Re: [galaxy-dev] Bismark installation dependencies error

Hi Jose, unfortunately the release_15.07 branch on Bitbucket seems to be missing all post-release updates, and I warmly suggest you to move to the Github releases as soon as you can.

The migration is documented at https://wiki.galaxyproject.org/Admin/SwitchingToGithubFromBitbucket

Cheers, Nicola

On 28/10/15 16:06, Jose Juan Almagro Armenteros wrote:

Hello again,

I have the from Bitbucket, so if I want to have that commit I suppose that I would have to switch my Galaxy instance from Bitbucket to Github. Is this correct?

Regards,

Jose

2015-10-28 17:00 GMT+01:00 Dave Bouvier <dave@bx.psu.edu mailto:dave@bx.psu.edu>:

Yes, this is definitely related to the issue I fixed part of, and
(I think) Nicola fixed the rest of.

-
Dave Bouvier
http://galaxyproject.org
http://usegalaxy.org

On 10/28/2015 11:46 AM, Nicola Soranzo wrote:

    Hi Jose,
    can you check that your release_15.07 is updated and contains
    git commit
    197c7b21b209a7b6fbdb9a8a11c232a2b88523fc (
    https://github.com/galaxyproject/galaxy/commit/197c7b21b209a7b6fbdb9a8a11c232a2b88523fc
    )?

    Cheers,
    Nicola

    On 28/10/15 14:53, Jose Juan Almagro Armenteros wrote:

        Hello Björn,

        I am using Galaxy 15.07, so everything should be updated.

        Regards,

        Jose

        2015-10-28 15:43 GMT+01:00 Björn Grüning
        <bjoern.gruening@gmail.com <mailto:bjoern.gruening@gmail.com>
        <mailto:bjoern.gruening@gmail.com
        <mailto:bjoern.gruening@gmail.com>>>:


            Hi Jose,

            which version of Galaxy are you using?
            @Dave can this be one of the old un-compressing changes?

            Cheers,
            Bjoern

            Am 28.10.2015 um 15:31 schrieb Jose Juan Almagro
        Armenteros:
            > Hello,
            >
            > I have tried to install the last version of Bismark
        from the
            toolshed and I
            > got an error while installing. Basically it can't
        install bowtie and
            > bowtie2 because the folder name
            > is written twice in the download directory. Here is
        the error:
            >
            > File
        "/steno-internal/projects/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py",
            > line 142, in install_and_build_package_via_fabric
            >     tool_dependency = self.install_and_build_package(
            > tool_shed_repository, tool_dependency, actions_dict )
            >   File
        "/steno-internal/projects/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py",
            > line 100, in install_and_build_package
            >     initial_download=True )
            >   File
        "/steno-internal/projects/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py",
            > line 32, in execute_step
            >     initial_download=initial_download )
            >   File
        "/steno-internal/projects/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py",
            > line 685, in execute_step
            >     dir = self.url_download( work_dir,
        downloaded_filename, url,
            > extract=True, checksums=checksums )
            >   File
        "/steno-internal/projects/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py",
            > line 223, in url_download
            >     extraction_path = archive.extract( install_dir )
            >   File
        "/steno-internal/projects/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py",
            > line 89, in extract
            >     os.chmod( absolute_filepath, unix_permissions )
            >
            > [Errno 2] No such file or directory:
            >
        './database/tmp/tmp-toolshed-mtdM4XBx_/bowtie-0.12.8/bowtie-0.12.8/'
            >
            > As you see "bowtie-0.12.8" is twice in the path and
        when I check the
            > directory, the last "bowtie-0.12.8" folder doesn't
        exists.
            >
            > Do you know what could go wrong or an alternative way of
            specifying the
            > correct path?
            >
            >
            > Best regards,
            >
            > Jose
            >
            >
            >
            >
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