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Package Details: picard-tools 3.1.1-1

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:	2023-11-15 00:03 (UTC)

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:

Popularity:

0.000000

First Submitted:

2013-11-25 11:23 (UTC)

Last Updated:

2023-11-15 00:03 (UTC)

Latest Comments

« First ‹ Previous 1 2 3 Next › Last »

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?

wookietreiber commented on 2015-03-18 13:41 (UTC)

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 (UTC)

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 (UTC)

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

greyltc commented on 2015-03-17 11:46 (UTC)

@wookietreiber, could you please add the following two lines to package(): mkdir -p $pkgdir/etc/profile.d echo 'export PICARDROOT="/usr/share/java/picard-tools"' > $pkgdir/etc/profile.d/picard-tools.sh thanks!

wookietreiber commented on 2014-11-20 10:38 (UTC)

1.125 just got released [1], see PKGBUILD [2]. [1]: https://github.com/broadinstitute/picard/releases/tag/1.125 [2]: https://github.com/wookietreiber/PKGBUILDs/tree/master/picard-tools