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authorRicardo Wurmus <rekado@elephly.net>2017-03-16 13:38:39 +0100
committerRicardo Wurmus <rekado@elephly.net>2017-03-16 13:38:39 +0100
commit558e23074e258202421e8e675927ec35f35db493 (patch)
tree2e8720a6d00e4ef1b6dfc4b6ee050ef12dc37e19 /gnu/packages
parent701111989e446ef2d2ac2d0d67a1ae78c5e1499a (diff)
downloadguix-558e23074e258202421e8e675927ec35f35db493.tar.gz
gnu: ncbi-vdb: Override search path for java-ngs.
* gnu/packages/bioinformatics.scm (ncbi-vdb)[arguments]: Patch "package.prl"
to ensure that java-ngs is found by the configure script; remove configure
flag "--with-ngs-java-prefix".
Diffstat (limited to 'gnu/packages')
-rw-r--r--gnu/packages/bioinformatics.scm7
1 files changed, 5 insertions, 2 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 7238446aaf..eb74da6b28 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -4483,6 +4483,11 @@ simultaneously.")
                  (("CFLAGS	=" prefix)
                   (string-append prefix "-msse2 ")))
 
+               ;; Override search path for ngs-java
+               (substitute* "setup/package.prl"
+                 (("/usr/local/ngs/ngs-java")
+                  (assoc-ref inputs "java-ngs")))
+
                ;; The 'configure' script doesn't recognize things like
                ;; '--enable-fast-install'.
                (zero? (system*
@@ -4494,8 +4499,6 @@ simultaneously.")
                                       (assoc-ref inputs "libxml2"))
                        (string-append "--with-ngs-sdk-prefix="
                                       (assoc-ref inputs "ngs-sdk"))
-                       (string-append "--with-ngs-java-prefix="
-                                      (assoc-ref inputs "java-ngs"))
                        (string-append "--with-hdf5-prefix="
                                       (assoc-ref inputs "hdf5")))))))
          (add-after 'install 'install-interfaces