From 558e23074e258202421e8e675927ec35f35db493 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 16 Mar 2017 13:38:39 +0100
Subject: [PATCH] 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 7238446aaf0..eb74da6b284 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -4483,6 +4483,11 @@ (define-public ncbi-vdb
(("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 @@ (define-public ncbi-vdb
(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
--
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