Hello list,
installing the dependency package_picard_1_136 results in the following
error:
---
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
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