The main problem for me was that I was not aware that the tophat tool had a dependency on a command line tool outside of galaxy installation. I see in the admin interface that tophat has a dependency on samtools of type package and I assumed that should provide the samtools binary. Of course I have not read the manuals regarding tool sheds, dependencies, etc so thats probably where my problem started in the first place...
> On Feb 24, 2015, at 3:18 AM, John Chilton <jmchil...@gmail.com> wrote: > > Sorry for this messy situation. With the next release Galaxy will be > able to set metadata using any version of samtools due to an excellent > fix by Nate - so this hopefully will become less of an issue. > > -John > > On Mon, Feb 23, 2015 at 10:01 AM, Peter Cock <p.j.a.c...@googlemail.com> > wrote: >> On Mon, Feb 23, 2015 at 2:13 PM, Michael Thon <mike.t...@gmail.com> wrote: >>> >>> I figured that galaxy must be finding a samtools v1.1 even though the tool >>> was not installed, according to the admin page. I uninstalled the samtools >>> that was installed system-wide on the server. Now I get this error: >>> >>> 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 1107, 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 250, >>> in set_meta >>> raise Exception, "Error Setting BAM Metadata: %s" % stderr >>> Exception: Error Setting BAM Metadata: /bin/sh: 1: samtools: not found >>> >>> So, galaxy is not using the samtools from the installed galaxy package and >>> is instead using the system one. I'll try to reinstall samtools and see if >>> that fixes it... >> >> In this case Galaxy itself expects samtools on the $PATH for managing >> BAM files separately from which ever tool you are using within Galaxy. >> >> The Galaxy Tool Shed dependencies are on a per-tool basis, and not >> used by Galaxy itself. >> >> This ought to be on the wiki somewhere, but I failed to find it... >> >> Peter >> ___________________________________________________________ >> 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/
