Hi: I just installed hisat2 and the data manager from the toolshed ….
Some macros seem not to be expanded when I load the tool in the UI (even across galaxy restarts) e.g. I see @FTYPE@ instead of fastqsanger
the data manager produces this error:
Fatal error: Exit code 1 () Traceback (most recent call last): File "/mnt/galaxy/data/galaxy/galaxy-toolshed-tools/toolshed.g2.bx.psu.edu/repos/iuc/data_manager_hisat2_index_builder/98a60a4cfb9a/data_manager_hisat2_index_builder/data_manager/hisat2_index_builder.pyhttp://toolshed.g2.bx.psu.edu/repos/iuc/data_manager_hisat2_index_builder/98a60a4cfb9a/data_manager_hisat2_index_builder/data_manager/hisat2_index_builder.py", line 85, in <module> main() File "/mnt/galaxy/data/galaxy/galaxy-toolshed-tools/toolshed.g2.bx.psu.edu/repos/iuc/data_manager_hisat2_index_builder/98a60a4cfb9a/data_manager_hisat2_index_builder/data_manager/hisat2_index_builder.pyhttp://toolshed.g2.bx.psu.edu/repos/iuc/data_manager_hisat2_index_builder/98a60a4cfb9a/data_manager_hisat2_index_builder/data_manager/hisat2_index_builder.py", line 79, in main build_hisat_index( data_manager_dict, options, params, sequence_id, sequence_name ) File "/mnt/galaxy/data/galaxy/galaxy-toolshed-tools/toolshed.g2.bx.psu.edu/repos/iuc/data_manager_hisat2_index_builder/98a60a4cfb9a/data_manager_hisat2_index_builder/data_manager/hisat2_index_builder.pyhttp://toolshed.g2.bx.psu.edu/repos/iuc/data_manager_hisat2_index_builder/98a60a4cfb9a/data_manager_hisat2_index_builder/data_manager/hisat2_index_builder.py", line 41, in build_hisat_index proc = subprocess.Popen( args=args, shell=False, cwd=target_directory ) File "/mnt/galaxy/data/galaxy/sw/lib/python2.7/subprocess.py", line 710, in __init__ errread, errwrite) File "/mnt/galaxy/data/galaxy/sw/lib/python2.7/subprocess.py", line 1327, in _execute_child raise child_exception OSError: [Errno 13] Permission denied
that seems to be a result of a missing execute bit for the binaries in
tool-deps/hisat/2.0/iuc/package_hisat_2_0/c65f00072e57/bin
Should I file issues, or did my installation go wrong?
Any hints to get this running?
Brad
-- Brad Langhorst, Ph.D. Development Scientist New England Biolabs