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 < jjalmagro@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 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/197c7b21b209a7b6fbdb9a8a11c23... )?
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 > > > > ___________________________________________________________ > 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/
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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/