diff options
Diffstat (limited to 'gn/packages')
| -rw-r--r-- | gn/packages/bioinformatics.scm | 31 |
1 files changed, 20 insertions, 11 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index 0533371..d6fd7d3 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -15,7 +15,6 @@ #: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 autotools) #:use-module (gnu packages algebra) #:use-module (gnu packages base) @@ -37,7 +36,6 @@ #:use-module (gnu packages graphviz) #:use-module (gnu packages java) #:use-module (gnu packages linux) - #:use-module (gn packages ldc) #:use-module (gnu packages machine-learning) #:use-module (gnu packages maths) #:use-module (gnu packages mpi) @@ -61,6 +59,9 @@ #:use-module (gnu packages xml) #:use-module (gnu packages zip) #:use-module (gnu packages bootstrap) + #:use-module (gn packages ldc) + #:use-module (gn packages ldc) + #:use-module (gn packages shell) #:use-module (srfi srfi-1)) (define-public contra @@ -921,10 +922,10 @@ association studies (GWAS).") (license license:gpl3)))) (define-public sambamba - (let ((commit "91096e78c81162f855b1044a4b2d41895bd27262")) + (let ((commit "6ae174bcb50d3a8f1b6dd10de9c68bbc4770e56a")) (package (name "sambamba") - (version (string-append "0.6.6-pre2-" (string-take commit 7))) + (version (string-append "0.6.6-pre3-" (string-take commit 7))) (source (origin (method git-fetch) (uri (git-reference @@ -933,7 +934,7 @@ association studies (GWAS).") (file-name (string-append name "-" version "-checkout")) (sha256 (base32 - "0d7d0f3ri8qi5r9wq2wy9wzkr1wm68alfsn20q61lqzrfrfwm93k")))) + "1m26i8icllclynqia4yi2mp7zfs2zajllva6bzxn188fhlyjwzqr")))) (build-system gnu-build-system) (outputs '("out" "debug")) @@ -962,14 +963,22 @@ association studies (GWAS).") ,(origin (method git-fetch) (uri (git-reference - (url "https://github.com/biod/BioD.git") - (commit "1248586b54af4bd4dfb28ebfebfc6bf012e7a587"))) + (url "https://github.com/pjotrp/BioD.git") + (commit "b7f1db860d212ee5fb6f9adfb36c6e783aaeb6f5"))) (file-name (string-append "biod-src-" (string-take commit 7) "-checkout")) (sha256 - (base32 "1m8hi1n7x0ri4l6s9i0x6jg4z4v94xrfdzp7mbizdipfag0m17g3")))))) + (base32 "01xkdjdn9lb2b4b5ykzhnrk2rjikagav8b3fyac3zafcfq600cr4")))) + ("dlang-undeaD-src" + ,(origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/dlang/undeaD.git") + (commit "610234f159132f91046d4fb893889fb8ee14cd2f"))) + (file-name (string-append "dlang-undeaD-src-" (string-take commit 7) "-checkout")) + (sha256 + (base32 "12zxsgvka4a82ghp2gaviph6kz13jzjb5pbc8v6i3rmcnifzpbrl")))))) (arguments - `(#:tests? #f ; no tests available - #:phases + `(#:phases (modify-phases %standard-phases (delete 'configure) (delete 'check) @@ -981,7 +990,7 @@ association studies (GWAS).") (and (with-directory-excursion "htslib" (zero? (system* "tar" "xvf" (assoc-ref inputs "htslib-src") "--strip-components=1"))) - ;; (zero? (system* "cp" "--recursive" (string-append (assoc-ref inputs "biod-src") "/*") "BioD/"))))) + (copy-recursively (assoc-ref inputs "dlang-undeaD-src") "undeaD") (copy-recursively (assoc-ref inputs "biod-src") "BioD")))) (replace 'build |