diff options
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 109 |
1 files changed, 54 insertions, 55 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index c9f901f32d..7238446aaf 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -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" "'"))) - - ;; 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 "))) - - ;; 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)))) + (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)")) + + (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"))))))) + (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) |