Hi Nate,

thanks for all your help! I attached the full installation log file.

Best regards,
Sarah

----- Original Message -----
From: "Nate Coraor" <n...@bx.psu.edu>
To: "Sarah Diehl" <di...@ie-freiburg.mpg.de>
Cc: "galaxy-dev@lists.bx.psu.edu List" <galaxy-dev@lists.bx.psu.edu>
Sent: Tuesday, February 25, 2014 3:57:36 PM
Subject: Re: [galaxy-dev] Error when installing package_galaxy_utils


Hi Sarah, 


Could you include the installation stdout as well? The dependency installation 
log separates stdout and stderr into two sections, there might be more detail 
about exactly where it's failing in the stdout. 


--nate 



On Fri, Feb 21, 2014 at 4:21 AM, Sarah Diehl < di...@ie-freiburg.mpg.de > 
wrote: 


Hi Nate, 

I tried it multiple times and always got the same error. I did successfully 
install other tools before and after that. I didn't notice any issues with the 
filesystem. Is there a way to find out what exactly the installation tries to 
do at that point? 

Thanks, 
Sarah 




----- Original Message ----- 
From: "Nate Coraor" < n...@bx.psu.edu > 
To: "Sarah Diehl" < di...@ie-freiburg.mpg.de > 
Cc: " galaxy-dev@lists.bx.psu.edu List" < galaxy-dev@lists.bx.psu.edu > 
Sent: Friday, February 21, 2014 5:10:46 AM 
Subject: Re: [galaxy-dev] Error when installing package_galaxy_utils 


Hi Sarah, 


This looks a lot like a transient filesystem error. If you attempt to reinstall 
the repository, do you get the same error? 


--nate 



On Thu, Feb 20, 2014 at 10:48 AM, Sarah Diehl < di...@ie-freiburg.mpg.de > 
wrote: 


Hi everyone, 

I just updated our local Galaxy installation to the latest dist version and 
also did the tool migration steps (./scripts/migrate_tools/0009_tools.sh). 
However, the package galaxy_utils gave me an error and I don't have the 
slightest idea what happened. So any help to figure out the issue is greatly 
appreciated! 

Thanks, 
Sarah 


############################################# 
export 
PYTHONPATH=$PYTHONPATH:/galaxy/galaxy_data/tools/galaxy_sequence_utils/1.0.0/devteam/package_galaxy_utils_1_0/0643676ad5f7/lib/python
 && python setup.py install --home /galaxy/galaxy_data/tools/galaxy_seq 
uence_utils/1.0.0/devteam/package_galaxy_utils_1_0/0643676ad5f7 
STDERR 
Downloading 
http://pypi.python.org/packages/source/d/distribute/distribute-0.6.38.tar.gz 
Extracting in /tmp/tmpo9Zxdz 
Now working in /tmp/tmpo9Zxdz/distribute-0.6.38 
Building a Distribute egg in 
/galaxy/galaxy_server/database/tmp/tmp-toolshed-mtd00x35_/galaxy_sequence_utils-1.0.0
 
/galaxy/galaxy_server/database/tmp/tmp-toolshed-mtd00x35_/galaxy_sequence_utils-1.0.0/distribute-0.6.38-py2.7.egg
 
error: site.py: Resource temporarily unavailable 
############################################# 
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#############################################
export PYTHONPATH=$PYTHONPATH:/galaxy/galaxy_data/tools/galaxy_sequence_utils/1.0.0/devteam/package_galaxy_utils_1_0/0643676ad5f7/lib/python && python setup.py install --home /galaxy/galaxy_data/tools/galaxy_sequence_utils/1.0.0/devteam/package_galaxy_utils_1_0/0643676ad5f7
STDOUT
running install
running bdist_egg
running egg_info
creating lib/galaxy_sequence_utils.egg-info
writing lib/galaxy_sequence_utils.egg-info/PKG-INFO
writing top-level names to lib/galaxy_sequence_utils.egg-info/top_level.txt
writing dependency_links to lib/galaxy_sequence_utils.egg-info/dependency_links.txt
writing manifest file 'lib/galaxy_sequence_utils.egg-info/SOURCES.txt'
reading manifest file 'lib/galaxy_sequence_utils.egg-info/SOURCES.txt'
writing manifest file 'lib/galaxy_sequence_utils.egg-info/SOURCES.txt'
installing library code to build/bdist.linux-x86_64/egg
running install_lib
running build_py
creating build
creating build/lib
creating build/lib/galaxy_utils
copying lib/galaxy_utils/__init__.py -> build/lib/galaxy_utils
creating build/lib/galaxy_utils/sequence
copying lib/galaxy_utils/sequence/__init__.py -> build/lib/galaxy_utils/sequence
copying lib/galaxy_utils/sequence/fasta.py -> build/lib/galaxy_utils/sequence
copying lib/galaxy_utils/sequence/fastq.py -> build/lib/galaxy_utils/sequence
copying lib/galaxy_utils/sequence/sequence.py -> build/lib/galaxy_utils/sequence
copying lib/galaxy_utils/sequence/transform.py -> build/lib/galaxy_utils/sequence
copying lib/galaxy_utils/sequence/vcf.py -> build/lib/galaxy_utils/sequence
creating build/bdist.linux-x86_64
creating build/bdist.linux-x86_64/egg
creating build/bdist.linux-x86_64/egg/galaxy_utils
copying build/lib/galaxy_utils/__init__.py -> build/bdist.linux-x86_64/egg/galaxy_utils
creating build/bdist.linux-x86_64/egg/galaxy_utils/sequence
copying build/lib/galaxy_utils/sequence/__init__.py -> build/bdist.linux-x86_64/egg/galaxy_utils/sequence
copying build/lib/galaxy_utils/sequence/fasta.py -> build/bdist.linux-x86_64/egg/galaxy_utils/sequence
copying build/lib/galaxy_utils/sequence/fastq.py -> build/bdist.linux-x86_64/egg/galaxy_utils/sequence
copying build/lib/galaxy_utils/sequence/sequence.py -> build/bdist.linux-x86_64/egg/galaxy_utils/sequence
copying build/lib/galaxy_utils/sequence/transform.py -> build/bdist.linux-x86_64/egg/galaxy_utils/sequence
copying build/lib/galaxy_utils/sequence/vcf.py -> build/bdist.linux-x86_64/egg/galaxy_utils/sequence
byte-compiling build/bdist.linux-x86_64/egg/galaxy_utils/__init__.py to __init__.pyc
byte-compiling build/bdist.linux-x86_64/egg/galaxy_utils/sequence/__init__.py to __init__.pyc
byte-compiling build/bdist.linux-x86_64/egg/galaxy_utils/sequence/fasta.py to fasta.pyc
byte-compiling build/bdist.linux-x86_64/egg/galaxy_utils/sequence/fastq.py to fastq.pyc
byte-compiling build/bdist.linux-x86_64/egg/galaxy_utils/sequence/sequence.py to sequence.pyc
byte-compiling build/bdist.linux-x86_64/egg/galaxy_utils/sequence/transform.py to transform.pyc
byte-compiling build/bdist.linux-x86_64/egg/galaxy_utils/sequence/vcf.py to vcf.pyc
creating build/bdist.linux-x86_64/egg/EGG-INFO
copying lib/galaxy_sequence_utils.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO
copying lib/galaxy_sequence_utils.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying lib/galaxy_sequence_utils.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying lib/galaxy_sequence_utils.egg-info/not-zip-safe -> build/bdist.linux-x86_64/egg/EGG-INFO
copying lib/galaxy_sequence_utils.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
creating dist
creating 'dist/galaxy_sequence_utils-1.0.0-py2.7.egg' and adding 'build/bdist.linux-x86_64/egg' to it
removing 'build/bdist.linux-x86_64/egg' (and everything under it)
#############################################

#############################################
export PYTHONPATH=$PYTHONPATH:/galaxy/galaxy_data/tools/galaxy_sequence_utils/1.0.0/devteam/package_galaxy_utils_1_0/0643676ad5f7/lib/python && python setup.py install --home /galaxy/galaxy_data/tools/galaxy_sequence_utils/1.0.0/devteam/package_galaxy_utils_1_0/0643676ad5f7
STDERR
Downloading http://pypi.python.org/packages/source/d/distribute/distribute-0.6.38.tar.gz
Extracting in /tmp/tmpOOFrT4
Now working in /tmp/tmpOOFrT4/distribute-0.6.38
Building a Distribute egg in /galaxy/galaxy_server/database/tmp/tmp-toolshed-mtdhhsI3z/galaxy_sequence_utils-1.0.0
/galaxy/galaxy_server/database/tmp/tmp-toolshed-mtdhhsI3z/galaxy_sequence_utils-1.0.0/distribute-0.6.38-py2.7.egg
error: site.py: Resource temporarily unavailable
#############################################
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
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  http://lists.bx.psu.edu/

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