diff options
| author | Efraim Flashner <efraim@flashner.co.il> | 2023-09-24 09:59:31 +0300 |
|---|---|---|
| committer | Efraim Flashner <efraim@flashner.co.il> | 2023-09-24 11:15:17 +0300 |
| commit | 0792d9946602a54a5318f7818cfe3307e9ef333d (patch) | |
| tree | 24183d459003cd7ed0cf1d726a67d610d5de3303 | |
| parent | a338a553e3bed0d33b964b87f5acc153e2b424bf (diff) | |
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.
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 29 |
1 files changed, 24 insertions, 5 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 2ea856d23f..1ed8b6c7a5 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -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 |