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authorRicardo Wurmus <ricardo.wurmus@mdc-berlin.de>2018-03-01 19:41:39 +0100
committerRicardo Wurmus <rekado@elephly.net>2018-03-03 21:27:41 +0100
commitf09d16e5949b5d84529be9022034e217fbaad54d (patch)
tree717faba12cee343cfb1ddf647da52a56bcc81763
parent93abc975feca4d877b0a14a0dd8f3613dcbd7c9b (diff)
downloadpatches-f09d16e5949b5d84529be9022034e217fbaad54d.tar
patches-f09d16e5949b5d84529be9022034e217fbaad54d.tar.gz
gnu: Add java-forester.
* gnu/packages/bioinformatics.scm (java-forester): New variable.
-rw-r--r--gnu/packages/bioinformatics.scm76
1 files changed, 76 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 4a90f30128..ef1e8606a9 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -11950,6 +11950,82 @@ 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")