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| author | Roel Janssen <roel@gnu.org> | 2020-03-26 18:08:27 +0100 |
|---|---|---|
| committer | Roel Janssen <roel@gnu.org> | 2020-03-26 18:08:27 +0100 |
| commit | 79c395dde318605fed7d0ba429c8d82d8e77202a (patch) | |
| tree | a67ae0bd1b95ba896bed23aef2f4a8710f3475a5 /gnu/packages/bioinformatics.scm | |
| parent | db47adb0c767c373958d892411da2c89fe5503a3 (diff) | |
| download | patches-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.
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 25 |
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))) |