Package Details: samtools 1.15.1-1

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: 29
Popularity: 0.000251
First Submitted: 2009-11-04 21:48 (UTC)
Last Updated: 2022-04-08 01:42 (UTC)

Dependencies (2)

Sources (1)

Latest Comments

viralstitch commented on 2021-07-31 15:54 (UTC)

I'm sorry for not getting back to you sooner. I no longer have time to maintain the package. Anyone is welcome to pick it up.

zethson commented on 2021-07-13 13:18 (UTC)

Installation fails because 7 tests are failing. I would appreciate a fix.

Thanks!

viralstitch commented on 2020-09-23 00:13 (UTC)

Thanks for the comment. I've pushed a pkgrel update with the new checksums. They changed at some point today. These files worked for me this morning.

Rhinoceros commented on 2020-09-22 23:17 (UTC)

The checksum is wrong. This worked for me:

sha256sums=('e283cebd6c1c49f0cf8a3ca4fa56e1d651496b4d2e42f80ab75991a9ece4e5b6')

iosonofabio commented on 2020-03-30 00:06 (UTC)

Same problem here, had this for a few months already. 1 test fails during the installation and that breaks the build process.

Anything we can do about this?

Thank you

linearleopard commented on 2020-03-03 21:56 (UTC) (edited on 2020-03-03 21:57 (UTC) by linearleopard)

Hello, thank you for maintaining the package.

You do a great job.

But today I had to reinstall the package and met with unexpected behavior: samtools didn't install due to some failing tests. But when I've started investigate it, I found out that that tests were failing due to perl in their pipelines, which wrote a message about unspecified locale. :)

I think that some warning in 3rd party software shouldn't prevent the package from installation.

Regards.

Rhinoceros commented on 2019-12-18 20:56 (UTC)

Oops sorry @viralstitch. Missed it somehow. Thank you!

viralstitch commented on 2019-12-18 15:32 (UTC)

If you've installed samtools-1.10-2, you'll need to upgrade to samtools-1.10-3 before upgrading htslib in order to solve the dependency issue.

Let me know if there are any other issues. Thanks!

Rhinoceros commented on 2019-12-18 08:55 (UTC)

@viralstitch Did you mean to depend on htslib=1.10 or htslib>=1.10? Currently htslib is 1.10.1, so samtools cannot be installed.

viralstitch commented on 2019-12-10 16:15 (UTC) (edited on 2019-12-10 16:15 (UTC) by viralstitch)

I think this is an issue with htslib changing its type names. I've updated the package to require htslib=1.10

dschrempf commented on 2019-12-09 09:59 (UTC)

Compilation worked at the third attempt. No idea what has changed, I did a clean build three times ... Sorry for the fuzz.

dschrempf commented on 2019-12-09 09:49 (UTC) (edited on 2019-12-09 09:50 (UTC) by dschrempf)

Hi,

With the new update, I am getting the following compilation error:

bam_index.c:117:32: error: unknown type name ‘sam_hdr_t’; did you mean ‘bam_hdr_t’? 117 | int slow_idxstats(samFile fp, sam_hdr_t header) { | ^~~~~~~~~ | bam_hdr_t

Is this a problem of the package, or of samtools?

Thanks!

alexpe87 commented on 2017-11-05 16:01 (UTC)

Ncurses update from today fixed the issue again: ncurses 6.0+20170902-3 (works) ncurses 6.0+20170902-2 (does not work) If your core repo isn't up to date yet, you could manually download the most current ncurses package and install manually with pacman -U <pkgname>. https://www.archlinux.org/packages/core/x86_64/ncurses/

alexpe87 commented on 2017-11-01 13:10 (UTC)

Hm, looks like ncurses was updated 7 days ago (https://git.archlinux.org/svntogit/packages.git/log/trunk?h=packages/ncurses) and that seems to break the package. I'll have a look.

alienzj commented on 2017-11-01 02:29 (UTC)

make: *** [Makefile:126:bam_tview_curses.o] error 1 Compiled failed! Hele me, please! Thanks very much!

wookietreiber commented on 2017-05-20 15:03 (UTC)

updated.

Rhinoceros commented on 2017-05-20 11:49 (UTC)

Yes, this worked fine for me too, when the PKGBUILD was updated five days ago. However, I just tested again for you, and now it doesn't verify. I'm getting 4860d6a8f85c6965a7e82fb11afbde13

alexpe87 commented on 2017-05-20 11:01 (UTC)

Maybe they changed the uploaded file? It did for me ~2 days ago!

greyltc commented on 2017-05-20 09:46 (UTC)

the checksum here isn't verifying for me

wookietreiber commented on 2015-10-25 17:09 (UTC)

Thanks for letting me know, updated pkgrel.

masonmlai commented on 2015-10-24 01:09 (UTC)

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 (UTC)

@MikeDacre: Done. Package now includes headers.

MikeDacre commented on 2014-09-11 22:23 (UTC)

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 (UTC)

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

wookietreiber commented on 2014-08-19 06:06 (UTC)

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 (UTC)

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 (UTC)

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 (UTC)

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 (UTC)

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 (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.

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?

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

stratust commented on 2012-01-16 04:07 (UTC)

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! :-)

commented on 2011-11-01 10:04 (UTC)

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