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authorEfraim Flashner2023-09-21 15:31:42 +0300
committerEfraim Flashner2023-09-21 15:31:42 +0300
commitc944663d2d64824d7f947dc3f65bd5489fa1f8df (patch)
treead319426ce6679b78683d08284932151d9a3d156 /gn/packages
parent86583628060872edc5adb08cc73425087b153825 (diff)
downloadguix-bioinformatics-c944663d2d64824d7f947dc3f65bd5489fa1f8df.tar.gz
rtg: Update package definition.
Diffstat (limited to 'gn/packages')
-rw-r--r--gn/packages/java.scm85
1 files changed, 46 insertions, 39 deletions
diff --git a/gn/packages/java.scm b/gn/packages/java.scm
index cdd9d00..c8e1e9b 100644
--- a/gn/packages/java.scm
+++ b/gn/packages/java.scm
@@ -19,6 +19,7 @@
(define-module (gn packages java)
#:use-module ((guix licenses) #:prefix license:)
#:use-module (guix packages)
+ #:use-module (guix gexp)
#:use-module (guix utils)
#:use-module (guix download)
#:use-module (guix git-download)
@@ -27,11 +28,11 @@
#:use-module (guix build-system ant)
#:use-module (gnu packages)
#:use-module (gnu packages autotools)
+ #:use-module (gnu packages bash)
#: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)
@@ -325,8 +326,7 @@ piece of information.")
(("\"git\"") "\"echo\"")
(("\\$\\{vcs\\.cmd\\.out\\}") "${product.version}")
(("\\$\\{build\\.time\\}") "1970-01-01")
- (("-\\$\\{rtg\\.vcs\\.commit\\.revision\\}") ""))
- #t))
+ (("-\\$\\{rtg\\.vcs\\.commit\\.revision\\}") ""))))
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out"))
@@ -337,52 +337,59 @@ piece of information.")
(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-file (string-append pkg "-nojre.zip"))))))
(add-after 'install 'create-rtg.cfg
- (lambda* (#:key outputs #:allow-other-keys)
+ (lambda* (#:key inputs outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out")))
(with-output-to-file (string-append out "/rtg.cfg")
(lambda _
(format #t "RTG_JAVA=\"~a\"~@
RTG_TALKBACK=false~@
RTG_USAGE=false~%"
- (which "java"))))
- #t)))
- (add-after 'install 'install-completions
- (lambda* (#:key outputs #:allow-other-keys)
- (install-file "installer/resources/common/scripts/rtg-bash-completion"
- (string-append (assoc-ref outputs "out")
- "/share/bash-completion/completions"))
- #t))
+ (search-input-file inputs "/bin/java")))))))
+ (add-after 'install 'create-wrapper-script
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (let* ((out (assoc-ref outputs "out"))
+ (wrapper (string-append out "/bin/rtg")))
+ ;; We want an executable in the bin directory without rewriting
+ ;; the existing wrapper script.
+ (mkdir-p (dirname wrapper))
+ (with-output-to-file wrapper
+ (lambda _
+ (format #t "#!~a~@
+ exec -a \"$0\" \"~a/rtg\" \"$@\"~%"
+ (search-input-file inputs "/bin/bash")
+ out)))
+ (chmod wrapper #o555))))
+ (add-after 'install 'install-completions
+ (lambda* (#:key outputs #:allow-other-keys)
+ (install-file "installer/resources/common/scripts/rtg-bash-completion"
+ (string-append (assoc-ref outputs "out")
+ "/share/bash-completion/completions"))))
(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)
- ))
+ (list bash-minimal ; for the wrapper script
+ java-commons-collections
+ java-commons-compress
+ java-commons-lang
+ ;java-gzipfix
+ ;java-sam-rtg
+ ;java-json-simple
+ ;java-rplot
+ java-snappy
+ ;java-velocity
+ ;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)))
+ (list ;java-findbugs-annotations
+ ;java-findbugs-jsr305
+ ;java-jumble-annotations
+ ;; for tests
+ java-hamcrest-core
+ java-junit
+ ;java-spelling
+ ;; For the 'install phase.
+ 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