From 69223db92f597d829cc408a218e75eead35afb9a Mon Sep 17 00:00:00 2001
From: Efraim Flashner
Date: Thu, 15 Jul 2021 12:19:08 +0300
Subject: gn: Provide rtg.cfg for rtg-tools.

---
 gn/packages/bioinformatics.scm |  6 ++----
 gn/packages/java.scm           | 16 ++++++++++++++++
 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)
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