Update JBrowse2 to 2.17.0 #1553
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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.
| e = os.environ | ||
| e["SHELL"] = "/bin/sh" | ||
| cmd = ["jbrowse", "text-index"] | ||
| subprocess.run(cmd, env=e, shell=True) |
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Is shell=true needed? It's discouraged and has some security implications afaik
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Unless the environment has that variable added, there is a problem with node.js trying to read the password file, remember?
We discussed changing the biocontainer env to avoid the need for this but that is an even worse option.
This is the fourth place where that could happen and allows text indexing to be turned back on.
If you really want, this one could be reverted but reverting any of the other three cases at line 760,1114 and 1542 will result in failure trying to read /etc/passwd. Only two of the four involve any user input - one a gff being sorted and the other a paf being indexed - so buffer overflow might be possible if anyone really wants to try - but it runs in a container...
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I don't remember at all ;) but now that you say it :)
Can you maybe add a comment to this part of the code? Feel free to merge after that.
another update without any breakage of the config generator.