diff options
Diffstat (limited to 'gn/packages/java.scm')
| -rw-r--r-- | gn/packages/java.scm | 81 |
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))) |