Re: [galaxy-dev] samtools: command not found in bowtie2
Could you try going to Admin -> Manage Installed tool shed repositories uninstall -> reinstall package_samtools_0_1_18 On 26 November 2014 at 16:55, Anna Terry <iseeglass@googlemail.com> wrote:
yway, I am also getting the problem with samtools filter sam or bam
-- Central Veterinary Institute of Wageningen UR (CVI) Department of Infection Biology PO box 65, 8200 AB Lelystad, NL Visiting address: ASG, Edelhertweg 15, 8219 PH Lelystad Tel: +31-(0)320-293391 Fax: +31-(0)320-238153 E-mail: eric.kuijt@wur.nl Web: http://www.cvi.wur.nl
I just tried still the same problem. I ran bowtie2 to test, again I saw samtools come up on top, but same error: Traceback (most recent call last): File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/runners/local.py", line 129, in queue_job job_wrapper.finish( stdout, stderr, exit_code ) File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 998, in finish dataset.datatype.set_meta( dataset, overwrite=False ) # call datatype.set_meta directly for the initial set_meta call during dataset creation File "/home/galaxy/galaxy-dist/lib/galaxy/datatypes/binary.py", line 251, in set_meta raise Exception, "Error Setting BAM Metadata: %s" % stderr Exception: Error Setting BAM Metadata: /bin/sh: samtools: command not found On 26 November 2014 at 16:01, Eric Kuyt <eric.kuijt@wur.nl> wrote:
Could you try going to Admin -> Manage Installed tool shed repositories
uninstall -> reinstall package_samtools_0_1_18
On 26 November 2014 at 16:55, Anna Terry <iseeglass@googlemail.com> wrote:
yway, I am also getting the problem with samtools filter sam or bam
-- Central Veterinary Institute of Wageningen UR (CVI) Department of Infection Biology PO box 65, 8200 AB Lelystad, NL Visiting address: ASG, Edelhertweg 15, 8219 PH Lelystad
Tel: +31-(0)320-293391 Fax: +31-(0)320-238153 E-mail: eric.kuijt@wur.nl Web: http://www.cvi.wur.nl
The problem is that bowtie and Galaxy (can) use a different samtools version. Galaxy needs samtools to create metadata for BAM files, so this process is actually running ofter bowtie has finished. You need a samtools version globally accessible for Galaxy. Make sure you have smatools in your $PATH and than restart Galaxy. Cheers, Bjoern 2014-11-26 17:14 GMT+01:00 Anna Terry <iseeglass@googlemail.com>:
I just tried still the same problem. I ran bowtie2 to test, again I saw samtools come up on top, but same error:
Traceback (most recent call last): File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/runners/local.py", line 129, in queue_job job_wrapper.finish( stdout, stderr, exit_code ) File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 998, in finish dataset.datatype.set_meta( dataset, overwrite=False ) # call datatype.set_meta directly for the initial set_meta call during dataset creation File "/home/galaxy/galaxy-dist/lib/galaxy/datatypes/binary.py", line 251, in set_meta raise Exception, "Error Setting BAM Metadata: %s" % stderr Exception: Error Setting BAM Metadata: /bin/sh: samtools: command not found
On 26 November 2014 at 16:01, Eric Kuyt <eric.kuijt@wur.nl> wrote:
Could you try going to Admin -> Manage Installed tool shed repositories
uninstall -> reinstall package_samtools_0_1_18
On 26 November 2014 at 16:55, Anna Terry <iseeglass@googlemail.com> wrote:
yway, I am also getting the problem with samtools filter sam or bam
-- Central Veterinary Institute of Wageningen UR (CVI) Department of Infection Biology PO box 65, 8200 AB Lelystad, NL Visiting address: ASG, Edelhertweg 15, 8219 PH Lelystad
Tel: +31-(0)320-293391 Fax: +31-(0)320-238153 E-mail: eric.kuijt@wur.nl Web: http://www.cvi.wur.nl
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is bash_profile the best place for this, or is somewhere else better? Cheers Anna On 26 November 2014 at 16:29, bjoern.gruening@googlemail.com < bjoern.gruening@gmail.com> wrote:
The problem is that bowtie and Galaxy (can) use a different samtools version. Galaxy needs samtools to create metadata for BAM files, so this process is actually running ofter bowtie has finished. You need a samtools version globally accessible for Galaxy. Make sure you have smatools in your $PATH and than restart Galaxy.
Cheers, Bjoern
2014-11-26 17:14 GMT+01:00 Anna Terry <iseeglass@googlemail.com>:
I just tried still the same problem. I ran bowtie2 to test, again I saw samtools come up on top, but same error:
Traceback (most recent call last): File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/runners/local.py", line 129, in queue_job job_wrapper.finish( stdout, stderr, exit_code ) File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 998, in finish dataset.datatype.set_meta( dataset, overwrite=False ) # call datatype.set_meta directly for the initial set_meta call during dataset creation File "/home/galaxy/galaxy-dist/lib/galaxy/datatypes/binary.py", line 251, in set_meta raise Exception, "Error Setting BAM Metadata: %s" % stderr Exception: Error Setting BAM Metadata: /bin/sh: samtools: command not found
On 26 November 2014 at 16:01, Eric Kuyt <eric.kuijt@wur.nl> wrote:
Could you try going to Admin -> Manage Installed tool shed repositories
uninstall -> reinstall package_samtools_0_1_18
On 26 November 2014 at 16:55, Anna Terry <iseeglass@googlemail.com> wrote:
yway, I am also getting the problem with samtools filter sam or bam
-- Central Veterinary Institute of Wageningen UR (CVI) Department of Infection Biology PO box 65, 8200 AB Lelystad, NL Visiting address: ASG, Edelhertweg 15, 8219 PH Lelystad
Tel: +31-(0)320-293391 Fax: +31-(0)320-238153 E-mail: eric.kuijt@wur.nl Web: http://www.cvi.wur.nl
___________________________________________________________ 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/
I would use .bashrc. You can also try to symlib the default dir to the actual /bin directory. Maybe this works for you. 2014-11-26 17:36 GMT+01:00 Anna Terry <iseeglass@googlemail.com>:
is bash_profile the best place for this, or is somewhere else better?
Cheers Anna
On 26 November 2014 at 16:29, bjoern.gruening@googlemail.com < bjoern.gruening@gmail.com> wrote:
The problem is that bowtie and Galaxy (can) use a different samtools version. Galaxy needs samtools to create metadata for BAM files, so this process is actually running ofter bowtie has finished. You need a samtools version globally accessible for Galaxy. Make sure you have smatools in your $PATH and than restart Galaxy.
Cheers, Bjoern
2014-11-26 17:14 GMT+01:00 Anna Terry <iseeglass@googlemail.com>:
I just tried still the same problem. I ran bowtie2 to test, again I saw samtools come up on top, but same error:
Traceback (most recent call last): File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/runners/local.py", line 129, in queue_job job_wrapper.finish( stdout, stderr, exit_code ) File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 998, in finish dataset.datatype.set_meta( dataset, overwrite=False ) # call datatype.set_meta directly for the initial set_meta call during dataset creation File "/home/galaxy/galaxy-dist/lib/galaxy/datatypes/binary.py", line 251, in set_meta raise Exception, "Error Setting BAM Metadata: %s" % stderr Exception: Error Setting BAM Metadata: /bin/sh: samtools: command not found
On 26 November 2014 at 16:01, Eric Kuyt <eric.kuijt@wur.nl> wrote:
Could you try going to Admin -> Manage Installed tool shed repositories
uninstall -> reinstall package_samtools_0_1_18
On 26 November 2014 at 16:55, Anna Terry <iseeglass@googlemail.com> wrote:
yway, I am also getting the problem with samtools filter sam or bam
-- Central Veterinary Institute of Wageningen UR (CVI) Department of Infection Biology PO box 65, 8200 AB Lelystad, NL Visiting address: ASG, Edelhertweg 15, 8219 PH Lelystad
Tel: +31-(0)320-293391 Fax: +31-(0)320-238153 E-mail: eric.kuijt@wur.nl Web: http://www.cvi.wur.nl
___________________________________________________________ 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/
great, thanks On 26 November 2014 at 16:39, bjoern.gruening@googlemail.com < bjoern.gruening@gmail.com> wrote:
I would use .bashrc. You can also try to symlib the default dir to the actual /bin directory. Maybe this works for you.
2014-11-26 17:36 GMT+01:00 Anna Terry <iseeglass@googlemail.com>:
is bash_profile the best place for this, or is somewhere else better?
Cheers Anna
On 26 November 2014 at 16:29, bjoern.gruening@googlemail.com < bjoern.gruening@gmail.com> wrote:
The problem is that bowtie and Galaxy (can) use a different samtools version. Galaxy needs samtools to create metadata for BAM files, so this process is actually running ofter bowtie has finished. You need a samtools version globally accessible for Galaxy. Make sure you have smatools in your $PATH and than restart Galaxy.
Cheers, Bjoern
2014-11-26 17:14 GMT+01:00 Anna Terry <iseeglass@googlemail.com>:
I just tried still the same problem. I ran bowtie2 to test, again I saw samtools come up on top, but same error:
Traceback (most recent call last): File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/runners/local.py", line 129, in queue_job job_wrapper.finish( stdout, stderr, exit_code ) File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 998, in finish dataset.datatype.set_meta( dataset, overwrite=False ) # call datatype.set_meta directly for the initial set_meta call during dataset creation File "/home/galaxy/galaxy-dist/lib/galaxy/datatypes/binary.py", line 251, in set_meta raise Exception, "Error Setting BAM Metadata: %s" % stderr Exception: Error Setting BAM Metadata: /bin/sh: samtools: command not found
On 26 November 2014 at 16:01, Eric Kuyt <eric.kuijt@wur.nl> wrote:
Could you try going to Admin -> Manage Installed tool shed repositories
uninstall -> reinstall package_samtools_0_1_18
On 26 November 2014 at 16:55, Anna Terry <iseeglass@googlemail.com> wrote:
yway, I am also getting the problem with samtools filter sam or bam
-- Central Veterinary Institute of Wageningen UR (CVI) Department of Infection Biology PO box 65, 8200 AB Lelystad, NL Visiting address: ASG, Edelhertweg 15, 8219 PH Lelystad
Tel: +31-(0)320-293391 Fax: +31-(0)320-238153 E-mail: eric.kuijt@wur.nl Web: http://www.cvi.wur.nl
___________________________________________________________ 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/
participants (3)
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Anna Terry -
bjoern.gruening＠googlemail.com -
Eric Kuyt