Problem using FastQC in Galaxy

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Problem using FastQC in Galaxy

Waldron, Michael H
Having a problem with directing FastQC output in Galaxy. User is running a job whose command line looks like this:

# FastQC cl = /nas02/apps/galaxy-prod/galaxy-dist/tool-data/shared/jars/FastQC/fastqc --outdir=/proj/galaxy/job_working_directory/010/10467/dataset_13836_files /proj/galaxy/job_working_directory/010/10467/dataset_13836_files/SRR016862.fastq

Job output looks like this:

## odpath=None: No output found in None. Output for the run was:

# FastQC cl = /nas02/apps/galaxy-prod/galaxy-dist/tool-data/shared/jars/FastQC/fastqc --outdir=/proj/galaxy/job_working_directory/010/10467/dataset_13827_files /proj/galaxy/job_working_directory/010/10467/dataset_13827_files/SRR016862.fastq

Started analysis of SRR016862.fastq

Approx 5% complete for SRR016862.fastq

Approx 10% complete for SRR016862.fastq

Approx 15% complete for SRR016862.fastq

Approx 20% complete for SRR016862.fastq

Approx 25% complete for SRR016862.fastq

Approx 30% complete for SRR016862.fastq

Approx 35% complete for SRR016862.fastq

Approx 40% complete for SRR016862.fastq

Approx 45% complete for SRR016862.fastq

Approx 50% complete for SRR016862.fastq

Approx 55% complete for SRR016862.fastq

Approx 60% complete for SRR016862.fastq

Approx 65% complete for SRR016862.fastq

Approx 70% complete for SRR016862.fastq

Approx 75% complete for SRR016862.fastq

Approx 80% complete for SRR016862.fastq

Approx 85% complete for SRR016862.fastq

Approx 90% complete for SRR016862.fastq

Approx 95% complete for SRR016862.fastq

Analysis complete for SRR016862.fastq

 
The job_working_directory/010/10467 directory is created, however it is empty. It appears this "odpath" needs to be set somehow?

Does anyone know a solution for this?

Mike Waldron
Systems Specialist
ITS - Research Computing Center
University of North Carolina at Chapel Hill


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Re: Problem using FastQC in Galaxy

Björn Grüning-3
Hi Michael,

which version of the FASTQC wrapper are you running? Can you point us to
the exact build and toolshed version?

Thanks,
Bjoern

Am 02.01.2015 um 21:22 schrieb Waldron, Michael H:

> Having a problem with directing FastQC output in Galaxy. User is running a job whose command line looks like this:
>
> # FastQC cl = /nas02/apps/galaxy-prod/galaxy-dist/tool-data/shared/jars/FastQC/fastqc --outdir=/proj/galaxy/job_working_directory/010/10467/dataset_13836_files /proj/galaxy/job_working_directory/010/10467/dataset_13836_files/SRR016862.fastq
>
> Job output looks like this:
>
> ## odpath=None: No output found in None. Output for the run was:
> # FastQC cl = /nas02/apps/galaxy-prod/galaxy-dist/tool-data/shared/jars/FastQC/fastqc --outdir=/proj/galaxy/job_working_directory/010/10467/dataset_13827_files /proj/galaxy/job_working_directory/010/10467/dataset_13827_files/SRR016862.fastq
> Started analysis of SRR016862.fastq
> Approx 5% complete for SRR016862.fastq
> Approx 10% complete for SRR016862.fastq
> Approx 15% complete for SRR016862.fastq
> Approx 20% complete for SRR016862.fastq
> Approx 25% complete for SRR016862.fastq
> Approx 30% complete for SRR016862.fastq
> Approx 35% complete for SRR016862.fastq
> Approx 40% complete for SRR016862.fastq
> Approx 45% complete for SRR016862.fastq
> Approx 50% complete for SRR016862.fastq
> Approx 55% complete for SRR016862.fastq
> Approx 60% complete for SRR016862.fastq
> Approx 65% complete for SRR016862.fastq
> Approx 70% complete for SRR016862.fastq
> Approx 75% complete for SRR016862.fastq
> Approx 80% complete for SRR016862.fastq
> Approx 85% complete for SRR016862.fastq
> Approx 90% complete for SRR016862.fastq
> Approx 95% complete for SRR016862.fastq
> Analysis complete for SRR016862.fastq
>
> The job_working_directory/010/10467 directory is created, however it is empty. It appears this "odpath" needs to be set somehow?
>
> Does anyone know a solution for this?
>
> Mike Waldron
> Systems Specialist
> ITS - Research Computing Center
> University of North Carolina at Chapel Hill
>
>
>
>
> ___________________________________________________________
> 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/
>
___________________________________________________________
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in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

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Re: Problem using FastQC in Galaxy

Waldron, Michael H
It is FastQC-0.11.2. It's a separate install from Galaxy, and a symlink points to it under tool-data/shared/jars:

$ pwd
/nas02/apps/galaxy-prod/galaxy-dist/tool-data/shared/jars

FastQC -> /nas02/apps/galaxy-prod/fastqc-0.11.2/FastQC


Mike Waldron
Systems Specialist
ITS - Research Computing Center
University of North Carolina at Chapel Hill


________________________________________
From: Björn Grüning [[hidden email]]
Sent: Saturday, January 03, 2015 6:42 AM
To: Waldron, Michael H; [hidden email]
Subject: Re: [galaxy-dev] Problem using FastQC in Galaxy

Hi Michael,

which version of the FASTQC wrapper are you running? Can you point us to
the exact build and toolshed version?

Thanks,
Bjoern

Am 02.01.2015 um 21:22 schrieb Waldron, Michael H:

> Having a problem with directing FastQC output in Galaxy. User is running a job whose command line looks like this:
>
> # FastQC cl = /nas02/apps/galaxy-prod/galaxy-dist/tool-data/shared/jars/FastQC/fastqc --outdir=/proj/galaxy/job_working_directory/010/10467/dataset_13836_files /proj/galaxy/job_working_directory/010/10467/dataset_13836_files/SRR016862.fastq
>
> Job output looks like this:
>
> ## odpath=None: No output found in None. Output for the run was:
> # FastQC cl = /nas02/apps/galaxy-prod/galaxy-dist/tool-data/shared/jars/FastQC/fastqc --outdir=/proj/galaxy/job_working_directory/010/10467/dataset_13827_files /proj/galaxy/job_working_directory/010/10467/dataset_13827_files/SRR016862.fastq
> Started analysis of SRR016862.fastq
> Approx 5% complete for SRR016862.fastq
> Approx 10% complete for SRR016862.fastq
> Approx 15% complete for SRR016862.fastq
> Approx 20% complete for SRR016862.fastq
> Approx 25% complete for SRR016862.fastq
> Approx 30% complete for SRR016862.fastq
> Approx 35% complete for SRR016862.fastq
> Approx 40% complete for SRR016862.fastq
> Approx 45% complete for SRR016862.fastq
> Approx 50% complete for SRR016862.fastq
> Approx 55% complete for SRR016862.fastq
> Approx 60% complete for SRR016862.fastq
> Approx 65% complete for SRR016862.fastq
> Approx 70% complete for SRR016862.fastq
> Approx 75% complete for SRR016862.fastq
> Approx 80% complete for SRR016862.fastq
> Approx 85% complete for SRR016862.fastq
> Approx 90% complete for SRR016862.fastq
> Approx 95% complete for SRR016862.fastq
> Analysis complete for SRR016862.fastq
>
> The job_working_directory/010/10467 directory is created, however it is empty. It appears this "odpath" needs to be set somehow?
>
> Does anyone know a solution for this?
>
> Mike Waldron
> Systems Specialist
> ITS - Research Computing Center
> University of North Carolina at Chapel Hill
>
>
>
>
> ___________________________________________________________
> 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:
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Re: Problem using FastQC in Galaxy

Björn Grüning-3
Hi Mike,

it can happen that wrappers versions do not work well with older/newer
FASTQC versions. This is the reason we try to couple "binary" versions
of tools to wrappers versions.

Any reason you don't use the toolshed installation with dependencies?

Cheers,
Bjoern

Am 03.01.2015 um 17:44 schrieb Waldron, Michael H:

> It is FastQC-0.11.2. It's a separate install from Galaxy, and a symlink points to it under tool-data/shared/jars:
>
> $ pwd
> /nas02/apps/galaxy-prod/galaxy-dist/tool-data/shared/jars
>
> FastQC -> /nas02/apps/galaxy-prod/fastqc-0.11.2/FastQC
>
>
> Mike Waldron
> Systems Specialist
> ITS - Research Computing Center
> University of North Carolina at Chapel Hill
>
>
> ________________________________________
> From: Björn Grüning [[hidden email]]
> Sent: Saturday, January 03, 2015 6:42 AM
> To: Waldron, Michael H; [hidden email]
> Subject: Re: [galaxy-dev] Problem using FastQC in Galaxy
>
> Hi Michael,
>
> which version of the FASTQC wrapper are you running? Can you point us to
> the exact build and toolshed version?
>
> Thanks,
> Bjoern
>
> Am 02.01.2015 um 21:22 schrieb Waldron, Michael H:
>> Having a problem with directing FastQC output in Galaxy. User is running a job whose command line looks like this:
>>
>> # FastQC cl = /nas02/apps/galaxy-prod/galaxy-dist/tool-data/shared/jars/FastQC/fastqc --outdir=/proj/galaxy/job_working_directory/010/10467/dataset_13836_files /proj/galaxy/job_working_directory/010/10467/dataset_13836_files/SRR016862.fastq
>>
>> Job output looks like this:
>>
>> ## odpath=None: No output found in None. Output for the run was:
>> # FastQC cl = /nas02/apps/galaxy-prod/galaxy-dist/tool-data/shared/jars/FastQC/fastqc --outdir=/proj/galaxy/job_working_directory/010/10467/dataset_13827_files /proj/galaxy/job_working_directory/010/10467/dataset_13827_files/SRR016862.fastq
>> Started analysis of SRR016862.fastq
>> Approx 5% complete for SRR016862.fastq
>> Approx 10% complete for SRR016862.fastq
>> Approx 15% complete for SRR016862.fastq
>> Approx 20% complete for SRR016862.fastq
>> Approx 25% complete for SRR016862.fastq
>> Approx 30% complete for SRR016862.fastq
>> Approx 35% complete for SRR016862.fastq
>> Approx 40% complete for SRR016862.fastq
>> Approx 45% complete for SRR016862.fastq
>> Approx 50% complete for SRR016862.fastq
>> Approx 55% complete for SRR016862.fastq
>> Approx 60% complete for SRR016862.fastq
>> Approx 65% complete for SRR016862.fastq
>> Approx 70% complete for SRR016862.fastq
>> Approx 75% complete for SRR016862.fastq
>> Approx 80% complete for SRR016862.fastq
>> Approx 85% complete for SRR016862.fastq
>> Approx 90% complete for SRR016862.fastq
>> Approx 95% complete for SRR016862.fastq
>> Analysis complete for SRR016862.fastq
>>
>> The job_working_directory/010/10467 directory is created, however it is empty. It appears this "odpath" needs to be set somehow?
>>
>> Does anyone know a solution for this?
>>
>> Mike Waldron
>> Systems Specialist
>> ITS - Research Computing Center
>> University of North Carolina at Chapel Hill
>>
>>
>>
>>
>> ___________________________________________________________
>> 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/
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Re: Problem using FastQC in Galaxy

Waldron, Michael H
It's mostly due to my lack of thorough knowledge about Galaxy. So should I just try to do the tool shed install by going to Admin->Tool Sheds and selecting fastqc from there?

Mike Waldron
Systems Specialist
ITS - Research Computing Center
University of North Carolina at Chapel Hill


________________________________________
From: Björn Grüning [[hidden email]]
Sent: Sunday, January 04, 2015 12:46 PM
To: Waldron, Michael H; Björn Grüning; [hidden email]
Subject: Re: [galaxy-dev] Problem using FastQC in Galaxy

Hi Mike,

it can happen that wrappers versions do not work well with older/newer
FASTQC versions. This is the reason we try to couple "binary" versions
of tools to wrappers versions.

Any reason you don't use the toolshed installation with dependencies?

Cheers,
Bjoern

Am 03.01.2015 um 17:44 schrieb Waldron, Michael H:

> It is FastQC-0.11.2. It's a separate install from Galaxy, and a symlink points to it under tool-data/shared/jars:
>
> $ pwd
> /nas02/apps/galaxy-prod/galaxy-dist/tool-data/shared/jars
>
> FastQC -> /nas02/apps/galaxy-prod/fastqc-0.11.2/FastQC
>
>
> Mike Waldron
> Systems Specialist
> ITS - Research Computing Center
> University of North Carolina at Chapel Hill
>
>
> ________________________________________
> From: Björn Grüning [[hidden email]]
> Sent: Saturday, January 03, 2015 6:42 AM
> To: Waldron, Michael H; [hidden email]
> Subject: Re: [galaxy-dev] Problem using FastQC in Galaxy
>
> Hi Michael,
>
> which version of the FASTQC wrapper are you running? Can you point us to
> the exact build and toolshed version?
>
> Thanks,
> Bjoern
>
> Am 02.01.2015 um 21:22 schrieb Waldron, Michael H:
>> Having a problem with directing FastQC output in Galaxy. User is running a job whose command line looks like this:
>>
>> # FastQC cl = /nas02/apps/galaxy-prod/galaxy-dist/tool-data/shared/jars/FastQC/fastqc --outdir=/proj/galaxy/job_working_directory/010/10467/dataset_13836_files /proj/galaxy/job_working_directory/010/10467/dataset_13836_files/SRR016862.fastq
>>
>> Job output looks like this:
>>
>> ## odpath=None: No output found in None. Output for the run was:
>> # FastQC cl = /nas02/apps/galaxy-prod/galaxy-dist/tool-data/shared/jars/FastQC/fastqc --outdir=/proj/galaxy/job_working_directory/010/10467/dataset_13827_files /proj/galaxy/job_working_directory/010/10467/dataset_13827_files/SRR016862.fastq
>> Started analysis of SRR016862.fastq
>> Approx 5% complete for SRR016862.fastq
>> Approx 10% complete for SRR016862.fastq
>> Approx 15% complete for SRR016862.fastq
>> Approx 20% complete for SRR016862.fastq
>> Approx 25% complete for SRR016862.fastq
>> Approx 30% complete for SRR016862.fastq
>> Approx 35% complete for SRR016862.fastq
>> Approx 40% complete for SRR016862.fastq
>> Approx 45% complete for SRR016862.fastq
>> Approx 50% complete for SRR016862.fastq
>> Approx 55% complete for SRR016862.fastq
>> Approx 60% complete for SRR016862.fastq
>> Approx 65% complete for SRR016862.fastq
>> Approx 70% complete for SRR016862.fastq
>> Approx 75% complete for SRR016862.fastq
>> Approx 80% complete for SRR016862.fastq
>> Approx 85% complete for SRR016862.fastq
>> Approx 90% complete for SRR016862.fastq
>> Approx 95% complete for SRR016862.fastq
>> Analysis complete for SRR016862.fastq
>>
>> The job_working_directory/010/10467 directory is created, however it is empty. It appears this "odpath" needs to be set somehow?
>>
>> Does anyone know a solution for this?
>>
>> Mike Waldron
>> Systems Specialist
>> ITS - Research Computing Center
>> University of North Carolina at Chapel Hill
>>
>>
>>
>>
>> ___________________________________________________________
>> 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:
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Re: Problem using FastQC in Galaxy

Martin Čech
Hi Mike, 

give it a shot for sure. If you want some details have a look at https://wiki.galaxyproject.org/Admin/Tools/AddToolFromToolShedTutorial

M.

On Sun Jan 04 2015 at 7:53:51 PM Waldron, Michael H <[hidden email]> wrote:
It's mostly due to my lack of thorough knowledge about Galaxy. So should I just try to do the tool shed install by going to Admin->Tool Sheds and selecting fastqc from there?

Mike Waldron
Systems Specialist
ITS - Research Computing Center
University of North Carolina at Chapel Hill


________________________________________
From: Björn Grüning [[hidden email]]
Sent: Sunday, January 04, 2015 12:46 PM
To: Waldron, Michael H; Björn Grüning; [hidden email]
Subject: Re: [galaxy-dev] Problem using FastQC in Galaxy

Hi Mike,

it can happen that wrappers versions do not work well with older/newer
FASTQC versions. This is the reason we try to couple "binary" versions
of tools to wrappers versions.

Any reason you don't use the toolshed installation with dependencies?

Cheers,
Bjoern

Am 03.01.2015 um 17:44 schrieb Waldron, Michael H:
> It is FastQC-0.11.2. It's a separate install from Galaxy, and a symlink points to it under tool-data/shared/jars:
>
> $ pwd
> /nas02/apps/galaxy-prod/galaxy-dist/tool-data/shared/jars
>
> FastQC -> /nas02/apps/galaxy-prod/fastqc-0.11.2/FastQC
>
>
> Mike Waldron
> Systems Specialist
> ITS - Research Computing Center
> University of North Carolina at Chapel Hill
>
>
> ________________________________________
> From: Björn Grüning [[hidden email]]
> Sent: Saturday, January 03, 2015 6:42 AM
> To: Waldron, Michael H; [hidden email]
> Subject: Re: [galaxy-dev] Problem using FastQC in Galaxy
>
> Hi Michael,
>
> which version of the FASTQC wrapper are you running? Can you point us to
> the exact build and toolshed version?
>
> Thanks,
> Bjoern
>
> Am 02.01.2015 um 21:22 schrieb Waldron, Michael H:
>> Having a problem with directing FastQC output in Galaxy. User is running a job whose command line looks like this:
>>
>> # FastQC cl = /nas02/apps/galaxy-prod/galaxy-dist/tool-data/shared/jars/FastQC/fastqc --outdir=/proj/galaxy/job_working_directory/010/10467/dataset_13836_files /proj/galaxy/job_working_directory/010/10467/dataset_13836_files/SRR016862.fastq
>>
>> Job output looks like this:
>>
>> ## odpath=None: No output found in None. Output for the run was:
>> # FastQC cl = /nas02/apps/galaxy-prod/galaxy-dist/tool-data/shared/jars/FastQC/fastqc --outdir=/proj/galaxy/job_working_directory/010/10467/dataset_13827_files /proj/galaxy/job_working_directory/010/10467/dataset_13827_files/SRR016862.fastq
>> Started analysis of SRR016862.fastq
>> Approx 5% complete for SRR016862.fastq
>> Approx 10% complete for SRR016862.fastq
>> Approx 15% complete for SRR016862.fastq
>> Approx 20% complete for SRR016862.fastq
>> Approx 25% complete for SRR016862.fastq
>> Approx 30% complete for SRR016862.fastq
>> Approx 35% complete for SRR016862.fastq
>> Approx 40% complete for SRR016862.fastq
>> Approx 45% complete for SRR016862.fastq
>> Approx 50% complete for SRR016862.fastq
>> Approx 55% complete for SRR016862.fastq
>> Approx 60% complete for SRR016862.fastq
>> Approx 65% complete for SRR016862.fastq
>> Approx 70% complete for SRR016862.fastq
>> Approx 75% complete for SRR016862.fastq
>> Approx 80% complete for SRR016862.fastq
>> Approx 85% complete for SRR016862.fastq
>> Approx 90% complete for SRR016862.fastq
>> Approx 95% complete for SRR016862.fastq
>> Analysis complete for SRR016862.fastq
>>
>> The job_working_directory/010/10467 directory is created, however it is empty. It appears this "odpath" needs to be set somehow?
>>
>> Does anyone know a solution for this?
>>
>> Mike Waldron
>> Systems Specialist
>> ITS - Research Computing Center
>> University of North Carolina at Chapel Hill
>>
>>
>>
>>
>> ___________________________________________________________
>> 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/

___________________________________________________________
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:
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Re: Problem using FastQC in Galaxy

Waldron, Michael H
I attempted to install fastqc via the tool shed, and got an error. The log information is listed below. The main error appears to be "too many values to unpack".

152.2.204.5 - - [05/Jan/2015:09:09:00 -0400] "GET /admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/&repository_ids=ca249a25748b71a3&changeset_revisions=0b201de108b9 HTTP/1.1" 500 - "https://toolshed.g2.bx.psu.edu/repository/preview_tools_in_changeset?repository_id=ca249a25748b71a3&changeset_revision=0b201de108b9" "Mozilla/5.0 (X11; Linux x86_64; rv:34.0) Gecko/20100101 Firefox/34.0"
Error - <type 'exceptions.ValueError'>: too many values to unpack
URL: https://galaxy.its.unc.edu/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/&repository_ids=ca249a25748b71a3&changeset_revisions=0b201de108b9
File '/nas02/apps/galaxy-prod/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py', line 143 in __call__
  app_iter = self.application(environ, start_response)
File '/nas02/apps/galaxy-prod/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__
  return self.application(environ, start_response)
File '/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/web/framework/middleware/remoteuser.py', line 91 in __call__
  return self.app( environ, start_response )
File '/nas02/apps/galaxy-prod/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__
  return self.application(environ, start_response)
File '/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/web/framework/base.py', line 132 in __call__
  return self.handle_request( environ, start_response )
File '/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/web/framework/base.py', line 185 in handle_request
  body = method( trans, **kwargs )
File '/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 216 in decorator
  return func( self, trans, *args, **kwargs )
File '/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py', line 1345 in prepare_for_install
  shed_util.get_dependencies_for_repository( trans, tool_shed_url, repo_info_dict, includes_tool_dependencies )
File '/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/util/shed_util.py', line 601 in get_dependencies_for_repository
  installed_rd, missing_rd = get_installed_and_missing_repository_dependencies_for_new_install( trans, repo_info_tuple )
File '/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/util/shed_util.py', line 715 in get_installed_and_missing_repository_dependencies_for_new_install
  tool_shed, name, owner, changeset_revision = rd_tup
ValueError: too many values to unpack

Configuration
-------------
  __file__: '/nas02/apps/galaxy-prod/galaxy-dist/universe_wsgi.ini'
  admin_users: '[hidden email],[hidden email],[hidden email],[hidden email]'
  allow_user_dataset_purge: 'True'
  database_connection: 'postgres://galaxy@localhost/galaxy'
  database_engine_option_server_side_cursors: 'True'
  database_engine_option_strategy: 'threadlocal'
  debug: 'False'
  default_cluster_job_runner: 'drmaa://-q pgalaxy_q -M 41900000 /'
  enable_quotas: 'True'
  enable_tracks: 'True'
  file_path: '/proj/galaxy'
  ftp_upload_dir: 'database/ftp'
  ftp_upload_site: 'galaxy.its.unc.edu:2021'
  here: '/nas02/apps/galaxy-prod/galaxy-dist'
  job_working_directory: '/proj/galaxy/job_working_directory'
  len_file_path: 'tool-data/shared/ucsc/chrom'
  library_import_dir: '/proj/seq/galaxy'
  local_job_queue_workers: '10'
  nglims_config_file: 'tool-data/nglims.yaml'
  remote_user_maildomain: 'email.unc.edu'
  retry_job_output_collection: '30'
  start_job_runners: 'drmaa'
  static_cache_time: '360'
  static_dir: '/nas02/apps/galaxy-prod/galaxy-dist/static/'
  static_enabled: 'True'
  static_favicon_dir: '/nas02/apps/galaxy-prod/galaxy-dist/static/favicon.ico'
  static_images_dir: '/nas02/apps/galaxy-prod/galaxy-dist/static/images'
  static_scripts_dir: '/nas02/apps/galaxy-prod/galaxy-dist/static/scripts/'
  static_style_dir: '/nas02/apps/galaxy-prod/galaxy-dist/static/june_2007_style/blue'
  tool_config_file: 'tool_conf.xml,shed_tool_conf.xml'
  tool_dependency_dir: '../tool_dependencies'
  tool_path: 'tools'
  use_interactive: 'False'
  use_nglims: 'False'
  use_remote_user: 'True'


WSGI Variables
--------------
  application: <paste.recursive.RecursiveMiddleware object at 0x1fa05fd0>
  original_wsgi.url_scheme: 'http'
  paste.cookies: (<SimpleCookie: VCLACTIVENODE='12' VCLAUTH='laCke775oUL18xKNIRgrIGOkWV8TDHKwq647BxYTcK1NkdOlvh0%2B8glvFC%2BdvpkoiYg7qttH2AXyWKGmw2aqWVJKp%2BeLJFauRWutlotbDElWn6CfZYeYesGHlWgWMnWbxAW8EYmsmecDsM0xV3KW5%2BFrMdBpDdseXYKCEXzpIIvvwp7F8gX%2BU%2BEUjPE3lb4JzGWf3Ie9XgfEqlPycbiJXPHXCrsGkanB3NXDzJJeUwe9PFO5bc0%2BA1vP7X3YxYdfjLxVAK9ZVqv8tpVwkyh26Mc%2BJ6ei5j9oYmOgQSGdoBuI3y6JmQuivN0z0I6%2FdFy1LBAH74Ri%2FZMgdL7%2Bgjj79A%3D%3D' VCLLOCALE='en_US' VCLSKIN='default' __unam='74abf65-13ed3051d32-51a5d500-40' __utma='117910737.2001824546.1373325050.1407267272.1407768470.35' __utmc='180505699' __utmz='117910737.1401999139.26.11.utmcsr=help.unc.edu|utmccn=(referral)|utmcmd=referral|utmcct=/help/research-computing-application-matrix/' _ga='GA1.2.83593674.1365452191' _shibsession_64656661756c7468747470733a2f2f67616c6178792e6974732e756e632e6564752f73686962626f6c657468='_881cda95b24d6988ef78dd775a463719' galaxysession='c6ca0ddb55be603a6569c0b408144f8320f2758b32c93176f6b2d0daddb6375a8a07f508556...f78dd775a463719')
  paste.expected_exceptions: [<class 'paste.httpexceptions.HTTPException'>]
  paste.httpexceptions: <paste.httpexceptions.HTTPExceptionHandler object at 0x1f83e690>
  paste.httpserver.thread_pool: <paste.httpserver.ThreadPool object at 0x18ec9110>
  paste.parsed_querystring: ([('tool_shed_url', 'https://toolshed.g2.bx.psu.edu/'), ('repository_ids', 'ca249a25748b71a3'), ('changeset_revisions', '0b201de108b9')], 'tool_shed_url=https://toolshed.g2.bx.psu.edu/&repository_ids=ca249a25748b71a3&changeset_revisions=0b201de108b9')
  paste.recursive.forward: <paste.recursive.Forwarder from />
  paste.recursive.include: <paste.recursive.Includer from />
  paste.recursive.include_app_iter: <paste.recursive.IncluderAppIter from />
  paste.recursive.script_name: ''
  paste.throw_errors: True
  webob._parsed_query_vars: (MultiDict([('tool_shed_url', 'https://toolshed.g2.bx.psu.edu/'), ('repository_ids', 'ca249a25748b71a3'), ('changeset_revisions', '0b201de108b9')]), 'tool_shed_url=https://toolshed.g2.bx.psu.edu/&repository_ids=ca249a25748b71a3&changeset_revisions=0b201de108b9')
  wsgi process: 'Multithreaded'
------------------------------------------------------------


Mike Waldron
Systems Specialist
ITS - Research Computing Center
University of North Carolina at Chapel Hill


From: Martin Čech [[hidden email]]
Sent: Monday, January 05, 2015 8:06 AM
To: Waldron, Michael H; Björn Grüning; [hidden email]
Subject: Re: [galaxy-dev] Problem using FastQC in Galaxy

Hi Mike, 

give it a shot for sure. If you want some details have a look at https://wiki.galaxyproject.org/Admin/Tools/AddToolFromToolShedTutorial

M.

On Sun Jan 04 2015 at 7:53:51 PM Waldron, Michael H <[hidden email]> wrote:
It's mostly due to my lack of thorough knowledge about Galaxy. So should I just try to do the tool shed install by going to Admin->Tool Sheds and selecting fastqc from there?

Mike Waldron
Systems Specialist
ITS - Research Computing Center
University of North Carolina at Chapel Hill


________________________________________
From: Björn Grüning [[hidden email]]
Sent: Sunday, January 04, 2015 12:46 PM
To: Waldron, Michael H; Björn Grüning; [hidden email]
Subject: Re: [galaxy-dev] Problem using FastQC in Galaxy

Hi Mike,

it can happen that wrappers versions do not work well with older/newer
FASTQC versions. This is the reason we try to couple "binary" versions
of tools to wrappers versions.

Any reason you don't use the toolshed installation with dependencies?

Cheers,
Bjoern

Am 03.01.2015 um 17:44 schrieb Waldron, Michael H:
> It is FastQC-0.11.2. It's a separate install from Galaxy, and a symlink points to it under tool-data/shared/jars:
>
> $ pwd
> /nas02/apps/galaxy-prod/galaxy-dist/tool-data/shared/jars
>
> FastQC -> /nas02/apps/galaxy-prod/fastqc-0.11.2/FastQC
>
>
> Mike Waldron
> Systems Specialist
> ITS - Research Computing Center
> University of North Carolina at Chapel Hill
>
>
> ________________________________________
> From: Björn Grüning [[hidden email]]
> Sent: Saturday, January 03, 2015 6:42 AM
> To: Waldron, Michael H; [hidden email]
> Subject: Re: [galaxy-dev] Problem using FastQC in Galaxy
>
> Hi Michael,
>
> which version of the FASTQC wrapper are you running? Can you point us to
> the exact build and toolshed version?
>
> Thanks,
> Bjoern
>
> Am 02.01.2015 um 21:22 schrieb Waldron, Michael H:
>> Having a problem with directing FastQC output in Galaxy. User is running a job whose command line looks like this:
>>
>> # FastQC cl = /nas02/apps/galaxy-prod/galaxy-dist/tool-data/shared/jars/FastQC/fastqc --outdir=/proj/galaxy/job_working_directory/010/10467/dataset_13836_files /proj/galaxy/job_working_directory/010/10467/dataset_13836_files/SRR016862.fastq
>>
>> Job output looks like this:
>>
>> ## odpath=None: No output found in None. Output for the run was:
>> # FastQC cl = /nas02/apps/galaxy-prod/galaxy-dist/tool-data/shared/jars/FastQC/fastqc --outdir=/proj/galaxy/job_working_directory/010/10467/dataset_13827_files /proj/galaxy/job_working_directory/010/10467/dataset_13827_files/SRR016862.fastq
>> Started analysis of SRR016862.fastq
>> Approx 5% complete for SRR016862.fastq
>> Approx 10% complete for SRR016862.fastq
>> Approx 15% complete for SRR016862.fastq
>> Approx 20% complete for SRR016862.fastq
>> Approx 25% complete for SRR016862.fastq
>> Approx 30% complete for SRR016862.fastq
>> Approx 35% complete for SRR016862.fastq
>> Approx 40% complete for SRR016862.fastq
>> Approx 45% complete for SRR016862.fastq
>> Approx 50% complete for SRR016862.fastq
>> Approx 55% complete for SRR016862.fastq
>> Approx 60% complete for SRR016862.fastq
>> Approx 65% complete for SRR016862.fastq
>> Approx 70% complete for SRR016862.fastq
>> Approx 75% complete for SRR016862.fastq
>> Approx 80% complete for SRR016862.fastq
>> Approx 85% complete for SRR016862.fastq
>> Approx 90% complete for SRR016862.fastq
>> Approx 95% complete for SRR016862.fastq
>> Analysis complete for SRR016862.fastq
>>
>> The job_working_directory/010/10467 directory is created, however it is empty. It appears this "odpath" needs to be set somehow?
>>
>> Does anyone know a solution for this?
>>
>> Mike Waldron
>> Systems Specialist
>> ITS - Research Computing Center
>> University of North Carolina at Chapel Hill
>>
>>
>>
>>
>> ___________________________________________________________
>> 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/

___________________________________________________________
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/
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Re: Problem using FastQC in Galaxy

John Chilton-4
This looks like a bug - but unfortunately it appears you are running a
fairly old version of Galaxy  - I don't think the file
lib/galaxy/util/shed_util.py has existed for the better part of a
year. It should be possible to get the FastQC wrapper to work with the
old version if you figure out the exact version of fastqc you need -
but if you want to use the tool shed you will probably want to upgrade
to the latest stable release of Galaxy.

-John

On Mon, Jan 5, 2015 at 9:17 AM, Waldron, Michael H
<[hidden email]> wrote:

> I attempted to install fastqc via the tool shed, and got an error. The log
> information is listed below. The main error appears to be "too many values
> to unpack".
>
> 152.2.204.5 - - [05/Jan/2015:09:09:00 -0400] "GET
> /admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/&repository_ids=ca249a25748b71a3&changeset_revisions=0b201de108b9
> HTTP/1.1" 500 -
> "https://toolshed.g2.bx.psu.edu/repository/preview_tools_in_changeset?repository_id=ca249a25748b71a3&changeset_revision=0b201de108b9"
> "Mozilla/5.0 (X11; Linux x86_64; rv:34.0) Gecko/20100101 Firefox/34.0"
> Error - <type 'exceptions.ValueError'>: too many values to unpack
> URL:
> https://galaxy.its.unc.edu/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/&repository_ids=ca249a25748b71a3&changeset_revisions=0b201de108b9
> File
> '/nas02/apps/galaxy-prod/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py',
> line 143 in __call__
>   app_iter = self.application(environ, start_response)
> File
> '/nas02/apps/galaxy-prod/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py',
> line 80 in __call__
>   return self.application(environ, start_response)
> File
> '/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/web/framework/middleware/remoteuser.py',
> line 91 in __call__
>   return self.app( environ, start_response )
> File
> '/nas02/apps/galaxy-prod/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py',
> line 632 in __call__
>   return self.application(environ, start_response)
> File '/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/web/framework/base.py',
> line 132 in __call__
>   return self.handle_request( environ, start_response )
> File '/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/web/framework/base.py',
> line 185 in handle_request
>   body = method( trans, **kwargs )
> File
> '/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/web/framework/__init__.py',
> line 216 in decorator
>   return func( self, trans, *args, **kwargs )
> File
> '/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py',
> line 1345 in prepare_for_install
>   shed_util.get_dependencies_for_repository( trans, tool_shed_url,
> repo_info_dict, includes_tool_dependencies )
> File '/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/util/shed_util.py',
> line 601 in get_dependencies_for_repository
>   installed_rd, missing_rd =
> get_installed_and_missing_repository_dependencies_for_new_install( trans,
> repo_info_tuple )
> File '/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/util/shed_util.py',
> line 715 in
> get_installed_and_missing_repository_dependencies_for_new_install
>   tool_shed, name, owner, changeset_revision = rd_tup
> ValueError: too many values to unpack
>
> Configuration
> -------------
>   __file__: '/nas02/apps/galaxy-prod/galaxy-dist/universe_wsgi.ini'
>   admin_users:
> '[hidden email],[hidden email],[hidden email],[hidden email]'
>   allow_user_dataset_purge: 'True'
>   database_connection: 'postgres://galaxy@localhost/galaxy'
>   database_engine_option_server_side_cursors: 'True'
>   database_engine_option_strategy: 'threadlocal'
>   debug: 'False'
>   default_cluster_job_runner: 'drmaa://-q pgalaxy_q -M 41900000 /'
>   enable_quotas: 'True'
>   enable_tracks: 'True'
>   file_path: '/proj/galaxy'
>   ftp_upload_dir: 'database/ftp'
>   ftp_upload_site: 'galaxy.its.unc.edu:2021'
>   here: '/nas02/apps/galaxy-prod/galaxy-dist'
>   job_working_directory: '/proj/galaxy/job_working_directory'
>   len_file_path: 'tool-data/shared/ucsc/chrom'
>   library_import_dir: '/proj/seq/galaxy'
>   local_job_queue_workers: '10'
>   nglims_config_file: 'tool-data/nglims.yaml'
>   remote_user_maildomain: 'email.unc.edu'
>   retry_job_output_collection: '30'
>   start_job_runners: 'drmaa'
>   static_cache_time: '360'
>   static_dir: '/nas02/apps/galaxy-prod/galaxy-dist/static/'
>   static_enabled: 'True'
>   static_favicon_dir:
> '/nas02/apps/galaxy-prod/galaxy-dist/static/favicon.ico'
>   static_images_dir: '/nas02/apps/galaxy-prod/galaxy-dist/static/images'
>   static_scripts_dir: '/nas02/apps/galaxy-prod/galaxy-dist/static/scripts/'
>   static_style_dir:
> '/nas02/apps/galaxy-prod/galaxy-dist/static/june_2007_style/blue'
>   tool_config_file: 'tool_conf.xml,shed_tool_conf.xml'
>   tool_dependency_dir: '../tool_dependencies'
>   tool_path: 'tools'
>   use_interactive: 'False'
>   use_nglims: 'False'
>   use_remote_user: 'True'
>
>
> WSGI Variables
> --------------
>   application: <paste.recursive.RecursiveMiddleware object at 0x1fa05fd0>
>   original_wsgi.url_scheme: 'http'
>   paste.cookies: (<SimpleCookie: VCLACTIVENODE='12'
> VCLAUTH='laCke775oUL18xKNIRgrIGOkWV8TDHKwq647BxYTcK1NkdOlvh0%2B8glvFC%2BdvpkoiYg7qttH2AXyWKGmw2aqWVJKp%2BeLJFauRWutlotbDElWn6CfZYeYesGHlWgWMnWbxAW8EYmsmecDsM0xV3KW5%2BFrMdBpDdseXYKCEXzpIIvvwp7F8gX%2BU%2BEUjPE3lb4JzGWf3Ie9XgfEqlPycbiJXPHXCrsGkanB3NXDzJJeUwe9PFO5bc0%2BA1vP7X3YxYdfjLxVAK9ZVqv8tpVwkyh26Mc%2BJ6ei5j9oYmOgQSGdoBuI3y6JmQuivN0z0I6%2FdFy1LBAH74Ri%2FZMgdL7%2Bgjj79A%3D%3D'
> VCLLOCALE='en_US' VCLSKIN='default' __unam='74abf65-13ed3051d32-51a5d500-40'
> __utma='117910737.2001824546.1373325050.1407267272.1407768470.35'
> __utmc='180505699'
> __utmz='117910737.1401999139.26.11.utmcsr=help.unc.edu|utmccn=(referral)|utmcmd=referral|utmcct=/help/research-computing-application-matrix/'
> _ga='GA1.2.83593674.1365452191'
> _shibsession_64656661756c7468747470733a2f2f67616c6178792e6974732e756e632e6564752f73686962626f6c657468='_881cda95b24d6988ef78dd775a463719'
> galaxysession='c6ca0ddb55be603a6569c0b408144f8320f2758b32c93176f6b2d0daddb6375a8a07f508556...f78dd775a463719')
>   paste.expected_exceptions: [<class 'paste.httpexceptions.HTTPException'>]
>   paste.httpexceptions: <paste.httpexceptions.HTTPExceptionHandler object at
> 0x1f83e690>
>   paste.httpserver.thread_pool: <paste.httpserver.ThreadPool object at
> 0x18ec9110>
>   paste.parsed_querystring: ([('tool_shed_url',
> 'https://toolshed.g2.bx.psu.edu/'), ('repository_ids', 'ca249a25748b71a3'),
> ('changeset_revisions', '0b201de108b9')],
> 'tool_shed_url=https://toolshed.g2.bx.psu.edu/&repository_ids=ca249a25748b71a3&changeset_revisions=0b201de108b9')
>   paste.recursive.forward: <paste.recursive.Forwarder from />
>   paste.recursive.include: <paste.recursive.Includer from />
>   paste.recursive.include_app_iter: <paste.recursive.IncluderAppIter from />
>   paste.recursive.script_name: ''
>   paste.throw_errors: True
>   webob._parsed_query_vars: (MultiDict([('tool_shed_url',
> 'https://toolshed.g2.bx.psu.edu/'), ('repository_ids', 'ca249a25748b71a3'),
> ('changeset_revisions', '0b201de108b9')]),
> 'tool_shed_url=https://toolshed.g2.bx.psu.edu/&repository_ids=ca249a25748b71a3&changeset_revisions=0b201de108b9')
>   wsgi process: 'Multithreaded'
> ------------------------------------------------------------
>
>
> Mike Waldron
> Systems Specialist
> ITS - Research Computing Center
> University of North Carolina at Chapel Hill
>
> ________________________________
> From: Martin Čech [[hidden email]]
> Sent: Monday, January 05, 2015 8:06 AM
>
> To: Waldron, Michael H; Björn Grüning; [hidden email]
> Subject: Re: [galaxy-dev] Problem using FastQC in Galaxy
>
> Hi Mike,
>
> give it a shot for sure. If you want some details have a look at
> https://wiki.galaxyproject.org/Admin/Tools/AddToolFromToolShedTutorial
>
> M.
>
> On Sun Jan 04 2015 at 7:53:51 PM Waldron, Michael H <[hidden email]>
> wrote:
>>
>> It's mostly due to my lack of thorough knowledge about Galaxy. So should I
>> just try to do the tool shed install by going to Admin->Tool Sheds and
>> selecting fastqc from there?
>>
>> Mike Waldron
>> Systems Specialist
>> ITS - Research Computing Center
>> University of North Carolina at Chapel Hill
>>
>>
>> ________________________________________
>> From: Björn Grüning [[hidden email]]
>> Sent: Sunday, January 04, 2015 12:46 PM
>> To: Waldron, Michael H; Björn Grüning; [hidden email]
>> Subject: Re: [galaxy-dev] Problem using FastQC in Galaxy
>>
>> Hi Mike,
>>
>> it can happen that wrappers versions do not work well with older/newer
>> FASTQC versions. This is the reason we try to couple "binary" versions
>> of tools to wrappers versions.
>>
>> Any reason you don't use the toolshed installation with dependencies?
>>
>> Cheers,
>> Bjoern
>>
>> Am 03.01.2015 um 17:44 schrieb Waldron, Michael H:
>> > It is FastQC-0.11.2. It's a separate install from Galaxy, and a symlink
>> > points to it under tool-data/shared/jars:
>> >
>> > $ pwd
>> > /nas02/apps/galaxy-prod/galaxy-dist/tool-data/shared/jars
>> >
>> > FastQC -> /nas02/apps/galaxy-prod/fastqc-0.11.2/FastQC
>> >
>> >
>> > Mike Waldron
>> > Systems Specialist
>> > ITS - Research Computing Center
>> > University of North Carolina at Chapel Hill
>> >
>> >
>> > ________________________________________
>> > From: Björn Grüning [[hidden email]]
>> > Sent: Saturday, January 03, 2015 6:42 AM
>> > To: Waldron, Michael H; [hidden email]
>> > Subject: Re: [galaxy-dev] Problem using FastQC in Galaxy
>> >
>> > Hi Michael,
>> >
>> > which version of the FASTQC wrapper are you running? Can you point us to
>> > the exact build and toolshed version?
>> >
>> > Thanks,
>> > Bjoern
>> >
>> > Am 02.01.2015 um 21:22 schrieb Waldron, Michael H:
>> >> Having a problem with directing FastQC output in Galaxy. User is
>> >> running a job whose command line looks like this:
>> >>
>> >> # FastQC cl =
>> >> /nas02/apps/galaxy-prod/galaxy-dist/tool-data/shared/jars/FastQC/fastqc
>> >> --outdir=/proj/galaxy/job_working_directory/010/10467/dataset_13836_files
>> >> /proj/galaxy/job_working_directory/010/10467/dataset_13836_files/SRR016862.fastq
>> >>
>> >> Job output looks like this:
>> >>
>> >> ## odpath=None: No output found in None. Output for the run was:
>> >> # FastQC cl =
>> >> /nas02/apps/galaxy-prod/galaxy-dist/tool-data/shared/jars/FastQC/fastqc
>> >> --outdir=/proj/galaxy/job_working_directory/010/10467/dataset_13827_files
>> >> /proj/galaxy/job_working_directory/010/10467/dataset_13827_files/SRR016862.fastq
>> >> Started analysis of SRR016862.fastq
>> >> Approx 5% complete for SRR016862.fastq
>> >> Approx 10% complete for SRR016862.fastq
>> >> Approx 15% complete for SRR016862.fastq
>> >> Approx 20% complete for SRR016862.fastq
>> >> Approx 25% complete for SRR016862.fastq
>> >> Approx 30% complete for SRR016862.fastq
>> >> Approx 35% complete for SRR016862.fastq
>> >> Approx 40% complete for SRR016862.fastq
>> >> Approx 45% complete for SRR016862.fastq
>> >> Approx 50% complete for SRR016862.fastq
>> >> Approx 55% complete for SRR016862.fastq
>> >> Approx 60% complete for SRR016862.fastq
>> >> Approx 65% complete for SRR016862.fastq
>> >> Approx 70% complete for SRR016862.fastq
>> >> Approx 75% complete for SRR016862.fastq
>> >> Approx 80% complete for SRR016862.fastq
>> >> Approx 85% complete for SRR016862.fastq
>> >> Approx 90% complete for SRR016862.fastq
>> >> Approx 95% complete for SRR016862.fastq
>> >> Analysis complete for SRR016862.fastq
>> >>
>> >> The job_working_directory/010/10467 directory is created, however it is
>> >> empty. It appears this "odpath" needs to be set somehow?
>> >>
>> >> Does anyone know a solution for this?
>> >>
>> >> Mike Waldron
>> >> Systems Specialist
>> >> ITS - Research Computing Center
>> >> University of North Carolina at Chapel Hill
>> >>
>> >>
>> >>
>> >>
>> >> ___________________________________________________________
>> >> 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/
>
>
> ___________________________________________________________
> 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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___________________________________________________________
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Re: Problem using FastQC in Galaxy

Waldron, Michael H
Ok, we have run several previous version of fastqc with it, we'll try one of those.

Our history of galaxy upgrade attempts has been very problematic. Things always seem to break, items disappear from menus, and I'm lost in trying to figure out the problems, so we tend to leave it alone.

Mike

________________________________________
From: John Chilton [[hidden email]]
Sent: Monday, January 05, 2015 10:25 AM
To: Waldron, Michael H
Cc: Martin Čech; Björn Grüning; [hidden email]
Subject: Re: [galaxy-dev] Problem using FastQC in Galaxy

This looks like a bug - but unfortunately it appears you are running a
fairly old version of Galaxy  - I don't think the file
lib/galaxy/util/shed_util.py has existed for the better part of a
year. It should be possible to get the FastQC wrapper to work with the
old version if you figure out the exact version of fastqc you need -
but if you want to use the tool shed you will probably want to upgrade
to the latest stable release of Galaxy.

-John

On Mon, Jan 5, 2015 at 9:17 AM, Waldron, Michael H
<[hidden email]> wrote:

> I attempted to install fastqc via the tool shed, and got an error. The log
> information is listed below. The main error appears to be "too many values
> to unpack".
>
> 152.2.204.5 - - [05/Jan/2015:09:09:00 -0400] "GET
> /admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/&repository_ids=ca249a25748b71a3&changeset_revisions=0b201de108b9
> HTTP/1.1" 500 -
> "https://toolshed.g2.bx.psu.edu/repository/preview_tools_in_changeset?repository_id=ca249a25748b71a3&changeset_revision=0b201de108b9"
> "Mozilla/5.0 (X11; Linux x86_64; rv:34.0) Gecko/20100101 Firefox/34.0"
> Error - <type 'exceptions.ValueError'>: too many values to unpack
> URL:
> https://galaxy.its.unc.edu/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/&repository_ids=ca249a25748b71a3&changeset_revisions=0b201de108b9
> File
> '/nas02/apps/galaxy-prod/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py',
> line 143 in __call__
>   app_iter = self.application(environ, start_response)
> File
> '/nas02/apps/galaxy-prod/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py',
> line 80 in __call__
>   return self.application(environ, start_response)
> File
> '/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/web/framework/middleware/remoteuser.py',
> line 91 in __call__
>   return self.app( environ, start_response )
> File
> '/nas02/apps/galaxy-prod/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py',
> line 632 in __call__
>   return self.application(environ, start_response)
> File '/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/web/framework/base.py',
> line 132 in __call__
>   return self.handle_request( environ, start_response )
> File '/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/web/framework/base.py',
> line 185 in handle_request
>   body = method( trans, **kwargs )
> File
> '/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/web/framework/__init__.py',
> line 216 in decorator
>   return func( self, trans, *args, **kwargs )
> File
> '/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py',
> line 1345 in prepare_for_install
>   shed_util.get_dependencies_for_repository( trans, tool_shed_url,
> repo_info_dict, includes_tool_dependencies )
> File '/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/util/shed_util.py',
> line 601 in get_dependencies_for_repository
>   installed_rd, missing_rd =
> get_installed_and_missing_repository_dependencies_for_new_install( trans,
> repo_info_tuple )
> File '/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/util/shed_util.py',
> line 715 in
> get_installed_and_missing_repository_dependencies_for_new_install
>   tool_shed, name, owner, changeset_revision = rd_tup
> ValueError: too many values to unpack
>
> Configuration
> -------------
>   __file__: '/nas02/apps/galaxy-prod/galaxy-dist/universe_wsgi.ini'
>   admin_users:
> '[hidden email],[hidden email],[hidden email],[hidden email]'
>   allow_user_dataset_purge: 'True'
>   database_connection: 'postgres://galaxy@localhost/galaxy'
>   database_engine_option_server_side_cursors: 'True'
>   database_engine_option_strategy: 'threadlocal'
>   debug: 'False'
>   default_cluster_job_runner: 'drmaa://-q pgalaxy_q -M 41900000 /'
>   enable_quotas: 'True'
>   enable_tracks: 'True'
>   file_path: '/proj/galaxy'
>   ftp_upload_dir: 'database/ftp'
>   ftp_upload_site: 'galaxy.its.unc.edu:2021'
>   here: '/nas02/apps/galaxy-prod/galaxy-dist'
>   job_working_directory: '/proj/galaxy/job_working_directory'
>   len_file_path: 'tool-data/shared/ucsc/chrom'
>   library_import_dir: '/proj/seq/galaxy'
>   local_job_queue_workers: '10'
>   nglims_config_file: 'tool-data/nglims.yaml'
>   remote_user_maildomain: 'email.unc.edu'
>   retry_job_output_collection: '30'
>   start_job_runners: 'drmaa'
>   static_cache_time: '360'
>   static_dir: '/nas02/apps/galaxy-prod/galaxy-dist/static/'
>   static_enabled: 'True'
>   static_favicon_dir:
> '/nas02/apps/galaxy-prod/galaxy-dist/static/favicon.ico'
>   static_images_dir: '/nas02/apps/galaxy-prod/galaxy-dist/static/images'
>   static_scripts_dir: '/nas02/apps/galaxy-prod/galaxy-dist/static/scripts/'
>   static_style_dir:
> '/nas02/apps/galaxy-prod/galaxy-dist/static/june_2007_style/blue'
>   tool_config_file: 'tool_conf.xml,shed_tool_conf.xml'
>   tool_dependency_dir: '../tool_dependencies'
>   tool_path: 'tools'
>   use_interactive: 'False'
>   use_nglims: 'False'
>   use_remote_user: 'True'
>
>
> WSGI Variables
> --------------
>   application: <paste.recursive.RecursiveMiddleware object at 0x1fa05fd0>
>   original_wsgi.url_scheme: 'http'
>   paste.cookies: (<SimpleCookie: VCLACTIVENODE='12'
> VCLAUTH='laCke775oUL18xKNIRgrIGOkWV8TDHKwq647BxYTcK1NkdOlvh0%2B8glvFC%2BdvpkoiYg7qttH2AXyWKGmw2aqWVJKp%2BeLJFauRWutlotbDElWn6CfZYeYesGHlWgWMnWbxAW8EYmsmecDsM0xV3KW5%2BFrMdBpDdseXYKCEXzpIIvvwp7F8gX%2BU%2BEUjPE3lb4JzGWf3Ie9XgfEqlPycbiJXPHXCrsGkanB3NXDzJJeUwe9PFO5bc0%2BA1vP7X3YxYdfjLxVAK9ZVqv8tpVwkyh26Mc%2BJ6ei5j9oYmOgQSGdoBuI3y6JmQuivN0z0I6%2FdFy1LBAH74Ri%2FZMgdL7%2Bgjj79A%3D%3D'
> VCLLOCALE='en_US' VCLSKIN='default' __unam='74abf65-13ed3051d32-51a5d500-40'
> __utma='117910737.2001824546.1373325050.1407267272.1407768470.35'
> __utmc='180505699'
> __utmz='117910737.1401999139.26.11.utmcsr=help.unc.edu|utmccn=(referral)|utmcmd=referral|utmcct=/help/research-computing-application-matrix/'
> _ga='GA1.2.83593674.1365452191'
> _shibsession_64656661756c7468747470733a2f2f67616c6178792e6974732e756e632e6564752f73686962626f6c657468='_881cda95b24d6988ef78dd775a463719'
> galaxysession='c6ca0ddb55be603a6569c0b408144f8320f2758b32c93176f6b2d0daddb6375a8a07f508556...f78dd775a463719')
>   paste.expected_exceptions: [<class 'paste.httpexceptions.HTTPException'>]
>   paste.httpexceptions: <paste.httpexceptions.HTTPExceptionHandler object at
> 0x1f83e690>
>   paste.httpserver.thread_pool: <paste.httpserver.ThreadPool object at
> 0x18ec9110>
>   paste.parsed_querystring: ([('tool_shed_url',
> 'https://toolshed.g2.bx.psu.edu/'), ('repository_ids', 'ca249a25748b71a3'),
> ('changeset_revisions', '0b201de108b9')],
> 'tool_shed_url=https://toolshed.g2.bx.psu.edu/&repository_ids=ca249a25748b71a3&changeset_revisions=0b201de108b9')
>   paste.recursive.forward: <paste.recursive.Forwarder from />
>   paste.recursive.include: <paste.recursive.Includer from />
>   paste.recursive.include_app_iter: <paste.recursive.IncluderAppIter from />
>   paste.recursive.script_name: ''
>   paste.throw_errors: True
>   webob._parsed_query_vars: (MultiDict([('tool_shed_url',
> 'https://toolshed.g2.bx.psu.edu/'), ('repository_ids', 'ca249a25748b71a3'),
> ('changeset_revisions', '0b201de108b9')]),
> 'tool_shed_url=https://toolshed.g2.bx.psu.edu/&repository_ids=ca249a25748b71a3&changeset_revisions=0b201de108b9')
>   wsgi process: 'Multithreaded'
> ------------------------------------------------------------
>
>
> Mike Waldron
> Systems Specialist
> ITS - Research Computing Center
> University of North Carolina at Chapel Hill
>
> ________________________________
> From: Martin Čech [[hidden email]]
> Sent: Monday, January 05, 2015 8:06 AM
>
> To: Waldron, Michael H; Björn Grüning; [hidden email]
> Subject: Re: [galaxy-dev] Problem using FastQC in Galaxy
>
> Hi Mike,
>
> give it a shot for sure. If you want some details have a look at
> https://wiki.galaxyproject.org/Admin/Tools/AddToolFromToolShedTutorial
>
> M.
>
> On Sun Jan 04 2015 at 7:53:51 PM Waldron, Michael H <[hidden email]>
> wrote:
>>
>> It's mostly due to my lack of thorough knowledge about Galaxy. So should I
>> just try to do the tool shed install by going to Admin->Tool Sheds and
>> selecting fastqc from there?
>>
>> Mike Waldron
>> Systems Specialist
>> ITS - Research Computing Center
>> University of North Carolina at Chapel Hill
>>
>>
>> ________________________________________
>> From: Björn Grüning [[hidden email]]
>> Sent: Sunday, January 04, 2015 12:46 PM
>> To: Waldron, Michael H; Björn Grüning; [hidden email]
>> Subject: Re: [galaxy-dev] Problem using FastQC in Galaxy
>>
>> Hi Mike,
>>
>> it can happen that wrappers versions do not work well with older/newer
>> FASTQC versions. This is the reason we try to couple "binary" versions
>> of tools to wrappers versions.
>>
>> Any reason you don't use the toolshed installation with dependencies?
>>
>> Cheers,
>> Bjoern
>>
>> Am 03.01.2015 um 17:44 schrieb Waldron, Michael H:
>> > It is FastQC-0.11.2. It's a separate install from Galaxy, and a symlink
>> > points to it under tool-data/shared/jars:
>> >
>> > $ pwd
>> > /nas02/apps/galaxy-prod/galaxy-dist/tool-data/shared/jars
>> >
>> > FastQC -> /nas02/apps/galaxy-prod/fastqc-0.11.2/FastQC
>> >
>> >
>> > Mike Waldron
>> > Systems Specialist
>> > ITS - Research Computing Center
>> > University of North Carolina at Chapel Hill
>> >
>> >
>> > ________________________________________
>> > From: Björn Grüning [[hidden email]]
>> > Sent: Saturday, January 03, 2015 6:42 AM
>> > To: Waldron, Michael H; [hidden email]
>> > Subject: Re: [galaxy-dev] Problem using FastQC in Galaxy
>> >
>> > Hi Michael,
>> >
>> > which version of the FASTQC wrapper are you running? Can you point us to
>> > the exact build and toolshed version?
>> >
>> > Thanks,
>> > Bjoern
>> >
>> > Am 02.01.2015 um 21:22 schrieb Waldron, Michael H:
>> >> Having a problem with directing FastQC output in Galaxy. User is
>> >> running a job whose command line looks like this:
>> >>
>> >> # FastQC cl =
>> >> /nas02/apps/galaxy-prod/galaxy-dist/tool-data/shared/jars/FastQC/fastqc
>> >> --outdir=/proj/galaxy/job_working_directory/010/10467/dataset_13836_files
>> >> /proj/galaxy/job_working_directory/010/10467/dataset_13836_files/SRR016862.fastq
>> >>
>> >> Job output looks like this:
>> >>
>> >> ## odpath=None: No output found in None. Output for the run was:
>> >> # FastQC cl =
>> >> /nas02/apps/galaxy-prod/galaxy-dist/tool-data/shared/jars/FastQC/fastqc
>> >> --outdir=/proj/galaxy/job_working_directory/010/10467/dataset_13827_files
>> >> /proj/galaxy/job_working_directory/010/10467/dataset_13827_files/SRR016862.fastq
>> >> Started analysis of SRR016862.fastq
>> >> Approx 5% complete for SRR016862.fastq
>> >> Approx 10% complete for SRR016862.fastq
>> >> Approx 15% complete for SRR016862.fastq
>> >> Approx 20% complete for SRR016862.fastq
>> >> Approx 25% complete for SRR016862.fastq
>> >> Approx 30% complete for SRR016862.fastq
>> >> Approx 35% complete for SRR016862.fastq
>> >> Approx 40% complete for SRR016862.fastq
>> >> Approx 45% complete for SRR016862.fastq
>> >> Approx 50% complete for SRR016862.fastq
>> >> Approx 55% complete for SRR016862.fastq
>> >> Approx 60% complete for SRR016862.fastq
>> >> Approx 65% complete for SRR016862.fastq
>> >> Approx 70% complete for SRR016862.fastq
>> >> Approx 75% complete for SRR016862.fastq
>> >> Approx 80% complete for SRR016862.fastq
>> >> Approx 85% complete for SRR016862.fastq
>> >> Approx 90% complete for SRR016862.fastq
>> >> Approx 95% complete for SRR016862.fastq
>> >> Analysis complete for SRR016862.fastq
>> >>
>> >> The job_working_directory/010/10467 directory is created, however it is
>> >> empty. It appears this "odpath" needs to be set somehow?
>> >>
>> >> Does anyone know a solution for this?
>> >>
>> >> Mike Waldron
>> >> Systems Specialist
>> >> ITS - Research Computing Center
>> >> University of North Carolina at Chapel Hill
>> >>
>> >>
>> >>
>> >>
>> >> ___________________________________________________________
>> >> 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/
>
>
> ___________________________________________________________
> 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:
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To search Galaxy mailing lists use the unified search at:
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Re: Problem using FastQC in Galaxy

Nate Coraor (nate@bx.psu.edu)
Hi Michael,

I understand your frustration in this regard. We do make an effort to respond to and fix issues that people encounter when upgrading Galaxy releases. We've also made pretty significant strides in increasing the quality of our releases, including a feature freeze for at least 2 weeks prior to each release. The galaxy-dev mailing list is fairly active, as is our IRC channel (#galaxyproject on Freenode) for more real-time help.

If you're not familiar with the Galaxy News Briefs, these are the primary means of communicating the changes you should expect to see between Galaxy releases and any config changes that might be necessary between releases:


We also recommend having a Test/QA Galaxy server (or cloning your production Galaxy instance) to test an upgrade before deploying it on your production instance(s) so most problems can be caught beforehand.

Unfortunately, due to the wide range of platforms, deployment scenarios, site-specific factors, and large scope of Galaxy functionality, we can't catch all potential issues. I don't think this is outside the rate typically experienced with major releases of large open source software, but it is still frustrating when it occurs. That said, we'll do our best to assist and improve documentation when you do encounter upgrade problems.

--nate

On Mon, Jan 5, 2015 at 10:34 AM, Waldron, Michael H <[hidden email]> wrote:
Ok, we have run several previous version of fastqc with it, we'll try one of those.

Our history of galaxy upgrade attempts has been very problematic. Things always seem to break, items disappear from menus, and I'm lost in trying to figure out the problems, so we tend to leave it alone.

Mike

________________________________________
From: John Chilton [[hidden email]]
Sent: Monday, January 05, 2015 10:25 AM
To: Waldron, Michael H
Cc: Martin Čech; Björn Grüning; [hidden email]
Subject: Re: [galaxy-dev] Problem using FastQC in Galaxy

This looks like a bug - but unfortunately it appears you are running a
fairly old version of Galaxy  - I don't think the file
lib/galaxy/util/shed_util.py has existed for the better part of a
year. It should be possible to get the FastQC wrapper to work with the
old version if you figure out the exact version of fastqc you need -
but if you want to use the tool shed you will probably want to upgrade
to the latest stable release of Galaxy.

-John

On Mon, Jan 5, 2015 at 9:17 AM, Waldron, Michael H
<[hidden email]> wrote:
> I attempted to install fastqc via the tool shed, and got an error. The log
> information is listed below. The main error appears to be "too many values
> to unpack".
>
> 152.2.204.5 - - [05/Jan/2015:09:09:00 -0400] "GET
> /admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/&repository_ids=ca249a25748b71a3&changeset_revisions=0b201de108b9
> HTTP/1.1" 500 -
> "https://toolshed.g2.bx.psu.edu/repository/preview_tools_in_changeset?repository_id=ca249a25748b71a3&changeset_revision=0b201de108b9"
> "Mozilla/5.0 (X11; Linux x86_64; rv:34.0) Gecko/20100101 Firefox/34.0"
> Error - <type 'exceptions.ValueError'>: too many values to unpack
> URL:
> https://galaxy.its.unc.edu/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/&repository_ids=ca249a25748b71a3&changeset_revisions=0b201de108b9
> File
> '/nas02/apps/galaxy-prod/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py',
> line 143 in __call__
>   app_iter = self.application(environ, start_response)
> File
> '/nas02/apps/galaxy-prod/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py',
> line 80 in __call__
>   return self.application(environ, start_response)
> File
> '/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/web/framework/middleware/remoteuser.py',
> line 91 in __call__
>   return self.app( environ, start_response )
> File
> '/nas02/apps/galaxy-prod/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py',
> line 632 in __call__
>   return self.application(environ, start_response)
> File '/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/web/framework/base.py',
> line 132 in __call__
>   return self.handle_request( environ, start_response )
> File '/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/web/framework/base.py',
> line 185 in handle_request
>   body = method( trans, **kwargs )
> File
> '/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/web/framework/__init__.py',
> line 216 in decorator
>   return func( self, trans, *args, **kwargs )
> File
> '/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py',
> line 1345 in prepare_for_install
>   shed_util.get_dependencies_for_repository( trans, tool_shed_url,
> repo_info_dict, includes_tool_dependencies )
> File '/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/util/shed_util.py',
> line 601 in get_dependencies_for_repository
>   installed_rd, missing_rd =
> get_installed_and_missing_repository_dependencies_for_new_install( trans,
> repo_info_tuple )
> File '/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/util/shed_util.py',
> line 715 in
> get_installed_and_missing_repository_dependencies_for_new_install
>   tool_shed, name, owner, changeset_revision = rd_tup
> ValueError: too many values to unpack
>
> Configuration
> -------------
>   __file__: '/nas02/apps/galaxy-prod/galaxy-dist/universe_wsgi.ini'
>   admin_users:
> '[hidden email],[hidden email],[hidden email],[hidden email]'
>   allow_user_dataset_purge: 'True'
>   database_connection: 'postgres://galaxy@localhost/galaxy'
>   database_engine_option_server_side_cursors: 'True'
>   database_engine_option_strategy: 'threadlocal'
>   debug: 'False'
>   default_cluster_job_runner: 'drmaa://-q pgalaxy_q -M 41900000 /'
>   enable_quotas: 'True'
>   enable_tracks: 'True'
>   file_path: '/proj/galaxy'
>   ftp_upload_dir: 'database/ftp'
>   ftp_upload_site: 'galaxy.its.unc.edu:2021'
>   here: '/nas02/apps/galaxy-prod/galaxy-dist'
>   job_working_directory: '/proj/galaxy/job_working_directory'
>   len_file_path: 'tool-data/shared/ucsc/chrom'
>   library_import_dir: '/proj/seq/galaxy'
>   local_job_queue_workers: '10'
>   nglims_config_file: 'tool-data/nglims.yaml'
>   remote_user_maildomain: 'email.unc.edu'
>   retry_job_output_collection: '30'
>   start_job_runners: 'drmaa'
>   static_cache_time: '360'
>   static_dir: '/nas02/apps/galaxy-prod/galaxy-dist/static/'
>   static_enabled: 'True'
>   static_favicon_dir:
> '/nas02/apps/galaxy-prod/galaxy-dist/static/favicon.ico'
>   static_images_dir: '/nas02/apps/galaxy-prod/galaxy-dist/static/images'
>   static_scripts_dir: '/nas02/apps/galaxy-prod/galaxy-dist/static/scripts/'
>   static_style_dir:
> '/nas02/apps/galaxy-prod/galaxy-dist/static/june_2007_style/blue'
>   tool_config_file: 'tool_conf.xml,shed_tool_conf.xml'
>   tool_dependency_dir: '../tool_dependencies'
>   tool_path: 'tools'
>   use_interactive: 'False'
>   use_nglims: 'False'
>   use_remote_user: 'True'
>
>
> WSGI Variables
> --------------
>   application: <paste.recursive.RecursiveMiddleware object at 0x1fa05fd0>
>   original_wsgi.url_scheme: 'http'
>   paste.cookies: (<SimpleCookie: VCLACTIVENODE='12'
> VCLAUTH='laCke775oUL18xKNIRgrIGOkWV8TDHKwq647BxYTcK1NkdOlvh0%2B8glvFC%2BdvpkoiYg7qttH2AXyWKGmw2aqWVJKp%2BeLJFauRWutlotbDElWn6CfZYeYesGHlWgWMnWbxAW8EYmsmecDsM0xV3KW5%2BFrMdBpDdseXYKCEXzpIIvvwp7F8gX%2BU%2BEUjPE3lb4JzGWf3Ie9XgfEqlPycbiJXPHXCrsGkanB3NXDzJJeUwe9PFO5bc0%2BA1vP7X3YxYdfjLxVAK9ZVqv8tpVwkyh26Mc%2BJ6ei5j9oYmOgQSGdoBuI3y6JmQuivN0z0I6%2FdFy1LBAH74Ri%2FZMgdL7%2Bgjj79A%3D%3D'
> VCLLOCALE='en_US' VCLSKIN='default' __unam='74abf65-13ed3051d32-51a5d500-40'
> __utma='117910737.2001824546.1373325050.1407267272.1407768470.35'
> __utmc='180505699'
> __utmz='117910737.1401999139.26.11.utmcsr=help.unc.edu|utmccn=(referral)|utmcmd=referral|utmcct=/help/research-computing-application-matrix/'
> _ga='GA1.2.83593674.1365452191'
> _shibsession_64656661756c7468747470733a2f2f67616c6178792e6974732e756e632e6564752f73686962626f6c657468='_881cda95b24d6988ef78dd775a463719'
> galaxysession='c6ca0ddb55be603a6569c0b408144f8320f2758b32c93176f6b2d0daddb6375a8a07f508556...f78dd775a463719')
>   paste.expected_exceptions: [<class 'paste.httpexceptions.HTTPException'>]
>   paste.httpexceptions: <paste.httpexceptions.HTTPExceptionHandler object at
> 0x1f83e690>
>   paste.httpserver.thread_pool: <paste.httpserver.ThreadPool object at
> 0x18ec9110>
>   paste.parsed_querystring: ([('tool_shed_url',
> 'https://toolshed.g2.bx.psu.edu/'), ('repository_ids', 'ca249a25748b71a3'),
> ('changeset_revisions', '0b201de108b9')],
> 'tool_shed_url=https://toolshed.g2.bx.psu.edu/&repository_ids=ca249a25748b71a3&changeset_revisions=0b201de108b9')
>   paste.recursive.forward: <paste.recursive.Forwarder from />
>   paste.recursive.include: <paste.recursive.Includer from />
>   paste.recursive.include_app_iter: <paste.recursive.IncluderAppIter from />
>   paste.recursive.script_name: ''
>   paste.throw_errors: True
>   webob._parsed_query_vars: (MultiDict([('tool_shed_url',
> 'https://toolshed.g2.bx.psu.edu/'), ('repository_ids', 'ca249a25748b71a3'),
> ('changeset_revisions', '0b201de108b9')]),
> 'tool_shed_url=https://toolshed.g2.bx.psu.edu/&repository_ids=ca249a25748b71a3&changeset_revisions=0b201de108b9')
>   wsgi process: 'Multithreaded'
> ------------------------------------------------------------
>
>
> Mike Waldron
> Systems Specialist
> ITS - Research Computing Center
> University of North Carolina at Chapel Hill
>
> ________________________________
> From: Martin Čech [[hidden email]]
> Sent: Monday, January 05, 2015 8:06 AM
>
> To: Waldron, Michael H; Björn Grüning; [hidden email]
> Subject: Re: [galaxy-dev] Problem using FastQC in Galaxy
>
> Hi Mike,
>
> give it a shot for sure. If you want some details have a look at
> https://wiki.galaxyproject.org/Admin/Tools/AddToolFromToolShedTutorial
>
> M.
>
> On Sun Jan 04 2015 at 7:53:51 PM Waldron, Michael H <[hidden email]>
> wrote:
>>
>> It's mostly due to my lack of thorough knowledge about Galaxy. So should I
>> just try to do the tool shed install by going to Admin->Tool Sheds and
>> selecting fastqc from there?
>>
>> Mike Waldron
>> Systems Specialist
>> ITS - Research Computing Center
>> University of North Carolina at Chapel Hill
>>
>>
>> ________________________________________
>> From: Björn Grüning [[hidden email]]
>> Sent: Sunday, January 04, 2015 12:46 PM
>> To: Waldron, Michael H; Björn Grüning; [hidden email]
>> Subject: Re: [galaxy-dev] Problem using FastQC in Galaxy
>>
>> Hi Mike,
>>
>> it can happen that wrappers versions do not work well with older/newer
>> FASTQC versions. This is the reason we try to couple "binary" versions
>> of tools to wrappers versions.
>>
>> Any reason you don't use the toolshed installation with dependencies?
>>
>> Cheers,
>> Bjoern
>>
>> Am 03.01.2015 um 17:44 schrieb Waldron, Michael H:
>> > It is FastQC-0.11.2. It's a separate install from Galaxy, and a symlink
>> > points to it under tool-data/shared/jars:
>> >
>> > $ pwd
>> > /nas02/apps/galaxy-prod/galaxy-dist/tool-data/shared/jars
>> >
>> > FastQC -> /nas02/apps/galaxy-prod/fastqc-0.11.2/FastQC
>> >
>> >
>> > Mike Waldron
>> > Systems Specialist
>> > ITS - Research Computing Center
>> > University of North Carolina at Chapel Hill
>> >
>> >
>> > ________________________________________
>> > From: Björn Grüning [[hidden email]]
>> > Sent: Saturday, January 03, 2015 6:42 AM
>> > To: Waldron, Michael H; [hidden email]
>> > Subject: Re: [galaxy-dev] Problem using FastQC in Galaxy
>> >
>> > Hi Michael,
>> >
>> > which version of the FASTQC wrapper are you running? Can you point us to
>> > the exact build and toolshed version?
>> >
>> > Thanks,
>> > Bjoern
>> >
>> > Am 02.01.2015 um 21:22 schrieb Waldron, Michael H:
>> >> Having a problem with directing FastQC output in Galaxy. User is
>> >> running a job whose command line looks like this:
>> >>
>> >> # FastQC cl =
>> >> /nas02/apps/galaxy-prod/galaxy-dist/tool-data/shared/jars/FastQC/fastqc
>> >> --outdir=/proj/galaxy/job_working_directory/010/10467/dataset_13836_files
>> >> /proj/galaxy/job_working_directory/010/10467/dataset_13836_files/SRR016862.fastq
>> >>
>> >> Job output looks like this:
>> >>
>> >> ## odpath=None: No output found in None. Output for the run was:
>> >> # FastQC cl =
>> >> /nas02/apps/galaxy-prod/galaxy-dist/tool-data/shared/jars/FastQC/fastqc
>> >> --outdir=/proj/galaxy/job_working_directory/010/10467/dataset_13827_files
>> >> /proj/galaxy/job_working_directory/010/10467/dataset_13827_files/SRR016862.fastq
>> >> Started analysis of SRR016862.fastq
>> >> Approx 5% complete for SRR016862.fastq
>> >> Approx 10% complete for SRR016862.fastq
>> >> Approx 15% complete for SRR016862.fastq
>> >> Approx 20% complete for SRR016862.fastq
>> >> Approx 25% complete for SRR016862.fastq
>> >> Approx 30% complete for SRR016862.fastq
>> >> Approx 35% complete for SRR016862.fastq
>> >> Approx 40% complete for SRR016862.fastq
>> >> Approx 45% complete for SRR016862.fastq
>> >> Approx 50% complete for SRR016862.fastq
>> >> Approx 55% complete for SRR016862.fastq
>> >> Approx 60% complete for SRR016862.fastq
>> >> Approx 65% complete for SRR016862.fastq
>> >> Approx 70% complete for SRR016862.fastq
>> >> Approx 75% complete for SRR016862.fastq
>> >> Approx 80% complete for SRR016862.fastq
>> >> Approx 85% complete for SRR016862.fastq
>> >> Approx 90% complete for SRR016862.fastq
>> >> Approx 95% complete for SRR016862.fastq
>> >> Analysis complete for SRR016862.fastq
>> >>
>> >> The job_working_directory/010/10467 directory is created, however it is
>> >> empty. It appears this "odpath" needs to be set somehow?
>> >>
>> >> Does anyone know a solution for this?
>> >>
>> >> Mike Waldron
>> >> Systems Specialist
>> >> ITS - Research Computing Center
>> >> University of North Carolina at Chapel Hill
>> >>
>> >>
>> >>
>> >>
>> >> ___________________________________________________________
>> >> 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/
>
>
> ___________________________________________________________
> 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/


___________________________________________________________
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/
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Re: Problem using FastQC in Galaxy

Waldron, Michael H
In reply to this post by John Chilton-4
We reverted back to fastqc version 0.10.1 and that is working.

Given that our current galaxy version is old and problematic to upgrade, going forward we're going to stand up a new separate galaxy installation on another server. We'll be able to test everything on it before switching over to it.

Thanks to all for the help.

Mike


________________________________________
From: John Chilton [[hidden email]]
Sent: Monday, January 05, 2015 10:25 AM
To: Waldron, Michael H
Cc: Martin Čech; Björn Grüning; [hidden email]
Subject: Re: [galaxy-dev] Problem using FastQC in Galaxy

This looks like a bug - but unfortunately it appears you are running a
fairly old version of Galaxy  - I don't think the file
lib/galaxy/util/shed_util.py has existed for the better part of a
year. It should be possible to get the FastQC wrapper to work with the
old version if you figure out the exact version of fastqc you need -
but if you want to use the tool shed you will probably want to upgrade
to the latest stable release of Galaxy.

-John

On Mon, Jan 5, 2015 at 9:17 AM, Waldron, Michael H
<[hidden email]> wrote:

> I attempted to install fastqc via the tool shed, and got an error. The log
> information is listed below. The main error appears to be "too many values
> to unpack".
>
> 152.2.204.5 - - [05/Jan/2015:09:09:00 -0400] "GET
> /admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/&repository_ids=ca249a25748b71a3&changeset_revisions=0b201de108b9
> HTTP/1.1" 500 -
> "https://toolshed.g2.bx.psu.edu/repository/preview_tools_in_changeset?repository_id=ca249a25748b71a3&changeset_revision=0b201de108b9"
> "Mozilla/5.0 (X11; Linux x86_64; rv:34.0) Gecko/20100101 Firefox/34.0"
> Error - <type 'exceptions.ValueError'>: too many values to unpack
> URL:
> https://galaxy.its.unc.edu/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/&repository_ids=ca249a25748b71a3&changeset_revisions=0b201de108b9
> File
> '/nas02/apps/galaxy-prod/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py',
> line 143 in __call__
>   app_iter = self.application(environ, start_response)
> File
> '/nas02/apps/galaxy-prod/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py',
> line 80 in __call__
>   return self.application(environ, start_response)
> File
> '/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/web/framework/middleware/remoteuser.py',
> line 91 in __call__
>   return self.app( environ, start_response )
> File
> '/nas02/apps/galaxy-prod/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py',
> line 632 in __call__
>   return self.application(environ, start_response)
> File '/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/web/framework/base.py',
> line 132 in __call__
>   return self.handle_request( environ, start_response )
> File '/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/web/framework/base.py',
> line 185 in handle_request
>   body = method( trans, **kwargs )
> File
> '/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/web/framework/__init__.py',
> line 216 in decorator
>   return func( self, trans, *args, **kwargs )
> File
> '/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py',
> line 1345 in prepare_for_install
>   shed_util.get_dependencies_for_repository( trans, tool_shed_url,
> repo_info_dict, includes_tool_dependencies )
> File '/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/util/shed_util.py',
> line 601 in get_dependencies_for_repository
>   installed_rd, missing_rd =
> get_installed_and_missing_repository_dependencies_for_new_install( trans,
> repo_info_tuple )
> File '/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/util/shed_util.py',
> line 715 in
> get_installed_and_missing_repository_dependencies_for_new_install
>   tool_shed, name, owner, changeset_revision = rd_tup
> ValueError: too many values to unpack
>
> Configuration
> -------------
>   __file__: '/nas02/apps/galaxy-prod/galaxy-dist/universe_wsgi.ini'
>   admin_users:
> '[hidden email],[hidden email],[hidden email],[hidden email]'
>   allow_user_dataset_purge: 'True'
>   database_connection: 'postgres://galaxy@localhost/galaxy'
>   database_engine_option_server_side_cursors: 'True'
>   database_engine_option_strategy: 'threadlocal'
>   debug: 'False'
>   default_cluster_job_runner: 'drmaa://-q pgalaxy_q -M 41900000 /'
>   enable_quotas: 'True'
>   enable_tracks: 'True'
>   file_path: '/proj/galaxy'
>   ftp_upload_dir: 'database/ftp'
>   ftp_upload_site: 'galaxy.its.unc.edu:2021'
>   here: '/nas02/apps/galaxy-prod/galaxy-dist'
>   job_working_directory: '/proj/galaxy/job_working_directory'
>   len_file_path: 'tool-data/shared/ucsc/chrom'
>   library_import_dir: '/proj/seq/galaxy'
>   local_job_queue_workers: '10'
>   nglims_config_file: 'tool-data/nglims.yaml'
>   remote_user_maildomain: 'email.unc.edu'
>   retry_job_output_collection: '30'
>   start_job_runners: 'drmaa'
>   static_cache_time: '360'
>   static_dir: '/nas02/apps/galaxy-prod/galaxy-dist/static/'
>   static_enabled: 'True'
>   static_favicon_dir:
> '/nas02/apps/galaxy-prod/galaxy-dist/static/favicon.ico'
>   static_images_dir: '/nas02/apps/galaxy-prod/galaxy-dist/static/images'
>   static_scripts_dir: '/nas02/apps/galaxy-prod/galaxy-dist/static/scripts/'
>   static_style_dir:
> '/nas02/apps/galaxy-prod/galaxy-dist/static/june_2007_style/blue'
>   tool_config_file: 'tool_conf.xml,shed_tool_conf.xml'
>   tool_dependency_dir: '../tool_dependencies'
>   tool_path: 'tools'
>   use_interactive: 'False'
>   use_nglims: 'False'
>   use_remote_user: 'True'
>
>
> WSGI Variables
> --------------
>   application: <paste.recursive.RecursiveMiddleware object at 0x1fa05fd0>
>   original_wsgi.url_scheme: 'http'
>   paste.cookies: (<SimpleCookie: VCLACTIVENODE='12'
> VCLAUTH='laCke775oUL18xKNIRgrIGOkWV8TDHKwq647BxYTcK1NkdOlvh0%2B8glvFC%2BdvpkoiYg7qttH2AXyWKGmw2aqWVJKp%2BeLJFauRWutlotbDElWn6CfZYeYesGHlWgWMnWbxAW8EYmsmecDsM0xV3KW5%2BFrMdBpDdseXYKCEXzpIIvvwp7F8gX%2BU%2BEUjPE3lb4JzGWf3Ie9XgfEqlPycbiJXPHXCrsGkanB3NXDzJJeUwe9PFO5bc0%2BA1vP7X3YxYdfjLxVAK9ZVqv8tpVwkyh26Mc%2BJ6ei5j9oYmOgQSGdoBuI3y6JmQuivN0z0I6%2FdFy1LBAH74Ri%2FZMgdL7%2Bgjj79A%3D%3D'
> VCLLOCALE='en_US' VCLSKIN='default' __unam='74abf65-13ed3051d32-51a5d500-40'
> __utma='117910737.2001824546.1373325050.1407267272.1407768470.35'
> __utmc='180505699'
> __utmz='117910737.1401999139.26.11.utmcsr=help.unc.edu|utmccn=(referral)|utmcmd=referral|utmcct=/help/research-computing-application-matrix/'
> _ga='GA1.2.83593674.1365452191'
> _shibsession_64656661756c7468747470733a2f2f67616c6178792e6974732e756e632e6564752f73686962626f6c657468='_881cda95b24d6988ef78dd775a463719'
> galaxysession='c6ca0ddb55be603a6569c0b408144f8320f2758b32c93176f6b2d0daddb6375a8a07f508556...f78dd775a463719')
>   paste.expected_exceptions: [<class 'paste.httpexceptions.HTTPException'>]
>   paste.httpexceptions: <paste.httpexceptions.HTTPExceptionHandler object at
> 0x1f83e690>
>   paste.httpserver.thread_pool: <paste.httpserver.ThreadPool object at
> 0x18ec9110>
>   paste.parsed_querystring: ([('tool_shed_url',
> 'https://toolshed.g2.bx.psu.edu/'), ('repository_ids', 'ca249a25748b71a3'),
> ('changeset_revisions', '0b201de108b9')],
> 'tool_shed_url=https://toolshed.g2.bx.psu.edu/&repository_ids=ca249a25748b71a3&changeset_revisions=0b201de108b9')
>   paste.recursive.forward: <paste.recursive.Forwarder from />
>   paste.recursive.include: <paste.recursive.Includer from />
>   paste.recursive.include_app_iter: <paste.recursive.IncluderAppIter from />
>   paste.recursive.script_name: ''
>   paste.throw_errors: True
>   webob._parsed_query_vars: (MultiDict([('tool_shed_url',
> 'https://toolshed.g2.bx.psu.edu/'), ('repository_ids', 'ca249a25748b71a3'),
> ('changeset_revisions', '0b201de108b9')]),
> 'tool_shed_url=https://toolshed.g2.bx.psu.edu/&repository_ids=ca249a25748b71a3&changeset_revisions=0b201de108b9')
>   wsgi process: 'Multithreaded'
> ------------------------------------------------------------
>
>
> Mike Waldron
> Systems Specialist
> ITS - Research Computing Center
> University of North Carolina at Chapel Hill
>
> ________________________________
> From: Martin Čech [[hidden email]]
> Sent: Monday, January 05, 2015 8:06 AM
>
> To: Waldron, Michael H; Björn Grüning; [hidden email]
> Subject: Re: [galaxy-dev] Problem using FastQC in Galaxy
>
> Hi Mike,
>
> give it a shot for sure. If you want some details have a look at
> https://wiki.galaxyproject.org/Admin/Tools/AddToolFromToolShedTutorial
>
> M.
>
> On Sun Jan 04 2015 at 7:53:51 PM Waldron, Michael H <[hidden email]>
> wrote:
>>
>> It's mostly due to my lack of thorough knowledge about Galaxy. So should I
>> just try to do the tool shed install by going to Admin->Tool Sheds and
>> selecting fastqc from there?
>>
>> Mike Waldron
>> Systems Specialist
>> ITS - Research Computing Center
>> University of North Carolina at Chapel Hill
>>
>>
>> ________________________________________
>> From: Björn Grüning [[hidden email]]
>> Sent: Sunday, January 04, 2015 12:46 PM
>> To: Waldron, Michael H; Björn Grüning; [hidden email]
>> Subject: Re: [galaxy-dev] Problem using FastQC in Galaxy
>>
>> Hi Mike,
>>
>> it can happen that wrappers versions do not work well with older/newer
>> FASTQC versions. This is the reason we try to couple "binary" versions
>> of tools to wrappers versions.
>>
>> Any reason you don't use the toolshed installation with dependencies?
>>
>> Cheers,
>> Bjoern
>>
>> Am 03.01.2015 um 17:44 schrieb Waldron, Michael H:
>> > It is FastQC-0.11.2. It's a separate install from Galaxy, and a symlink
>> > points to it under tool-data/shared/jars:
>> >
>> > $ pwd
>> > /nas02/apps/galaxy-prod/galaxy-dist/tool-data/shared/jars
>> >
>> > FastQC -> /nas02/apps/galaxy-prod/fastqc-0.11.2/FastQC
>> >
>> >
>> > Mike Waldron
>> > Systems Specialist
>> > ITS - Research Computing Center
>> > University of North Carolina at Chapel Hill
>> >
>> >
>> > ________________________________________
>> > From: Björn Grüning [[hidden email]]
>> > Sent: Saturday, January 03, 2015 6:42 AM
>> > To: Waldron, Michael H; [hidden email]
>> > Subject: Re: [galaxy-dev] Problem using FastQC in Galaxy
>> >
>> > Hi Michael,
>> >
>> > which version of the FASTQC wrapper are you running? Can you point us to
>> > the exact build and toolshed version?
>> >
>> > Thanks,
>> > Bjoern
>> >
>> > Am 02.01.2015 um 21:22 schrieb Waldron, Michael H:
>> >> Having a problem with directing FastQC output in Galaxy. User is
>> >> running a job whose command line looks like this:
>> >>
>> >> # FastQC cl =
>> >> /nas02/apps/galaxy-prod/galaxy-dist/tool-data/shared/jars/FastQC/fastqc
>> >> --outdir=/proj/galaxy/job_working_directory/010/10467/dataset_13836_files
>> >> /proj/galaxy/job_working_directory/010/10467/dataset_13836_files/SRR016862.fastq
>> >>
>> >> Job output looks like this:
>> >>
>> >> ## odpath=None: No output found in None. Output for the run was:
>> >> # FastQC cl =
>> >> /nas02/apps/galaxy-prod/galaxy-dist/tool-data/shared/jars/FastQC/fastqc
>> >> --outdir=/proj/galaxy/job_working_directory/010/10467/dataset_13827_files
>> >> /proj/galaxy/job_working_directory/010/10467/dataset_13827_files/SRR016862.fastq
>> >> Started analysis of SRR016862.fastq
>> >> Approx 5% complete for SRR016862.fastq
>> >> Approx 10% complete for SRR016862.fastq
>> >> Approx 15% complete for SRR016862.fastq
>> >> Approx 20% complete for SRR016862.fastq
>> >> Approx 25% complete for SRR016862.fastq
>> >> Approx 30% complete for SRR016862.fastq
>> >> Approx 35% complete for SRR016862.fastq
>> >> Approx 40% complete for SRR016862.fastq
>> >> Approx 45% complete for SRR016862.fastq
>> >> Approx 50% complete for SRR016862.fastq
>> >> Approx 55% complete for SRR016862.fastq
>> >> Approx 60% complete for SRR016862.fastq
>> >> Approx 65% complete for SRR016862.fastq
>> >> Approx 70% complete for SRR016862.fastq
>> >> Approx 75% complete for SRR016862.fastq
>> >> Approx 80% complete for SRR016862.fastq
>> >> Approx 85% complete for SRR016862.fastq
>> >> Approx 90% complete for SRR016862.fastq
>> >> Approx 95% complete for SRR016862.fastq
>> >> Analysis complete for SRR016862.fastq
>> >>
>> >> The job_working_directory/010/10467 directory is created, however it is
>> >> empty. It appears this "odpath" needs to be set somehow?
>> >>
>> >> Does anyone know a solution for this?
>> >>
>> >> Mike Waldron
>> >> Systems Specialist
>> >> ITS - Research Computing Center
>> >> University of North Carolina at Chapel Hill
>> >>
>> >>
>> >>
>> >>
>> >> ___________________________________________________________
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>> >>
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>> >>
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>
>
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Re: Problem using FastQC in Galaxy

ryang
In reply to this post by Nate Coraor (nate@bx.psu.edu)
I hate to hijack this thread, but I was thinking about this over the holiday in how we are going to maintain a local up to date copy of Galaxy ourselves.  One thought would be to standardize on a single supported platform aka an Amazon instance and make sure everything works on that single platform.  This frees you from having to support many different platforms and versions.  Have you guys given this some thought?

On Mon, Jan 5, 2015 at 12:05 PM, Nate Coraor <[hidden email]> wrote:
Hi Michael,

I understand your frustration in this regard. We do make an effort to respond to and fix issues that people encounter when upgrading Galaxy releases. We've also made pretty significant strides in increasing the quality of our releases, including a feature freeze for at least 2 weeks prior to each release. The galaxy-dev mailing list is fairly active, as is our IRC channel (#galaxyproject on Freenode) for more real-time help.

If you're not familiar with the Galaxy News Briefs, these are the primary means of communicating the changes you should expect to see between Galaxy releases and any config changes that might be necessary between releases:


We also recommend having a Test/QA Galaxy server (or cloning your production Galaxy instance) to test an upgrade before deploying it on your production instance(s) so most problems can be caught beforehand.

Unfortunately, due to the wide range of platforms, deployment scenarios, site-specific factors, and large scope of Galaxy functionality, we can't catch all potential issues. I don't think this is outside the rate typically experienced with major releases of large open source software, but it is still frustrating when it occurs. That said, we'll do our best to assist and improve documentation when you do encounter upgrade problems.

--nate



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Re: Problem using FastQC in Galaxy

Björn Grüning-3
Hi Ryan,

I have tried to collect a minimal set of dependencies you need to have
installed:

https://wiki.galaxyproject.org/Admin/Config/ToolDependenciesList

And we have a Galaxy Docker container that is working and should define
and test a fresh Galaxy installation:

https://github.com/bgruening/docker-galaxy-stable

Please also have a look at the Galaxy playbook:
https://github.com/galaxyproject/usegalaxy-playbook

This defines a installation and deployment strategy of Galaxy for
several platforms.
I don't think that the Galaxy project is going to focus on one single
platform. But this is only my opinion. I think one of Galaxy strength
is, that it is working on everything besides Windows (without docker).

Cheers,
Bjoern

Am 05.01.2015 um 23:36 schrieb Ryan G:

> I hate to hijack this thread, but I was thinking about this over the
> holiday in how we are going to maintain a local up to date copy of Galaxy
> ourselves.  One thought would be to standardize on a single supported
> platform aka an Amazon instance and make sure everything works on that
> single platform.  This frees you from having to support many different
> platforms and versions.  Have you guys given this some thought?
>
> On Mon, Jan 5, 2015 at 12:05 PM, Nate Coraor <[hidden email]> wrote:
>
>> Hi Michael,
>>
>> I understand your frustration in this regard. We do make an effort to
>> respond to and fix issues that people encounter when upgrading Galaxy
>> releases. We've also made pretty significant strides in increasing the
>> quality of our releases, including a feature freeze for at least 2 weeks
>> prior to each release. The galaxy-dev mailing list is fairly active, as is
>> our IRC channel (#galaxyproject on Freenode) for more real-time help.
>>
>> If you're not familiar with the Galaxy News Briefs, these are the primary
>> means of communicating the changes you should expect to see between Galaxy
>> releases and any config changes that might be necessary between releases:
>>
>>     https://wiki.galaxyproject.org/DevNewsBriefs
>>
>> We also recommend having a Test/QA Galaxy server (or cloning your
>> production Galaxy instance) to test an upgrade before deploying it on your
>> production instance(s) so most problems can be caught beforehand.
>>
>> Unfortunately, due to the wide range of platforms, deployment scenarios,
>> site-specific factors, and large scope of Galaxy functionality, we can't
>> catch all potential issues. I don't think this is outside the rate
>> typically experienced with major releases of large open source software,
>> but it is still frustrating when it occurs. That said, we'll do our best to
>> assist and improve documentation when you do encounter upgrade problems.
>>
>> --nate
>>
>>
>
>
>
> ___________________________________________________________
> 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/
>
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