Error when installing package_galaxy_utils

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Error when installing package_galaxy_utils

Sarah Diehl-2
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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Re: Error when installing package_galaxy_utils

Nate Coraor (nate@bx.psu.edu)
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 <[hidden email]> 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/

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___________________________________________________________
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Re: Error when installing package_galaxy_utils

Sarah Diehl-2
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" <[hidden email]>
To: "Sarah Diehl" <[hidden email]>
Cc: "[hidden email] List" <[hidden email]>
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 < [hidden email] > 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:
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To search Galaxy mailing lists use the unified search at:
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Re: Error when installing package_galaxy_utils

Nate Coraor (nate@bx.psu.edu)
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 <[hidden email]> 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" <[hidden email]>
To: "Sarah Diehl" <[hidden email]>
Cc: "[hidden email] List" <[hidden email]>
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 < [hidden email] > 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/

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Re: Error when installing package_galaxy_utils

Sarah Diehl-2
Hi Nate,

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

Best regards,
Sarah

----- Original Message -----
From: "Nate Coraor" <[hidden email]>
To: "Sarah Diehl" <[hidden email]>
Cc: "[hidden email] List" <[hidden email]>
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 < [hidden email] > 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" < [hidden email] >
To: "Sarah Diehl" < [hidden email] >
Cc: " [hidden email] List" < [hidden email] >
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 < [hidden email] > 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/

INSTALLATION.log (6K) Download Attachment