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-rw-r--r--gn/packages/java.scm81
1 files changed, 79 insertions, 2 deletions
diff --git a/gn/packages/java.scm b/gn/packages/java.scm
index 6d835b1..23b59be 100644
--- a/gn/packages/java.scm
+++ b/gn/packages/java.scm
@@ -28,12 +28,14 @@
#:use-module (gnu packages)
#:use-module (gnu packages autotools)
#:use-module (gnu packages bioinformatics)
+ #:use-module (gnu packages certs)
#:use-module (gnu packages compression)
#:use-module (gnu packages gcc)
+ #:use-module (gnu packages icu4c)
#:use-module (gnu packages java)
+ #:use-module (gnu packages java-compression)
#:use-module (gnu packages perl)
- #:use-module (gnu packages certs)
- )
+ #:use-module (srfi srfi-1))
;; ----------------------------------------------------------------------------
;; WORKING PACKAGES
@@ -297,3 +299,78 @@ comprehension tool. Based on the concept of a project object model (POM),
Maven can manage a project's build, reporting and documentation from a central
piece of information.")
(license license:asl2.0)))
+
+;; TODO: Remove bundled jars from buildLib, lib, testLib and javascript
+(define-public rtg-tools
+ (package
+ (name "rtg-tools")
+ (version "3.11")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/RealTimeGenomics/rtg-tools")
+ (commit version)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "13fjhhcjgnynxscaymkn3rpdciplbg2m2qmihc7fxsylgn4m6gxk"))))
+ (build-system ant-build-system)
+ (arguments
+ `(#:build-target "zip-nojre"
+ #:test-target "runalltests"
+ #:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'adjust-source
+ (lambda _
+ (substitute* "build.xml"
+ (("\"git\"") "\"echo\"")
+ (("\\$\\{vcs\\.cmd\\.out\\}") "${product.version}")
+ (("\\$\\{build\\.time\\}") "1970-01-01")
+ (("-\\$\\{rtg\\.vcs\\.commit\\.revision\\}") ""))
+ #t))
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((out (assoc-ref outputs "out"))
+ (pkg (string-append ,name "-" ,version)))
+ (install-file (string-append "dist/" pkg "-nojre.zip")
+ out)
+ (with-directory-excursion out
+ (invoke "unzip" (string-append pkg "-nojre.zip"))
+ (copy-recursively (string-append pkg "/") ".")
+ (delete-file-recursively pkg)
+ (delete-file (string-append pkg "-nojre.zip")))
+ #t)))
+ (delete 'generate-jar-indices)))) ; manually installed
+ (inputs
+ `(("java-commons-collections" ,java-commons-collections)
+ ("java-commons-compress" ,java-commons-compress)
+ ("java-commons-lang" ,java-commons-lang)
+ ;("java-graal-sdk" ,java-graal-sdk)
+ ;("java-gzipfix" ,java-gzipfix)
+ ;("java-htsjdk" ,java-sam-rtg)
+ ("java-icu4j" ,java-icu4j)
+ ;("java-js" ,java-js)
+ ;("java-js-scriptengine" ,java-js-scriptengine)
+ ;("java-json-simple" ,java-json-simple)
+ ;("java-regex" ,java-regex)
+ ;("java-rplot" ,java-rplot)
+ ("java-snappy" ,java-snappy)
+ ;("java-truffle-api" ,java-truffle-api)
+ ;("java-velocity" ,java-velocity)
+ ;("java-velocity-tools-generic" ,java-velocity-tools-generic)
+ ))
+ (native-inputs
+ `(;("java-findbugs-annotations" ,java-findbugs-annotations)
+ ;("java-findbugs-jsr305" ,java-findbugs-jsr305)
+ ;("java-jumble-annotations" ,java-jumble-annotations)
+ ;; for tests
+ ("java-hamcrest-core" ,java-hamcrest-core)
+ ("java-junit" ,java-junit)
+ ;("java-spelling" ,java-spelling)
+ ("unzip" ,unzip)))
+ (home-page "https://github.com/RealTimeGenomics/rtg-tools/")
+ (synopsis "Utilities for accurate VCF comparison and manipulation")
+ (description "RTG Tools is a subset of RTG Core that includes several useful
+utilities for dealing with VCF files and sequence data. Probably the most
+interesting is the @code{vcfeval} command which performs sophisticated
+comparison of VCF files.")
+ (license license:bsd-2)))