Package Details: htslib 1.15.1-1

Git Clone URL: https://aur.archlinux.org/htslib.git (read-only, click to copy)
Package Base: htslib
Description: A C library for high-throughput sequencing data formats
Upstream URL: https://github.com/samtools/htslib
Licenses: custom
Conflicts: tabix
Provides: tabix
Replaces: tabix
Submitter: wookietreiber
Maintainer: meanjollies
Last Packager: meanjollies
Votes: 18
Popularity: 0.001142
First Submitted: 2014-08-18 18:58 (UTC)
Last Updated: 2022-05-19 23:44 (UTC)

Latest Comments

rmagno commented on 2022-05-20 00:08 (UTC)

Thank you @meanjollies, it is working now.

$> pacman -Ql htslib | grep -P 'hts.+a$'
htslib /usr/lib/libhts.a

meanjollies commented on 2022-05-19 23:46 (UTC)

@magno can you try again? By default, makepkg will clean up any static libs. I've enabled the option to keep it here, so you should be good to go now.

rmagno commented on 2022-05-19 15:35 (UTC) (edited on 2022-05-19 15:38 (UTC) by rmagno)

Hi Andrew,

I tried to install htslib-git but got this error about the htscodecs submodule...

Motivation for installing htslib-git is to check whether the newest version provides the static library libhts.a required by SHAPEIT4, please see https://github.com/odelaneau/shapeit4/issues/74.

$> yay -S htslib-git
:: Checking for conflicts...
:: Checking for inner conflicts...
 -> 
Package conflicts found:
 -> Installing htslib-git will remove: htslib
 -> Conflicting packages will have to be confirmed manually
[Aur:1]  htslib-git-1.10.2.r134.ge9447f86-2

:: (1/1) Downloaded PKGBUILD: htslib-git
  1 htslib-git                       (Build Files Exist)
==> Diffs to show?
==> [N]one [A]ll [Ab]ort [I]nstalled [No]tInstalled or (1 2 3, 1-3, ^4)
==> 
:: (1/1) Parsing SRCINFO: htslib-git
==> Making package: htslib-git 1.10.2.r134.ge9447f86-2 (Thu 19 May 2022 04:27:55 PM WEST)
==> Retrieving sources...
  -> Cloning htslib git repo...
Cloning into bare repository '/home/rmagno/.cache/yay/htslib-git/htslib'...
remote: Enumerating objects: 19249, done.
remote: Counting objects: 100% (1187/1187), done.
remote: Compressing objects: 100% (511/511), done.
remote: Total 19249 (delta 835), reused 845 (delta 676), pack-reused 18062
Receiving objects: 100% (19249/19249), 13.17 MiB | 3.21 MiB/s, done.
Resolving deltas: 100% (13927/13927), done.
==> Validating source files with sha256sums...
    htslib ... Skipped
==> Making package: htslib-git 1.10.2.r134.ge9447f86-2 (Thu 19 May 2022 04:28:03 PM WEST)
==> Checking runtime dependencies...
==> Checking buildtime dependencies...
==> Retrieving sources...
  -> Updating htslib git repo...
Fetching origin
==> Validating source files with sha256sums...
    htslib ... Skipped
==> Removing existing $srcdir/ directory...
==> Extracting sources...
  -> Creating working copy of htslib git repo...
Cloning into 'htslib'...
done.
==> Starting pkgver()...
==> Updated version: htslib-git 1.15.1.r20.g46c56fcc-1
==> Sources are ready.
==> Making package: htslib-git 1.15.1.r20.g46c56fcc-1 (Thu 19 May 2022 04:28:10 PM WEST)
==> Checking runtime dependencies...
==> Checking buildtime dependencies...
==> WARNING: Using existing $srcdir/ tree
==> Starting pkgver()...
==> Starting build()...
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C... yes
checking whether gcc accepts -g... yes
checking for gcc option to enable C11 features... none needed
checking for ranlib... ranlib
checking for grep that handles long lines and -e... /usr/bin/grep
checking for C compiler warning flags... -Wall
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
checking shared library type for unknown-Linux... plain .so
checking whether the compiler accepts -fvisibility=hidden... yes
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking for stdio.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for strings.h... yes
checking for sys/stat.h... yes
checking for sys/types.h... yes
checking for unistd.h... yes
checking for sys/param.h... yes
checking for getpagesize... yes
checking for working mmap... yes
checking for gmtime_r... yes
checking for fsync... yes
checking for drand48... yes
checking for srand48_deterministic... no
checking for gcc options needed to detect all undeclared functions... none needed
checking whether fdatasync is declared... yes
checking for fdatasync... yes
checking for library containing dlsym... -ldl
checking whether the compiler accepts -rdynamic... yes
checking for library containing log... -lm
checking for zlib.h... yes
checking for inflate in -lz... yes
checking for library containing recv... none required
checking for bzlib.h... yes
checking for BZ2_bzBuffToBuffCompress in -lbz2... yes
checking for lzma.h... yes
checking for lzma_easy_buffer_encode in -llzma... yes
checking whether htscodecs files are present... no
configure: error: htscodecs submodule files not present.

HTSlib uses some functions from the htscodecs project, which is normally
included as a submodule.  Try running:

  git submodule update --init --recursive

in  the top-level htslib directory to update it, and then re-run configure.

==> ERROR: A failure occurred in build().
    Aborting...
 -> error making: htslib-git

meanjollies commented on 2021-08-12 12:52 (UTC)

No worries - I got it.

aorth commented on 2021-08-12 07:50 (UTC)

Hi, I can maintain it. I maintain htslib/samtools elsewhere on an HPC and I use Arch locally so I have an interest in having this be available. Cheers...

viralstitch commented on 2021-07-31 15:55 (UTC)

I no longer have time to maintain this package and am disowning it.

meanjollies commented on 2021-07-22 02:15 (UTC)

Hey @viralstitch, would you be able to update this to 1.13?

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 23:15 (UTC)

Package also fails to build for me. This worked:

sha256sums=('cffadd9baa6fce27b8fe0b01a462b489f06a5433dfe92121f667f40f632538d7')

meanjollies commented on 2020-09-22 15:43 (UTC)

The sha256sum is incorrect.

wookietreiber commented on 2014-12-16 10:13 (UTC)

The new release now properly conflicts/provides/replaces tabix.