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AUR (en) - picard-tools

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Package Details: picard-tools 2.8.2-1

Git Clone URL: https://aur-dev.archlinux.org/picard-tools.git (read-only)
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: GPL2
Submitter: mschu
Maintainer: wookietreiber
Last Packager: wookietreiber
Votes: 5
Popularity: 0.002028
First Submitted: 2013-11-25 11:23
Last Updated: 2017-01-24 07:48

Latest Comments

1 2 Next › Last »

wookietreiber commented on 2016-07-04 11:23

Done, thanks for letting me know, @greyltc.

greyltc commented on 2016-07-02 11:06

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

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

updated to 2.0.1

greyltc commented on 2015-03-18 14:33

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

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

greyltc commented on 2015-03-18 13:47

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

wookietreiber commented on 2015-03-18 13:41

Then, for now, you should either do this in your bashrc / bash_profile only (or inside your build environment, however you are setting it up).

Considering the code you are writing: if you really want this to be portable, ask the picard-tools upstream devs to include such an environment variable for all to use in their project. Maybe they already have a solution for this issue.

greyltc commented on 2015-03-18 03:29

No, this variable is not required by any software that I'm aware of. It's a nice to have as a pointer to where the .jar files end up.

The picard.sh script that this package includes is a nice way to call the tool in Arch, but I'm trying to write code that is portable to non-Arch environments where picard.sh is not available. Having an environment variable created by the installer which tells the user where the tool was installed is a simple and elegant way to enable the user to write portable code.

wookietreiber commented on 2015-03-17 13:08

@greyltc: is this variable required by some other software?