diff options
| -rw-r--r-- | gn/packages/lmm.scm | 1 | ||||
| -rw-r--r-- | gn/packages/sambamba.scm | 22 |
2 files changed, 13 insertions, 10 deletions
diff --git a/gn/packages/lmm.scm b/gn/packages/lmm.scm index 3761db7..40e9551 100644 --- a/gn/packages/lmm.scm +++ b/gn/packages/lmm.scm @@ -11,6 +11,7 @@ #:use-module (guix build-system ruby) #:use-module (guix build-system r) #:use-module (guix build-system trivial) + #:use-module (gn packages statistics) #:use-module (gnu packages) #:use-module (gnu packages algebra) #:use-module (gnu packages base) diff --git a/gn/packages/sambamba.scm b/gn/packages/sambamba.scm index 6463689..f5a384f 100644 --- a/gn/packages/sambamba.scm +++ b/gn/packages/sambamba.scm @@ -19,10 +19,10 @@ #:use-module (srfi srfi-1)) (define-public sambamba - (let ((commit "54778aea4c054702d34740d229bbf03e5b907482")) + (let ((commit "52ab1eff7070cd3dafad94a15c9fd6e243a45a4d")) (package (name "sambamba") - (version (string-append "0.6.6-pre4-" (string-take commit 7))) + (version (string-append "0.6.6-" (string-take commit 7))) (source (origin (method git-fetch) (uri (git-reference @@ -31,9 +31,9 @@ (file-name (string-append name "-" version "-checkout")) (sha256 (base32 - "131311h0ccz3r74yvw20f96pc86s760cvvnzgxin0kks7wgixmmz")))) + "16nfvmipa1gj7f8c9lqhh5yffdmaic1pzcrm9281dqwywl9w8hsg")))) (build-system gnu-build-system) - (outputs '("out" + (outputs '("out" ; disable all checks for speed "debug")) (inputs `(("samtools" ,samtools) ; for pileup @@ -87,7 +87,7 @@ (lambda* (#:key inputs #:allow-other-keys) (substitute* "sambamba/pileup.d" (("string samtoolsBin = null;") (string-append "string samtoolsBin = \"" (which "samtools") "\";")) - (("string samtoolsBin = null;") (string-append "string samtoolsBin = \"" (which "samtools") "\";")) + (("string bcftoolsBin = null;") (string-append "string bcftoolsBin = \"" (which "bcftools") "\";")) ((" this_app = args[0];") (string-append " this_app = \"" (which "sambamba") "\";"))))) (add-after 'unpack 'unpack-htslib-sources (lambda* (#:key inputs #:allow-other-keys) @@ -101,11 +101,13 @@ (copy-recursively (assoc-ref inputs "biod-src") "BioD")))) (replace 'build - (lambda* (#:key inputs make-flags #:allow-other-keys) - (zero? (system* "make" "-f" "Makefile.guix" "guix-debug" - (string-append "LDC_LIB_PATH=" - (assoc-ref inputs "ldc") - "/lib"))))) + (lambda* (#:key inputs outputs make-flags #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (debug-out (assoc-ref outputs "debug"))) + (zero? (system* "make" "-f" "Makefile.guix" "guix" + (string-append "LDC_LIB_PATH=" + (assoc-ref inputs "ldc") + "/lib")))))) (replace 'install (lambda* (#:key outputs #:allow-other-keys) |