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
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/
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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 bjoern.gruening@pharmazie.uni-freiburg.de 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/
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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 bioinformatics.umd@gmail.com 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 bjoern.gruening@pharmazie.uni-freiburg.de 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/
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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 <bioinformatics.umd@gmail.com mailto:bioinformatics.umd@gmail.com> 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 <bjoern.gruening@pharmazie.uni-freiburg.de mailto:bjoern.gruening@pharmazie.uni-freiburg.de> 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/
Dave,
Here is my information on the revision.
$ hg heads | more changeset: 10421:a477486bf18e branch: stable tag: tip user: Nate Coraor nate@bx.psu.edu 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 dave@bx.psu.edu 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 <bioinformatics.umd@gmail.com mailto:bioinformatics.umd@gmail.com> 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 <bjoern.gruening@pharmazie.uni-freiburg.de mailto:bjoern.gruening@pharmazie.uni-freiburg.de> 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/
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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 nate@bx.psu.edu 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 dave@bx.psu.edu 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 <bioinformatics.umd@gmail.com mailto:bioinformatics.umd@gmail.com> 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 <bjoern.gruening@pharmazie.uni-freiburg.de mailto:bjoern.gruening@pharmazie.uni-freiburg.de> 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/
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 dave@bx.psu.edu 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 nate@bx.psu.edu 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 dave@bx.psu.edu 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 <bioinformatics.umd@gmail.com mailto:bioinformatics.umd@gmail.com> 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 <bjoern.gruening@pharmazie.uni-freiburg.de mailto:bjoern.gruening@pharmazie.uni-freiburg.de> 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/
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
On Oct 14, 2013, at 9:16 PM, Brad Chapman chapmanb@50mail.com 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
On Mon, Oct 14, 2013 at 9:20 PM, UMD Bioinformatics bioinformatics.umd@gmail.com wrote:
On Oct 14, 2013, at 9:16 PM, Brad Chapman chapmanb@50mail.com 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 $PATH so I'm not quite sure why Galaxy cannot "see" them.
Hi Ian,
In the past I had trouble making sure Galaxy would run jobs with the proper environment settings. I think there are a few moving parts depending on your local configuration(ex. local vs cluster jobs). All of my problems went away after I started using something like this in my 'universe_wsgi.ini': environment_setup_file = /local/opt/galaxy/.bashrc
Any env configuration I want Galaxy to use, I put it in that bashrc file.
Hope it helps, Carlos
Carlos,
Thank you very much. What I ended up doing to fix this issue was to uninstall fastx_toolkit from the tool shed then I created a .bashrc file for galaxy. I added this to the environmental_setup_file path and restarted galaxy. This was the fix I needed. Things seem to be working now. Here is the contents of my .bashrc file for others having issues.
export PATH=${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 carlos.borroto@gmail.com wrote:
On Mon, Oct 14, 2013 at 9:20 PM, UMD Bioinformatics bioinformatics.umd@gmail.com wrote:
On Oct 14, 2013, at 9:16 PM, Brad Chapman chapmanb@50mail.com 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
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 dave@bx.psu.edu 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 nate@bx.psu.edu 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 dave@bx.psu.edu 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 <bioinformatics.umd@gmail.com mailto:bioinformatics.umd@gmail.com> 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 <bjoern.gruening@pharmazie.uni-freiburg.de mailto:bjoern.gruening@pharmazie.uni-freiburg.de> 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/
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Björn Grüning -
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UMD Bioinformatics