Re: [galaxy-dev] Problems uploading files to galaxy

2016-03-11 Thread Lemley, Rob 
Hi everyone,

I didn’t see any response to my email below. Does anyone have any thoughts? I'm 
pretty stuck.

Thanks again,

-Rob

Rob Lemley
Systems Administrator – CIRC
University of Rochester

-Original Message-
From: galaxy-dev [mailto:galaxy-dev-boun...@lists.galaxyproject.org] On Behalf 
Of Lemley, Rob
Sent: Monday, March 7, 2016 2:03 PM
To: galaxy-dev@lists.galaxyproject.org
Subject: [galaxy-dev] Problems uploading files to galaxy

Hi,

I'm hoping you can help out with a problem we are experiencing uploading files 
to our own Galaxy instance.

When a user tries to upload a file to Galaxy through their web browser, the job 
errors out:

Traceback (most recent call last):
  File "/gpfs/fs1/sfw/cibem_galaxy/app/galaxy/tools/data_source/upload.py", 
line 430, in 
__main__()
  File "/gpfs/fs1/sfw/cibem_galaxy/app/galaxy/tools/data_source/upload.py", 
line 407, in __main__
for line in open( sys.argv[3], 'r' ):
IOError: [Errno 13] Permission denied: 
'/scratch/XX/XX/galaxy/tmp/tmpSlG2pC'

The permissions on the referenced file:
-rw---+ 1 rlemley  rlemley  317 Mar  7 13:42 tmpSlG2pC

As the Galaxy daemons run as XX_galaxy, it does not have permission to read 
the file.

I tried modifying external_chown_script.py so that XX_galaxy has permission 
to read that file, but that caused problems elsewhere so I backed out the 
changes.

Any suggestions?

Many thanks,

-Rob


Rob Lemley
Systems Administrator - CIRC
University of Rochester

___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  
https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.galaxyproject.org_=BQIGaQ=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOU=d-Zn2Sbc-XheRlOYkSFXPupZ8ZmuYq52isQBiI3MBWA=xTXPxT_d1oq2TJoB3W7P0xfhV52TZzeUjoGhvts8xNU=yW1eNcfXnR8Rut3-T62JBQMRJXblVpOZEA0w7DxiJ04=
 

To search Galaxy mailing lists use the unified search at:
  
https://urldefense.proofpoint.com/v2/url?u=http-3A__galaxyproject.org_search_mailinglists_=BQIGaQ=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOU=d-Zn2Sbc-XheRlOYkSFXPupZ8ZmuYq52isQBiI3MBWA=xTXPxT_d1oq2TJoB3W7P0xfhV52TZzeUjoGhvts8xNU=sQNOB73SDBa-fat4oHkeYucMCsvheL3eXDp3qoUndLU=
 
___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] Missing dependency issue

2016-03-11 Thread Dannon Baker 
Scott,

I'm not sure what's going on here, but maybe it'd be useful to try to run
the build by hand to see what's going on here?

cd /readline/6.2/iuc/package_readline_6_2/52d6f646b3b5/

./configure


On Fri, Mar 11, 2016 at 8:25 AM, Scott Szakonyi 
wrote:

> Sorry, I was a bit premature. I did find the INSTALLATION.log file, but it
> only contains the original error message. I can't seem to find a config.log
> file anywhere.
>
> Thanks!
>
> Scott
>
> On Fri, Mar 11, 2016 at 8:19 AM, Scott Szakonyi  > wrote:
>
>> Hello Peter,
>>
>> Sadly, when I look in '../Galaxy/shed_tools/
>> toolshed.g2.bx.psu.edu/repos/iuc/package_readline_6_2/52d6f646b3b5/package_readline_6_2'
>> I don't see an installation log anywhere in the tree. I don't know what is
>> going on... I've always installed via the toolshed, so I don't think I've
>> done anything to mess it up through manual installations or so forth. I'll
>> keep looking, but if you or other folks on the list have additional
>> suggestions I would welcome them.
>>
>> Best,
>>
>> Scott
>>
>> On Thu, Mar 10, 2016 at 7:28 AM, Peter Briggs <
>> peter.bri...@manchester.ac.uk> wrote:
>>
>>> Hello Scott
>>>
>>> I don't have any insight into your specific problem with the readline
>>> package, however it might be worth looking for the INSTALLATION.log file
>>> from the tool install process.
>>>
>>> Assuming that this is the iuc version of package_readline_6_2 then you
>>> can try looking for it under
>>>
>>>
>>> .../tool_dependencies/readline/6.2/iuc/package_readline_6_2/52d6f646b3b5/
>>>
>>> (the final subdirectory corresponds to the version hash so might be
>>> different for your installation).
>>>
>>> If present the INSTALLATION.log file should be in there and hopefully
>>> will give you some clues as to what the problem could be.
>>>
>>> HTH
>>>
>>> Best wishes
>>>
>>> Peter
>>>
>>> On 09/03/16 20:33, Scott Szakonyi wrote:
>>>
 Hello all,

 I'm having an issue with a missing dependency for readline 6.2. When I
 try to install or repair, I get the following error message:

 configure: error: in
 `/vectorbase/web/Galaxy/galaxy/data/galaxy/tmp/tmp-toolshed-mtd3fhemK/readline-6.2':
 configure: error: cannot compute suffix of object files: cannot
 compile
 See `config.log' for more details.


 I've tried to locate the config.log file without success, so this is all
 I have to go on. Has anyone else encountered this sort of issue, and if
 so, how did you solve it?

 Thanks!

 --
 Scott B. Szakonyi
 Research Programmer

 *Center for Research Computing*
 107 Information Technology Center
 Notre Dame, IN 46556
 http://crc.nd.edu 


 ___
 Please keep all replies on the list by using "reply all"
 in your mail client.  To manage your subscriptions to this
 and other Galaxy lists, please use the interface at:
https://lists.galaxyproject.org/

 To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/


>>> --
>>> Peter Briggs peter.bri...@manchester.ac.uk
>>> Bioinformatics Core Facility University of Manchester
>>> B.1083 Michael Smith Bldg Tel: (0161) 2751482
>>>
>>
>>
>>
>> --
>> Scott B. Szakonyi
>> Research Programmer
>>
>> *Center for Research Computing*
>> 107 Information Technology Center
>> Notre Dame, IN 46556
>> http://crc.nd.edu
>>
>
>
>
> --
> Scott B. Szakonyi
> Research Programmer
>
> *Center for Research Computing*
> 107 Information Technology Center
> Notre Dame, IN 46556
> http://crc.nd.edu
>
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>   https://lists.galaxyproject.org/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/
>
___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] Missing dependency issue

2016-03-11 Thread Scott Szakonyi 
Sorry, I was a bit premature. I did find the INSTALLATION.log file, but it
only contains the original error message. I can't seem to find a config.log
file anywhere.

Thanks!

Scott

On Fri, Mar 11, 2016 at 8:19 AM, Scott Szakonyi 
wrote:

> Hello Peter,
>
> Sadly, when I look in '../Galaxy/shed_tools/
> toolshed.g2.bx.psu.edu/repos/iuc/package_readline_6_2/52d6f646b3b5/package_readline_6_2'
> I don't see an installation log anywhere in the tree. I don't know what is
> going on... I've always installed via the toolshed, so I don't think I've
> done anything to mess it up through manual installations or so forth. I'll
> keep looking, but if you or other folks on the list have additional
> suggestions I would welcome them.
>
> Best,
>
> Scott
>
> On Thu, Mar 10, 2016 at 7:28 AM, Peter Briggs <
> peter.bri...@manchester.ac.uk> wrote:
>
>> Hello Scott
>>
>> I don't have any insight into your specific problem with the readline
>> package, however it might be worth looking for the INSTALLATION.log file
>> from the tool install process.
>>
>> Assuming that this is the iuc version of package_readline_6_2 then you
>> can try looking for it under
>>
>>
>> .../tool_dependencies/readline/6.2/iuc/package_readline_6_2/52d6f646b3b5/
>>
>> (the final subdirectory corresponds to the version hash so might be
>> different for your installation).
>>
>> If present the INSTALLATION.log file should be in there and hopefully
>> will give you some clues as to what the problem could be.
>>
>> HTH
>>
>> Best wishes
>>
>> Peter
>>
>> On 09/03/16 20:33, Scott Szakonyi wrote:
>>
>>> Hello all,
>>>
>>> I'm having an issue with a missing dependency for readline 6.2. When I
>>> try to install or repair, I get the following error message:
>>>
>>> configure: error: in
>>> `/vectorbase/web/Galaxy/galaxy/data/galaxy/tmp/tmp-toolshed-mtd3fhemK/readline-6.2':
>>> configure: error: cannot compute suffix of object files: cannot
>>> compile
>>> See `config.log' for more details.
>>>
>>>
>>> I've tried to locate the config.log file without success, so this is all
>>> I have to go on. Has anyone else encountered this sort of issue, and if
>>> so, how did you solve it?
>>>
>>> Thanks!
>>>
>>> --
>>> Scott B. Szakonyi
>>> Research Programmer
>>>
>>> *Center for Research Computing*
>>> 107 Information Technology Center
>>> Notre Dame, IN 46556
>>> http://crc.nd.edu 
>>>
>>>
>>> ___
>>> Please keep all replies on the list by using "reply all"
>>> in your mail client.  To manage your subscriptions to this
>>> and other Galaxy lists, please use the interface at:
>>>https://lists.galaxyproject.org/
>>>
>>> To search Galaxy mailing lists use the unified search at:
>>>http://galaxyproject.org/search/mailinglists/
>>>
>>>
>> --
>> Peter Briggs peter.bri...@manchester.ac.uk
>> Bioinformatics Core Facility University of Manchester
>> B.1083 Michael Smith Bldg Tel: (0161) 2751482
>>
>
>
>
> --
> Scott B. Szakonyi
> Research Programmer
>
> *Center for Research Computing*
> 107 Information Technology Center
> Notre Dame, IN 46556
> http://crc.nd.edu
>



-- 
Scott B. Szakonyi
Research Programmer

*Center for Research Computing*
107 Information Technology Center
Notre Dame, IN 46556
http://crc.nd.edu
___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] Missing dependency issue

2016-03-11 Thread Scott Szakonyi 
Hello Peter,

Sadly, when I look in '../Galaxy/shed_tools/
toolshed.g2.bx.psu.edu/repos/iuc/package_readline_6_2/52d6f646b3b5/package_readline_6_2'
I don't see an installation log anywhere in the tree. I don't know what is
going on... I've always installed via the toolshed, so I don't think I've
done anything to mess it up through manual installations or so forth. I'll
keep looking, but if you or other folks on the list have additional
suggestions I would welcome them.

Best,

Scott

On Thu, Mar 10, 2016 at 7:28 AM, Peter Briggs  wrote:

> Hello Scott
>
> I don't have any insight into your specific problem with the readline
> package, however it might be worth looking for the INSTALLATION.log file
> from the tool install process.
>
> Assuming that this is the iuc version of package_readline_6_2 then you can
> try looking for it under
>
>
> .../tool_dependencies/readline/6.2/iuc/package_readline_6_2/52d6f646b3b5/
>
> (the final subdirectory corresponds to the version hash so might be
> different for your installation).
>
> If present the INSTALLATION.log file should be in there and hopefully will
> give you some clues as to what the problem could be.
>
> HTH
>
> Best wishes
>
> Peter
>
> On 09/03/16 20:33, Scott Szakonyi wrote:
>
>> Hello all,
>>
>> I'm having an issue with a missing dependency for readline 6.2. When I
>> try to install or repair, I get the following error message:
>>
>> configure: error: in
>> `/vectorbase/web/Galaxy/galaxy/data/galaxy/tmp/tmp-toolshed-mtd3fhemK/readline-6.2':
>> configure: error: cannot compute suffix of object files: cannot
>> compile
>> See `config.log' for more details.
>>
>>
>> I've tried to locate the config.log file without success, so this is all
>> I have to go on. Has anyone else encountered this sort of issue, and if
>> so, how did you solve it?
>>
>> Thanks!
>>
>> --
>> Scott B. Szakonyi
>> Research Programmer
>>
>> *Center for Research Computing*
>> 107 Information Technology Center
>> Notre Dame, IN 46556
>> http://crc.nd.edu 
>>
>>
>> ___
>> Please keep all replies on the list by using "reply all"
>> in your mail client.  To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
>>https://lists.galaxyproject.org/
>>
>> To search Galaxy mailing lists use the unified search at:
>>http://galaxyproject.org/search/mailinglists/
>>
>>
> --
> Peter Briggs peter.bri...@manchester.ac.uk
> Bioinformatics Core Facility University of Manchester
> B.1083 Michael Smith Bldg Tel: (0161) 2751482
>



-- 
Scott B. Szakonyi
Research Programmer

*Center for Research Computing*
107 Information Technology Center
Notre Dame, IN 46556
http://crc.nd.edu
___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/