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-rw-r--r--gn/packages/bioinformatics.scm36
1 files changed, 20 insertions, 16 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index cfc5dae..3363ea2 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -35,6 +35,7 @@
#:use-module (gnu packages popt)
#:use-module (gnu packages protobuf)
#:use-module (gnu packages python)
+ #:use-module (gnu packages ruby)
#:use-module (gnu packages statistics)
#:use-module (gnu packages tbb)
#:use-module (gnu packages textutils)
@@ -310,22 +311,19 @@ and freshness without requiring additional information from the user.")
(license license:boost1.0))))
(define-public sambamba
- (let ((commit "8fe1bda92423c7c97a52ef81c6871fd6569fd1da"))
- ;;(let ((commit "2ca5a2dbac5ab90c3b4c588519edc3edcb71df84"))
+ (let ((commit "2ca5a2dbac5ab90c3b4c588519edc3edcb71df84"))
(package
(name "sambamba")
- (version (string-append "0.5.9-" commit))
+ (version (string-append "0.5.9-1." (string-take commit 7)))
(source (origin
(method git-fetch)
(uri (git-reference
- ;; https://github.com/pjotrp/sambamba.git
- (url "https://github.com/roelj/sambamba.git")
+ (url "https://github.com/pjotrp/sambamba.git")
(commit commit)))
- (file-name (string-append name "-" (string-take commit 7)))
+ (file-name (string-append name "-" version "-checkout"))
(sha256
(base32
- ;;"1f14wn9aaxwjkmla6pzq3s28741carbr2v0fd2v2mm1dcpwnrqz5"
- "14gx0hhn039xhgkf5hbvffn9d0ld4zn9ka2zvvdi16k441sc8wjh"))))
+ "1f14wn9aaxwjkmla6pzq3s28741carbr2v0fd2v2mm1dcpwnrqz5"))))
(build-system gnu-build-system)
;; (inputs
;; `(("ldc" ,ldc)
@@ -340,13 +338,16 @@ and freshness without requiring additional information from the user.")
("lz4" ,lz4)
("rdmd" ,rdmd)
("zlib" ,zlib)
+ ("perl" ,perl) ; Needed for htslib
+ ("ruby" ,ruby) ; Needed for htslib
+ ("python" ,python) ; Needed for htslib
("gcc" ,gcc)
("lz4-src"
,(origin
(method url-fetch)
(uri (string-append
"https://github.com/Cyan4973/lz4/archive/r131.tar.gz"))
- (file-name "lz4-131.tar.gz")
+ (file-name "lz4-r131.tar.gz")
(sha256
(base32 "1vfg305zvj50hwscad24wan9jar6nqj14gdk2hqyr7bb9mhh0kcx"))))
("htslib-src"
@@ -354,7 +355,7 @@ and freshness without requiring additional information from the user.")
(method url-fetch)
(uri (string-append
"https://github.com/lomereiter/htslib/archive/0.2.0-rc10.tar.gz"))
- (file-name (string-append name "-" version ".tar.gz"))
+ (file-name "htslib-0.2.0-rc10.tar.gz")
(sha256
(base32 "1k6dlf6m8yayhcp7b4yisgw1xqdy1xg2xyrllss6ld0wg00hfcbs"))))
("biod-src"
@@ -363,15 +364,16 @@ and freshness without requiring additional information from the user.")
(uri (git-reference
(url "https://github.com/biod/BioD.git")
(commit "7efdb8a2f7fdcd71c9ad9596be48d1262bb1bd5b")))
+ (file-name "biod-src")
(sha256
- (base32 "09icc2bjsg9y4hxjim4ql275izadf0kh1nnmapg8manyz6bc8svf"))
- (file-name "biod-src")))))
+ (base32 "09icc2bjsg9y4hxjim4ql275izadf0kh1nnmapg8manyz6bc8svf"))))))
(arguments
`(#:tests? #f
- #:make-flags (list "CC=gcc" "D_COMPILER=ldc2")
+ ;;#:make-flags
#:phases
(modify-phases %standard-phases
(delete 'configure)
+ (delete 'check)
(add-after 'unpack 'unpack-htslib-sources
(lambda* (#:key inputs #:allow-other-keys)
;; Unfortunately, the current build compiles htslib statically
@@ -384,14 +386,16 @@ and freshness without requiring additional information from the user.")
(with-directory-excursion "lz4"
(zero? (system* "tar" "xvf" (assoc-ref inputs "lz4-src")
"--strip-components=1")))
- (zero? (system* "ln" "--symbolic" (assoc-ref inputs "biod-src") "BioD")))))
+ (and (zero? (system* "rm" "-r" "BioD"))
+ (zero? (system* "ln" "--symbolic" "--no-target-directory"
+ (assoc-ref inputs "biod-src") "BioD"))))))
;; Building a production-quality executable is done with a
;; non-default make target. Adding it with #:make-flags breaks
;; building tests. Therefore, the default make got replaced by this.
(replace
'build
- (lambda* (#:key inputs #:allow-other-keys)
- (zero? (system* "make" "sambamba-ldmd2-64")))))))
+ (lambda* (#:key inputs make-flags #:allow-other-keys)
+ (zero? (system* "make" "-f" "Makefile.guix" "CC=gcc" "D_COMPILER=ldc2")))))))
(home-page "https://github.com/lomereiter/sambamba")
(synopsis "A tool for working with SAM and BAM files written in D.")
(description