Fastx toolkit broken pipe

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Fastx toolkit broken pipe

UMD Bioinformatics
Hello,

I've got a local install of galaxy with fastx tools installed. I'm getting a broken pipe error but I'm not sure why. I install fastx using the compiler outside galaxy and it was working fine inside galaxy previously. Fastx works fine via the command line. I've checked the xml files and I don't see how galaxy cannot find the commands. I am running this off and external volume, but I don't think that matters.

Cheers
Ian





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Re: Fastx toolkit broken pipe

Björn Grüning
Hi Ian,

what mean broken pipe error, can you post the error message here?

Thanks,
Bjoern

> Hello,
>
> I've got a local install of galaxy with fastx tools installed. I'm getting a broken pipe error but I'm not sure why. I install fastx using the compiler outside galaxy and it was working fine inside galaxy previously. Fastx works fine via the command line. I've checked the xml files and I don't see how galaxy cannot find the commands. I am running this off and external volume, but I don't think that matters.
>
> Cheers
> Ian
>
>
>
>
>
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>   http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/



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Re: Fastx toolkit broken pipe

UMD Bioinformatics
Bjöern,

Here is the error message. 

An error occurred with this dataset:/bin/sh: fastq_to_fasta: command not found gzip: stdout: Broken pipe


On Oct 10, 2013, at 7:06 PM, Björn Grüning <[hidden email]> wrote:

Hi Ian,

what mean broken pipe error, can you post the error message here?

Thanks,
Bjoern

Hello,

I've got a local install of galaxy with fastx tools installed. I'm getting a broken pipe error but I'm not sure why. I install fastx using the compiler outside galaxy and it was working fine inside galaxy previously. Fastx works fine via the command line. I've checked the xml files and I don't see how galaxy cannot find the commands. I am running this off and external volume, but I don't think that matters.

Cheers
Ian





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Re: Fastx toolkit broken pipe

UMD Bioinformatics
Hello all,

I'm still dealing with an error regarding Fastx toolkit. I all of the fastx commands in my /usr/local and I have installed fastx via the toolshed. I'm am still receiving the following error. Any help would be great.

Cheers
Ian

An error occurred with this dataset:/bin/sh: fasta_formatter: command not found cat: stdout: Broken pipe


On Oct 11, 2013, at 9:24 AM, UMD Bioinformatics <[hidden email]> wrote:

Bjöern,

Here is the error message. 

An error occurred with this dataset:/bin/sh: fastq_to_fasta: command not found gzip: stdout: Broken pipe


On Oct 10, 2013, at 7:06 PM, Björn Grüning <[hidden email]> wrote:

Hi Ian,

what mean broken pipe error, can you post the error message here?

Thanks,
Bjoern

Hello,

I've got a local install of galaxy with fastx tools installed. I'm getting a broken pipe error but I'm not sure why. I install fastx using the compiler outside galaxy and it was working fine inside galaxy previously. Fastx works fine via the command line. I've checked the xml files and I don't see how galaxy cannot find the commands. I am running this off and external volume, but I don't think that matters.

Cheers
Ian





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Re: Fastx toolkit broken pipe

Dave Bouvier
Ian,

To help track down this issue, could you provide the revision of Galaxy
you're running?

    --Dave B.

On 10/14/2013 08:09 AM, UMD Bioinformatics wrote:

> Hello all,
>
> I'm still dealing with an error regarding Fastx toolkit. I all of the
> fastx commands in my /usr/local and I have installed fastx via the
> toolshed. I'm am still receiving the following error. Any help would be
> great.
>
> Cheers
> Ian
>
> An error occurred with this dataset://bin/sh: fasta_formatter: command
> not found cat: stdout: Broken pipe/
> /
> /
> /
> /
> On Oct 11, 2013, at 9:24 AM, UMD Bioinformatics
> <[hidden email] <mailto:[hidden email]>> wrote:
>
>> Bjöern,
>>
>> Here is the error message.
>>
>> An error occurred with this dataset://bin/sh: fastq_to_fasta: command
>> not found gzip: stdout: Broken pipe/
>> /
>> /
>> /
>> /
>> On Oct 10, 2013, at 7:06 PM, Björn Grüning
>> <[hidden email]
>> <mailto:[hidden email]>> wrote:
>>
>>> Hi Ian,
>>>
>>> what mean broken pipe error, can you post the error message here?
>>>
>>> Thanks,
>>> Bjoern
>>>
>>>> Hello,
>>>>
>>>> I've got a local install of galaxy with fastx tools installed. I'm
>>>> getting a broken pipe error but I'm not sure why. I install fastx
>>>> using the compiler outside galaxy and it was working fine inside
>>>> galaxy previously. Fastx works fine via the command line. I've
>>>> checked the xml files and I don't see how galaxy cannot find the
>>>> commands. I am running this off and external volume, but I don't
>>>> think that matters.
>>>>
>>>> Cheers
>>>> Ian
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> ___________________________________________________________
>>>> Please keep all replies on the list by using "reply all"
>>>> in your mail client.  To manage your subscriptions to this
>>>> and other Galaxy lists, please use the interface at:
>>>> http://lists.bx.psu.edu/
>>>>
>>>> To search Galaxy mailing lists use the unified search at:
>>>> http://galaxyproject.org/search/mailinglists/
>>>
>>>
>>>
>>> ___________________________________________________________
>>> Please keep all replies on the list by using "reply all"
>>> in your mail client.  To manage your subscriptions to this
>>> and other Galaxy lists, please use the interface at:
>>> http://lists.bx.psu.edu/
>>>
>>> To search Galaxy mailing lists use the unified search at:
>>> http://galaxyproject.org/search/mailinglists/
>>
>
>
>
> ___________________________________________________________
> 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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>
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Re: Fastx toolkit broken pipe

UMD Bioinformatics
Dave,

Here is my information on the revision.

$ hg heads | more
changeset:   10421:a477486bf18e
branch:      stable
tag:         tip
user:        Nate Coraor <[hidden email]>
date:        Thu Sep 26 11:02:58 2013 -0400
summary:     Bugfix for tool-to-destination mapping, tool ids are lowercased but the mapping id was not lowercased.

changeset:   10411:c42567f43aa7
user:        greg
date:        Mon Aug 19 13:19:56 2013 -0400
summary:     Filter invalid objects when generating the list of repository_dependencies objects that are associated with a tool shed repository installed into Galaxy.

On Oct 14, 2013, at 9:11 AM, Dave Bouvier <[hidden email]> wrote:

> Ian,
>
> To help track down this issue, could you provide the revision of Galaxy you're running?
>
>   --Dave B.
>
> On 10/14/2013 08:09 AM, UMD Bioinformatics wrote:
>> Hello all,
>>
>> I'm still dealing with an error regarding Fastx toolkit. I all of the
>> fastx commands in my /usr/local and I have installed fastx via the
>> toolshed. I'm am still receiving the following error. Any help would be
>> great.
>>
>> Cheers
>> Ian
>>
>> An error occurred with this dataset://bin/sh: fasta_formatter: command
>> not found cat: stdout: Broken pipe/
>> /
>> /
>> /
>> /
>> On Oct 11, 2013, at 9:24 AM, UMD Bioinformatics
>> <[hidden email] <mailto:[hidden email]>> wrote:
>>
>>> Bjöern,
>>>
>>> Here is the error message.
>>>
>>> An error occurred with this dataset://bin/sh: fastq_to_fasta: command
>>> not found gzip: stdout: Broken pipe/
>>> /
>>> /
>>> /
>>> /
>>> On Oct 10, 2013, at 7:06 PM, Björn Grüning
>>> <[hidden email]
>>> <mailto:[hidden email]>> wrote:
>>>
>>>> Hi Ian,
>>>>
>>>> what mean broken pipe error, can you post the error message here?
>>>>
>>>> Thanks,
>>>> Bjoern
>>>>
>>>>> Hello,
>>>>>
>>>>> I've got a local install of galaxy with fastx tools installed. I'm
>>>>> getting a broken pipe error but I'm not sure why. I install fastx
>>>>> using the compiler outside galaxy and it was working fine inside
>>>>> galaxy previously. Fastx works fine via the command line. I've
>>>>> checked the xml files and I don't see how galaxy cannot find the
>>>>> commands. I am running this off and external volume, but I don't
>>>>> think that matters.
>>>>>
>>>>> Cheers
>>>>> Ian
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> ___________________________________________________________
>>>>> Please keep all replies on the list by using "reply all"
>>>>> in your mail client.  To manage your subscriptions to this
>>>>> and other Galaxy lists, please use the interface at:
>>>>> http://lists.bx.psu.edu/
>>>>>
>>>>> To search Galaxy mailing lists use the unified search at:
>>>>> http://galaxyproject.org/search/mailinglists/
>>>>
>>>>
>>>>
>>>> ___________________________________________________________
>>>> Please keep all replies on the list by using "reply all"
>>>> in your mail client.  To manage your subscriptions to this
>>>> and other Galaxy lists, please use the interface at:
>>>> http://lists.bx.psu.edu/
>>>>
>>>> To search Galaxy mailing lists use the unified search at:
>>>> http://galaxyproject.org/search/mailinglists/
>>>
>>
>>
>>
>> ___________________________________________________________
>> Please keep all replies on the list by using "reply all"
>> in your mail client.  To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
>>   http://lists.bx.psu.edu/
>>
>> To search Galaxy mailing lists use the unified search at:
>>   http://galaxyproject.org/search/mailinglists/
>>


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Re: Fastx toolkit broken pipe

Dave Bouvier
Ian,

Although the fastx tools have been migrated to the tool shed, this
migration has not yet been released to the stable branch, but is planned
to be included in the upcoming release. In the meantime, I would suggest
maintaining the binary installation of the fastx dependencies using one
of the options described on this page:

http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies

After the release, you can then run the automated process to install the
migrated tools from the tool shed as described here:

http://wiki.galaxyproject.org/MigratingToolsFromGalaxyDistribution

    --Dave B.

On 10/14/2013 09:14 AM, UMD Bioinformatics wrote:

> Dave,
>
> Here is my information on the revision.
>
> $ hg heads | more
> changeset:   10421:a477486bf18e
> branch:      stable
> tag:         tip
> user:        Nate Coraor <[hidden email]>
> date:        Thu Sep 26 11:02:58 2013 -0400
> summary:     Bugfix for tool-to-destination mapping, tool ids are lowercased but the mapping id was not lowercased.
>
> changeset:   10411:c42567f43aa7
> user:        greg
> date:        Mon Aug 19 13:19:56 2013 -0400
> summary:     Filter invalid objects when generating the list of repository_dependencies objects that are associated with a tool shed repository installed into Galaxy.
>
> On Oct 14, 2013, at 9:11 AM, Dave Bouvier <[hidden email]> wrote:
>
>> Ian,
>>
>> To help track down this issue, could you provide the revision of Galaxy you're running?
>>
>>    --Dave B.
>>
>> On 10/14/2013 08:09 AM, UMD Bioinformatics wrote:
>>> Hello all,
>>>
>>> I'm still dealing with an error regarding Fastx toolkit. I all of the
>>> fastx commands in my /usr/local and I have installed fastx via the
>>> toolshed. I'm am still receiving the following error. Any help would be
>>> great.
>>>
>>> Cheers
>>> Ian
>>>
>>> An error occurred with this dataset://bin/sh: fasta_formatter: command
>>> not found cat: stdout: Broken pipe/
>>> /
>>> /
>>> /
>>> /
>>> On Oct 11, 2013, at 9:24 AM, UMD Bioinformatics
>>> <[hidden email] <mailto:[hidden email]>> wrote:
>>>
>>>> Bjöern,
>>>>
>>>> Here is the error message.
>>>>
>>>> An error occurred with this dataset://bin/sh: fastq_to_fasta: command
>>>> not found gzip: stdout: Broken pipe/
>>>> /
>>>> /
>>>> /
>>>> /
>>>> On Oct 10, 2013, at 7:06 PM, Björn Grüning
>>>> <[hidden email]
>>>> <mailto:[hidden email]>> wrote:
>>>>
>>>>> Hi Ian,
>>>>>
>>>>> what mean broken pipe error, can you post the error message here?
>>>>>
>>>>> Thanks,
>>>>> Bjoern
>>>>>
>>>>>> Hello,
>>>>>>
>>>>>> I've got a local install of galaxy with fastx tools installed. I'm
>>>>>> getting a broken pipe error but I'm not sure why. I install fastx
>>>>>> using the compiler outside galaxy and it was working fine inside
>>>>>> galaxy previously. Fastx works fine via the command line. I've
>>>>>> checked the xml files and I don't see how galaxy cannot find the
>>>>>> commands. I am running this off and external volume, but I don't
>>>>>> think that matters.
>>>>>>
>>>>>> Cheers
>>>>>> Ian
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> ___________________________________________________________
>>>>>> Please keep all replies on the list by using "reply all"
>>>>>> in your mail client.  To manage your subscriptions to this
>>>>>> and other Galaxy lists, please use the interface at:
>>>>>> http://lists.bx.psu.edu/
>>>>>>
>>>>>> To search Galaxy mailing lists use the unified search at:
>>>>>> http://galaxyproject.org/search/mailinglists/
>>>>>
>>>>>
>>>>>
>>>>> ___________________________________________________________
>>>>> Please keep all replies on the list by using "reply all"
>>>>> in your mail client.  To manage your subscriptions to this
>>>>> and other Galaxy lists, please use the interface at:
>>>>> http://lists.bx.psu.edu/
>>>>>
>>>>> To search Galaxy mailing lists use the unified search at:
>>>>> http://galaxyproject.org/search/mailinglists/
>>>>
>>>
>>>
>>>
>>> ___________________________________________________________
>>> Please keep all replies on the list by using "reply all"
>>> in your mail client.  To manage your subscriptions to this
>>> and other Galaxy lists, please use the interface at:
>>>    http://lists.bx.psu.edu/
>>>
>>> To search Galaxy mailing lists use the unified search at:
>>>    http://galaxyproject.org/search/mailinglists/
>>>
>
>
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Re: Fastx toolkit broken pipe

UMD Bioinformatics
Dave,

Thanks for the information. I've added the bin folder to the fastx_toolkit as described in the document. I also copied the executables from /usr/local/bin for fastx_toolkit to the devteam/backage_fastx_toolkit/0_0_13/ec66ae4c269b/bin as described. I've restarted Galaxy but I'm still getting an error.  My PATH has both /usr/local/bin and the devfolder in therm. I'm not sure why this won't work. 

error
An error occurred with this dataset:/bin/sh: fastq_quality_trimmer: command not found cat: stdout: Broken pipe

I have my PATH set as well as the env.sh and my ./bash_profile. Again this all works fine from the command line. I don't know where else Galaxy is trying to find the fastx commands. This is very frustrating.

Cheers
Ian

On Oct 14, 2013, at 12:05 PM, Dave Bouvier <[hidden email]> wrote:

Ian,

Although the fastx tools have been migrated to the tool shed, this migration has not yet been released to the stable branch, but is planned to be included in the upcoming release. In the meantime, I would suggest maintaining the binary installation of the fastx dependencies using one of the options described on this page:

http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies

After the release, you can then run the automated process to install the migrated tools from the tool shed as described here:

http://wiki.galaxyproject.org/MigratingToolsFromGalaxyDistribution

  --Dave B.

On 10/14/2013 09:14 AM, UMD Bioinformatics wrote:
Dave,

Here is my information on the revision.

$ hg heads | more
changeset:   10421:a477486bf18e
branch:      stable
tag:         tip
user:        Nate Coraor <[hidden email]>
date:        Thu Sep 26 11:02:58 2013 -0400
summary:     Bugfix for tool-to-destination mapping, tool ids are lowercased but the mapping id was not lowercased.

changeset:   10411:c42567f43aa7
user:        greg
date:        Mon Aug 19 13:19:56 2013 -0400
summary:     Filter invalid objects when generating the list of repository_dependencies objects that are associated with a tool shed repository installed into Galaxy.

On Oct 14, 2013, at 9:11 AM, Dave Bouvier <[hidden email]> wrote:

Ian,

To help track down this issue, could you provide the revision of Galaxy you're running?

  --Dave B.

On 10/14/2013 08:09 AM, UMD Bioinformatics wrote:
Hello all,

I'm still dealing with an error regarding Fastx toolkit. I all of the
fastx commands in my /usr/local and I have installed fastx via the
toolshed. I'm am still receiving the following error. Any help would be
great.

Cheers
Ian

An error occurred with this dataset://bin/sh: fasta_formatter: command
not found cat: stdout: Broken pipe/
/
/
/
/
On Oct 11, 2013, at 9:24 AM, UMD Bioinformatics
<[hidden email] <mailto:[hidden email]>> wrote:

Bjöern,

Here is the error message.

An error occurred with this dataset://bin/sh: fastq_to_fasta: command
not found gzip: stdout: Broken pipe/
/
/
/
/
On Oct 10, 2013, at 7:06 PM, Björn Grüning
<[hidden email]
<mailto:[hidden email]>> wrote:

Hi Ian,

what mean broken pipe error, can you post the error message here?

Thanks,
Bjoern

Hello,

I've got a local install of galaxy with fastx tools installed. I'm
getting a broken pipe error but I'm not sure why. I install fastx
using the compiler outside galaxy and it was working fine inside
galaxy previously. Fastx works fine via the command line. I've
checked the xml files and I don't see how galaxy cannot find the
commands. I am running this off and external volume, but I don't
think that matters.

Cheers
Ian





___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/

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



___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
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To search Galaxy mailing lists use the unified search at:
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: Fastx toolkit broken pipe

UMD Bioinformatics
In reply to this post by Dave Bouvier
Hello Dave,

Here is the full log info for the failed fastx runs

galaxy.jobs.runners.local DEBUG 2013-10-14 14:24:32,512 (306) executing: cat '/Volumes/Jose-Drobo/WholeGenomeSequencingDataOfInterest/Ruvkun_mut16_smallRNAs/SRR087428/SRR087428.fastq' | fastx_reverse_complement  -Q 64  -v -o '/Volumes/Jose-Drobo/galaxy-dist/database/files/000/dataset_313.dat'
galaxy.jobs DEBUG 2013-10-14 14:24:32,581 (306) Persisting job destination (destination id: local:///)
galaxy.jobs.runners.local DEBUG 2013-10-14 14:24:32,722 execution finished: cat '/Volumes/Jose-Drobo/WholeGenomeSequencingDataOfInterest/Ruvkun_mut16_smallRNAs/SRR087428/SRR087428.fastq' | fastx_reverse_complement  -Q 64  -v -o '/Volumes/Jose-Drobo/galaxy-dist/database/files/000/dataset_313.dat'
galaxy.jobs.runners DEBUG 2013-10-14 14:24:32,866 executing external set_meta script for job 306: /Volumes/Jose-Drobo/galaxy-dist/set_metadata.sh ./database/files /Volumes/Jose-Drobo/galaxy-dist/database/job_working_directory/000/306 . /Volumes/Jose-Drobo/galaxy-dist/universe_wsgi.ini /Volumes/Jose-Drobo/galaxy-dist/database/tmp/tmprYzdng /Volumes/Jose-Drobo/galaxy-dist/database/job_working_directory/000/306/galaxy.json /Volumes/Jose-Drobo/galaxy-dist/database/job_working_directory/000/306/metadata_in_HistoryDatasetAssociation_312_XtTL8q,/Volumes/Jose-Drobo/galaxy-dist/database/job_working_directory/000/306/metadata_kwds_HistoryDatasetAssociation_312_3MJoHa,/Volumes/Jose-Drobo/galaxy-dist/database/job_working_directory/000/306/metadata_out_HistoryDatasetAssociation_312_82_iZG,/Volumes/Jose-Drobo/galaxy-dist/database/job_working_directory/000/306/metadata_results_HistoryDatasetAssociation_312_k5blD2,,/Volumes/Jose-Drobo/galaxy-dist/database/job_working_directory/000/306/metadata_override_HistoryDatasetAssociation_312_tFX5kW
galaxy.jobs.runners DEBUG 2013-10-14 14:24:35,692 execution of external set_meta for job 306 finished
galaxy.jobs DEBUG 2013-10-14 14:24:35,781 setting dataset state to ERROR
galaxy.jobs DEBUG 2013-10-14 14:24:35,949 job 306 ended

Cheers
Ian
On Oct 14, 2013, at 12:05 PM, Dave Bouvier <[hidden email]> wrote:

> Ian,
>
> Although the fastx tools have been migrated to the tool shed, this migration has not yet been released to the stable branch, but is planned to be included in the upcoming release. In the meantime, I would suggest maintaining the binary installation of the fastx dependencies using one of the options described on this page:
>
> http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies
>
> After the release, you can then run the automated process to install the migrated tools from the tool shed as described here:
>
> http://wiki.galaxyproject.org/MigratingToolsFromGalaxyDistribution
>
>   --Dave B.
>
> On 10/14/2013 09:14 AM, UMD Bioinformatics wrote:
>> Dave,
>>
>> Here is my information on the revision.
>>
>> $ hg heads | more
>> changeset:   10421:a477486bf18e
>> branch:      stable
>> tag:         tip
>> user:        Nate Coraor <[hidden email]>
>> date:        Thu Sep 26 11:02:58 2013 -0400
>> summary:     Bugfix for tool-to-destination mapping, tool ids are lowercased but the mapping id was not lowercased.
>>
>> changeset:   10411:c42567f43aa7
>> user:        greg
>> date:        Mon Aug 19 13:19:56 2013 -0400
>> summary:     Filter invalid objects when generating the list of repository_dependencies objects that are associated with a tool shed repository installed into Galaxy.
>>
>> On Oct 14, 2013, at 9:11 AM, Dave Bouvier <[hidden email]> wrote:
>>
>>> Ian,
>>>
>>> To help track down this issue, could you provide the revision of Galaxy you're running?
>>>
>>>   --Dave B.
>>>
>>> On 10/14/2013 08:09 AM, UMD Bioinformatics wrote:
>>>> Hello all,
>>>>
>>>> I'm still dealing with an error regarding Fastx toolkit. I all of the
>>>> fastx commands in my /usr/local and I have installed fastx via the
>>>> toolshed. I'm am still receiving the following error. Any help would be
>>>> great.
>>>>
>>>> Cheers
>>>> Ian
>>>>
>>>> An error occurred with this dataset://bin/sh: fasta_formatter: command
>>>> not found cat: stdout: Broken pipe/
>>>> /
>>>> /
>>>> /
>>>> /
>>>> On Oct 11, 2013, at 9:24 AM, UMD Bioinformatics
>>>> <[hidden email] <mailto:[hidden email]>> wrote:
>>>>
>>>>> Bjöern,
>>>>>
>>>>> Here is the error message.
>>>>>
>>>>> An error occurred with this dataset://bin/sh: fastq_to_fasta: command
>>>>> not found gzip: stdout: Broken pipe/
>>>>> /
>>>>> /
>>>>> /
>>>>> /
>>>>> On Oct 10, 2013, at 7:06 PM, Björn Grüning
>>>>> <[hidden email]
>>>>> <mailto:[hidden email]>> wrote:
>>>>>
>>>>>> Hi Ian,
>>>>>>
>>>>>> what mean broken pipe error, can you post the error message here?
>>>>>>
>>>>>> Thanks,
>>>>>> Bjoern
>>>>>>
>>>>>>> Hello,
>>>>>>>
>>>>>>> I've got a local install of galaxy with fastx tools installed. I'm
>>>>>>> getting a broken pipe error but I'm not sure why. I install fastx
>>>>>>> using the compiler outside galaxy and it was working fine inside
>>>>>>> galaxy previously. Fastx works fine via the command line. I've
>>>>>>> checked the xml files and I don't see how galaxy cannot find the
>>>>>>> commands. I am running this off and external volume, but I don't
>>>>>>> think that matters.
>>>>>>>
>>>>>>> Cheers
>>>>>>> Ian
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> ___________________________________________________________
>>>>>>> Please keep all replies on the list by using "reply all"
>>>>>>> in your mail client.  To manage your subscriptions to this
>>>>>>> and other Galaxy lists, please use the interface at:
>>>>>>> http://lists.bx.psu.edu/
>>>>>>>
>>>>>>> To search Galaxy mailing lists use the unified search at:
>>>>>>> http://galaxyproject.org/search/mailinglists/
>>>>>>
>>>>>>
>>>>>>
>>>>>> ___________________________________________________________
>>>>>> Please keep all replies on the list by using "reply all"
>>>>>> in your mail client.  To manage your subscriptions to this
>>>>>> and other Galaxy lists, please use the interface at:
>>>>>> http://lists.bx.psu.edu/
>>>>>>
>>>>>> To search Galaxy mailing lists use the unified search at:
>>>>>> http://galaxyproject.org/search/mailinglists/
>>>>>
>>>>
>>>>
>>>>
>>>> ___________________________________________________________
>>>> Please keep all replies on the list by using "reply all"
>>>> in your mail client.  To manage your subscriptions to this
>>>> and other Galaxy lists, please use the interface at:
>>>>   http://lists.bx.psu.edu/
>>>>
>>>> To search Galaxy mailing lists use the unified search at:
>>>>   http://galaxyproject.org/search/mailinglists/
>>>>
>>
>>


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Re: Fastx toolkit broken pipe

Brad Chapman
In reply to this post by UMD Bioinformatics

Ian;

> I have my PATH set as well as the env.sh and my ./bash_profile. Again
> this all works fine from the command line. I don't know where else
> Galaxy is trying to find the fastx commands.

I know zero about setting up fastx_toolkit from the toolshed but from
reading your error messages:

> command not found cat: stdout: Broken pipe
> command not found gzip: stdout: Broken pipe/

It looks like it's not having trouble finding fastx_toolkit, but rather
standard unix commands 'cat' and 'gzip'. Is it possible the PATH you're
feeding to Galaxy somehow avoids include `/bin` and `/usr/bin` (or
wherever cat and gzip are on your system)?

Brad
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Re: Fastx toolkit broken pipe

UMD Bioinformatics

On Oct 14, 2013, at 9:16 PM, Brad Chapman <[hidden email]> wrote:

>
> Ian;
>
>> I have my PATH set as well as the env.sh and my ./bash_profile. Again
>> this all works fine from the command line. I don't know where else
>> Galaxy is trying to find the fastx commands.
>
> I know zero about setting up fastx_toolkit from the toolshed but from
> reading your error messages:
>
>> command not found cat: stdout: Broken pipe
>> command not found gzip: stdout: Broken pipe/
>
> It looks like it's not having trouble finding fastx_toolkit, but rather
> standard unix commands 'cat' and 'gzip'. Is it possible the PATH you're
> feeding to Galaxy somehow avoids include `/bin` and `/usr/bin` (or
> wherever cat and gzip are on your system)?

This is what I have for cat and gzip

$ which cat
/bin/cat
$ which gzip
/usr/bin/gzip
$ echo $PATH
/opt/local/bin:/opt/local/sbin:/usr/bin:/bin:

>From what i can tell they should be available on the $PATH so I'm not quite sure why Galaxy cannot "see" them.

Ian

>
> Brad


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Re: Fastx toolkit broken pipe

Carlos Borroto
On Mon, Oct 14, 2013 at 9:20 PM, UMD Bioinformatics
<[hidden email]> wrote:

> On Oct 14, 2013, at 9:16 PM, Brad Chapman <[hidden email]> wrote:
>
>>
>> Ian;
>>
>>> I have my PATH set as well as the env.sh and my ./bash_profile. Again
>>> this all works fine from the command line. I don't know where else
>>> Galaxy is trying to find the fastx commands.
>>
>> I know zero about setting up fastx_toolkit from the toolshed but from
>> reading your error messages:
>>
>>> command not found cat: stdout: Broken pipe
>>> command not found gzip: stdout: Broken pipe/
>>
>> It looks like it's not having trouble finding fastx_toolkit, but rather
>> standard unix commands 'cat' and 'gzip'. Is it possible the PATH you're
>> feeding to Galaxy somehow avoids include `/bin` and `/usr/bin` (or
>> wherever cat and gzip are on your system)?
>
> This is what I have for cat and gzip
>
> $ which cat
> /bin/cat
> $ which gzip
> /usr/bin/gzip
> $ echo $PATH
> /opt/local/bin:/opt/local/sbin:/usr/bin:/bin:
>
> >From what i can tell they should be available on the $PATH so I'm not quite sure why Galaxy cannot "see" them.
>

Hi Ian,

In the past I had trouble making sure Galaxy would run jobs with the
proper environment settings. I think there are a few moving parts
depending on your local configuration(ex. local vs cluster jobs). All
of my problems went away after I started using something like this in
my 'universe_wsgi.ini':
environment_setup_file = /local/opt/galaxy/.bashrc

Any env configuration I want Galaxy to use, I put it in that bashrc file.

Hope it helps,
Carlos
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Re: Fastx toolkit broken pipe

UMD Bioinformatics
Carlos,

Thank you very much. What I ended up doing to fix this issue was to uninstall fastx_toolkit from the tool shed then I created a .bashrc file for galaxy. I added this to the environmental_setup_file path and restarted galaxy. This was the fix I needed. Things seem to be working now. Here is the contents of my .bashrc file for others having issues.

export PATH=${PATH}:/usr/bin:/usr/local/bin:/bin:/opt/local/bin:/opt/local/sbin

I placed the .bashrc file in the galaxy-dist folder and source it from there.

Cheers
Ian

On Oct 15, 2013, at 9:53 AM, Carlos Borroto <[hidden email]> wrote:

> On Mon, Oct 14, 2013 at 9:20 PM, UMD Bioinformatics
> <[hidden email]> wrote:
>> On Oct 14, 2013, at 9:16 PM, Brad Chapman <[hidden email]> wrote:
>>
>>>
>>> Ian;
>>>
>>>> I have my PATH set as well as the env.sh and my ./bash_profile. Again
>>>> this all works fine from the command line. I don't know where else
>>>> Galaxy is trying to find the fastx commands.
>>>
>>> I know zero about setting up fastx_toolkit from the toolshed but from
>>> reading your error messages:
>>>
>>>> command not found cat: stdout: Broken pipe
>>>> command not found gzip: stdout: Broken pipe/
>>>
>>> It looks like it's not having trouble finding fastx_toolkit, but rather
>>> standard unix commands 'cat' and 'gzip'. Is it possible the PATH you're
>>> feeding to Galaxy somehow avoids include `/bin` and `/usr/bin` (or
>>> wherever cat and gzip are on your system)?
>>
>> This is what I have for cat and gzip
>>
>> $ which cat
>> /bin/cat
>> $ which gzip
>> /usr/bin/gzip
>> $ echo $PATH
>> /opt/local/bin:/opt/local/sbin:/usr/bin:/bin:
>>
>>> From what i can tell they should be available on the $PATH so I'm not quite sure why Galaxy cannot "see" them.
>>
>
> Hi Ian,
>
> In the past I had trouble making sure Galaxy would run jobs with the
> proper environment settings. I think there are a few moving parts
> depending on your local configuration(ex. local vs cluster jobs). All
> of my problems went away after I started using something like this in
> my 'universe_wsgi.ini':
> environment_setup_file = /local/opt/galaxy/.bashrc
>
> Any env configuration I want Galaxy to use, I put it in that bashrc file.
>
> Hope it helps,
> Carlos


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