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JBrowse2: Revert from pif indexes for paf #1522
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…m/fubar2/nftoolmaker It actually does work. Sort of. Hope this is useful to someone.
…ply to all future generated tools :)
Allows single ended fastq or fasta to be mapped, or a pair of forward and reverse - both must be fastq
…dio replacement...
Pity the built in fails in biocontainers.
revert to paf until sorted
…y is broken tabix does not do this.
I guess we should try to find out why the container does not work. Indicates some permission problems. Which is very likely in a container setting. |
@bgruening: yes - likely a file permission error and well beyond my skills. Meanwhile, synteny tracks do not work right. At least this reverts to working paf and retains the code - just need to set canPif true. Would prefer to merge this while someone figures out the real cause and fixes it. |
@bgruening: Until someone (not me!) figures out the fix, the current JBrowse2 is broken and this PR will fix it by reverting. |
Sorry, not a good week here ... |
Sorry you don't have enough monkeys to make every week a good one - sorry to add to your woes - thanks! |
Painful.
The pif index is a GMOD thing - not tabix.
The utility works when tested with planemo/conda but fails with this node-js error using biocontainers so cannot be used. Tried making all the paths local - no difference. Something odd about node-js wanting to call uv_os_get_passwd in the biocontainer. Apparently it happens if a path cannot be found or is RO?