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01/02: gnu: sra-tools: Use "modify-phases" syntax.
From: |
Ricardo Wurmus |
Subject: |
01/02: gnu: sra-tools: Use "modify-phases" syntax. |
Date: |
Wed, 5 Apr 2017 12:07:06 -0400 (EDT) |
rekado pushed a commit to branch master
in repository guix.
commit beebe43176b6e63f35932f280f43969c46d951d8
Author: Ricardo Wurmus <address@hidden>
Date: Wed Apr 5 17:48:26 2017 +0200
gnu: sra-tools: Use "modify-phases" syntax.
* gnu/packages/bioinformatics.scm (sra-tools)[arguments]: Use
"modify-phases"
syntax.
---
gnu/packages/bioinformatics.scm | 87 ++++++++++++++++++++---------------------
1 file changed, 43 insertions(+), 44 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 9244ae3..6a04e69 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -4790,50 +4790,49 @@ sequence itself can be retrieved from these databases.")
"/lib64"
"/lib32")))
#:phases
- (alist-replace
- 'configure
- (lambda* (#:key inputs outputs #:allow-other-keys)
- ;; The build system expects a directory containing the sources and
- ;; raw build output of ncbi-vdb, including files that are not
- ;; installed. Since we are building against an installed version of
- ;; ncbi-vdb, the following modifications are needed.
- (substitute* "setup/konfigure.perl"
- ;; Make the configure script look for the "ilib" directory of
- ;; "ncbi-vdb" without first checking for the existence of a
- ;; matching library in its "lib" directory.
- (("^ my \\$f = File::Spec->catdir\\(\\$libdir,
\\$lib\\);")
- "my $f = File::Spec->catdir($ilibdir, $ilib);")
- ;; Look for interface libraries in ncbi-vdb's "ilib" directory.
- (("my \\$ilibdir = File::Spec->catdir\\(\\$builddir, 'ilib'\\);")
- "my $ilibdir = File::Spec->catdir($dir, 'ilib');"))
-
- ;; Dynamic linking
- (substitute* "tools/copycat/Makefile"
- (("smagic-static") "lmagic"))
-
- ;; 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-fuse-prefix="
- (assoc-ref inputs "fuse"))
- (string-append "--with-magic-prefix="
- (assoc-ref inputs "libmagic"))
- ;; TODO: building with libxml2 fails with linker errors
- ;; (string-append "--with-xml2-prefix="
- ;; (assoc-ref inputs "libxml2"))
- (string-append "--with-ncbi-vdb-sources="
- (assoc-ref inputs "ncbi-vdb"))
- (string-append "--with-ncbi-vdb-build="
- (assoc-ref inputs "ncbi-vdb"))
- (string-append "--with-ngs-sdk-prefix="
- (assoc-ref inputs "ngs-sdk"))
- (string-append "--with-hdf5-prefix="
- (assoc-ref inputs "hdf5")))))
- %standard-phases)))
+ (modify-phases %standard-phases
+ (replace 'configure
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ ;; The build system expects a directory containing the sources and
+ ;; raw build output of ncbi-vdb, including files that are not
+ ;; installed. Since we are building against an installed version
of
+ ;; ncbi-vdb, the following modifications are needed.
+ (substitute* "setup/konfigure.perl"
+ ;; Make the configure script look for the "ilib" directory of
+ ;; "ncbi-vdb" without first checking for the existence of a
+ ;; matching library in its "lib" directory.
+ (("^ my \\$f = File::Spec->catdir\\(\\$libdir,
\\$lib\\);")
+ "my $f = File::Spec->catdir($ilibdir, $ilib);")
+ ;; Look for interface libraries in ncbi-vdb's "ilib" directory.
+ (("my \\$ilibdir = File::Spec->catdir\\(\\$builddir,
'ilib'\\);")
+ "my $ilibdir = File::Spec->catdir($dir, 'ilib');"))
+
+ ;; Dynamic linking
+ (substitute* "tools/copycat/Makefile"
+ (("smagic-static") "lmagic"))
+
+ ;; 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-fuse-prefix="
+ (assoc-ref inputs "fuse"))
+ (string-append "--with-magic-prefix="
+ (assoc-ref inputs "libmagic"))
+ ;; TODO: building with libxml2 fails with linker errors
+ ;; (string-append "--with-xml2-prefix="
+ ;; (assoc-ref inputs "libxml2"))
+ (string-append "--with-ncbi-vdb-sources="
+ (assoc-ref inputs "ncbi-vdb"))
+ (string-append "--with-ncbi-vdb-build="
+ (assoc-ref inputs "ncbi-vdb"))
+ (string-append "--with-ngs-sdk-prefix="
+ (assoc-ref inputs "ngs-sdk"))
+ (string-append "--with-hdf5-prefix="
+ (assoc-ref inputs "hdf5")))))))))
(native-inputs `(("perl" ,perl)))
(inputs
`(("ngs-sdk" ,ngs-sdk)