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 <d...@bx.psu.edu <mailto:d...@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.gruen...@gmail.com <mailto:bjoern.gruen...@gmail.com>
            <mailto:bjoern.gruen...@gmail.com
            <mailto:bjoern.gruen...@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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