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-linux-x86_64.tgz


On 26 November 2014 at 13:26, Eric Kuyt <eric.kuijt@wur.nl<mailto: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



--
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