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authorRoel Janssen <roel@gnu.org>2020-03-26 18:08:27 +0100
committerRoel Janssen <roel@gnu.org>2020-03-26 18:08:27 +0100
commit79c395dde318605fed7d0ba429c8d82d8e77202a (patch)
treea67ae0bd1b95ba896bed23aef2f4a8710f3475a5
parentdb47adb0c767c373958d892411da2c89fe5503a3 (diff)
downloadpatches-79c395dde318605fed7d0ba429c8d82d8e77202a.tar
patches-79c395dde318605fed7d0ba429c8d82d8e77202a.tar.gz
gnu: Update sambamba to 0.7.1.
* gnu/packages/bioinformatics.scm (sambamba): Update to 0.7.1; Remove unneeded undead input.
-rw-r--r--gnu/packages/bioinformatics.scm25
1 files changed, 6 insertions, 19 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index d1032cba1c..da3fe1d2c9 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10977,7 +10977,7 @@ droplet sequencing. It has been particularly tailored for Drop-seq.")
(define-public sambamba
(package
(name "sambamba")
- (version "0.6.8")
+ (version "0.7.1")
(source
(origin
(method git-fetch)
@@ -10987,7 +10987,7 @@ droplet sequencing. It has been particularly tailored for Drop-seq.")
(file-name (string-append name "-" version "-checkout"))
(sha256
(base32
- "0k0cz3qcv98p6cq09zlbgnjsggxcqbcmzxg5zikgcgbr2nfq4lry"))))
+ "111h05b60pj8dxbidiamy4imc92x2962b3lmb7wgysl6lx064qis"))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f ; there is no test target
@@ -11006,7 +11006,6 @@ droplet sequencing. It has been particularly tailored for Drop-seq.")
(add-after 'unpack 'place-biod-and-undead
(lambda* (#:key inputs #:allow-other-keys)
(copy-recursively (assoc-ref inputs "biod") "BioD")
- (copy-recursively (assoc-ref inputs "undead") "undeaD")
#t))
(add-after 'unpack 'unbundle-prerequisites
(lambda _
@@ -11020,14 +11019,15 @@ droplet sequencing. It has been particularly tailored for Drop-seq.")
(let* ((out (assoc-ref outputs "out"))
(bin (string-append out "/bin")))
(mkdir-p bin)
- (install-file "bin/sambamba" bin)
+ (copy-file (string-append "bin/sambamba-" ,version)
+ (string-append bin "/sambamba"))
#t))))))
(native-inputs
`(("ldc" ,ldc)
("rdmd" ,rdmd)
("python" ,python)
("biod"
- ,(let ((commit "4f1a7d2fb7ef3dfe962aa357d672f354ebfbe42e"))
+ ,(let ((commit "7969eb0a847b05874e83ffddead26e193ece8101"))
(origin
(method git-fetch)
(uri (git-reference
@@ -11038,20 +11038,7 @@ droplet sequencing. It has been particularly tailored for Drop-seq.")
"-checkout"))
(sha256
(base32
- "1k5pdjv1qvi0a3rwd1sfq6zbj37l86i7bf710m4c0y6737lxj426")))))
- ("undead"
- ,(let ((commit "9be93876982b5f14fcca60832563b3cd767dd84d"))
- (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/biod/undeaD.git")
- (commit commit)))
- (file-name (string-append "undead-"
- (string-take commit 9)
- "-checkout"))
- (sha256
- (base32
- "1xfarj0nqlmi5jd1vmcmm7pabzaf9hxyvk6hp0d6jslb5k9r8r3d")))))))
+ "0mjxsmbmv0jxl3pq21p8j5r829d648if8q58ka50b2956lc6qkpm")))))))
(inputs
`(("lz4" ,lz4)
("htslib" ,htslib-for-sambamba)))