So I actually still have a problem, (I guess the setting was still there somewhere from the bash_profile)
Anyway, I am also getting the problem with samtools filter sam or bam
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
I have tried also what you said, linking the samtools binary to default, but still the same problem.
Any other ideas?
On 26 November 2014 at 14:01, Anna Terry iseeglass@googlemail.com wrote:
Great, I've done it and it works.
galaxy-dist/tools/samtools/default cd galaxy-dist/tools/samtools/default/ cp -rs ~/galaxy-dist/tools/samtools/0.1.19/* .
Thanks Bjoern and Eric
On 26 November 2014 at 13:54, Eric Kuyt eric.kuijt@wur.nl wrote:
Bjoerns comment was the right one, samtools isn't automatically installed as a dependency somehow.
so the best option is to install samtools https://toolshed.g2.bx.psu.edu/view/devteam/package_samtools_0_1_19
and link the installed binary to ~/tool_deps/samtools/0.19/iuc/2828727744/ to ~/tool_deps/samtools/default
Eric
On 26 November 2014 at 14:44, Anna Terry iseeglass@googlemail.com wrote:
Here is the contents of the log file:
Successfully downloaded from url: http://depot.galaxyproject.org/package/linux/x86_64/bowtie2/bowtie2-2.1.0-li...
On 26 November 2014 at 13:26, Eric Kuyt <eric.kuijt@wur.nlmailto: eric.kuijt@wur.nl> wrote: Hi Anna,
Setting your own path variables shouldn't be necessary for toolshed tools, so probably something is wrong with the installation. could you post your
tooldependencies/bowtie2/2.1.0/devteam/package_bowtie2_2_1_0/017a00c265f1/INSTALLATION.log
file?
On 26 November 2014 at 13:49, Anna Terry <iseeglass@googlemail.com mailto:iseeglass@googlemail.com> wrote: Hi, I installed bowtie2 from the toolshed, but get the following error when I run it:
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
I'm not sure why this won't work? samtools is a dependency for the bowtie2 tool and is installed, but cannot seem to find it. There must me something slightly wrong on my server as I can't see loads of errors like this on this mailing list.
I have added the path from the samtools env file to .bash_profile for galaxy and this allows this tool to run, but is not the correct solution, as doesn't work when versions change.
Could you let me know where I'm going wrong Thanks Anna
-- 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.nlmailto:eric.kuijt@wur.nl Web: http://www.cvi.wur.nl
-- 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
What is really weird is when running the bowtie2 tool, before it quits, I can see samtools come up in top
On 26 November 2014 at 15:55, Anna Terry iseeglass@googlemail.com wrote:
So I actually still have a problem, (I guess the setting was still there somewhere from the bash_profile)
Anyway, I am also getting the problem with samtools filter sam or bam
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
I have tried also what you said, linking the samtools binary to default, but still the same problem.
Any other ideas?
On 26 November 2014 at 14:01, Anna Terry iseeglass@googlemail.com wrote:
Great, I've done it and it works.
galaxy-dist/tools/samtools/default cd galaxy-dist/tools/samtools/default/ cp -rs ~/galaxy-dist/tools/samtools/0.1.19/* .
Thanks Bjoern and Eric
On 26 November 2014 at 13:54, Eric Kuyt eric.kuijt@wur.nl wrote:
Bjoerns comment was the right one, samtools isn't automatically installed as a dependency somehow.
so the best option is to install samtools https://toolshed.g2.bx.psu.edu/view/devteam/package_samtools_0_1_19
and link the installed binary to ~/tool_deps/samtools/0.19/iuc/2828727744/ to ~/tool_deps/samtools/default
Eric
On 26 November 2014 at 14:44, Anna Terry iseeglass@googlemail.com wrote:
Here is the contents of the log file:
Successfully downloaded from url: http://depot.galaxyproject.org/package/linux/x86_64/bowtie2/bowtie2-2.1.0-li...
On 26 November 2014 at 13:26, Eric Kuyt <eric.kuijt@wur.nlmailto: eric.kuijt@wur.nl> wrote: Hi Anna,
Setting your own path variables shouldn't be necessary for toolshed tools, so probably something is wrong with the installation. could you post your
tooldependencies/bowtie2/2.1.0/devteam/package_bowtie2_2_1_0/017a00c265f1/INSTALLATION.log
file?
On 26 November 2014 at 13:49, Anna Terry <iseeglass@googlemail.com mailto:iseeglass@googlemail.com> wrote: Hi, I installed bowtie2 from the toolshed, but get the following error when I run it:
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
I'm not sure why this won't work? samtools is a dependency for the bowtie2 tool and is installed, but cannot seem to find it. There must me something slightly wrong on my server as I can't see loads of errors like this on this mailing list.
I have added the path from the samtools env file to .bash_profile for galaxy and this allows this tool to run, but is not the correct solution, as doesn't work when versions change.
Could you let me know where I'm going wrong Thanks Anna
-- 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.nlmailto:eric.kuijt@wur.nl Web: http://www.cvi.wur.nl
-- 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
galaxy-dev@lists.galaxyproject.org
-
Anna Terry