Re: [galaxy-dev] migrated BWA installed but missing dependencies

8 Oct 2012


      Hi Derrick!
...
I saw that printed message but I decided not to
append install_dependencies flag to the command because we have had
BWA binary in the galaxy running environment.
...
I don't think the use of install_dependencies is compulsory?
Sorry, im not sure if it is compulsory. But i would advise you do use
that. One idea of the toolshed is to log all version informations about
all dependencies, enabling reproducibility. Also the toolshed can create
environments for each tool, so that you can run different versions of
your tool. So it can be that the bwa-wrapper does not know about your
local install. But i haven’t looked at it. 

Regards,
Bjoern
...
Derrick
On Mon, Oct 8, 2012 at 5:14 PM, Björn Grüning
<bjoern.gruening@pharmazie.uni-freiburg.de> wrote:
        Hi Derrick,
i think during the migration something like that was printed
        on your
        screen:
---------
        The tool dependencies listed above will be installed along
        with the
        repositories if you add the 'install_dependencies' option to
        the above
        command like this:
vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv
        sh ./scripts/migrate_tools/0005_tools.sh install_dependencies
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Tool dependencies can be installed after the repositories have
        been
        installed as well.
        ---------
I think you should run that command by yourself to get BWA
        working
        again.
Kind regards,
        Bjoern
> Hi guys,
        >
        >
        > I have updated the galaxy to Oct 5 dist, and BWA has been
        reinstalled
        > via the migration script. However, I couldn't find any entry
        has been
        > added in migrated_tools_conf.xml (thus the BWA tools are not
        display
        > in the tool panel).
        >
        >
        > I check in the admin "Installed tool shed repositories"
        section and
        > BWA repos status is "Installed, missing dependencies", is
        that why it
        > didn't get added into the migrated_tools_conf.xml?
        >
        >
        > I have had BWA 0.5.9-r16 in path, and been used by the old
        BWA wrapper
        > without an issue before. How can I fix this dependencies
        issue for a
        > Shed Tool? Should I add something like:
        >
        >
        > <tool_dependency_dir>/bowtie/0.12.7/env.sh
        >
        >
        > thanks,
        > Derrick
> ___________________________________________________________
        > 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:
        >
        >   http://lists.bx.psu.edu/