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authorEfraim Flashner2021-07-15 12:19:08 +0300
committerEfraim Flashner2021-07-15 12:19:08 +0300
commit69223db92f597d829cc408a218e75eead35afb9a (patch)
treed2f4413ebbccd410184b5788d681b3361952c0ad
parenteecc939c493e1d5d0aa11c2831ce847be47a1c6f (diff)
downloadguix-bioinformatics-69223db92f597d829cc408a218e75eead35afb9a.tar.gz
gn: Provide rtg.cfg for rtg-tools.
-rw-r--r--gn/packages/bioinformatics.scm6
-rw-r--r--gn/packages/java.scm16
2 files changed, 18 insertions, 4 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index bb11987..de66599 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -2063,10 +2063,8 @@ cases include:
(lambda* (#:key inputs #:allow-other-keys)
(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"
- (string-append dest "/rtg.cfg"))
+ (mkdir-p (dirname dest))
+ (symlink rtg-tools dest)
#t)))
(replace 'configure
(lambda* (#:key outputs (configure-flags '()) (out-of-source? #t)
diff --git a/gn/packages/java.scm b/gn/packages/java.scm
index 23b59be..cdd9d00 100644
--- a/gn/packages/java.scm
+++ b/gn/packages/java.scm
@@ -339,6 +339,22 @@ piece of information.")
(delete-file-recursively pkg)
(delete-file (string-append pkg "-nojre.zip")))
#t)))
+ (add-after 'install 'create-rtg.cfg
+ (lambda* (#:key 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))
(delete 'generate-jar-indices)))) ; manually installed
(inputs
`(("java-commons-collections" ,java-commons-collections)