Package Details: bbmap 39.42-1

Git Clone URL: https://aur.archlinux.org/bbmap.git (read-only, click to copy)
Package Base: bbmap
Description: A short read aligner and other bioinformatic tools
Upstream URL: https://jgi.doe.gov/data-and-tools/bbtools/
Licenses: BSD
Submitter: clintval
Maintainer: malacology (BioArchLinuxBot)
Last Packager: BioArchLinuxBot
Votes: 1
Popularity: 0.000000
First Submitted: 2017-12-25 07:34 (UTC)
Last Updated: 2025-10-31 18:06 (UTC)

Dependencies (4)

Required by (1)

Sources (1)

Latest Comments

clintval commented on 2018-04-20 04:23 (UTC)

For those interested, this package will build the companion jni shared objects.

To make use of the speedups you have to pass usejni=t to BBMerge, BBMap, and Dedupe!

fennerm commented on 2018-04-19 21:27 (UTC)

Thanks @clintval that seems to having fixed it.

clintval commented on 2018-04-19 20:40 (UTC) (edited on 2018-04-19 20:40 (UTC) by clintval)

I can confirm I can at least run the test case succesfully:

❯ stats.sh /usr/share/java/bbmap/resources/phix174_ill.ref.fa.gz
A       C       G       T       N       IUPAC   Other   GC      GC_stdev
0.2399  0.2144  0.2326  0.3130  0.0000  0.0000  0.0000  0.4471  0.0000
...

clintval commented on 2018-04-19 20:29 (UTC)

Hi @fennerm, I've only just started maintaining this package and will likely need more help from testers since bbtools relies so heavily on hardcoded paths and/or env-modules.

I just updated the PKGBUILD to source v37.99. Please let me know if you have any more trouble. You can email me too for faster chat.

fennerm commented on 2018-04-14 22:30 (UTC)

This isn't installing correctly for me. I get a series of errors like this one:

/usr/bin/repair.sh: line 71: /usr/share/java/bbmap//calcmem.sh: No such file or directory

BBMap is looking for scripts in /usr/share/java/bbmap but they're placed in /usr/bin instead.