Tool cant find datasets even though they exist correctly

Question: Tool cant find datasets even though they exist correctly

2.8 years ago by

alepfu • 10

alepfu • 10 wrote:

Hi,

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

Thanks

Alex

pindel tool software error galaxy • 716 views

ADD COMMENT • link •

modified 2.8 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.8 years ago by alepfu • 10

2.8 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

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 galaxy-dev@lists.galaxyproject.org mailing list (many tool developers follow this).
https://wiki.galaxyproject.org/MailingLists

Thanks, Jen, Galaxy team

ADD COMMENT • link written 2.8 years ago by Jennifer Hillman Jackson ♦ 25k

Similar posts • Search »