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.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.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.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