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Package Details: bbmap 39.13-1
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Git Clone URL: | https://aur.archlinux.org/bbmap.git (read-only, click to copy) |
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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: | 2024-11-19 00:14 (UTC) |
Dependencies (4)
- java-environment (jdk12AUR, jdk10AUR, jdk10-openj9-binAUR, jdk7AUR, amazon-corretto-16AUR, jdk8-graalvm-binAUR, jdk16-graalvm-binAUR, jdk16-adoptopenjdkAUR, liberica-jre-11-binAUR, jdk11-j9-binAUR, jdk11-jbr-xdgAUR, jdk16-openjdkAUR, jdk14-openjdkAUR, jdk18-openjdkAUR, amazon-corretto-19-binAUR, jdk19-graalvm-binAUR, liberica-jre-11-full-binAUR, jdk19-graalvm-ee-binAUR, jdk13-openjdk-binAUR, liberica-jre-8-full-binAUR, jdk11-graalvm-binAUR, jdk-openj9AUR, jdk11-graalvm-ee-binAUR, jdk12-openjdkAUR, jdk11-dragonwell-standard-binAUR, jdk11-jetbrains-binAUR, jdk20-graalvm-binAUR, jdk17-graalvm-binAUR, jdk8-graalvm-ee-binAUR, jdk20-openj9-binAUR, zulu-13-binAUR, jdk8-dragonwell-extended-binAUR, jdk8-dragonwell-standard-binAUR, jdk11-dragonwell-extended-binAUR, jdk17-dragonwell-standard-binAUR, jdk8-j9-binAUR, jdk7-j9-binAUR, jdk7r1-j9-binAUR, jdk8-dragonwell-extendedAUR, jdk13-openjdkAUR, jdk15-openjdkAUR, jdk21-graalvm-binAUR, jdk17-jetbrainsAUR, jdk8-openj9-binAUR, jdk-ltsAUR, microsoft-openjdk-11-binAUR, microsoft-openjdk-17-binAUR, microsoft-openjdk-21-binAUR, liberica-nik-24-full-binAUR, jdk21-jetbrains-gitAUR, zulu-17-binAUR, zulu-11-binAUR, zulu-8-binAUR, mandrel-binAUR, mandrel24-binAUR, liberica-jdk-17-full-binAUR, liberica-jdk-11-lite-binAUR, liberica-jdk-11-full-binAUR, liberica-jdk-11-binAUR, jdk17-graalvm-ee-binAUR, jdk21-graalvm-ee-binAUR, jdk22-graalvm-ee-binAUR, jdk20-graalvm-ee-binAUR, jdk22-graalvm-binAUR, jdk19-openjdkAUR, jdk17-jetbrains-binAUR, zulu-jdk-fx-binAUR, jabba-binAUR, jdk21-jetbrainsAUR, jdk17-zulu-prime-binAUR, java-openjdk-binAUR, amazon-corretto-17AUR, amazon-corretto-21-binAUR, jdk21-temurinAUR, amazon-corretto-8AUR, amazon-corretto-11AUR, jdk11-temurinAUR, liberica-jdk-full-binAUR, liberica-jdk-21-full-binAUR, liberica-jdk-8-full-binAUR, jdk17-temurinAUR, jdk8-temurinAUR, zulu-21-binAUR, jdk-temurinAUR, jdk8AUR, zulu-17-fx-binAUR, jdk8-perfAUR, zulu-fx-binAUR, zulu8-fx-binAUR, zulu11-fx-binAUR, zulu17-fx-binAUR, zulu21-fx-binAUR, jdk-openj9-binAUR, jdk11-openj9-binAUR, jre-jetbrainsAUR, jdk-openjdk-wakefieldAUR, jdk21-openj9-binAUR, zulu-23-binAUR, jdkAUR, jre-zulu-binAUR, jre-zulu-fx-binAUR, jdk21-dragonwell-standard-binAUR, jdk21-dragonwell-extended-binAUR, jdk-android-studioAUR, jdk17-openj9-binAUR, jdk23-graalvm-ee-binAUR, zing-8-binAUR, zing-21-binAUR, java-openjdk-ea-binAUR, jdk21-jetbrains-binAUR, openjdk-zulu-ca-fx-binAUR, openjdk-zulu8-ca-fx-binAUR, openjdk-zulu11-ca-fx-binAUR, openjdk-zulu17-ca-fx-binAUR, openjdk-zulu21-ca-fx-binAUR, jdk11AUR, jdk-openjdk, jdk11-openjdk, jdk17-openjdk, jdk21-openjdk, jdk8-openjdk)
- env-modulesAUR (lmodAUR) (optional) – for any scripts requiring `module`
- pigz (pigz-gitAUR) (optional) – for parallel GZIP (de)compression
- samtoolsAUR (samtools-gitAUR) (optional) – for BAM output
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:
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.