Package Details: picard-tools 2.27.5-4

Git Clone URL: https://aur.archlinux.org/picard-tools.git (read-only, click to copy)
Package Base: picard-tools
Description: set of tools for working with next generation sequencing data in the BAM format
Upstream URL: https://github.com/broadinstitute/picard
Licenses: MIT
Submitter: mschu
Maintainer: malacology (BioArchLinuxBot)
Last Packager: BioArchLinuxBot
Votes: 8
Popularity: 0.000005
First Submitted: 2013-11-25 11:23 (UTC)
Last Updated: 2022-12-02 10:36 (UTC)

Dependencies (4)

Required by (0)

Sources (1)

Latest Comments

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luscinius commented on 2022-02-23 14:51 (UTC)

Does building the jar file ourselves instead of downloading one from Broad Institute give us any benefits? AUR guidelines (https://wiki.archlinux.org/title/AUR_submission_guidelines#Rules_of_submission) explicitly allow the use of prebuilt deliverables for Java packages without adding the -bin suffix. I think using the prebuilt jar as it was in the PKGBUILDs for the earlier versions would simplify things significantly.

fujoyaki commented on 2021-12-29 03:30 (UTC) (edited on 2021-12-29 03:39 (UTC) by fujoyaki)

Not compatible with Gradle version 7 and up, due to the following:

https://docs.gradle.org/7.0/userguide/upgrading_version_6.html#removal_of_the_legacy_maven_plugin

https://docs.gradle.org/7.0/userguide/publishing_maven.html#publishing_maven

Gradle version 5.6.* is needed for this to work, but unfortunately the gradle5 AUR package is also broken. So it must be installed manually, using one of the methods listed here: https://gradle.org/install/

luscinius commented on 2021-06-11 19:33 (UTC) (edited on 2021-06-11 19:35 (UTC) by luscinius)

Fails to build in a chroot using aurutils, gradle complains about the maven plugin:

FAILURE: Build failed with an exception.

  • Where: Build file '/build/picard-tools/src/picard-2.24.1/build.gradle' line: 13

  • What went wrong: Plugin [id: 'maven'] was not found in any of the following sources:

  • Gradle Core Plugins (not a core plugin, please see https://docs.gradle.org/7.0.2/userguide/standard_plugins.html for available core plugins)

  • Plugin Repositories (plugin dependency must include a version number for this source)

  • Try: Run with --stacktrace option to get the stack trace. Run with --info or --debug option to get more log output. Run with --scan to get full insights.

  • Get more help at https://help.gradle.org

wookietreiber commented on 2016-07-04 11:23 (UTC)

Done, thanks for letting me know, @greyltc.

greyltc commented on 2016-07-02 11:06 (UTC)

From the github repo's README.md: As of version 2.0.1 (Nov. 2015) Picard requires Java 1.8 (jdk8u66). The last version to support Java 1.7 was release 1.141. @wookietreiber, I think you need to update the dependencies here.

greyltc commented on 2016-07-02 10:56 (UTC)

I'm getting an "Unsupported major.minor version 52.0" error: Exception in thread "main" java.lang.UnsupportedClassVersionError: picard/cmdline/PicardCommandLine : Unsupported major.minor version 52.0 at java.lang.ClassLoader.defineClass1(Native Method) at java.lang.ClassLoader.defineClass(ClassLoader.java:803) at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142) at java.net.URLClassLoader.defineClass(URLClassLoader.java:449) at java.net.URLClassLoader.access$100(URLClassLoader.java:71) at java.net.URLClassLoader$1.run(URLClassLoader.java:361) at java.net.URLClassLoader$1.run(URLClassLoader.java:355) at java.security.AccessController.doPrivileged(Native Method) at java.net.URLClassLoader.findClass(URLClassLoader.java:354) at java.lang.ClassLoader.loadClass(ClassLoader.java:425) at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:308) at java.lang.ClassLoader.loadClass(ClassLoader.java:358) at sun.launcher.LauncherHelper.checkAndLoadMain(LauncherHelper.java:482)

wookietreiber commented on 2016-01-19 10:09 (UTC)

updated to 2.0.1

greyltc commented on 2015-03-18 14:33 (UTC)

Thanks for adding it. I'm not sure how this issue could be addressed by upstream (outside of a line in the readme that says "For portability, packagers should export the PICARDROOT variable which points to the picard.jar install directory"), since the .jar install location on any given distro is up to the package maintainer.

wookietreiber commented on 2015-03-18 14:12 (UTC)

There is no harm in it. There is, however, harm in not involving the larger community.

greyltc commented on 2015-03-18 13:47 (UTC)

Oh come on. This should clearly be addressed by the packaging. What's the harm in adding the environment variable anyway?

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