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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