On Dec 10, 2015, at 5:02 PM, John Chilton <jmchilton@gmail.com> wrote:

Hey Brad,

 What version of Galaxy are you on? Parameterized macros are pretty
new and will not work on older Galaxies.

-John

On Fri, Dec 4, 2015 at 3:36 AM, Langhorst, Brad <Langhorst@neb.com> wrote:
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.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



--
Brad Langhorst, Ph.D.
Development Scientist
New England Biolabs


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