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> 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

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