Docker Galaxy & HISAT2: ValueError: Parameter index requires a value, but has no legal values defined.
I'm trying to use HISAT2 using a Docker-ized Galaxy (bgruening/galaxy-rna-seq:dev - Galaxy 17.05). I installed the HISAT2 index builder from the toolshed and built an index for the dm3 genome (resulting in an index in /galaxy-central/tool-data/dm3/hisat2_index/dm3). When I try and run HISAT2 with this newly created genome, I get the following error:
Traceback (most recent call last):
File "/galaxy-central/lib/galaxy/jobs/runners/__init__.py", line 170, in prepare_job
File "/galaxy-central/lib/galaxy/jobs/__init__.py", line 878, in prepare
The "index" parameter is the one used in selecting between the genome from the History and the built-in genome options. Curiously if I spend some time changing this selection before running the tool the HISAT2 run completes successfully. This looks like a bug though - any workarounds or suggestions?
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