diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 25 |
1 files changed, 13 insertions, 12 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 58cee5cbbe..1a7199241a 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -11158,7 +11158,7 @@ droplet sequencing. It has been particularly tailored for Drop-seq.") (define-public sambamba (package (name "sambamba") - (version "0.6.7-10-g223fa20") + (version "0.6.8") (source (origin (method git-fetch) @@ -11168,7 +11168,7 @@ droplet sequencing. It has been particularly tailored for Drop-seq.") (file-name (string-append name "-" version "-checkout")) (sha256 (base32 - "1zb9hrxglxqh13ava9wwri30cvf85hjnbn8ccnr8l60a3k5avczn")))) + "0k0cz3qcv98p6cq09zlbgnjsggxcqbcmzxg5zikgcgbr2nfq4lry")))) (build-system gnu-build-system) (arguments `(#:tests? #f ; there is no test target @@ -11179,9 +11179,10 @@ droplet sequencing. It has been particularly tailored for Drop-seq.") (add-after 'unpack 'fix-ldc-version (lambda _ (substitute* "gen_ldc_version_info.py" - (("/usr/bin/env.*") (which "python"))) + (("/usr/bin/env.*") (which "python3"))) (substitute* "Makefile" - (("\\$\\(shell which ldmd2\\)") (which "ldmd2"))) + ;; 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) @@ -11193,21 +11194,21 @@ droplet sequencing. It has been particularly tailored for Drop-seq.") (substitute* "Makefile" (("htslib/libhts.a lz4/lib/liblz4.a") "-L-lhts -L-llz4") - ((" htslib-static lz4-static") "")) + ((" lz4-static htslib-static") "")) #t)) (replace 'install (lambda* (#:key outputs #:allow-other-keys) (let* ((out (assoc-ref outputs "out")) (bin (string-append out "/bin"))) (mkdir-p bin) - (install-file "build/sambamba" bin) + (install-file "bin/sambamba" bin) #t)))))) (native-inputs `(("ldc" ,ldc) ("rdmd" ,rdmd) - ("python" ,python2-minimal) + ("python" ,python-minimal) ("biod" - ,(let ((commit "c778e4f2d8bacea7499283ce39f5577b232732c6")) + ,(let ((commit "4f1a7d2fb7ef3dfe962aa357d672f354ebfbe42e")) (origin (method git-fetch) (uri (git-reference @@ -11218,20 +11219,20 @@ droplet sequencing. It has been particularly tailored for Drop-seq.") "-checkout")) (sha256 (base32 - "1z90562hg47i63gx042wb3ak2vqjg5z7hwgn9bp2pdxfg3nxrw37"))))) + "1k5pdjv1qvi0a3rwd1sfq6zbj37l86i7bf710m4c0y6737lxj426"))))) ("undead" - ,(let ((commit "92803d25c88657e945511f0976a0c79d8da46e89")) + ,(let ((commit "9be93876982b5f14fcca60832563b3cd767dd84d")) (origin (method git-fetch) (uri (git-reference - (url "https://github.com/dlang/undeaD.git") + (url "https://github.com/biod/undeaD.git") (commit commit))) (file-name (string-append "undead-" (string-take commit 9) "-checkout")) (sha256 (base32 - "0vq6n81vzqvgphjw54lz2isc1j8lcxwjdbrhqz1h5gwrvw9w5138"))))))) + "1xfarj0nqlmi5jd1vmcmm7pabzaf9hxyvk6hp0d6jslb5k9r8r3d"))))))) (inputs `(("lz4" ,lz4) ("htslib" ,htslib-for-sambamba))) |