diff options
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 83 |
1 files changed, 83 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index fe43b04dcc..89f8041d56 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -5537,6 +5537,89 @@ manipulating HTS data.") (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 |