Package Details: samtools 1.12-1

Git Clone URL: (read-only, click to copy)
Package Base: samtools
Description: tools for manipulating next-generation sequencing data
Upstream URL:
Licenses: custom
Submitter: Vrob
Maintainer: viralstitch
Last Packager: viralstitch
Votes: 28
Popularity: 0.000055
First Submitted: 2009-11-04 21:48
Last Updated: 2021-03-17 16:57

Latest Comments

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viralstitch commented on 2020-09-23 00:13

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

The checksum is wrong. This worked for me:


iosonofabio commented on 2020-03-30 00:06

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

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.


Rhinoceros commented on 2019-12-18 20:56

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

viralstitch commented on 2019-12-18 15:32

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

@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

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

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


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?