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gnu: Add java-forester-1.005.
* gnu/packages/bioinformatics.scm (java-forester-1.005): New variable.
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@ -12026,6 +12026,101 @@ (define-public java-forester
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reading, writing, and exporting phylogenetic trees.")
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(license license:lgpl2.1+))))
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(define-public java-forester-1.005
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(package
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(name "java-forester")
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(version "1.005")
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(source (origin
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(method url-fetch)
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(uri (string-append "http://search.maven.org/remotecontent?"
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"filepath=org/biojava/thirdparty/forester/"
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version "/forester-" version "-sources.jar"))
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(file-name (string-append name "-" version ".jar"))
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(sha256
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(base32
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"04r8qv4rk3p71z4ajrvp11py1z46qrx0047j3zzs79s6lnsm3lcv"))))
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(build-system ant-build-system)
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(arguments
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`(#:tests? #f ; there are none
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#:jdk ,icedtea-8
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#:modules ((guix build ant-build-system)
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(guix build utils)
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(guix build java-utils)
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(sxml simple)
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(sxml transform))
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#:phases
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(modify-phases %standard-phases
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(add-after 'unpack 'fix-dependencies
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(lambda* (#:key inputs #:allow-other-keys)
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(call-with-output-file "build.xml"
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(lambda (port)
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(sxml->xml
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(pre-post-order
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(with-input-from-file "src/build.xml"
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(lambda _ (xml->sxml #:trim-whitespace? #t)))
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`(;; Remove all unjar tags to avoid repacking classes.
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(unjar . ,(lambda _ '()))
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(*default* . ,(lambda (tag . kids) `(,tag ,@kids)))
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(*text* . ,(lambda (_ txt) txt))))
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port)))
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(copy-file (assoc-ref inputs "synth_look_and_feel_1.xml")
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"synth_look_and_feel_1.xml")
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(copy-file (assoc-ref inputs "phyloxml.xsd")
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"phyloxml.xsd")
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(substitute* "build.xml"
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(("../resources/synth_laf/synth_look_and_feel_1.xml")
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"synth_look_and_feel_1.xml")
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(("../resources/phyloxml_schema/1.10/phyloxml.xsd")
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"phyloxml.xsd"))
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#t))
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;; FIXME: itext is difficult to package as it depends on a few
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;; unpackaged libraries.
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(add-after 'unpack 'remove-dependency-on-unpackaged-itext
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(lambda _
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(delete-file "src/org/forester/archaeopteryx/PdfExporter.java")
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(substitute* '("src/org/forester/archaeopteryx/MainFrame.java"
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"src/org/forester/archaeopteryx/MainFrameApplication.java")
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(("pdf_written_to = PdfExporter.*")
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"throw new IOException(\"PDF export is not available.\"); /*")
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((".getPrintSizeX\\(\\), getOptions\\(\\).getPrintSizeY\\(\\) \\);") "*/")
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(("getCurrentTreePanel\\(\\).getHeight\\(\\) \\);") "*/"))
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#t))
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(add-after 'unpack 'delete-pre-built-classes
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(lambda _ (delete-file-recursively "src/classes") #t))
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;; There is no install target
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(replace 'install (install-jars ".")))))
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(propagated-inputs
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`(("java-commons-codec" ,java-commons-codec)
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("java-openchart2" ,java-openchart2)))
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;; The source archive does not contain the resources.
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(native-inputs
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`(("phyloxml.xsd"
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,(origin
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(method url-fetch)
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(uri (string-append "https://raw.githubusercontent.com/cmzmasek/forester/"
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"b61cc2dcede0bede317db362472333115756b8c6/"
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"forester/resources/phyloxml_schema/1.10/phyloxml.xsd"))
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(file-name (string-append name "-phyloxml-" version ".xsd"))
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(sha256
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(base32
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"1zxc4m8sn4n389nqdnpxa8d0k17qnr3pm2y5y6g6vh4k0zm52npv"))))
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("synth_look_and_feel_1.xml"
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,(origin
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(method url-fetch)
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(uri (string-append "https://raw.githubusercontent.com/cmzmasek/forester/"
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"29e04321615da6b35c1e15c60e52caf3f21d8e6a/"
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"forester/java/classes/resources/synth_look_and_feel_1.xml"))
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(file-name (string-append name "-synth-look-and-feel-" version ".xml"))
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(sha256
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(base32
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"1gv5602gv4k7y7713y75a4jvj7i9s7nildsbdl7n9q10sc2ikg8h"))))))
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(home-page "https://sites.google.com/site/cmzmasek/home/software/forester")
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(synopsis "Phylogenomics libraries for Java")
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(description "Forester is a collection of Java libraries for
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phylogenomics and evolutionary biology research. It includes support for
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reading, writing, and exporting phylogenetic trees.")
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(license license:lgpl2.1+)))
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(define-public java-biojava-core
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(package
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(name "java-biojava-core")
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