From b0926f0df4f76b24dbb99da3f10a87e606fac993 Mon Sep 17 00:00:00 2001
From: Efraim Flashner
Date: Mon, 5 Aug 2019 07:41:00 -0500
Subject: gn: varscan: Fix build.

* gn/packages/bioinformatics.scm (varscan)[arguments]: Disable tests.
Update all custom phases.
[home-page]: Use https.
[description]: Add it.
---
 gn/packages/bioinformatics.scm | 55 ++++++++++++++++++++----------------------
 1 file changed, 26 insertions(+), 29 deletions(-)

diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index e5914c2..b7db927 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -881,45 +881,42 @@ reads.")
        (base32 "0y45ympkza7qwcbcisg006286pwjbr5978n03hx5nvl09f0mapk8"))))
     (build-system ant-build-system)
     (arguments
-     `(#:phases
+     `(#:tests? #f ; build.xml does not exist
+       #:phases
        (modify-phases %standard-phases
          (replace 'unpack
            (lambda _
              (mkdir "source")
              (chdir "source")
-             (and
-              ;; Unpack the Java archive containing the source files.
-              (zero? (system* "jar" "xf" (assoc-ref %build-inputs "source")))
-              ;; Remove existing compiled output.
-              (with-directory-excursion "net/sf/varscan/"
-                (for-each (lambda (file)
-                            (unless (string= (string-take-right file 5) ".java")
-                              (zero? (system* "rm" file))))
-                          (find-files "." #:directories? #f))))))
+             ;; Unpack the Java archive containing the source files.
+             (invoke "jar" "xf" (assoc-ref %build-inputs "source"))
+             ;; Remove existing compiled output.
+             (with-directory-excursion "net/sf/varscan/"
+               (for-each (lambda (file)
+                           (delete-file file))
+                         (find-files "." "^.java$" #:directories? #f)))
+             #t))
          (replace 'build
            (lambda _
-             (let ((classes '()))
-             (and
-              ;; Compile the source files.
-              (with-directory-excursion "net/sf/varscan/"
-                (for-each (lambda (file)
-                            (when (string= (string-take-right file 5) ".java")
-                              (zero? (system* "javac" file))
-                              (cons ))
-                          (find-files "." #:directories? #f)))
-              ;; Construct the new Java archive.
-              (zero? (system* "jar" "cfm" "varscan-2.4.1.jar"
-                              "META-INF/MANIFEST.MF"
-                              "net/sf/varscan/*.java")))))))
+             ;; Compile the source files.
+             (with-directory-excursion "net/sf/varscan/"
+               (for-each (lambda (file)
+                           (invoke "javac" file))
+                         (find-files "." ".java$" #:directories? #f)))
+             ;; Construct the new Java archive.
+             (apply invoke "jar" "cfm"
+                    (string-append "varscan-" ,version ".jar")
+                    "META-INF/MANIFEST.MF"
+                    (find-files "net/sf/varscan" ".java$"))))
         (replace 'install
-          (lambda _
-            (let ((out (string-append (assoc-ref %outputs "out")
+          (lambda* (#:key outputs #:allow-other-keys)
+            (let ((out (string-append (assoc-ref outputs "out")
                                       "/share/java/varscan/")))
-              (mkdir-p out)
-              (install-file "varscan-2.4.1.jar" out)))))))
-    (home-page "http://dkoboldt.github.io/varscan/")
+              (install-file (string-append "varscan-" ,version ".jar") out))
+            #t)))))
+    (home-page "https://dkoboldt.github.io/varscan/")
     (synopsis "Variant detection in massively parallel sequencing data")
-    (description "")
+    (description "Variant detection in massively parallel sequencing data.")
     ;; Free for non-commercial use by academic, government, and
     ;; non-profit/not-for-profit institutions
     (license license:non-copyleft)))
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