diff options
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 87 |
1 files changed, 43 insertions, 44 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 9244ae327c..6a04e69be3 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) |