Re: [galaxy-dev] Error in SICER tool

2014-02-20 Thread Jennifer Jackson

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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[galaxy-dev] Error in SICER tool

2014-02-13 Thread Nikos Sidiropoulos
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,
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,
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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