Package Details: samtools 1.20-1

Git Clone URL: https://aur.archlinux.org/samtools.git (read-only, click to copy)
Package Base: samtools
Description: tools for manipulating next-generation sequencing data
Upstream URL: http://www.htslib.org/
Licenses: custom
Submitter: Vrob
Maintainer: r6eve
Last Packager: r6eve
Votes: 31
Popularity: 0.85
First Submitted: 2009-11-04 21:48 (UTC)
Last Updated: 2024-04-15 22:56 (UTC)

Dependencies (2)

Sources (1)

Latest Comments

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wookietreiber commented on 2013-11-21 16:31 (UTC)

Done.

stratust commented on 2013-11-21 16:13 (UTC)

Hi wookietreiber, I've been too busy lately to take care of this package. Feel free to adopt it!

wookietreiber commented on 2013-11-21 10:26 (UTC)

Hi, I have tried to sanitize the PKGBUILD, have a look: https://github.com/wookietreiber/PKGBUILDs/blob/master/samtools/PKGBUILD I have added your original, so you can view the diff: https://github.com/wookietreiber/PKGBUILDs/commit/330046f191d43956fd67a85242a79523b279c70d Would be nice if you could replace this with the current build.

<deleted-account> commented on 2013-05-24 12:42 (UTC)

Hi, this package is out of date, the current version is 0.1.19 Thanks!

stratust commented on 2012-10-31 04:04 (UTC)

bcftools now is installed as pointed out by buttons. Thanks.

buttons commented on 2012-09-24 20:18 (UTC)

To modify the pkgbuild: Change the make line to remove "all". For some reason "all" doesn't build bcftools, which is required for SNP calling. "Make" by itself does, though. Add the following: # Install bcftools cd bcftools for f in $(ls -l) do if [ -x "$f" ]; then install -m755 "$f" "$pkgdir/usr/bin" fi done And change the misc stuff to cd ../misc instead of directly to misc.

buttons commented on 2012-09-24 20:02 (UTC)

This package needs to install bcftools as well, which is distributed with samtools.

stratust commented on 2012-04-24 04:10 (UTC)

Hi superbobry, 1. Because I tried to install TopHat with libbam.a in /usr/lib and I couldn't. 2. Because other softwares (like TopHat and Bio::DB::Sam from Bioperl) seem to use libbam.a as a static library 3. I don't use any software that request libbcf.a. Do you know any?

<deleted-account> commented on 2012-04-23 18:51 (UTC)

Hello, three things here: 1. Why do you install libbam.a to /usr/local/lib instead of /usr/lib? 2. Why don't you build a dynamically loaded version (I know it's not in the 'Makefile', but still)? 3. There's also libbcf.a in the 'bcftools/' subdirectory, which probably should be installed as well. Cheers, Sergei

Vrob commented on 2012-01-16 09:20 (UTC)

Hey, actually I'm not an active bioinformatics student anymore, so don't keep track of whats going on with samtools etc. Therefore, I'm abandoning the package, so that any of you can pick it up and give it some love ;) Greets, Vrob

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