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gnu: ncbi-vdb: Use modify-phases syntax. 

* gnu/packages/bioinformatics.scm (ncbi-vdb)[arguments]: Use modify-phases
syntax.
master
Ricardo Wurmus 2017-03-16 10:20:56 +01:00
parent 5021f54787
commit 701111989e
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1 changed files with 51 additions and 52 deletions
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gnu/packages/bioinformatics.scm
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@ -4463,61 +4463,60 @@ simultaneously.")
`(#:parallel-build? #f ; not supported
#:tests? #f ; no "check" target
#:phases
(alist-replace
'configure
(lambda* (#:key inputs outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out")))
;; Override include path for libmagic
(substitute* "setup/package.prl"
(("name => 'magic', Include => '/usr/include'")
(string-append "name=> 'magic', Include => '"
(assoc-ref inputs "libmagic")
"/include" "'")))
(modify-phases %standard-phases
(replace 'configure
(lambda* (#:key inputs outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out")))
;; Override include path for libmagic
(substitute* "setup/package.prl"
(("name => 'magic', Include => '/usr/include'")
(string-append "name=> 'magic', Include => '"
(assoc-ref inputs "libmagic")
"/include" "'")))
;; Install kdf5 library (needed by sra-tools)
(substitute* "build/Makefile.install"
(("LIBRARIES_TO_INSTALL =")
"LIBRARIES_TO_INSTALL = kdf5.$(VERSION_LIBX) kdf5.$(VERSION_SHLX)"))
;; Install kdf5 library (needed by sra-tools)
(substitute* "build/Makefile.install"
(("LIBRARIES_TO_INSTALL =")
"LIBRARIES_TO_INSTALL = kdf5.$(VERSION_LIBX) kdf5.$(VERSION_SHLX)"))
(substitute* "build/Makefile.env"
(("CFLAGS =" prefix)
(string-append prefix "-msse2 ")))
(substitute* "build/Makefile.env"
(("CFLAGS =" prefix)
(string-append prefix "-msse2 ")))
;; The 'configure' script doesn't recognize things like
;; '--enable-fast-install'.
(zero? (system*
"./configure"
(string-append "--build-prefix=" (getcwd) "/build")
(string-append "--prefix=" (assoc-ref outputs "out"))
(string-append "--debug")
(string-append "--with-xml2-prefix="
(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"))))))
(alist-cons-after
'install 'install-interfaces
(lambda* (#:key outputs #:allow-other-keys)
;; Install interface libraries. On i686 the interface libraries
;; are installed to "linux/gcc/i386", so we need to use the Linux
;; architecture name ("i386") instead of the target system prefix
;; ("i686").
(mkdir (string-append (assoc-ref outputs "out") "/ilib"))
(copy-recursively (string-append "build/ncbi-vdb/linux/gcc/"
,(system->linux-architecture
(or (%current-target-system)
(%current-system)))
"/rel/ilib")
(string-append (assoc-ref outputs "out")
"/ilib"))
;; Install interface headers
(copy-recursively "interfaces"
(string-append (assoc-ref outputs "out")
"/include")))
%standard-phases))))
;; The 'configure' script doesn't recognize things like
;; '--enable-fast-install'.
(zero? (system*
"./configure"
(string-append "--build-prefix=" (getcwd) "/build")
(string-append "--prefix=" (assoc-ref outputs "out"))
(string-append "--debug")
(string-append "--with-xml2-prefix="
(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
(lambda* (#:key outputs #:allow-other-keys)
;; Install interface libraries. On i686 the interface libraries
;; are installed to "linux/gcc/i386", so we need to use the Linux
;; architecture name ("i386") instead of the target system prefix
;; ("i686").
(mkdir (string-append (assoc-ref outputs "out") "/ilib"))
(copy-recursively (string-append "build/ncbi-vdb/linux/gcc/"
,(system->linux-architecture
(or (%current-target-system)
(%current-system)))
"/rel/ilib")
(string-append (assoc-ref outputs "out")
"/ilib"))
;; Install interface headers
(copy-recursively "interfaces"
(string-append (assoc-ref outputs "out")
"/include"))
#t)))))
(inputs
`(("libxml2" ,libxml2)
("ngs-sdk" ,ngs-sdk)