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[bug#30666] [PATCH 07/17] gnu: Add java-forester.
From: |
Ricardo Wurmus |
Subject: |
[bug#30666] [PATCH 07/17] gnu: Add java-forester. |
Date: |
Thu, 1 Mar 2018 19:41:39 +0100 |
* gnu/packages/bioinformatics.scm (java-forester): New variable.
---
gnu/packages/bioinformatics.scm | 76 +++++++++++++++++++++++++++++++++++++++++
1 file changed, 76 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 60dbc956a..a41efc054 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -11887,6 +11887,82 @@ graphs. This library makes it easy to work with
@file{.loom} files for
single-cell RNA-seq data.")
(license license:bsd-3)))
+;; We cannot use the latest commit because it requires Java 9.
+(define-public java-forester
+ (let ((commit "86b07efe302d5094b42deed9260f719a4c4ac2e6")
+ (revision "1"))
+ (package
+ (name "java-forester")
+ (version (string-append "0-" revision "." (string-take commit 7)))
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/cmzmasek/forester.git")
+ (commit commit)))
+ (file-name (string-append name "-" version "-checkout"))
+ (sha256
+ (base32
+ "0vxavc1yrf84yrnf20dq26hi0lglidk8d382xrxsy4qmlbjd276z"))
+ (modules '((guix build utils)))
+ (snippet
+ '(begin
+ ;; Delete bundled jars and pre-built classes
+ (delete-file-recursively "forester/java/resources")
+ (delete-file-recursively "forester/java/classes")
+ (for-each delete-file (find-files "forester/java/"
"\\.jar$"))
+ ;; Delete bundled applications
+ (delete-file-recursively "forester_applications")
+ #t))))
+ (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 'chdir
+ (lambda _ (chdir "forester/java") #t))
+ (add-after 'chdir 'fix-dependencies
+ (lambda _
+ (chmod "build.xml" #o664)
+ (call-with-output-file "build.xml.new"
+ (lambda (port)
+ (sxml->xml
+ (pre-post-order
+ (with-input-from-file "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)))
+ (rename-file "build.xml.new" "build.xml")
+ #t))
+ ;; FIXME: itext is difficult to package as it depends on a few
+ ;; unpackaged libraries.
+ (add-after 'chdir 'remove-dependency-on-unpackaged-itext
+ (lambda _
+ (delete-file "src/org/forester/archaeopteryx/PdfExporter.java")
+ (substitute* "src/org/forester/archaeopteryx/MainFrame.java"
+ (("pdf_written_to = PdfExporter.*")
+ "throw new IOException(\"PDF export is not available.\");"))
+ #t))
+ ;; There is no install target
+ (replace 'install (install-jars ".")))))
+ (propagated-inputs
+ `(("java-commons-codec" ,java-commons-codec)
+ ("java-openchart2" ,java-openchart2)))
+ (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")
--
2.15.1
- [bug#30666] [PATCH 00/17] Add dropseq-tools., Ricardo Wurmus, 2018/03/01
- [bug#30666] [PATCH 01/17] gnu: Add java-la4j., Ricardo Wurmus, 2018/03/01
- [bug#30666] [PATCH 04/17] gnu: Add java-jdistlib., Ricardo Wurmus, 2018/03/01
- [bug#30666] [PATCH 05/17] gnu: Add java-biojava-core., Ricardo Wurmus, 2018/03/01
- [bug#30666] [PATCH 06/17] gnu: Add java-openchart2., Ricardo Wurmus, 2018/03/01
- [bug#30666] [PATCH 07/17] gnu: Add java-forester.,
Ricardo Wurmus <=
- [bug#30666] [PATCH 10/17] gnu: Add java-biojava-alignment., Ricardo Wurmus, 2018/03/01
- [bug#30666] [PATCH 08/17] gnu: Add java-forester-1.005., Ricardo Wurmus, 2018/03/01
- [bug#30666] [PATCH 11/17] gnu: Add java-biojava-core-4.0., Ricardo Wurmus, 2018/03/01
- [bug#30666] [PATCH 03/17] gnu: Add java-jtransforms., Ricardo Wurmus, 2018/03/01
- [bug#30666] [PATCH 09/17] gnu: Add java-biojava-phylo., Ricardo Wurmus, 2018/03/01
- [bug#30666] [PATCH 02/17] gnu: Add java-jlargearrays., Ricardo Wurmus, 2018/03/01
- [bug#30666] [PATCH 12/17] gnu: Add java-biojava-phylo-4.0., Ricardo Wurmus, 2018/03/01
- [bug#30666] [PATCH 13/17] gnu: Add java-biojava-alignment-4.0., Ricardo Wurmus, 2018/03/01
- [bug#30666] [PATCH 14/17] gnu: Add java-htsjdk-latest., Ricardo Wurmus, 2018/03/01
- [bug#30666] [PATCH 15/17] gnu: Add java-htsjdk-2.10.1., Ricardo Wurmus, 2018/03/01