diff options
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 51 |
1 files changed, 36 insertions, 15 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 88aa48cd9e..0e9e6b13fd 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10999,34 +10999,41 @@ droplet sequencing. It has been particularly tailored for Drop-seq.") (define-public sambamba (package (name "sambamba") - (version "0.6.5") + (version "0.6.7-10-g223fa20") (source (origin - (method url-fetch) - (uri (string-append "https://github.com/lomereiter/sambamba/" - "archive/v" version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/lomereiter/sambamba.git") + (commit (string-append "v" version)))) + (file-name (string-append name "-" version "-checkout")) (sha256 (base32 - "17076gijd65a3f07zns2gvbgahiz5lriwsa6dq353ss3jl85d8vy")))) + "1zb9hrxglxqh13ava9wwri30cvf85hjnbn8ccnr8l60a3k5avczn")))) (build-system gnu-build-system) (arguments - `(#:tests? #f ; there is no test target - #:make-flags - '("D_COMPILER=ldc2" - ;; Override "--compiler" flag only. - "D_FLAGS=--compiler=ldc2 -IBioD -g -d" - "sambamba-ldmd2-64") + `(#:tests? #f ; there is no test target + #:parallel-build? #f ; not supported #:phases (modify-phases %standard-phases (delete 'configure) - (add-after 'unpack 'place-biod + (add-after 'unpack 'fix-ldc-version + (lambda _ + (substitute* "gen_ldc_version_info.py" + (("/usr/bin/env.*") (which "python"))) + (substitute* "Makefile" + (("\\$\\(shell which ldmd2\\)") (which "ldmd2"))) + #t)) + (add-after 'unpack 'place-biod-and-undead (lambda* (#:key inputs #:allow-other-keys) (copy-recursively (assoc-ref inputs "biod") "BioD") + (copy-recursively (assoc-ref inputs "undead") "undeaD") #t)) (add-after 'unpack 'unbundle-prerequisites (lambda _ (substitute* "Makefile" + (("htslib/libhts.a lz4/lib/liblz4.a") + "-L-lhts -L-llz4") ((" htslib-static lz4-static") "")) #t)) (replace 'install @@ -11039,8 +11046,9 @@ droplet sequencing. It has been particularly tailored for Drop-seq.") (native-inputs `(("ldc" ,ldc) ("rdmd" ,rdmd) + ("python" ,python2-minimal) ("biod" - ,(let ((commit "1248586b54af4bd4dfb28ebfebfc6bf012e7a587")) + ,(let ((commit "c778e4f2d8bacea7499283ce39f5577b232732c6")) (origin (method git-fetch) (uri (git-reference @@ -11051,7 +11059,20 @@ droplet sequencing. It has been particularly tailored for Drop-seq.") "-checkout")) (sha256 (base32 - "1m8hi1n7x0ri4l6s9i0x6jg4z4v94xrfdzp7mbizdipfag0m17g3"))))))) + "1z90562hg47i63gx042wb3ak2vqjg5z7hwgn9bp2pdxfg3nxrw37"))))) + ("undead" + ,(let ((commit "92803d25c88657e945511f0976a0c79d8da46e89")) + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/dlang/undeaD.git") + (commit commit))) + (file-name (string-append "undead-" + (string-take commit 9) + "-checkout")) + (sha256 + (base32 + "0vq6n81vzqvgphjw54lz2isc1j8lcxwjdbrhqz1h5gwrvw9w5138"))))))) (inputs `(("lz4" ,lz4) ("htslib" ,htslib-for-sambamba))) |