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