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-rw-r--r--gn/packages/bioinformatics.scm32
-rw-r--r--gn/packages/java.scm81
2 files changed, 86 insertions, 27 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index 9e63a26..bb11987 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -15,6 +15,7 @@
#:use-module (guix build-system trivial)
#:use-module (guix build-system waf)
#:use-module (gnu packages)
+ #:use-module (gn packages java)
#:use-module (gn packages python)
#:use-module (gn packages twint)
#:use-module (gnu packages algebra)
@@ -2060,20 +2061,12 @@ cases include:
#t)))
(add-after 'fix-build 'insert-rtg-tools
(lambda* (#:key inputs #:allow-other-keys)
- (let ((rtg-tools (assoc-ref inputs "rtg-tools")))
- (mkdir "external/libexec")
- (invoke "unzip" "-j" rtg-tools
- "rtg-tools-3.12.1/rtg"
- "rtg-tools-3.12.1/RTG.jar"
- "rtg-tools-3.12.1/README.txt"
- "rtg-tools-3.12.1/LICENSE.txt"
- "rtg-tools-3.12.1/third-party/gzipfix.jar"
- "-d" "external/libexec/rtg-tools-install")
- (mkdir "external/libexec/rtg-tools-install/third-party")
- (rename-file "external/libexec/rtg-tools-install/gzipfix.jar"
- "external/libexec/rtg-tools-install/third-party/gzipfix.jar")
+ (let ((rtg-tools (assoc-ref inputs "rtg-tools"))
+ (dest "external/libexec/rtg-tools-install"))
+ (mkdir-p dest)
+ (copy-recursively rtg-tools dest)
(copy-file "external/rtg.cfg"
- "external/libexec/rtg-tools-install/rtg.cfg")
+ (string-append dest "/rtg.cfg"))
#t)))
(replace 'configure
(lambda* (#:key outputs (configure-flags '()) (out-of-source? #t)
@@ -2155,18 +2148,6 @@ cases include:
,(string-append samtools "/bin")))))
(find-files (string-append out "/bin") "\\.py$"))
#t))))))
- (native-inputs
- `(("rtg-tools"
- ;; When updating this package also update the insert-rtg-tools phase.
- ;; This bundled software is bsd-2 licensed.
- ,(origin
- (method url-fetch)
- (uri (string-append "https://github.com/RealTimeGenomics/rtg-tools"
- "/releases/download/3.12.1"
- "/rtg-tools-3.12.1-nojre.zip"))
- (sha256
- (base32 "1an4axkrj28br09xpj9g0a6k5hrx1cx4wcldrryvj6a0ljqqrz2y"))))
- ("unzip" ,unzip)))
(inputs
`(("bcftools" ,bcftools)
("boost" ,boost-static) ; has to be boost-static
@@ -2179,6 +2160,7 @@ cases include:
("python2-pandas" ,python2-pandas)
("python2-pysam" ,python2-pysam)
("python2-scipy" ,python2-scipy)
+ ("rtg-tools" ,rtg-tools)
("samtools" ,samtools)
("zlib" ,zlib)))
(home-page "https://github.com/Illumina/hap.py")
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)))