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Package Details: samtools 1.15.1-1
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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: | 0.000540 |
First Submitted: | 2009-11-04 21:48 (UTC) |
Last Updated: | 2022-04-08 01:42 (UTC) |
Dependencies (2)
- htslib (htslib-git)
- luajit (moonjit, luajit-2.1-lua52-git, luajit-openresty) (optional) – needed for r2plot.lua vcfutils.lua
Required by (10)
- abyss (optional)
- augustus
- bbmap (optional)
- bedtools (check)
- cufflinks
- cufflinks-git
- phantompeakqualtools
- ugene-bin (optional)
- ugene-git (optional)
- unicycler (optional)
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 tosamtools-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
orhtslib>=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)
alexpe87 commented on 2017-11-01 13:10 (UTC)
alienzj commented on 2017-11-01 02:29 (UTC)
wookietreiber commented on 2017-05-20 15:03 (UTC)
Rhinoceros commented on 2017-05-20 11:49 (UTC)
alexpe87 commented on 2017-05-20 11:01 (UTC)
greyltc commented on 2017-05-20 09:46 (UTC)
wookietreiber commented on 2015-10-25 17:09 (UTC)
masonmlai commented on 2015-10-24 01:09 (UTC)
wookietreiber commented on 2014-09-12 08:19 (UTC)
MikeDacre commented on 2014-09-11 22:23 (UTC)
Rhinoceros commented on 2014-08-20 10:37 (UTC)
wookietreiber commented on 2014-08-19 06:06 (UTC)
Rhinoceros commented on 2014-08-19 06:02 (UTC)
wookietreiber commented on 2014-08-19 05:57 (UTC)
Rhinoceros commented on 2014-08-19 05:17 (UTC)
lqs commented on 2013-12-16 07:10 (UTC)
wookietreiber commented on 2013-11-21 16:31 (UTC)
stratust commented on 2013-11-21 16:13 (UTC)
wookietreiber commented on 2013-11-21 10:26 (UTC)
commented on 2013-05-24 12:42 (UTC)
stratust commented on 2012-10-31 04:04 (UTC)
buttons commented on 2012-09-24 20:18 (UTC)
buttons commented on 2012-09-24 20:02 (UTC)
stratust commented on 2012-04-24 04:10 (UTC)
commented on 2012-04-23 18:51 (UTC)
Vrob commented on 2012-01-16 09:20 (UTC)
stratust commented on 2012-01-16 04:07 (UTC)
commented on 2011-11-01 10:04 (UTC)