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 <langho...@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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