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gnu: Add java-maxent.

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* gnu/packages/bioinformatics.scm (java-maxent): New variable.
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Ricardo Wurmus 2023-06-02 11:28:09 +02:00
parent 75bdd4b052
commit 341b4b2a97
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gnu/packages/bioinformatics.scm
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@ -5537,6 +5537,89 @@ (define-public java-htsjdk-2.10.1
(add-after 'unpack 'remove-tests
(lambda _ (delete-file-recursively "src/test") #t)))))))
(define-public java-maxent
(package
(name "java-maxent")
(version "3.4.4")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/mrmaxent/Maxent")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
"12q7hhly76l77vm8w8v9icga2gn6xs0bw33a7wb7zikcmvizcyp0"))))
(build-system ant-build-system)
(arguments
(list
#:tests? #false ;there are none
#:jdk icedtea-8
#:phases
#~(modify-phases %standard-phases
(replace 'build
(lambda* (#:key inputs #:allow-other-keys)
;; See https://github.com/mrmaxent/Maxent/pull/11
(substitute* "density/Extractor.java"
(("float") "double"))
(with-directory-excursion "gnu/getopt/"
(invoke "make"))
(mkdir-p "ptii")
(with-directory-excursion "ptii"
(invoke "tar" "xvf" (assoc-ref inputs "ptii")
"--strip-components=1")
(copy-recursively "com" "../com"))
(delete-file-recursively "ptii")
(apply invoke "javac" "-cp" (getcwd) "-g"
(find-files "com/microstar/xml" "\\.java$"))
(apply invoke "javac" "-cp" (getcwd) "-g"
(find-files "density" "\\.java$"))
;; This needs the proprietary com.sun.image.codec.jpeg module.
(delete-file "ptolemy/plot/servlet/PlotServlet.java")
(apply invoke "javac" "-cp"
(string-append (getcwd) ":" (getenv "CLASSPATH")) "-g"
(find-files "ptolemy/plot" "\\.java$"))
(apply invoke "javac" "-cp" (getcwd) "-g"
(find-files "com" "\\.java$"))
(apply invoke "javac" "-cp" (getcwd) "-g"
(find-files "gui" "\\.java$"))
(apply invoke "jar" "cvfm" "maxent.jar"
(cons* "density/mc.mf"
"density/parameters.csv"
(append (find-files "density" "\\.class$")
(find-files "density" "\\.html$")
(find-files "gnu/getopt" ".*")
(find-files "gui/layouts" "\\.class$")
(find-files "com/macfaq/io" "\\.class$")
(find-files "density/tools" "\\.class$")
(find-files "ptolemy/plot" "\\.class$"))))))
(replace 'install
(lambda _
(install-file "maxent.jar"
(string-append #$output "/share/java/maxent/")))))))
(inputs
(list java-classpathx-servletapi))
(native-inputs
`(("make" ,gnu-make)
;; For com.microstar.xml
("ptii"
,(let ((version "4.0.1"))
(origin
(method url-fetch)
(uri (string-append "https://ptolemy.berkeley.edu/ptolemyII/ptII"
(version-major+minor version)
"/ptII" version ".src.tar.gz"))
(sha256
(base32
"0ifmmvrcipcnd4b9im1g379ffrs7g7k99sw5vv9d9h3hzq6hqv21")))))))
(home-page "http://biodiversityinformatics.amnh.org/open_source/maxent")
(synopsis "Model species geographic distributions")
(description
"Maxent is a stand-alone Java application for modelling species
geographic distributions.")
(license license:expat)))
;; This version matches java-htsjdk 2.3.0. Later versions also require a more
;; recent version of java-htsjdk, which depends on gradle.
(define-public java-picard