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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".
master
Ricardo Wurmus 2017-03-16 13:38:39 +01:00
parent 701111989e
commit 558e23074e
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1 changed files with 5 additions and 2 deletions
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gnu/packages/bioinformatics.scm
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@ -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