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: BSD
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

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) before gatk fixes the issue for me. Please add gradle to makedepends.

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 package gatk-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 the Cannot 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:

Could not determine java version from '10.0.1'.

Could not determine java version from '9.0.4'.

With jdk8 it still fails, this time with the error message:

FAILURE: Build failed with an exception.

* Where:
Build file '/build/gatk/src/gatk-4.0.2.1/build.gradle' line: 141

* What went wrong:
A problem occurred evaluating root project 'gatk'.
> Cannot invoke method getURLs() on null object

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.