Hello list,
installing the dependency package_picard_1_136 results in the following error:
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File "/beegfs/common/galaxy/home/galaxy-15.07/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 "/beegfs/common/galaxy/home/galaxy-15.07/lib/tool_shed/galaxy_install/install_manager.py", line 100, in install_and_build_package initial_download=True ) File "/beegfs/common/galaxy/home/galaxy-15.07/lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py", line 32, in execute_step initial_download=initial_download ) File "/beegfs/common/galaxy/home/galaxy-15.07/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", line 685, in execute_step checksums = self.get_dict_checksums( action_dict ) File "/beegfs/common/galaxy/home/galaxy-15.07/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", line 223, in url_download archive = CompressedFile( file_path ) File "/beegfs/common/galaxy/home/galaxy-15.07/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", line 89, in extract print "foo"
[Errno 2] No such file or directory: './database/tmp/tmp-toolshed-mtdBC1_TE/picard-tools-1.136/picard-tools-1.136/'
---
Checking the directory './database/tmp/tmp-toolshed-mtdBC1_TE/picard-tools-1.136' returns:
$ ls -a ./database/tmp/tmp-toolshed-mtdBC1_TE/picard-tools-1.136 . .. htsjdk-1.136.jar libIntelDeflater.so picard-lib.jar picard.jar
The same thing happens with 'package_picard_1_126_0', whereas 'package_picard_1_56_0' installs fine. Is there an issue with '<source_directory>.</source_directory>' (in 126 and 136) vs '<source_directory>picard-tools-1.56</source_directory>'? I changed this in my local xml but it had no effect.
Any ideas?
Sven