Package Details: samtools 1.9-1

Git Clone URL: https://aur.archlinux.org/samtools.git (read-only)
Package Base: samtools
Description: tools for manipulating next-generation sequencing data
Upstream URL: http://www.htslib.org/
Licenses: custom
Submitter: Vrob
Maintainer: viralstitch
Last Packager: alexpe87
Votes: 27
Popularity: 0.457748
First Submitted: 2009-11-04 21:48
Last Updated: 2018-07-20 08:24

Latest Comments

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Anonymous comment on 2013-05-24 12:42

Hi, this package is out of date, the current version is 0.1.19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

stratust commented on 2012-10-31 04:04

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

buttons commented on 2012-09-24 20:18

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

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

stratust commented on 2012-04-24 04:10

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?

Anonymous comment on 2012-04-23 18:51

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

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

stratust commented on 2012-01-16 04:07

Hi, Vrob!

Thanks for the pkgbuild, would be nice if you could update it to version 0.1.18. :-)

Let me know if you are too busy to maintain the package because I can adopt it! :-)

Anonymous comment on 2011-11-01 10:04

Hi Vrob!

Thanks for the pkgbuild. 0.1.18 has been out for a while :-)