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-rw-r--r--gn/packages/bioinformatics.scm31
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