Hi Anna, you need to install samtools into your system or via the toolshed. If you install it via the toolshed you need to create a symlink. Lets assume you have samtools installed in: ~/tool_deps/samtools/0.19/iuc/2828727744/ than you need to create a symlink from ~/tool_deps/samtools/0.19/iuc/2828727744/ to ~/tool_deps/samtools/default Hope this helps, Bjoern Am 26.11.2014 um 13:49 schrieb Anna Terry:

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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