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Package Details: gatk 2:4.0.7.0-1
Git Clone URL: | https://aur.archlinux.org/gatk.git (read-only, click to copy) |
---|---|
Package Base: | gatk |
Description: | Variant discovery in high-throughput bioinformatics sequencing data |
Upstream URL: | https://software.broadinstitute.org/gatk |
Keywords: | bioinformatics |
Licenses: | |
Submitter: | clintval |
Maintainer: | mrwillbarnz |
Last Packager: | clintval |
Votes: | 1 |
Popularity: | 0.005214 |
First Submitted: | 2017-12-04 23:56 |
Last Updated: | 2018-07-31 01:58 |
Dependencies (3)
- python (python-dbg)
- java-runtime>=8 (jdk5, tuxjdk, jre7-openjdk-infinality, java-8-openjdk-shenandoah, jre8-openjdk-infinality, java-gcj-compat, jdk9, jre9, jdk-devel, jre10, jdk8-arm64, jdk6, jdk12-openj9-bin, zulu-12-bin, jre6, jre12, jdk8-openjdk-dcevm, jdk11-graalvm-ee-bin, server-jre, jdk8-arm, jdk13-openj9-bin, jdk9-openj9-bin, jdk10, jdk11-openjdk-dcevm, jre8-openjdk-jetbrains, jre8-openjdk-shenandoah, jdk10-openj9-bin, jdk14-openj9-bin, sapmachine-jdk-bin, jdk7, jre7, jdk8-j9-bin, jre14, jdk-arm, jdk-adoptopenjdk, jdk11-adoptopenjdk, liberica-jdk-full-bin, jdk8-jetbrains, zulu-embedded-jdk8, liberica-jdk-8-full-bin, liberica-jdk-11-bin, liberica-jdk-11-full-bin, liberica-jdk-11-lite-bin, liberica-jre-11-bin, liberica-jre-11-full-bin, liberica-jre-8-full-bin, jre11, zulu-embedded-jdk, jdk7r1-j9-bin, jdk7-j9-bin, zulu-15-bin, zulu-14-bin, zulu-13-bin, jre8-adoptopenjdk, zulu-embedded-jdk11, jdk-bcl, jre-bcl, jdk8-openj9-bin, zulu-11-bin, zulu-8-bin, amazon-corretto-15, jre-openj9, jre-jetbrains, java-openjdk-loom-ea-bin, jdk11-openj9-bin, jre11-jetbrains-imfix, jdk8-graalvm-bin, jdk11-graalvm-bin, java-openjdk-bin, amazon-corretto-8, amazon-corretto-11, jdk11-openjdk-dcevm-conflicts-fixed, jre8, jdk8, java-openjdk-ea-bin, jdk-openj9-bin, jre, jdk-jetbrains, jre-openjdk, jre11-openjdk, jre7-openjdk, jre8-openjdk)
- gradle (gradle-rc) (make)
Latest Comments
clintval commented on 2018-07-31 02:00
@Pastafarianist thanks for
gatk-bin
! I updated the PKGBUILD here to clone the repository and checkout the tagged commit for the version.Not ideal but the best I can do.
Anyone interested in installing this package should know it will clone a ~2Gb payload and with all the network calls, this takes a long time.
clintval commented on 2018-07-31 01:21
Thanks everyone!
I patched the currently listed PKGBUILD at
v4.0.2.1
and am working on a build from source solution for recent versions now.Pastafarianist commented on 2018-07-17 21:56
Manually installing
gradle
(with java8) beforegatk
fixes the issue for me. Please addgradle
tomakedepends
.Also, the latest version is 4.0.6.0, and it does not support building from the source code distribution. Only building from a
git clone
is supported. I have added a packagegatk-bin
that unpacks and installs the official binary distribution, but a proper up-to-date source-based package would also be appreciated.Pastafarianist commented on 2018-07-15 07:06
For me,
prepare()
fails on jdk10 with theCannot invoke method getURLs() on null object
message.eschwartz commented on 2018-04-26 05:34
No clue what that orphan request is about...
Note this still does currently fail to build in a clean chroot during prepare,
with either jdk9 or jdk10 displaying the erorr:
With jdk8 it still fails, this time with the error message:
clintval commented on 2018-04-12 23:21
Not sure why someone is making orphan requests on this. The package works for me. Please submit comments on why it is not working for you or how I can improve it.