gnu: sambamba Update to 0.8.0.
* gnu/packages/bioinformatics.scm (sambamba): Update to 0.8.0. [source, home-page]: Update to new upstream URI. [arguments]: Shorten 'fix-ldc-version phase. Remove 'place-biod-and-undead phase. Update 'unbundle-prerequisites and 'insatll phases. [native-inputs]: Remove rdmd, biod. Move ldc ... [inputs]: ... to here. Add zlib. (htslib-for-sambamba): Remove variable.
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@ -10513,41 +10513,20 @@ explore and perform basic analysis of single cell sequencing data coming from
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droplet sequencing. It has been particularly tailored for Drop-seq.")
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droplet sequencing. It has been particularly tailored for Drop-seq.")
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(license license:gpl3))))
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(license license:gpl3))))
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(define htslib-for-sambamba
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(let ((commit "2f3c3ea7b301f9b45737a793c0b2dcf0240e5ee5"))
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(package
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(inherit htslib)
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(name "htslib-for-sambamba")
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(version (string-append "1.3.1-1." (string-take commit 9)))
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(source
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(origin
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(method git-fetch)
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(uri (git-reference
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(url "https://github.com/lomereiter/htslib")
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(commit commit)))
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(file-name (string-append "htslib-" version "-checkout"))
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(sha256
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(base32
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"0g38g8s3npr0gjm9fahlbhiskyfws9l5i0x1ml3rakzj7az5l9c9"))))
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(native-inputs
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`(("autoconf" ,autoconf)
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("automake" ,automake)
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,@(package-native-inputs htslib))))))
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(define-public sambamba
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(define-public sambamba
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(package
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(package
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(name "sambamba")
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(name "sambamba")
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(version "0.7.1")
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(version "0.8.0")
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(source
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(source
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(origin
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(origin
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(method git-fetch)
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(method git-fetch)
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(uri (git-reference
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(uri (git-reference
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(url "https://github.com/lomereiter/sambamba")
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(url "https://github.com/biod/sambamba")
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(commit (string-append "v" version))))
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(commit (string-append "v" version))))
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(file-name (string-append name "-" version "-checkout"))
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(file-name (git-file-name name version))
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(sha256
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(sha256
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(base32
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(base32
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"111h05b60pj8dxbidiamy4imc92x2962b3lmb7wgysl6lx064qis"))))
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"07dznzl6m8k7sw84jxw2kx6i3ymrapbmcmyh0fxz8wrybhw8fmwc"))))
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(build-system gnu-build-system)
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(build-system gnu-build-system)
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(arguments
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(arguments
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`(#:tests? #f ; there is no test target
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`(#:tests? #f ; there is no test target
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@ -10557,52 +10536,30 @@ droplet sequencing. It has been particularly tailored for Drop-seq.")
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(delete 'configure)
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(delete 'configure)
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(add-after 'unpack 'fix-ldc-version
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(add-after 'unpack 'fix-ldc-version
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(lambda _
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(lambda _
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(substitute* "gen_ldc_version_info.py"
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(("/usr/bin/env.*") (which "python3")))
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(substitute* "Makefile"
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(substitute* "Makefile"
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;; We use ldc2 instead of ldmd2 to compile sambamba.
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;; We use ldc2 instead of ldmd2 to compile sambamba.
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(("\\$\\(shell which ldmd2\\)") (which "ldc2")))
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(("\\$\\(shell which ldmd2\\)") (which "ldc2")))
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#t))
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#t))
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(add-after 'unpack 'place-biod-and-undead
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(lambda* (#:key inputs #:allow-other-keys)
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(copy-recursively (assoc-ref inputs "biod") "BioD")
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#t))
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(add-after 'unpack 'unbundle-prerequisites
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(add-after 'unpack 'unbundle-prerequisites
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(lambda _
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(lambda _
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(substitute* "Makefile"
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(substitute* "Makefile"
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(("htslib/libhts.a lz4/lib/liblz4.a")
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(("= lz4/lib/liblz4.a") "= -L-llz4")
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"-L-lhts -L-llz4")
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(("ldc_version_info lz4-static") "ldc_version_info"))
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((" lz4-static htslib-static") ""))
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#t))
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#t))
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(replace 'install
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(replace 'install
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(lambda* (#:key outputs #:allow-other-keys)
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(lambda* (#:key outputs #:allow-other-keys)
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(let* ((out (assoc-ref outputs "out"))
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(let ((bin (string-append (assoc-ref outputs "out") "/bin")))
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(bin (string-append out "/bin")))
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(mkdir-p bin)
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(mkdir-p bin)
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(copy-file (string-append "bin/sambamba-" ,version)
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(copy-file (string-append "bin/sambamba-" ,version)
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(string-append bin "/sambamba"))
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(string-append bin "/sambamba"))
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#t))))))
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#t))))))
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(native-inputs
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(native-inputs
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`(("ldc" ,ldc)
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`(("python" ,python)))
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("rdmd" ,rdmd)
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("python" ,python)
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("biod"
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,(let ((commit "7969eb0a847b05874e83ffddead26e193ece8101"))
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(origin
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(method git-fetch)
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(uri (git-reference
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(url "https://github.com/biod/BioD")
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(commit commit)))
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(file-name (string-append "biod-"
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(string-take commit 9)
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"-checkout"))
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(sha256
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(base32
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"0mjxsmbmv0jxl3pq21p8j5r829d648if8q58ka50b2956lc6qkpm")))))))
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(inputs
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(inputs
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`(("lz4" ,lz4)
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`(("ldc" ,ldc)
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("htslib" ,htslib-for-sambamba)))
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("lz4" ,lz4)
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(home-page "https://lomereiter.github.io/sambamba/")
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("zlib" ,zlib)))
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(home-page "https://github.com/biod/sambamba")
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(synopsis "Tools for working with SAM/BAM data")
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(synopsis "Tools for working with SAM/BAM data")
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(description "Sambamba is a high performance modern robust and
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(description "Sambamba is a high performance modern robust and
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fast tool (and library), written in the D programming language, for
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fast tool (and library), written in the D programming language, for
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