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bcgsc / tigmint

⛓ Correct misassemblies using linked AND long reads
https://bcgsc.github.io/tigmint/
GNU General Public License v3.0
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Respect PATH and few more parent env variables to speedup sorting #64

Closed mmokrejs closed 2 years ago

mmokrejs commented 2 years ago

respect $TMPDIR so that sort places the files on large and fast enough storage, supposedly local

provide a SORT_OPTS variable to inject also sort-buffer -related settings like '-S 10G'

swap the if/else conditions so that preferably bgzip is picked over pigz

The installation procedure should be changed to get the files installed.

Makefiles need to have executable bit set to be executable.

Bug: https://github.com/bcgsc/tigmint/issues/63 https://github.com/bcgsc/tigmint/issues/62 https://github.com/bcgsc/tigmint/issues/60

lcoombe commented 2 years ago

Thanks for the comments, @mmokrejs - I think we are on the same page for most of the changes in the PR. When you have a chance to update the code in the PR accordingly (and CI passes), I'll be happy to accept and merge.

mmokrejs commented 2 years ago

Basically, you can add the use of SORT_OPTS and of TMPDIR in a different request, I think not much is left from this one. I have to leave now and not sure I get to it tomorrow.

lcoombe commented 2 years ago

Superseded by #73