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08/17: gnu: Add java-forester-1.005.
From: |
Ricardo Wurmus |
Subject: |
08/17: gnu: Add java-forester-1.005. |
Date: |
Sat, 3 Mar 2018 15:28:37 -0500 (EST) |
rekado pushed a commit to branch master
in repository guix.
commit 10645b9212d5eff74132edf60c90c3eb099a139f
Author: Ricardo Wurmus <address@hidden>
Date: Thu Mar 1 19:41:40 2018 +0100
gnu: Add java-forester-1.005.
* gnu/packages/bioinformatics.scm (java-forester-1.005): New variable.
---
gnu/packages/bioinformatics.scm | 95 +++++++++++++++++++++++++++++++++++++++++
1 file changed, 95 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index ef1e860..d64cda2 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")
- branch master updated (bd97583 -> 1adeef3), Ricardo Wurmus, 2018/03/03
- 02/17: gnu: Add java-jlargearrays., Ricardo Wurmus, 2018/03/03
- 03/17: gnu: Add java-jtransforms., Ricardo Wurmus, 2018/03/03
- 05/17: gnu: Add java-biojava-core., Ricardo Wurmus, 2018/03/03
- 06/17: gnu: Add java-openchart2., Ricardo Wurmus, 2018/03/03
- 04/17: gnu: Add java-jdistlib., Ricardo Wurmus, 2018/03/03
- 09/17: gnu: Add java-biojava-phylo., Ricardo Wurmus, 2018/03/03
- 08/17: gnu: Add java-forester-1.005.,
Ricardo Wurmus <=
- 01/17: gnu: Add java-la4j., Ricardo Wurmus, 2018/03/03
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- 11/17: gnu: Add java-biojava-core-4.0., Ricardo Wurmus, 2018/03/03
- 10/17: gnu: Add java-biojava-alignment., Ricardo Wurmus, 2018/03/03
- 12/17: gnu: Add java-biojava-phylo-4.0., Ricardo Wurmus, 2018/03/03
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