diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 67 |
1 files changed, 12 insertions, 55 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 84a9a4d208..77150e0dce 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10513,41 +10513,20 @@ explore and perform basic analysis of single cell sequencing data coming from droplet sequencing. It has been particularly tailored for Drop-seq.") (license license:gpl3)))) -(define htslib-for-sambamba - (let ((commit "2f3c3ea7b301f9b45737a793c0b2dcf0240e5ee5")) - (package - (inherit htslib) - (name "htslib-for-sambamba") - (version (string-append "1.3.1-1." (string-take commit 9))) - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/lomereiter/htslib") - (commit commit))) - (file-name (string-append "htslib-" version "-checkout")) - (sha256 - (base32 - "0g38g8s3npr0gjm9fahlbhiskyfws9l5i0x1ml3rakzj7az5l9c9")))) - (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ,@(package-native-inputs htslib)))))) - (define-public sambamba (package (name "sambamba") - (version "0.7.1") + (version "0.8.0") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/lomereiter/sambamba") + (url "https://github.com/biod/sambamba") (commit (string-append "v" version)))) - (file-name (string-append name "-" version "-checkout")) + (file-name (git-file-name name version)) (sha256 (base32 - "111h05b60pj8dxbidiamy4imc92x2962b3lmb7wgysl6lx064qis")))) + "07dznzl6m8k7sw84jxw2kx6i3ymrapbmcmyh0fxz8wrybhw8fmwc")))) (build-system gnu-build-system) (arguments `(#:tests? #f ; there is no test target @@ -10557,52 +10536,30 @@ droplet sequencing. It has been particularly tailored for Drop-seq.") (delete 'configure) (add-after 'unpack 'fix-ldc-version (lambda _ - (substitute* "gen_ldc_version_info.py" - (("/usr/bin/env.*") (which "python3"))) (substitute* "Makefile" ;; We use ldc2 instead of ldmd2 to compile sambamba. (("\\$\\(shell which ldmd2\\)") (which "ldc2"))) #t)) - (add-after 'unpack 'place-biod-and-undead - (lambda* (#:key inputs #:allow-other-keys) - (copy-recursively (assoc-ref inputs "biod") "BioD") - #t)) (add-after 'unpack 'unbundle-prerequisites (lambda _ (substitute* "Makefile" - (("htslib/libhts.a lz4/lib/liblz4.a") - "-L-lhts -L-llz4") - ((" lz4-static htslib-static") "")) + (("= lz4/lib/liblz4.a") "= -L-llz4") + (("ldc_version_info lz4-static") "ldc_version_info")) #t)) (replace 'install (lambda* (#:key outputs #:allow-other-keys) - (let* ((out (assoc-ref outputs "out")) - (bin (string-append out "/bin"))) + (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) (mkdir-p bin) (copy-file (string-append "bin/sambamba-" ,version) (string-append bin "/sambamba")) #t)))))) (native-inputs - `(("ldc" ,ldc) - ("rdmd" ,rdmd) - ("python" ,python) - ("biod" - ,(let ((commit "7969eb0a847b05874e83ffddead26e193ece8101")) - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/biod/BioD") - (commit commit))) - (file-name (string-append "biod-" - (string-take commit 9) - "-checkout")) - (sha256 - (base32 - "0mjxsmbmv0jxl3pq21p8j5r829d648if8q58ka50b2956lc6qkpm"))))))) + `(("python" ,python))) (inputs - `(("lz4" ,lz4) - ("htslib" ,htslib-for-sambamba))) - (home-page "https://lomereiter.github.io/sambamba/") + `(("ldc" ,ldc) + ("lz4" ,lz4) + ("zlib" ,zlib))) + (home-page "https://github.com/biod/sambamba") (synopsis "Tools for working with SAM/BAM data") (description "Sambamba is a high performance modern robust and fast tool (and library), written in the D programming language, for |