gnu: Add java-maxent.
* gnu/packages/bioinformatics.scm (java-maxent): New variable.master
Ricardo Wurmus
parent
75bdd4b052
commit
341b4b2a97
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@ -5537,6 +5537,89 @@ manipulating HTS data.")
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(add-after 'unpack 'remove-tests
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(lambda _ (delete-file-recursively "src/test") #t)))))))
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(define-public java-maxent
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(package
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(name "java-maxent")
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(version "3.4.4")
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(source (origin
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(method git-fetch)
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(uri (git-reference
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(url "https://github.com/mrmaxent/Maxent")
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(commit (string-append "v" version))))
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(file-name (git-file-name name version))
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(sha256
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(base32
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"12q7hhly76l77vm8w8v9icga2gn6xs0bw33a7wb7zikcmvizcyp0"))))
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(build-system ant-build-system)
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(arguments
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(list
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#:tests? #false ;there are none
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#:jdk icedtea-8
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#:phases
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#~(modify-phases %standard-phases
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(replace 'build
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(lambda* (#:key inputs #:allow-other-keys)
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;; See https://github.com/mrmaxent/Maxent/pull/11
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(substitute* "density/Extractor.java"
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(("float") "double"))
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(with-directory-excursion "gnu/getopt/"
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(invoke "make"))
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(mkdir-p "ptii")
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(with-directory-excursion "ptii"
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(invoke "tar" "xvf" (assoc-ref inputs "ptii")
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"--strip-components=1")
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(copy-recursively "com" "../com"))
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(delete-file-recursively "ptii")
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(apply invoke "javac" "-cp" (getcwd) "-g"
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(find-files "com/microstar/xml" "\\.java$"))
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(apply invoke "javac" "-cp" (getcwd) "-g"
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(find-files "density" "\\.java$"))
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;; This needs the proprietary com.sun.image.codec.jpeg module.
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(delete-file "ptolemy/plot/servlet/PlotServlet.java")
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(apply invoke "javac" "-cp"
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(string-append (getcwd) ":" (getenv "CLASSPATH")) "-g"
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(find-files "ptolemy/plot" "\\.java$"))
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(apply invoke "javac" "-cp" (getcwd) "-g"
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(find-files "com" "\\.java$"))
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(apply invoke "javac" "-cp" (getcwd) "-g"
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(find-files "gui" "\\.java$"))
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(apply invoke "jar" "cvfm" "maxent.jar"
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(cons* "density/mc.mf"
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"density/parameters.csv"
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(append (find-files "density" "\\.class$")
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(find-files "density" "\\.html$")
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(find-files "gnu/getopt" ".*")
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(find-files "gui/layouts" "\\.class$")
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(find-files "com/macfaq/io" "\\.class$")
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(find-files "density/tools" "\\.class$")
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(find-files "ptolemy/plot" "\\.class$"))))))
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(replace 'install
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(lambda _
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(install-file "maxent.jar"
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(string-append #$output "/share/java/maxent/")))))))
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(inputs
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(list java-classpathx-servletapi))
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(native-inputs
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`(("make" ,gnu-make)
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;; For com.microstar.xml
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("ptii"
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,(let ((version "4.0.1"))
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(origin
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(method url-fetch)
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(uri (string-append "https://ptolemy.berkeley.edu/ptolemyII/ptII"
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(version-major+minor version)
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"/ptII" version ".src.tar.gz"))
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(sha256
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(base32
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"0ifmmvrcipcnd4b9im1g379ffrs7g7k99sw5vv9d9h3hzq6hqv21")))))))
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(home-page "http://biodiversityinformatics.amnh.org/open_source/maxent")
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(synopsis "Model species geographic distributions")
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(description
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"Maxent is a stand-alone Java application for modelling species
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geographic distributions.")
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(license license:expat)))
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;; This version matches java-htsjdk 2.3.0. Later versions also require a more
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;; recent version of java-htsjdk, which depends on gradle.
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(define-public java-picard
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