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/
