Sicer Version 0.0.1 fails for not finding one of the output files during execution
Closed this issue · 4 comments
The error is reproducible both at Galaxy Main and Galaxy Freiburg.
- https://usegalaxy.org/u/jen/h/sicer-test
- https://galaxy.uni-freiburg.de/u/jenj/h/copy-of-test-history-sicer
Main
Traceback (most recent call last):
File "/galaxy/main/migrated_tools/toolshed.g2.bx.psu.edu/repos/devteam/sicer/82a8234e03f2/sicer/sicer_wrapper.py", line 157, in
if name=="main": main()
File "/galaxy/main/migrated_tools/toolshed.g2.bx.psu.edu/repos/devteam/sicer/82a8234e03f2/sicer/sicer_wrapper.py", line 153, in main
raise e
IOError: [Errno 2] No such file or directory: '/galaxy-repl/main/jobdir/017/652/17652579/_job_tmp/tmpcLZaF6/input_bed_file-W200-G600-islands-summary'
Freiburg
Traceback (most recent call last):
File "/usr/local/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/sicer/82a8234e03f2/sicer/sicer_wrapper.py", line 157, in
if name=="main": main()
File "/usr/local/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/sicer/82a8234e03f2/sicer/sicer_wrapper.py", line 153, in main
raise e
IOError: [Errno 2] No such file or directory: '/var/tmp/3819266.1.galaxy1.q/tmpmeKwRD/input_bed_file-W200-G600-islands-summary'
Moved from /galaxy repo: galaxyproject/galaxy#3355
A user reported this problem to usegalaxy.org galaxy-bugs last on 7/27/18.
Is there any update about the tool correction? Is SICER still supported?
EU now has version 0.0.2 - retesting
v 0.0.2 works at EU (test in the same history as above). Upgrading ORG to that version should resolve the prior issues.
Update tracking ticket for ORG: galaxyproject/usegalaxy-playbook#175
v 0.0.2 works at EU and ORG:
Closing this out and sicer update ticket for main