Closed gmauro closed 1 year ago
Circos tool needs to use a file in the karyotype directory, Pulsar prepare correctly the path in the command line:
karyotype
circos --version > /data/share/staging/33761204/outputs/COMMAND_VERSION 2>&1; mkdir -p circos/conf/ circos/data/ && cp '/data/share/staging/33761204/tool_files/karyotype/karyotype.mouse.mm9.txt' ...
but fails at the remote staging step, because it's not considering the karyotype folder:
{ "remote_staging": { "setup": [ { "name": "karyotype.mouse.mm9.txt", "type": "tool", "action": { "path": "/opt/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/iuc/circos/7f13dc906cb9/circos/karyotype/karyotype.mouse.mm9.txt", "source": { "path": "/opt/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/iuc/circos/7f13dc906cb9/circos/karyotype/karyotype.mouse.mm9.txt" }, "action_type": "remote_transfer", "url": "https://usegalaxy.eu/_job_files?job_id=11ac94870d0bb33ab848c86c299a7d6a&job_key=b269333ccac1e914130a3c7906c59a4f&path=/opt/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/iuc/circos/7f13dc906cb9/circos/karyotype/karyotype.mouse.mm9.txt&file_type=tool" } }, ...
in the end, the file karyotype.mouse.mm9.txt is copied into the tool_files directory without the karyotype folder
karyotype.mouse.mm9.txt
tool_files
[centos@vgcn-it01-central-manager 33761204]$ ll tool_files/ total 24 -rw-r--r--. 1 centos centos 242 Nov 10 11:31 karyotype-colors.py -rw-r--r--. 1 centos centos 17799 Nov 10 11:31 karyotype.mouse.mm9.txt
I am using pulsar-app==0.14.11
pulsar-app==0.14.11
this is the error message:
[centos@vgcn-it01-central-manager 33761204]$ cat stderr cp: can't stat '/data/share/staging/33761204/tool_files/karyotype/karyotype.mouse.mm9.txt': No such file or directory
That should be fixed by https://github.com/galaxyproject/pulsar/pull/261 and https://github.com/mvdbeek/galaxy/blob/2f9b7212e076a5e19c43892c099f2118e4df2a97/lib/galaxy/tools/__init__.py#L236
Circos tool needs to use a file in the
karyotype
directory, Pulsar prepare correctly the path in the command line:but fails at the remote staging step, because it's not considering the
karyotype
folder:in the end, the file
karyotype.mouse.mm9.txt
is copied into thetool_files
directory without thekaryotype
folderI am using
pulsar-app==0.14.11