Hi Alban,

After a few weeks on other work, I try again the integration of your suite Nebula in my local instance of Galaxy.

If possible, could you please help me to understand why the script "parseChipmunkOutput.pl " doesn't found results in my Galaxy instance.

Here are the steps performed:

*1* Command launched with sucess in a terminal :
ruby /usr/local/bioinfo/src/galaxy/galaxy-dist/tool-data/shared/jars/ChIPMunk/run_chiphorde.rb toto.log 3:10,2:10 mask yes 1.0 s:masked_sequence
s_for_CompleteMotifs.fasta 100 10 1 4

Ouput fles :
-rw-r--r-- 1 galaxy wbioinfo 256K 27 févr. 09:59 masked_sequences_for_CompleteMotifs.fasta
-rw-r--r-- 1 galaxy wbioinfo 61K 27 févr. 10:03 toto.log_chiphorde.log
-rw-r--r-- 1 galaxy wbioinfo 3,5K 27 févr. 10:03 toto.log_0.xml
-rw-r--r-- 1 galaxy wbioinfo 82K 27 févr. 10:03 toto.log_0.xml.png
-rw-r--r-- 1 galaxy wbioinfo 59K 27 févr. 10:03 toto.log_0_occurrences.txt

So ChIPMunk work.

*2*Command launched via Galaxy :
« /work/galaxy/database/job_working_directory/004/4397/galaxy_dataset_6397.dat_0.xml.png »: Aucun fichier ou dossier de ce type

So the error comes from next step (i.e. the parseChipmunkOutput.pl script). Do you have any idea ?

Thanks in advance,
Sarah

Here is your last message :

- Here is the error I get when running the tool ChIPmunk (thanks Alban
for you help (ChIPMunk v2 is used and all librairies are found) but
here is a new error, maybe a problem of "dirname" ?)

mv: impossible d'évaluer
« /work/galaxy/database/job_working_directory/004/4132/galaxy_dataset_5992.dat_0.xml.png »: Aucun fichier ou dossier de ce type
mv: impossible d'évaluer « /work/gala
        
Here, I think that the error is due to the ChIPMunk execution which doesn't work.

You can try the ChIPMunk execution this way:

Find the line containing:

ruby $CHIPMUNK_BIN_DIR/run_chiphorde.rb $LOG $motifs $MODE yes 1.0 s:$inputfile 100 10 1 4 >> /dev/null 2>> /dev/null

Add a line with:

echo "ruby $CHIPMUNK_BIN_DIR/run_chiphorde.rb $LOG $motifs $MODE yes 1.0 s:$inputfile 100 10 1 4 >> /dev/null 2>> /dev/null" > ~/ChIPMunk.log

Then try to launch the command in ~/ChIPMunk.log in a terminal and look at the output.

If ChIPMunk has run, the error comes from next step (i.e. the parseChipmunkOutput.pl script).

Else, try to debug ChIPMunk, and then the tool will work.