diff options
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 95 |
1 files changed, 95 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index ef1e8606a9..d64cda2340 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -12026,6 +12026,101 @@ phylogenomics and evolutionary biology research. It includes support for reading, writing, and exporting phylogenetic trees.") (license license:lgpl2.1+)))) +(define-public java-forester-1.005 + (package + (name "java-forester") + (version "1.005") + (source (origin + (method url-fetch) + (uri (string-append "http://search.maven.org/remotecontent?" + "filepath=org/biojava/thirdparty/forester/" + version "/forester-" version "-sources.jar")) + (file-name (string-append name "-" version ".jar")) + (sha256 + (base32 + "04r8qv4rk3p71z4ajrvp11py1z46qrx0047j3zzs79s6lnsm3lcv")))) + (build-system ant-build-system) + (arguments + `(#:tests? #f ; there are none + #:jdk ,icedtea-8 + #:modules ((guix build ant-build-system) + (guix build utils) + (guix build java-utils) + (sxml simple) + (sxml transform)) + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'fix-dependencies + (lambda* (#:key inputs #:allow-other-keys) + (call-with-output-file "build.xml" + (lambda (port) + (sxml->xml + (pre-post-order + (with-input-from-file "src/build.xml" + (lambda _ (xml->sxml #:trim-whitespace? #t))) + `(;; Remove all unjar tags to avoid repacking classes. + (unjar . ,(lambda _ '())) + (*default* . ,(lambda (tag . kids) `(,tag ,@kids))) + (*text* . ,(lambda (_ txt) txt)))) + port))) + (copy-file (assoc-ref inputs "synth_look_and_feel_1.xml") + "synth_look_and_feel_1.xml") + (copy-file (assoc-ref inputs "phyloxml.xsd") + "phyloxml.xsd") + (substitute* "build.xml" + (("../resources/synth_laf/synth_look_and_feel_1.xml") + "synth_look_and_feel_1.xml") + (("../resources/phyloxml_schema/1.10/phyloxml.xsd") + "phyloxml.xsd")) + #t)) + ;; FIXME: itext is difficult to package as it depends on a few + ;; unpackaged libraries. + (add-after 'unpack 'remove-dependency-on-unpackaged-itext + (lambda _ + (delete-file "src/org/forester/archaeopteryx/PdfExporter.java") + (substitute* '("src/org/forester/archaeopteryx/MainFrame.java" + "src/org/forester/archaeopteryx/MainFrameApplication.java") + (("pdf_written_to = PdfExporter.*") + "throw new IOException(\"PDF export is not available.\"); /*") + ((".getPrintSizeX\\(\\), getOptions\\(\\).getPrintSizeY\\(\\) \\);") "*/") + (("getCurrentTreePanel\\(\\).getHeight\\(\\) \\);") "*/")) + #t)) + (add-after 'unpack 'delete-pre-built-classes + (lambda _ (delete-file-recursively "src/classes") #t)) + ;; There is no install target + (replace 'install (install-jars "."))))) + (propagated-inputs + `(("java-commons-codec" ,java-commons-codec) + ("java-openchart2" ,java-openchart2))) + ;; The source archive does not contain the resources. + (native-inputs + `(("phyloxml.xsd" + ,(origin + (method url-fetch) + (uri (string-append "https://raw.githubusercontent.com/cmzmasek/forester/" + "b61cc2dcede0bede317db362472333115756b8c6/" + "forester/resources/phyloxml_schema/1.10/phyloxml.xsd")) + (file-name (string-append name "-phyloxml-" version ".xsd")) + (sha256 + (base32 + "1zxc4m8sn4n389nqdnpxa8d0k17qnr3pm2y5y6g6vh4k0zm52npv")))) + ("synth_look_and_feel_1.xml" + ,(origin + (method url-fetch) + (uri (string-append "https://raw.githubusercontent.com/cmzmasek/forester/" + "29e04321615da6b35c1e15c60e52caf3f21d8e6a/" + "forester/java/classes/resources/synth_look_and_feel_1.xml")) + (file-name (string-append name "-synth-look-and-feel-" version ".xml")) + (sha256 + (base32 + "1gv5602gv4k7y7713y75a4jvj7i9s7nildsbdl7n9q10sc2ikg8h")))))) + (home-page "https://sites.google.com/site/cmzmasek/home/software/forester") + (synopsis "Phylogenomics libraries for Java") + (description "Forester is a collection of Java libraries for +phylogenomics and evolutionary biology research. It includes support for +reading, writing, and exporting phylogenetic trees.") + (license license:lgpl2.1+))) + (define-public java-biojava-core (package (name "java-biojava-core") |