diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 21 |
1 files changed, 14 insertions, 7 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 169d0c4dd1..9986a4a563 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8979,7 +8979,7 @@ communication networks from scRNA-seq data.") (define-public sambamba (package (name "sambamba") - (version "0.8.0") + (version "0.8.2") (source (origin (method git-fetch) @@ -8989,7 +8989,7 @@ communication networks from scRNA-seq data.") (file-name (git-file-name name version)) (sha256 (base32 - "07dznzl6m8k7sw84jxw2kx6i3ymrapbmcmyh0fxz8wrybhw8fmwc")))) + "1zdkd1md5wk4la71p82pbclqqcm55abk23fk087da6186i1bsihl")))) (build-system gnu-build-system) (arguments `(#:tests? #f ; there is no test target @@ -8997,11 +8997,12 @@ communication networks from scRNA-seq data.") #:phases (modify-phases %standard-phases (delete 'configure) - (add-after 'unpack 'fix-ldc-version - (lambda _ + (add-after 'unpack 'prepare-build-tools + (lambda* (#:key inputs #:allow-other-keys) (substitute* "Makefile" - ;; We use ldc2 instead of ldmd2 to compile sambamba. - (("\\$\\(shell which ldmd2\\)") (which "ldc2"))))) + (("\\$\\(shell which ldmd2\\)") (which "ldmd2"))) + (setenv "CC" "gcc") + (setenv "D_LD" (which "ld.gold")))) (add-after 'unpack 'unbundle-prerequisites (lambda _ (substitute* "Makefile" @@ -9014,7 +9015,13 @@ communication networks from scRNA-seq data.") (copy-file (string-append "bin/sambamba-" ,version) (string-append bin "/sambamba")))))))) (native-inputs - (list python)) + `(("ld-gold-wrapper" + ;; Importing (gnu packages commencement) would introduce a cycle. + ,(module-ref (resolve-interface + '(gnu packages commencement)) + 'ld-gold-wrapper)) + ("binutils-gold" ,binutils-gold) + ("python" ,python))) (inputs (list ldc lz4 zlib)) (home-page "https://github.com/biod/sambamba") |