Galaxy itself will call samtools index on BAM files, so
they should be there on disk already, See for example:
https://github.com/peterjc/pico_galaxy/blob/master/tools/samtools_idxstats/samtools_idxstats.xml
Roberto -
Sorry for consistently taking so long to respond to these parallelism
inquires - you are doing awesome work but I am just constantly swamped
- I'll try to do more testing today.
I can confirm both of those tests fail - it has nothing to do with your setup.
compare_bam_as_sam was added
://lists.galaxyproject.org/pipermail/galaxy-dev/attachments/20150522/26eb90de/attachment-0001.html
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