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easybuilders / easybuild-easyconfigs

A collection of easyconfig files that describe which software to build using which build options with EasyBuild.
https://easybuild.io
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Prokka provides some binaries, so they should be deps as the current PATH does not contains their location. #15366

Open hajgato opened 2 years ago

hajgato commented 2 years ago

Prokka (1.14.5) provides couple of pre-compiled binaries:

[vsc43020@gligar07 ~]$ ls -lR /apps/gent/RHEL8/skylake-ib/software/prokka/1.14.5-gompi-2020b/binaries
/apps/gent/RHEL8/skylake-ib/software/prokka/1.14.5-gompi-2020b/binaries:
total 3
drwxr-xr-x 2 vsc40003 vsc40003 4096 Nov 11  2019 common
drwxr-xr-x 2 vsc40003 vsc40003 4096 Nov 11  2019 darwin
drwxr-xr-x 2 vsc40003 vsc40003 4096 Nov 11  2019 linux

/apps/gent/RHEL8/skylake-ib/software/prokka/1.14.5-gompi-2020b/binaries/common:
total 577
-rwxr-xr-x 1 vsc40003 vsc40003    791 Nov 11  2019 minced
-rw-r--r-- 1 vsc40003 vsc40003  24828 Nov 11  2019 minced.jar
-rwxr-xr-x 1 vsc40003 vsc40003 259064 Nov 11  2019 parallel

/apps/gent/RHEL8/skylake-ib/software/prokka/1.14.5-gompi-2020b/binaries/darwin:
total 167776
-rwxr-xr-x 1 vsc40003 vsc40003   454940 Nov 11  2019 aragorn
-rwxr-xr-x 1 vsc40003 vsc40003 24565940 Nov 11  2019 blastp
-rwxr-xr-x 1 vsc40003 vsc40003  2271284 Nov 11  2019 cmpress
-rwxr-xr-x 1 vsc40003 vsc40003  2341500 Nov 11  2019 cmscan
-rwxr-xr-x 1 vsc40003 vsc40003   397348 Nov 11  2019 hmmpress
-rwxr-xr-x 1 vsc40003 vsc40003   720908 Nov 11  2019 hmmscan
-rwxr-xr-x 1 vsc40003 vsc40003 17269136 Nov 11  2019 makeblastdb
-rwxr-xr-x 1 vsc40003 vsc40003 28025528 Nov 11  2019 prodigal
-rwxr-xr-x 1 vsc40003 vsc40003  9811768 Nov 11  2019 tbl2asn

/apps/gent/RHEL8/skylake-ib/software/prokka/1.14.5-gompi-2020b/binaries/linux:
total 199376
-rwxr-xr-x 1 vsc40003 vsc40003   445784 Nov 11  2019 aragorn
-rwxr-xr-x 1 vsc40003 vsc40003 43444288 Nov 11  2019 blastp
-rwxr-xr-x 1 vsc40003 vsc40003  2040704 Nov 11  2019 cmpress
-rwxr-xr-x 1 vsc40003 vsc40003  2107792 Nov 11  2019 cmscan
-rwxr-xr-x 1 vsc40003 vsc40003   335160 Nov 11  2019 hmmpress
-rwxr-xr-x 1 vsc40003 vsc40003   628552 Nov 11  2019 hmmscan
-rwxr-xr-x 1 vsc40003 vsc40003 31323968 Nov 11  2019 makeblastdb
-rwxr-xr-x 1 vsc40003 vsc40003 13507248 Nov 11  2019 prodigal
-rwxr-xr-x 1 vsc40003 vsc40003  8211360 Nov 11  2019 tbl2asn

Couple of stuff is already a dep, so we probably should give the rest also as a dep. Adding those locations to path might not be a good way (for example do not know how to check whether we should give linux or darwin)

Additionally I do not know how they evolved, whether they just provided and not used anymore. (blastp and parallel is already a dep)

hajgato commented 2 years ago

be aware, some of them called using hard coded locations, using ../binary/linux

branfosj commented 2 years ago

For tbl2asn we had the following error reported:

[10:01:14] Looking for 'tbl2asn' - found /rds/bear-apps/2019b/EL8-has/software/prokka/1.14.5-gompi-2019b/bin/../binaries/linux/tbl2asn
tbl2asn: error while loading shared libraries: libidn.so.11: cannot open shared object file: No such file or directory
[10:01:14] Could not determine version of tbl2asn - please install version 24.3 or higher

For our local copy, I've 'fixed' it with the changes in https://github.com/bear-rsg/easybuild-easyconfigs/blob/2019b/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2019b.eb, which includes a sanity check using the supplied data to that triggers use of tbl2asn.