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vscentrum / vsc-software-stack

Central repository of easyconfigs used in the software installations on VSC clusters.
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NextDenovo #397

Closed laraPPr closed 3 weeks ago

laraPPr commented 2 months ago
pavelToman commented 2 months ago

PR:

boegel commented 2 months ago

To fix the problem with HTSlib, we should add it as a dependency and make it is used, probably with something like HTSDIR=$EBROOTHTSLIB in buildopts, see also https://github.com/Nextomics/NextDenovo/blob/master/lib/Makefile#L4

pavelToman commented 2 months ago

It uses either minimap2 but modified one - https://nextdenovo.readthedocs.io/en/latest/UTILITY.html#minimap2-nd

pavelToman commented 2 months ago

I was unable to replace htslib by one from EB. I've tried even to build and use HTSlib-1.9 as they use this version. Most recent log is https://github.com/vscentrum/vsc-software-stack/blob/wip/397_NextDenovo/log5.txt There are a lot of undefined reference to for bsort.c during gcc -Wall -O3 -Wno-unused-function -o bam_sort bam_sort.c ../lib/bsort.c -I ../lib/htslib/ -lpthread -lcurl -lm -lz -lcrypto The finall WIP is there: https://github.com/vscentrum/vsc-software-stack/blob/wip/397_NextDenovo/nextdenovo_HTS_test_2.eb another one there: https://github.com/vscentrum/vsc-software-stack/blob/wip/397_NextDenovo/nextdenovo_HTS_test.eb

boegel commented 4 weeks ago

@pavelToman The undefined reference errors hint towards not linking to XZ + bzip2, that's probably what you should try and fix.

Maybe also ask upstream whether linking with your own HTSlib library makes sense/is supported

boegel commented 3 weeks ago

@pavelToman PR merged, software installed, ready for cleanup