gnu: Add kentutils.
* gnu/packages/bioinformatics.scm (kentutils): New variable.
This commit is contained in:
Ricardo Wurmus
parent
519bfc656c
commit
94820951d6
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@ -50,6 +50,7 @@ (define-module (gnu packages bioinformatics)
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#:use-module (gnu packages cpio)
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#:use-module (gnu packages curl)
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#:use-module (gnu packages documentation)
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#:use-module (gnu packages databases)
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#:use-module (gnu packages datastructures)
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#:use-module (gnu packages file)
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#:use-module (gnu packages flex)
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@ -84,6 +85,7 @@ (define-module (gnu packages bioinformatics)
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#:use-module (gnu packages readline)
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#:use-module (gnu packages ruby)
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#:use-module (gnu packages serialization)
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#:use-module (gnu packages shells)
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#:use-module (gnu packages statistics)
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#:use-module (gnu packages swig)
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#:use-module (gnu packages tbb)
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@ -9537,3 +9539,116 @@ (define-public tadbit
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interaction matrices, and finally, extract structural properties from the
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models. TADbit is complemented by TADkit for visualizing 3D models.")
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(license license:gpl3+)))
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(define-public kentutils
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(package
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(name "kentutils")
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;; 302.1.0 is out, but the only difference is the inclusion of
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;; pre-built binaries.
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(version "302.0.0")
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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/ENCODE-DCC/kentUtils/"
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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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(sha256
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(base32
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"134aja3k1cj32kbk1nnw0q9gxjb2krr15q6sga8qldzvc0585rmm"))
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(modules '((guix build utils)
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(srfi srfi-26)
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(ice-9 ftw)))
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(snippet
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'(begin
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;; Only the contents of the specified directories are free
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;; for all uses, so we remove the rest. "hg/autoSql" and
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;; "hg/autoXml" are nominally free, but they depend on a
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;; library that is built from the sources in "hg/lib",
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;; which is nonfree.
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(let ((free (list "." ".."
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"utils" "lib" "inc" "tagStorm"
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"parasol" "htslib"))
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(directory? (lambda (file)
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(eq? 'directory (stat:type (stat file))))))
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(for-each (lambda (file)
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(and (directory? file)
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(delete-file-recursively file)))
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(map (cut string-append "src/" <>)
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(scandir "src"
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(lambda (file)
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(not (member file free)))))))
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;; Only make the utils target, not the userApps target,
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;; because that requires libraries we won't build.
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(substitute* "Makefile"
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((" userApps") " utils"))
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;; Only build libraries that are free.
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(substitute* "src/makefile"
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(("DIRS =.*") "DIRS =\n")
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(("cd jkOwnLib.*") "")
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((" hgLib") "")
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(("cd hg.*") ""))
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(substitute* "src/utils/makefile"
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;; These tools depend on "jkhgap.a", which is part of the
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;; nonfree "src/hg/lib" directory.
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(("raSqlQuery") "")
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(("pslLiftSubrangeBlat") "")
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;; Do not build UCSC tools, which may require nonfree
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;; components.
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(("ALL_APPS =.*") "ALL_APPS = $(UTILS_APPLIST)\n"))
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#t))))
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(build-system gnu-build-system)
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(arguments
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`( ;; There is no global test target and the test target for
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;; individual tools depends on input files that are not
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;; included.
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#:tests? #f
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#:phases
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(modify-phases %standard-phases
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(add-after 'unpack 'fix-paths
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(lambda _
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(substitute* "Makefile"
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(("/bin/echo") (which "echo")))
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#t))
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(add-after 'unpack 'prepare-samtabix
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(lambda* (#:key inputs #:allow-other-keys)
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(copy-recursively (assoc-ref inputs "samtabix")
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"samtabix")
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#t))
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(delete 'configure)
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(replace 'install
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(lambda* (#:key outputs #:allow-other-keys)
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(let ((bin (string-append (assoc-ref outputs "out")
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"/bin")))
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(copy-recursively "bin" bin))
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#t)))))
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(native-inputs
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`(("samtabix"
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,(origin
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(method git-fetch)
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(uri (git-reference
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(url "http://genome-source.cse.ucsc.edu/samtabix.git")
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(commit "10fd107909c1ac4d679299908be4262a012965ba")))
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(sha256
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(base32
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"0c1nj64l42v395sa84n7az43xiap4i6f9n9dfz4058aqiwkhkmma"))))))
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(inputs
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`(("zlib" ,zlib)
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("tcsh" ,tcsh)
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("perl" ,perl)
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("libpng" ,libpng)
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("mysql" ,mysql)
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("openssl" ,openssl)))
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(home-page "http://genome.cse.ucsc.edu/index.html")
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(synopsis "Assorted bioinformatics utilities")
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(description "This package provides the kentUtils, a selection of
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bioinformatics utilities used in combination with the UCSC genome
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browser.")
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;; Only a subset of the sources are released under a non-copyleft
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;; free software license. All other sources are removed in a
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;; snippet. See this bug report for an explanation of how the
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;; license statements apply:
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;; https://github.com/ENCODE-DCC/kentUtils/issues/12
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(license (license:non-copyleft
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"http://genome.ucsc.edu/license/"
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"The contents of this package are free for all uses."))))
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