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.