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:
than you need to create a symlink from
~/tool_deps/samtools/0.19/iuc/2828727744/ to ~/tool_deps/samtools/default
Hope this helps,
Am 26.11.2014 um 13:49 schrieb Anna Terry:
> 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
> 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:
> To search Galaxy mailing lists use the unified search at:
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:
To search Galaxy mailing lists use the unified search at: