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gnu: sra-tools: Use "modify-phases" syntax. 

* gnu/packages/bioinformatics.scm (sra-tools)[arguments]: Use "modify-phases"
syntax.
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Ricardo Wurmus 2017-04-05 17:48:26 +02:00 committed by Ricardo Wurmus
parent fc5b12879f
commit beebe43176
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1 changed files with 41 additions and 42 deletions
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@ -4790,50 +4790,49 @@ sequence itself can be retrieved from these databases.")
"/lib64" "/lib64"
"/lib32"))) "/lib32")))
#:phases #:phases
(alist-replace (modify-phases %standard-phases
'configure (replace 'configure
(lambda* (#:key inputs outputs #:allow-other-keys) (lambda* (#:key inputs outputs #:allow-other-keys)
;; The build system expects a directory containing the sources and ;; The build system expects a directory containing the sources and
;; raw build output of ncbi-vdb, including files that are not ;; raw build output of ncbi-vdb, including files that are not
;; installed. Since we are building against an installed version of ;; installed. Since we are building against an installed version of
;; ncbi-vdb, the following modifications are needed. ;; ncbi-vdb, the following modifications are needed.
(substitute* "setup/konfigure.perl" (substitute* "setup/konfigure.perl"
;; Make the configure script look for the "ilib" directory of ;; Make the configure script look for the "ilib" directory of
;; "ncbi-vdb" without first checking for the existence of a ;; "ncbi-vdb" without first checking for the existence of a
;; matching library in its "lib" directory. ;; matching library in its "lib" directory.
(("^ my \\$f = File::Spec->catdir\\(\\$libdir, \\$lib\\);") (("^ my \\$f = File::Spec->catdir\\(\\$libdir, \\$lib\\);")
"my $f = File::Spec->catdir($ilibdir, $ilib);") "my $f = File::Spec->catdir($ilibdir, $ilib);")
;; Look for interface libraries in ncbi-vdb's "ilib" directory. ;; Look for interface libraries in ncbi-vdb's "ilib" directory.
(("my \\$ilibdir = File::Spec->catdir\\(\\$builddir, 'ilib'\\);") (("my \\$ilibdir = File::Spec->catdir\\(\\$builddir, 'ilib'\\);")
"my $ilibdir = File::Spec->catdir($dir, 'ilib');")) "my $ilibdir = File::Spec->catdir($dir, 'ilib');"))
;; Dynamic linking ;; Dynamic linking
(substitute* "tools/copycat/Makefile" (substitute* "tools/copycat/Makefile"
(("smagic-static") "lmagic")) (("smagic-static") "lmagic"))
;; The 'configure' script doesn't recognize things like ;; The 'configure' script doesn't recognize things like
;; '--enable-fast-install'. ;; '--enable-fast-install'.
(zero? (system* (zero? (system*
"./configure" "./configure"
(string-append "--build-prefix=" (getcwd) "/build") (string-append "--build-prefix=" (getcwd) "/build")
(string-append "--prefix=" (assoc-ref outputs "out")) (string-append "--prefix=" (assoc-ref outputs "out"))
(string-append "--debug") (string-append "--debug")
(string-append "--with-fuse-prefix=" (string-append "--with-fuse-prefix="
(assoc-ref inputs "fuse")) (assoc-ref inputs "fuse"))
(string-append "--with-magic-prefix=" (string-append "--with-magic-prefix="
(assoc-ref inputs "libmagic")) (assoc-ref inputs "libmagic"))
;; TODO: building with libxml2 fails with linker errors ;; TODO: building with libxml2 fails with linker errors
;; (string-append "--with-xml2-prefix=" ;; (string-append "--with-xml2-prefix="
;; (assoc-ref inputs "libxml2")) ;; (assoc-ref inputs "libxml2"))
(string-append "--with-ncbi-vdb-sources=" (string-append "--with-ncbi-vdb-sources="
(assoc-ref inputs "ncbi-vdb")) (assoc-ref inputs "ncbi-vdb"))
(string-append "--with-ncbi-vdb-build=" (string-append "--with-ncbi-vdb-build="
(assoc-ref inputs "ncbi-vdb")) (assoc-ref inputs "ncbi-vdb"))
(string-append "--with-ngs-sdk-prefix=" (string-append "--with-ngs-sdk-prefix="
(assoc-ref inputs "ngs-sdk")) (assoc-ref inputs "ngs-sdk"))
(string-append "--with-hdf5-prefix=" (string-append "--with-hdf5-prefix="
(assoc-ref inputs "hdf5"))))) (assoc-ref inputs "hdf5")))))))))
%standard-phases)))
(native-inputs `(("perl" ,perl))) (native-inputs `(("perl" ,perl)))
(inputs (inputs
`(("ngs-sdk" ,ngs-sdk) `(("ngs-sdk" ,ngs-sdk)