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gnu: htslib: Link against htscodecs. 

* gnu/packages/bioinformatics.scm (htslib)[source]: Add snippet to
remove bundled htscodecs.
[arguments]: Add configure-flag to link against htscodecs.
[propagated-inputs]: Add htscodecs.
(htslib-1.14, htslib-1.12): Use bundled htscodecs.
master
Efraim Flashner 2023-09-24 09:59:31 +03:00
parent a338a553e3
commit 0792d99466
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GPG Key ID: 41AAE7DCCA3D8351
1 changed files with 24 additions and 5 deletions
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29
gnu/packages/bioinformatics.scm
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@ -6721,7 +6721,11 @@ name/ID compression and quality score compression derived from fqzcomp.")
version "/htslib-" version ".tar.bz2"))
(sha256
(base32
"093r1n4s134k50m9a925yn95gyi90ps5dlgc6gq4qwvkzxx7qsv0"))))
"093r1n4s134k50m9a925yn95gyi90ps5dlgc6gq4qwvkzxx7qsv0"))
(snippet
#~(begin
(use-modules (guix build utils))
(delete-file-recursively "htscodecs")))))
(build-system gnu-build-system)
;; Let htslib translate "gs://" and "s3://" to regular https links with
;; "--enable-gcs" and "--enable-s3". For these options to work, we also
@ -6729,12 +6733,13 @@ name/ID compression and quality score compression derived from fqzcomp.")
(arguments
`(#:configure-flags '("--enable-gcs"
"--enable-libcurl"
"--enable-s3")))
"--enable-s3"
"--with-external-htscodecs")))
(inputs
(list bzip2 curl openssl xz))
;; This is referred to in the pkg-config file as a required library.
(propagated-inputs
(list zlib))
(list htscodecs zlib))
(native-inputs
(list perl))
(home-page "https://www.htslib.org")
@ -6757,7 +6762,14 @@ data. It also provides the @command{bgzip}, @command{htsfile}, and
version "/htslib-" version ".tar.bz2"))
(sha256
(base32
"0pwk8yhhvb85mi1d2qhwsb4samc3rmbcrq7b1s0jz0glaa7in8pd"))))))
"0pwk8yhhvb85mi1d2qhwsb4samc3rmbcrq7b1s0jz0glaa7in8pd"))))
(arguments
(substitute-keyword-arguments (package-arguments htslib)
((#:configure-flags cf #~'())
#~(delete "--with-external-htscodecs" #$cf))))
(propagated-inputs
(modify-inputs (package-propagated-inputs htslib)
(delete "htscodecs")))))
(define-public htslib-1.12
(package/inherit htslib
@ -6769,7 +6781,14 @@ data. It also provides the @command{bgzip}, @command{htsfile}, and
version "/htslib-" version ".tar.bz2"))
(sha256
(base32
"1jplnvizgr0fyyvvmkfmnsywrrpqhid3760vw15bllz98qdi9012"))))))
"1jplnvizgr0fyyvvmkfmnsywrrpqhid3760vw15bllz98qdi9012"))))
(arguments
(substitute-keyword-arguments (package-arguments htslib)
((#:configure-flags cf #~'())
#~(delete "--with-external-htscodecs" #$cf))))
(propagated-inputs
(modify-inputs (package-propagated-inputs htslib)
(delete "htscodecs")))))
(define-public htslib-1.10
(package/inherit htslib