmptCRyWo/files/000/dataset_2.dat;

job standard error:

cp: impossible d'évaluer «03_run_BLAST_with.K.filter.sh»: Aucun fichier ou dossier de ce type
cp: impossible d'évaluer «10_run_BLAST2_with.K.filter.sh»: Aucun fichier ou dossier de ce type
Traceback (most recent call last):
  File "/home/umr7144/abice/vmataigne/Documents/AdaptSearch/adaptsearch-master/galaxy_wrappers/02_Pairwise/03_organize_RBH.py", line 54, in <module>
    pipeline_patron = open("XXX_patronPipeline.sh", "r")
IOError: [Errno 2] No such file or directory: 'XXX_patronPipeline.sh'
ADD COMMENTlink modified 23 months ago • written 23 months ago by Mataivic0
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