2015-10-28 17:00 GMT+01:00 Dave Bouvier <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>>:

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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