Question: Tool cant find datasets even though they exist correctly
gravatar for alepfu
2.8 years ago by
alepfu10 wrote:


I just imported a workflow from another Galaxy instance and when running it, the tool pindel_test (from the Test Tool Shed) reports the following error concering missing datasets, even tough they exist:

Error message:

problem doing : samtools index /opt/galaxy/database/files/000/dataset_50.dat
[Errno 2] No such file or directory
problem doing : samtools faidx /opt/galaxy/database/files/000/dataset_3.dat
[Errno 2] No such file or directory

Additional output:

samtools index /opt/galaxy/database/files/000/dataset_50.dat
samtools faidx /opt/galaxy/database/files/000/dataset_3.dat
pindel -f /opt/galaxy/database/files/000/dataset_3.dat -i /opt/galaxy/database/tmp/tmpn7gvfu/pindel_configFile -o /opt/galaxy/database/tmp/tmpn7gvfu/pindel  --number_of_threads 1 --window_size 5 --sequencing_error_rate 0.010000 --sensitivity 0.950000 -u 0.020000 -n 2 -a 1 -m 3 -v 50 -d 30 -B 0 -A 0 -M 3 
commande = pindel2vcf -P /opt/galaxy/database/tmp/tmpn7gvfu/pindel -r /opt/galaxy/database/files/000/dataset_3.dat -R sample -d 03/02/16
pindel2vcf -P /opt/galaxy/database/tmp/tmpn7gvfu/pindel -r /opt/galaxy/database/files/000/dataset_3.dat -R sample -d 03/02/16
cp /opt/galaxy/database/tmp/tmpn7gvfu/pindel.vcf /opt/galaxy/database/files/000/dataset_54.dat




ADD COMMENTlink modified 2.8 years ago by Jennifer Hillman Jackson25k • written 2.8 years ago by alepfu10
gravatar for Jennifer Hillman Jackson
2.8 years ago by
United States
Jennifer Hillman Jackson25k wrote:


Tools obtained from the Test Tool Shed may not always be in a usable state across all Galaxy servers. This is a sandbox for testing and sharing. Using tools from the Main Tool Shed is recommended for the majority of users. 

That said, you could try to contact the tool author through the test tool shed utilities. Log in, then find "contact repository owner" in the upper right menu.

This would be true for most tools when problems come up on a local (including those in the Main tool shed). For those authored by individuals/groups other than devteam or iuc, this can be the primary point of contact. Other options for Main tool shed tool support is to try the mailing list (many tool developers follow this).

Thanks, Jen, Galaxy team

ADD COMMENTlink written 2.8 years ago by Jennifer Hillman Jackson25k
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