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 > > > > ___________________________________________________________ > 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: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ > ___________________________________________________________ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
