04/06: gnu: ncbi-vdb: Override search path for java-ngs.

[Ricardo Wurmus]

rekado pushed a commit to branch master
in repository guix.

commit 558e23074e258202421e8e675927ec35f35db493
Author: Ricardo Wurmus <address@hidden>
Date:   Thu Mar 16 13:38:39 2017 +0100

    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".
---
 gnu/packages/bioinformatics.scm | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 7238446..eb74da6 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