Package Details: picard-tools 3.4.0-1

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: 0.000000
First Submitted: 2013-11-25 11:23 (UTC)
Last Updated: 2025-04-13 18:31 (UTC)

Dependencies (4)

Required by (1)

Sources (1)

Latest Comments

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MarsSeed commented on 2023-07-29 08:02 (UTC)

Exactly how is this information harmful?

malacology commented on 2023-07-29 06:18 (UTC)

Welcome Mr Marcell Meszaros to comment useless and harmful information under my every pkg!!!

MarsSeed commented on 2023-07-28 23:14 (UTC)

As per project's build.xml:

ANT IS DEPRECATED FOR BUILDING Picard

Please remove ant from makedepends.

malacology commented on 2023-04-24 06:33 (UTC)

Okay, sorry for missing to reply, you can use BioArchLinux repository to use it directly, as recommended, we should use build scripts to build jar.

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)

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