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: 0.240739
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 ^_^

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