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gnu: sambamba: Update to 0.6.7-10-g223fa20.
* gnu/packages/bioinformatics.scm (sambamba)[source]: Fetch from git. [arguments]: Disable parallel build; rename build phase "place-biod" to "place-biod-and-undead"; add build phase "fix-ldc-version"; adjust phase "unbundle-prerequisites". [native-inputs]: Add python2-minimal; update biod sources; add undead sources.
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1 changed files with 36 additions and 15 deletions
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@ -10999,34 +10999,41 @@ (define htslib-for-sambamba
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(define-public sambamba
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(package
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(name "sambamba")
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(version "0.6.5")
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(version "0.6.7-10-g223fa20")
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(source
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(origin
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(method url-fetch)
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(uri (string-append "https://github.com/lomereiter/sambamba/"
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"archive/v" version ".tar.gz"))
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(file-name (string-append name "-" version ".tar.gz"))
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(method git-fetch)
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(uri (git-reference
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(url "https://github.com/lomereiter/sambamba.git")
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(commit (string-append "v" version))))
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(file-name (string-append name "-" version "-checkout"))
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(sha256
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(base32
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"17076gijd65a3f07zns2gvbgahiz5lriwsa6dq353ss3jl85d8vy"))))
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"1zb9hrxglxqh13ava9wwri30cvf85hjnbn8ccnr8l60a3k5avczn"))))
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(build-system gnu-build-system)
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(arguments
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`(#:tests? #f ; there is no test target
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#:make-flags
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'("D_COMPILER=ldc2"
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;; Override "--compiler" flag only.
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"D_FLAGS=--compiler=ldc2 -IBioD -g -d"
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"sambamba-ldmd2-64")
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#:parallel-build? #f ; not supported
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#:phases
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(modify-phases %standard-phases
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(delete 'configure)
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(add-after 'unpack 'place-biod
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(add-after 'unpack 'fix-ldc-version
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(lambda _
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(substitute* "gen_ldc_version_info.py"
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(("/usr/bin/env.*") (which "python")))
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(substitute* "Makefile"
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(("\\$\\(shell which ldmd2\\)") (which "ldmd2")))
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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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(copy-recursively (assoc-ref inputs "undead") "undeaD")
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#t))
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(add-after 'unpack 'unbundle-prerequisites
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(lambda _
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(substitute* "Makefile"
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(("htslib/libhts.a lz4/lib/liblz4.a")
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"-L-lhts -L-llz4")
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((" htslib-static lz4-static") ""))
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#t))
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(replace 'install
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@ -11039,8 +11046,9 @@ (define-public sambamba
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(native-inputs
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`(("ldc" ,ldc)
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("rdmd" ,rdmd)
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("python" ,python2-minimal)
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("biod"
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,(let ((commit "1248586b54af4bd4dfb28ebfebfc6bf012e7a587"))
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,(let ((commit "c778e4f2d8bacea7499283ce39f5577b232732c6"))
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(origin
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(method git-fetch)
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(uri (git-reference
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@ -11051,7 +11059,20 @@ (define-public sambamba
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"-checkout"))
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(sha256
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(base32
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"1m8hi1n7x0ri4l6s9i0x6jg4z4v94xrfdzp7mbizdipfag0m17g3")))))))
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"1z90562hg47i63gx042wb3ak2vqjg5z7hwgn9bp2pdxfg3nxrw37")))))
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("undead"
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,(let ((commit "92803d25c88657e945511f0976a0c79d8da46e89"))
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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/dlang/undeaD.git")
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(commit commit)))
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(file-name (string-append "undead-"
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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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"0vq6n81vzqvgphjw54lz2isc1j8lcxwjdbrhqz1h5gwrvw9w5138")))))))
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(inputs
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`(("lz4" ,lz4)
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("htslib" ,htslib-for-sambamba)))
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