gnu: ncbi-vdb: Ensure that vdb-sqlite is installed.
The most important change here is the addition of the 'install-libs phase. All other changes are just the result of switching to G-expressions. * gnu/packages/bioinformatics.scm (ncbi-vdb)[arguments]: Add 'install-libs phase; use G-expression; drop trailing #T from build phases. [inputs]: Drop package labels.
This commit is contained in:
Ricardo Wurmus
parent
263f235cd0
commit
8ba3bf6564
1 changed files with 88 additions and 88 deletions
|
|
@ -7561,99 +7561,99 @@ simultaneously.")
|
|||
"0m8hlxscidsfqm9x9fyi62q6lpf1dv5115kgjjgnrkl49q9c27m6"))))
|
||||
(build-system gnu-build-system)
|
||||
(arguments
|
||||
`(#:parallel-build? #f ; not supported
|
||||
#:tests? #f ; no "check" target
|
||||
#:make-flags '("HAVE_HDF5=1")
|
||||
#:phases
|
||||
(modify-phases %standard-phases
|
||||
(add-after 'unpack 'make-files-writable
|
||||
(lambda _ (for-each make-file-writable (find-files "." ".*")) #t))
|
||||
(add-before 'configure 'set-perl-search-path
|
||||
(lambda _
|
||||
;; Work around "dotless @INC" build failure.
|
||||
(setenv "PERL5LIB"
|
||||
(string-append (getcwd) "/setup:"
|
||||
(getenv "PERL5LIB")))
|
||||
#t))
|
||||
;; See https://github.com/ncbi/ncbi-vdb/issues/14
|
||||
(add-after 'unpack 'patch-krypto-flags
|
||||
(lambda _
|
||||
(substitute* "libs/krypto/Makefile"
|
||||
(("-Wa,-march=generic64\\+aes") "")
|
||||
(("-Wa,-march=generic64\\+sse4") ""))
|
||||
#t))
|
||||
(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" "'")))
|
||||
(list
|
||||
#:parallel-build? #f ; not supported
|
||||
#:tests? #f ; no "check" target
|
||||
#:make-flags '(list "HAVE_HDF5=1")
|
||||
#:phases
|
||||
#~(modify-phases %standard-phases
|
||||
#;
|
||||
(add-after 'unpack 'make-files-writable
|
||||
(lambda _ (for-each make-file-writable (find-files "." ".*"))))
|
||||
(add-before 'configure 'set-perl-search-path
|
||||
(lambda _
|
||||
;; Work around "dotless @INC" build failure.
|
||||
(setenv "PERL5LIB"
|
||||
(string-append (getcwd) "/setup:"
|
||||
(getenv "PERL5LIB")))))
|
||||
;; See https://github.com/ncbi/ncbi-vdb/issues/14
|
||||
(add-after 'unpack 'patch-krypto-flags
|
||||
(lambda _
|
||||
(substitute* "libs/krypto/Makefile"
|
||||
(("-Wa,-march=generic64\\+aes") "")
|
||||
(("-Wa,-march=generic64\\+sse4") ""))))
|
||||
(replace 'configure
|
||||
(lambda _
|
||||
;; Override include path for libmagic
|
||||
(substitute* "setup/package.prl"
|
||||
(("name => 'magic', Include => '/usr/include'")
|
||||
(string-append "name=> 'magic', Include => '"
|
||||
#$(this-package-input "file")
|
||||
"/include" "'")))
|
||||
|
||||
;; Install kdf5 library (needed by sra-tools)
|
||||
(substitute* "build/Makefile.install"
|
||||
(("LIBRARIES_TO_INSTALL =")
|
||||
"LIBRARIES_TO_INSTALL = kdf5.$(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.$(VERSION_SHLX)"))
|
||||
|
||||
(substitute* "build/Makefile.env"
|
||||
(("CFLAGS =" prefix)
|
||||
(string-append prefix "-msse2 ")))
|
||||
(substitute* "build/Makefile.env"
|
||||
(("CFLAGS =" prefix)
|
||||
(string-append prefix "-msse2 ")))
|
||||
|
||||
;; Override search path for ngs-java
|
||||
(substitute* "setup/package.prl"
|
||||
(("/usr/local/ngs/ngs-java")
|
||||
(assoc-ref inputs "java-ngs")))
|
||||
;; Override search path for ngs-java
|
||||
(substitute* "setup/package.prl"
|
||||
(("/usr/local/ngs/ngs-java")
|
||||
#$(this-package-input "java-ngs")))
|
||||
|
||||
;; The 'configure' script doesn't recognize things like
|
||||
;; '--enable-fast-install'.
|
||||
(invoke "./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-hdf5-prefix="
|
||||
(assoc-ref inputs "hdf5")))
|
||||
#t)))
|
||||
(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/"
|
||||
,(platform-linux-architecture
|
||||
(lookup-platform-by-target-or-system
|
||||
(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))
|
||||
;; These files are needed by sra-tools.
|
||||
(add-after 'install 'install-configuration-files
|
||||
(lambda* (#:key outputs #:allow-other-keys)
|
||||
(let ((target (string-append (assoc-ref outputs "out") "/kfg")))
|
||||
(mkdir target)
|
||||
(install-file "libs/kfg/default.kfg" target)
|
||||
(install-file "libs/kfg/certs.kfg" target))
|
||||
#t)))))
|
||||
;; The 'configure' script doesn't recognize things like
|
||||
;; '--enable-fast-install'.
|
||||
(invoke "./configure"
|
||||
(string-append "--build-prefix=" (getcwd) "/build")
|
||||
(string-append "--prefix=" #$output)
|
||||
(string-append "--debug")
|
||||
(string-append "--with-xml2-prefix="
|
||||
#$(this-package-input "libxml2"))
|
||||
(string-append "--with-ngs-sdk-prefix="
|
||||
#$(this-package-input "ngs-sdk"))
|
||||
(string-append "--with-hdf5-prefix="
|
||||
#$(this-package-input "hdf5")))))
|
||||
(add-after 'install 'install-interfaces
|
||||
(lambda _
|
||||
;; 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 #$output "/ilib"))
|
||||
(copy-recursively (string-append
|
||||
"build/ncbi-vdb/linux/gcc/"
|
||||
#$(platform-linux-architecture
|
||||
(lookup-platform-by-target-or-system
|
||||
(or (%current-target-system)
|
||||
(%current-system))))
|
||||
"/rel/ilib")
|
||||
(string-append #$output "/ilib"))
|
||||
;; Install interface headers
|
||||
(copy-recursively "interfaces"
|
||||
(string-append #$output "/include"))))
|
||||
(add-after 'install-interfaces 'install-libs
|
||||
(lambda _
|
||||
(copy-recursively (string-append
|
||||
"build/ncbi-vdb/linux/gcc/"
|
||||
#$(platform-linux-architecture
|
||||
(lookup-platform-by-target-or-system
|
||||
(or (%current-target-system)
|
||||
(%current-system))))
|
||||
"/rel/lib")
|
||||
(string-append #$output "/lib"))))
|
||||
;; These files are needed by sra-tools.
|
||||
(add-after 'install 'install-configuration-files
|
||||
(lambda _
|
||||
(let ((target (string-append #$output "/kfg")))
|
||||
(mkdir target)
|
||||
(install-file "libs/kfg/default.kfg" target)
|
||||
(install-file "libs/kfg/certs.kfg" target)))))))
|
||||
(inputs
|
||||
`(("libxml2" ,libxml2)
|
||||
("ngs-sdk" ,ngs-sdk)
|
||||
("java-ngs" ,java-ngs)
|
||||
("libmagic" ,file)
|
||||
("hdf5" ,hdf5)))
|
||||
(list file hdf5 java-ngs libxml2 ngs-sdk ))
|
||||
(native-inputs (list perl))
|
||||
;; NCBI-VDB requires SSE capability.
|
||||
(supported-systems '("i686-linux" "x86_64-linux"))
|
||||
|
|
|
|||
Reference in a new issue