diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 36167d0ba0..32f123a723 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6144,6 +6144,44 @@ to the user's query of interest.") (define-public samtools (package (name "samtools") + (version "1.14") + (source + (origin + (method url-fetch) + (uri + (string-append "mirror://sourceforge/samtools/samtools/" + version "/samtools-" version ".tar.bz2")) + (sha256 + (base32 + "0x3xdda78ac5vx66b3jdsv9sfhyz4npl4znl1zbaf3lbm6xdlhck")) + (modules '((guix build utils))) + (snippet '(begin + ;; Delete bundled htslib. + (delete-file-recursively "htslib-1.14"))))) + (build-system gnu-build-system) + (arguments + `(#:configure-flags (list "--with-ncurses") + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'patch-tests + (lambda _ + (substitute* "test/test.pl" + ;; The test script calls out to /bin/bash + (("/bin/bash") (which "bash")))))))) + (native-inputs (list pkg-config)) + (inputs + (list htslib ncurses perl python zlib)) + (home-page "http://samtools.sourceforge.net") + (synopsis "Utilities to efficiently manipulate nucleotide sequence alignments") + (description + "Samtools implements various utilities for post-processing nucleotide +sequence alignments in the SAM, BAM, and CRAM formats, including indexing, +variant calling (in conjunction with bcftools), and a simple alignment +viewer.") + (license license:expat))) + +(define-public samtools-1.12 + (package/inherit samtools (version "1.12") (source (origin @@ -6157,47 +6195,31 @@ to the user's query of interest.") (modules '((guix build utils))) (snippet '(begin ;; Delete bundled htslib. - (delete-file-recursively "htslib-1.12") - #t)))) - (build-system gnu-build-system) + (delete-file-recursively "htslib-1.12"))))) (arguments - `(#:modules ((ice-9 ftw) - (ice-9 regex) - (guix build gnu-build-system) - (guix build utils)) - #:configure-flags (list "--with-ncurses") - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'patch-tests - (lambda _ - (substitute* "test/test.pl" - ;; The test script calls out to /bin/bash - (("/bin/bash") (which "bash"))) - #t)) - (add-after 'install 'install-library - (lambda* (#:key outputs #:allow-other-keys) - (let ((lib (string-append (assoc-ref outputs "out") "/lib"))) - (install-file "libbam.a" lib) - #t))) - (add-after 'install 'install-headers - (lambda* (#:key outputs #:allow-other-keys) - (let ((include (string-append (assoc-ref outputs "out") - "/include/samtools/"))) - (for-each (lambda (file) - (install-file file include)) - (scandir "." (lambda (name) (string-match "\\.h$" name)))) - #t)))))) + (substitute-keyword-arguments (package-arguments samtools) + ((#:modules _ #f) + '((ice-9 ftw) + (ice-9 regex) + (guix build gnu-build-system) + (guix build utils))) + ((#:phases phases) + `(modify-phases ,phases + (add-after 'install 'install-library + (lambda* (#:key outputs #:allow-other-keys) + (let ((lib (string-append (assoc-ref outputs "out") "/lib"))) + (install-file "libbam.a" lib)))) + (add-after 'install 'install-headers + (lambda* (#:key outputs #:allow-other-keys) + (let ((include (string-append (assoc-ref outputs "out") + "/include/samtools/"))) + (for-each (lambda (file) + (install-file file include)) + (scandir "." (lambda (name) + (string-match "\\.h$" name))))))))))) (native-inputs (list pkg-config)) (inputs - (list htslib ncurses perl python zlib)) - (home-page "http://samtools.sourceforge.net") - (synopsis "Utilities to efficiently manipulate nucleotide sequence alignments") - (description - "Samtools implements various utilities for post-processing nucleotide -sequence alignments in the SAM, BAM, and CRAM formats, including indexing, -variant calling (in conjunction with bcftools), and a simple alignment -viewer.") - (license license:expat))) + (list htslib-1.12 ncurses perl python zlib)))) (define-public samtools-1.10 (package (inherit samtools)