diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 58 |
1 files changed, 47 insertions, 11 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 9163b5dc8a..cdb82aee8b 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1382,7 +1382,7 @@ gapped, local, and paired-end alignment modes.") ("python" ,python-2) ("perl" ,perl) ("zlib" ,zlib) - ("seqan" ,seqan))) + ("seqan" ,seqan-1))) (home-page "http://ccb.jhu.edu/software/tophat/index.shtml") (synopsis "Spliced read mapper for RNA-Seq data") (description @@ -5733,14 +5733,15 @@ writing files into the .sra format.") (define-public seqan (package (name "seqan") - (version "1.4.2") + (version "2.4.0") (source (origin (method url-fetch) - (uri (string-append "http://packages.seqan.de/seqan-library/" - "seqan-library-" version ".tar.bz2")) + (uri (string-append "https://github.com/seqan/seqan/releases/" + "download/seqan-v" version + "/seqan-library-" version ".tar.xz")) (sha256 (base32 - "05s3wrrwn50f81aklfm65i4a749zag1vr8z03k21xm0pdxy47yvp")))) + "19a1rlxx03qy1i1iriicly68w64yjxbv24g9gdywnfmq998v35yx")))) ;; The documentation is 7.8MB and the includes are 3.6MB heavy, so it ;; makes sense to split the outputs. (outputs '("out" "doc")) @@ -5750,11 +5751,11 @@ writing files into the .sra format.") #:builder (begin (use-modules (guix build utils)) - (let ((tar (assoc-ref %build-inputs "tar")) - (bzip (assoc-ref %build-inputs "bzip2")) - (out (assoc-ref %outputs "out")) - (doc (assoc-ref %outputs "doc"))) - (setenv "PATH" (string-append tar "/bin:" bzip "/bin")) + (let ((tar (assoc-ref %build-inputs "tar")) + (xz (assoc-ref %build-inputs "xz")) + (out (assoc-ref %outputs "out")) + (doc (assoc-ref %outputs "doc"))) + (setenv "PATH" (string-append tar "/bin:" xz "/bin")) (invoke "tar" "xvf" (assoc-ref %build-inputs "source")) (chdir (string-append "seqan-library-" ,version)) (copy-recursively "include" (string-append out "/include")) @@ -5763,7 +5764,7 @@ writing files into the .sra format.") (native-inputs `(("source" ,source) ("tar" ,tar) - ("bzip2" ,bzip2))) + ("xz" ,xz))) (home-page "http://www.seqan.de") (synopsis "Library for nucleotide sequence analysis") (description @@ -5774,6 +5775,41 @@ manipulation, online and indexed string search, efficient I/O of bioinformatics file formats, sequence alignment, and more.") (license license:bsd-3))) +(define-public seqan-1 + (package (inherit seqan) + (name "seqan") + (version "1.4.2") + (source (origin + (method url-fetch) + (uri (string-append "http://packages.seqan.de/seqan-library/" + "seqan-library-" version ".tar.bz2")) + (sha256 + (base32 + "05s3wrrwn50f81aklfm65i4a749zag1vr8z03k21xm0pdxy47yvp")))) + ;; The documentation is 7.8MB and the includes are 3.6MB heavy, so it + ;; makes sense to split the outputs. + (outputs '("out" "doc")) + (build-system trivial-build-system) + (arguments + `(#:modules ((guix build utils)) + #:builder + (begin + (use-modules (guix build utils)) + (let ((tar (assoc-ref %build-inputs "tar")) + (bzip (assoc-ref %build-inputs "bzip2")) + (out (assoc-ref %outputs "out")) + (doc (assoc-ref %outputs "doc"))) + (setenv "PATH" (string-append tar "/bin:" bzip "/bin")) + (invoke "tar" "xvf" (assoc-ref %build-inputs "source")) + (chdir (string-append "seqan-library-" ,version)) + (copy-recursively "include" (string-append out "/include")) + (copy-recursively "share" (string-append doc "/share")) + #t)))) + (native-inputs + `(("source" ,source) + ("tar" ,tar) + ("bzip2" ,bzip2))))) + (define-public seqmagick (package (name "seqmagick") |