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Package Details: picard-tools 2.27.5-4
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Git Clone URL: | https://aur.archlinux.org/picard-tools.git (read-only, click to copy) |
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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)
- java-runtime (java-gcj-compat, jre10, jdk12-openj9-bin, zulu-12-bin, jre6, jre12, server-jre, jdk13-openj9-bin, jdk9-openj9-bin, jdk10, jdk11-openjdk-dcevm, jdk10-openj9-bin, jdk14-openj9-bin, jdk7, jre7, zulu-14-bin, amazon-corretto-15, jdk11-openjdk-dcevm-conflicts-fixed, zulu-embedded-jdk8, sapmachine-jdk-bin, amazon-corretto-16, jdk8-graalvm-bin, jdk16-graalvm-bin, jre8-openjdk-shenandoah, zulu-16-bin, jdk11-graalvm-ee-bin, jdk16-adoptopenjdk, zulu-jdk-fx-bin, jdk11-microsoft-openjdk, jdk16-microsoft-openjdk, jdk11-msopenjdk-bin, jdk18-beta-temurin, jdk8-arm, jre17-jetbrains, liberica-jdk-11-bin, liberica-jdk-11-lite-bin, liberica-jre-11-bin, jre11-jetbrains-imfix, java-openjdk-loom-ea-bin, jdk17-dragonwell-bin, hmcl-zulu-bin, jdk7-j9-bin, jdk7r1-j9-bin, jdk8-j9-bin, jdk11-j9-bin, jdk-jetbrains, jre11-jbr-xdg, jre12-openjdk, jre15-openjdk, jre16-openjdk, jre13-openjdk, jre14-openjdk, jre-bcl, jdk-bcl, amazon-corretto-18, zulu-18-bin, zulu-13-bin, jre15, jre14, jre13, jre16, jre17, bishengjdk-17, bishengjre-17, jdk-arm, jdk11-openj9-bin, jdk-openj9-bin, jre-openj9, jre-lts, jre, zulu-15-bin, zulu-embedded-jdk, jre-jbr-xdg, jre-openjdk-xdg, jre-openjdk-xdg-bin, zulu-embedded-jdk11, jdk-microsoft-openjdk, jre18-openjdk, jdk17-openj9-bin, jdk17-jetbrains-bin, jdk11-jetbrains-bin, liberica-jdk-8-full-bin, liberica-jdk-17-full-bin, liberica-jdk-full-bin, liberica-jre-11-full-bin, liberica-jdk-11-full-bin, jre-jetbrains, zulu-jre-fx-bin, jdk8-dragonwell-extended-bin, jdk8-dragonwell-standard-bin, jdk11-dragonwell-extended-bin, jdk11-dragonwell-standard-bin, jdk17-dragonwell-standard-bin, jdk8-dragonwell-extended, jre8-adoptopenjdk, jdk18-openj9-bin, jdk8-openj9-bin, jre8, jdk8, jre11, jre17-jetbrains-imfix, jdk-android-studio, amazon-corretto-8, amazon-corretto-11, amazon-corretto-19-bin, amazon-corretto-17, zulu-8-bin, zulu-11-bin, zulu-17-bin, zulu-19-bin, jdk11-temurin, jdk17-temurin, jdk-temurin, jdk17-graalvm-ee-bin, java-openjdk-bin, liberica-jre-8-full-bin, jdk11-graalvm-bin, jdk17-graalvm-bin, jdk19-graalvm-bin, java-openjdk-ea-bin, jre-openjdk, jre11-openjdk, jre17-openjdk, jre8-openjdk)
- ant (ant-git) (make)
- git (git-vfs, git-git, git-run-command-patch-git) (make)
- java-environment (java-gcj-compat, zulu-10-bin, jdk12-openj9-bin, zulu-12-bin, jdk12, jdk13-openj9-bin, jdk9-openj9-bin, jdk10, jdk11-openjdk-dcevm, jdk10-openj9-bin, jdk14-openj9-bin, jdk7, zulu-14-bin, amazon-corretto-15, jdk11-openjdk-dcevm-conflicts-fixed, zulu-embedded-jdk8, sapmachine-jdk-bin, amazon-corretto-16, jdk8-graalvm-bin, jdk16-graalvm-bin, jdk8-openjdk-shenandoah, zulu-16-bin, jdk11-graalvm-ee-bin, jdk16-adoptopenjdk, jdk11-microsoft-openjdk, jdk16-microsoft-openjdk, jdk11-msopenjdk-bin, jdk18-beta-temurin, jdk8-arm, jdk17-jetbrains, liberica-jdk-11-bin, liberica-jdk-11-lite-bin, liberica-jre-11-bin, jdk11-jetbrains-imfix, java-openjdk-loom-ea-bin, jdk17-dragonwell-bin, jdk7-j9-bin, jdk7r1-j9-bin, jdk8-j9-bin, jdk11-j9-bin, jdk-jetbrains, jdk11-jbr-xdg, jdk12-openjdk, jdk15-openjdk, jdk16-openjdk, jdk13-openjdk, jdk14-openjdk, jdk-bcl, amazon-corretto-18, zulu-18-bin, zulu-13-bin, bishengjdk-17, jdk-arm, jdk11-openj9-bin, jdk-openj9-bin, jdk-openj9, jabba-bin, jdk-lts, jdk, zulu-15-bin, zulu-embedded-jdk, jdk-jbr-xdg, jdk-openjdk-xdg, jdk-openjdk-xdg-bin, zulu-embedded-jdk11, jdk-microsoft-openjdk, jdk18-openjdk, jdk17-openj9-bin, jdk17-jetbrains-bin, jdk11-jetbrains-bin, liberica-jdk-8-full-bin, liberica-jdk-17-full-bin, liberica-jdk-full-bin, liberica-jre-11-full-bin, liberica-jdk-11-full-bin, jre-jetbrains, jdk8-dragonwell-extended-bin, jdk8-dragonwell-standard-bin, jdk11-dragonwell-extended-bin, jdk11-dragonwell-standard-bin, jdk17-dragonwell-standard-bin, jdk8-dragonwell-extended, jdk8-adoptopenjdk, jdk18-openj9-bin, jdk8-openj9-bin, jdk8, jdk11, jdk17-jetbrains-imfix, jdk-android-studio, amazon-corretto-8, amazon-corretto-11, amazon-corretto-19-bin, amazon-corretto-17, zulu-8-bin, zulu-11-bin, zulu-17-bin, zulu-19-bin, jdk11-temurin, jdk17-temurin, jdk-temurin, jdk17-graalvm-ee-bin, java-openjdk-bin, liberica-jre-8-full-bin, jdk11-graalvm-bin, jdk17-graalvm-bin, jdk19-graalvm-bin, java-openjdk-ea-bin, jdk-openjdk, jdk11-openjdk, jdk17-openjdk, jdk8-openjdk) (make)
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)
greyltc commented on 2016-07-02 11:06 (UTC)
greyltc commented on 2016-07-02 10:56 (UTC)
wookietreiber commented on 2016-01-19 10:09 (UTC)
greyltc commented on 2015-03-18 14:33 (UTC)
wookietreiber commented on 2015-03-18 14:12 (UTC)
greyltc commented on 2015-03-18 13:47 (UTC)
1 2 3 Next › Last »