Package Details: samtools 1.3.1-1

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: wookietreiber
Last Packager: wookietreiber
Votes: 21
Popularity: 0.244004
First Submitted: 2009-11-04 21:48
Last Updated: 2016-05-29 18:27

Dependencies (3)

Sources (1)

Latest Comments

wookietreiber commented on 2015-10-25 17:09

Thanks for letting me know, updated pkgrel.

masonmlai commented on 2015-10-24 01:09

Recent update to ncurses seems to break samtools:

samtools: error while loading shared libraries: libncursesw.so.5: cannot open shared object file: No such file or directory

wookietreiber commented on 2014-09-12 08:19

@MikeDacre: Done. Package now includes headers.

MikeDacre commented on 2014-09-11 22:23

This package does not allow the successful compilation of cufflinks. In order for cufflinks to work all of the header files have to be included.

Adding the following lines to package() solves the problem:

mkdir -p "$pkgdir/usr/include/bam"

install -Dm644 $srcdir/$pkgname-$pkgver/*.h "$pkgdir/usr/include/bam"

Rhinoceros commented on 2014-08-20 10:37

I'm really not sure. I wouldn't know where to look, either.

wookietreiber commented on 2014-08-19 06:06

Do pacaur and packer use different compiler options? IIRC /etc/makepkg.conf should be the place where to set up your arch linux compilation ...

Rhinoceros commented on 2014-08-19 06:02

That's quite odd. I wanted to come back and report how I installed it. I tried `pacaur -Syu` and it failed twice. I then tried it with `packer -Syu`, and it now installed fine. Sorry for the noise, although it's quite odd that one worked and the other failed. (FWIW I had python2 but not luaji.)

wookietreiber commented on 2014-08-19 05:57

Did you install all the optional dependencies?

Would you please give more specific information about these failed tests?

Rhinoceros commented on 2014-08-19 05:17

Is any one else having troubles with installation? It fails with:

> Number of tests:
> total .. 375
> passed .. 339
> failed .. 2
> expected failure .. 34
> unexpected pass .. 0
>
> Makefile:172: recipe for target 'check' failed
> make: *** [check] Error 1
> ==> ERROR: A failure occurred in check().
> Aborting...

I scanned the tests above this, but could find nothing unusual.

lqs commented on 2013-12-16 07:10

Glad to see bio-software(or NGS program, like bwa, samtools).

Maybe we should catalog those software more specify so anybody can find it easily.

Thanks ^_^

wookietreiber commented on 2013-11-21 16:31

Done.

stratust commented on 2013-11-21 16:13

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

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.

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 :-)