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>:
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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