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gnu: sambamba: Update to 0.6.8. 

* gnu/packages/bioinformatics.scm (sambamba): Update to 0.6.8.
This commit is contained in:
Roel Janssen 2018-11-15 13:09:01 +01:00
parent 7413c31693
commit 2d86eaff5b
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GPG Key ID: C3EC1DCA843072E1
1 changed files with 13 additions and 12 deletions
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@ -11158,7 +11158,7 @@ droplet sequencing. It has been particularly tailored for Drop-seq.")
(define-public sambamba (define-public sambamba
(package (package
(name "sambamba") (name "sambamba")
(version "0.6.7-10-g223fa20") (version "0.6.8")
(source (source
(origin (origin
(method git-fetch) (method git-fetch)
@ -11168,7 +11168,7 @@ droplet sequencing. It has been particularly tailored for Drop-seq.")
(file-name (string-append name "-" version "-checkout")) (file-name (string-append name "-" version "-checkout"))
(sha256 (sha256
(base32 (base32
"1zb9hrxglxqh13ava9wwri30cvf85hjnbn8ccnr8l60a3k5avczn")))) "0k0cz3qcv98p6cq09zlbgnjsggxcqbcmzxg5zikgcgbr2nfq4lry"))))
(build-system gnu-build-system) (build-system gnu-build-system)
(arguments (arguments
`(#:tests? #f ; there is no test target `(#:tests? #f ; there is no test target
@ -11179,9 +11179,10 @@ droplet sequencing. It has been particularly tailored for Drop-seq.")
(add-after 'unpack 'fix-ldc-version (add-after 'unpack 'fix-ldc-version
(lambda _ (lambda _
(substitute* "gen_ldc_version_info.py" (substitute* "gen_ldc_version_info.py"
(("/usr/bin/env.*") (which "python"))) (("/usr/bin/env.*") (which "python3")))
(substitute* "Makefile" (substitute* "Makefile"
(("\\$\\(shell which ldmd2\\)") (which "ldmd2"))) ;; We use ldc2 instead of ldmd2 to compile sambamba.
(("\\$\\(shell which ldmd2\\)") (which "ldc2")))
#t)) #t))
(add-after 'unpack 'place-biod-and-undead (add-after 'unpack 'place-biod-and-undead
(lambda* (#:key inputs #:allow-other-keys) (lambda* (#:key inputs #:allow-other-keys)
@ -11193,21 +11194,21 @@ droplet sequencing. It has been particularly tailored for Drop-seq.")
(substitute* "Makefile" (substitute* "Makefile"
(("htslib/libhts.a lz4/lib/liblz4.a") (("htslib/libhts.a lz4/lib/liblz4.a")
"-L-lhts -L-llz4") "-L-lhts -L-llz4")
((" htslib-static lz4-static") "")) ((" lz4-static htslib-static") ""))
#t)) #t))
(replace 'install (replace 'install
(lambda* (#:key outputs #:allow-other-keys) (lambda* (#:key outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out")) (let* ((out (assoc-ref outputs "out"))
(bin (string-append out "/bin"))) (bin (string-append out "/bin")))
(mkdir-p bin) (mkdir-p bin)
(install-file "build/sambamba" bin) (install-file "bin/sambamba" bin)
#t)))))) #t))))))
(native-inputs (native-inputs
`(("ldc" ,ldc) `(("ldc" ,ldc)
("rdmd" ,rdmd) ("rdmd" ,rdmd)
("python" ,python2-minimal) ("python" ,python-minimal)
("biod" ("biod"
,(let ((commit "c778e4f2d8bacea7499283ce39f5577b232732c6")) ,(let ((commit "4f1a7d2fb7ef3dfe962aa357d672f354ebfbe42e"))
(origin (origin
(method git-fetch) (method git-fetch)
(uri (git-reference (uri (git-reference
@ -11218,20 +11219,20 @@ droplet sequencing. It has been particularly tailored for Drop-seq.")
"-checkout")) "-checkout"))
(sha256 (sha256
(base32 (base32
"1z90562hg47i63gx042wb3ak2vqjg5z7hwgn9bp2pdxfg3nxrw37"))))) "1k5pdjv1qvi0a3rwd1sfq6zbj37l86i7bf710m4c0y6737lxj426")))))
("undead" ("undead"
,(let ((commit "92803d25c88657e945511f0976a0c79d8da46e89")) ,(let ((commit "9be93876982b5f14fcca60832563b3cd767dd84d"))
(origin (origin
(method git-fetch) (method git-fetch)
(uri (git-reference (uri (git-reference
(url "https://github.com/dlang/undeaD.git") (url "https://github.com/biod/undeaD.git")
(commit commit))) (commit commit)))
(file-name (string-append "undead-" (file-name (string-append "undead-"
(string-take commit 9) (string-take commit 9)
"-checkout")) "-checkout"))
(sha256 (sha256
(base32 (base32
"0vq6n81vzqvgphjw54lz2isc1j8lcxwjdbrhqz1h5gwrvw9w5138"))))))) "1xfarj0nqlmi5jd1vmcmm7pabzaf9hxyvk6hp0d6jslb5k9r8r3d")))))))
(inputs (inputs
`(("lz4" ,lz4) `(("lz4" ,lz4)
("htslib" ,htslib-for-sambamba))) ("htslib" ,htslib-for-sambamba)))