Hello Nikos,
This is a known issue after the recent tool migrations. The ticket is
here: https://trello.com/c/h9LSdfdS
The root cause of the error is a missing fortran library. If you click
on the "eye" for the associated log dataset, and scroll down through the
full report down to the "Warnings" section: the details are at the
start, before any other warning are reported. The "missing file" errors
are all secondary issues related to the missing library.
Our team is actively working on a solution. Not just for the public Main
Galaxy instance, but for the Tool Shed repository installed dependencies
(to my knowledge). Follow the ticket and the tool shed repository for
updates.
This is important correction, but "up-votes" from our community also are
considered when setting priorities.
https://wiki.galaxyproject.org/Issues
Hopefully this helps to explain the issue,
Jen
Galaxy team
On 2/13/14 4:20 AM, Nikos Sidiropoulos wrote:
Hi all,
I'm getting the following error whenever I'm trying to run SICER
Traceback (most recent call last):
File
"/steno-internal/projects/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/sicer/82a8234e03f2/sicer/sicer_wrapper.py
<http://toolshed.g2.bx.psu.edu/repos/devteam/sicer/82a8234e03f2/sicer/sicer_wrapper.py>",
line 158, in <module>
if __name__=="__main__": __main__()
File
"/steno-internal/projects/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/sicer/82a8234e03f2/sicer/sicer_wrapper.py
<http://toolshed.g2.bx.psu.edu/repos/devteam/sicer/82a8234e03f2/sicer/sicer_wrapper.py>",
line 154, in __main__
raise e
IOError: [Errno 2] No such file or directory:
'/NextGenSeqData/galaxy-data/database/tmp/tmpHPGhcN/input_bed_file-W200-G600-E0.01.scoreisland'
Do you know if there's a workaround for this error?
I have installed SICER from the toolshed (devteam)
Bests,
Nikos
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--
Jennifer Hillman-Jackson
http://galaxyproject.org
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