Hi Jose,

I think that is a good idea. Please see the bottom of this page for some
hints: https://wiki.galaxyproject.org/Develop/SourceCode

Martin

On Wed, Oct 28, 2015 at 12:06 PM Jose Juan Almagro Armenteros <
jjalma...@gmail.com> wrote:

> Hello again,
>
> I have the release_15.07 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>:
>
>> 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>>:
>>>>
>>>>
>>>>     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
>>>>     >
>>>>     >
>>>>     >
>>>>     > ___________________________________________________________
>>>>     > 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/
>>>>
>>>
>>>
>>>
>>> ___________________________________________________________
>>> 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/
___________________________________________________________
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/

Reply via email to