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.dewrote: 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 # ___ 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: http://lists.bx.psu.edu/ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Error when installing package_galaxy_utils
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 # ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ # 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
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.dewrote: 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 # ___ 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: http://lists.bx.psu.edu/ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
