diff options
Diffstat (limited to 'gnu/packages')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 76 |
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") |