diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 41 |
1 files changed, 32 insertions, 9 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index ccee9d1f60..cb0bdf766e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6687,7 +6687,7 @@ performance.") (define-public htscodecs (package (name "htscodecs") - (version "1.5.0") + (version "1.5.1") (source (origin (method url-fetch) (uri (string-append "https://github.com/samtools/htscodecs/" @@ -6695,7 +6695,7 @@ performance.") version "/htscodecs-" version ".tar.gz")) (sha256 (base32 - "1cys6hp438m1rfmgq6xig3q0md7nh0m03jb17mc798q13lsggpil")))) + "0nykdf08wil6iiihgf5qlb04n70yv4zqqj7c27vpnpwpr2r2ns62")))) (build-system gnu-build-system) (inputs (list bzip2 zlib)) (home-page "https://github.com/samtools/htscodecs") @@ -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 @@ -11732,7 +11751,7 @@ replacement for strverscmp.") (copy-recursively (assoc-ref inputs "tests") "/tmp/tests") (with-directory-excursion "/tmp/tests" (invoke "multiqc" "data" "--ignore" "data/modules"))))))))) - (propagated-inputs + (inputs (list python-click python-coloredlogs python-future @@ -16412,7 +16431,11 @@ genomic scores), long range contacts and the visualization of viewpoints.") (lambda _ (substitute* "setup.py" (("matplotlib ==3.1.1") - "matplotlib >=3.1.1"))))))) + "matplotlib >=3.1.1")))) + (add-after 'unpack 'remove-invalid-syntax + (lambda _ + (substitute* "setup.py" + ((".\\*,") ","))))))) (propagated-inputs (list python-future python-gffutils |