gnu: sra-tools: Do link with libxml2.
* gnu/packages/bioinformatics.scm (sra-tools)[arguments]: Use G-expression for clarity; drop trailing #T from build phases; modify 'configure phase to dynamically link with libxml2. [inputs]: Drop package labels; add libxml2.
This commit is contained in:
Ricardo Wurmus
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8ba3bf6564
commit
0e20ed322d
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@ -8013,86 +8013,88 @@ (define-public sra-tools
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"1cr2mijkfs5sm35ffjs6861qsd1qkgnhnbavdv65zg5d655abbjf"))))
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(build-system gnu-build-system)
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(arguments
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`(#:parallel-build? #f ; not supported
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#:tests? #f ; no "check" target
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#:make-flags
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,#~(list (string-append "DEFAULT_CRT="
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#$(this-package-input "ncbi-vdb")
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"/kfg/certs.kfg")
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(string-append "DEFAULT_KFG="
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#$(this-package-input "ncbi-vdb")
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"/kfg/default.kfg")
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(string-append "VDB_LIBDIR="
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#$(this-package-input "ncbi-vdb")
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#$(if (string-prefix? "x86_64"
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(or (%current-target-system)
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(%current-system)))
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"/lib64"
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"/lib32")))
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(list
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#:parallel-build? #f ; not supported
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#:tests? #f ; no "check" target
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#:make-flags
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#~(list (string-append "DEFAULT_CRT="
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#$(this-package-input "ncbi-vdb")
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"/kfg/certs.kfg")
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(string-append "DEFAULT_KFG="
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#$(this-package-input "ncbi-vdb")
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"/kfg/default.kfg")
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(string-append "VDB_LIBDIR="
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#$(this-package-input "ncbi-vdb")
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#$(if (string-prefix? "x86_64"
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(or (%current-target-system)
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(%current-system)))
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"/lib64"
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"/lib32")))
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#:phases
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(modify-phases %standard-phases
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(add-before 'configure 'set-perl-search-path
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(lambda _
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;; Work around "dotless @INC" build failure.
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(setenv "PERL5LIB"
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(string-append (getcwd) "/setup:"
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(getenv "PERL5LIB")))
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#t))
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(replace 'configure
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(lambda* (#:key inputs outputs #:allow-other-keys)
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;; The build system expects a directory containing the sources and
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;; raw build output of ncbi-vdb, including files that are not
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;; installed. Since we are building against an installed version of
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;; ncbi-vdb, the following modifications are needed.
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(substitute* "setup/konfigure.perl"
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;; Make the configure script look for the "ilib" directory of
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;; "ncbi-vdb" without first checking for the existence of a
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;; matching library in its "lib" directory.
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(("^ my \\$f = File::Spec->catdir\\(\\$libdir, \\$lib\\);")
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"my $f = File::Spec->catdir($ilibdir, $ilib);")
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;; Look for interface libraries in ncbi-vdb's "ilib" directory.
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(("my \\$ilibdir = File::Spec->catdir\\(\\$builddir, 'ilib'\\);")
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"my $ilibdir = File::Spec->catdir($dir, 'ilib');"))
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#~(modify-phases %standard-phases
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(add-before 'configure 'set-perl-search-path
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(lambda _
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;; Work around "dotless @INC" build failure.
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(setenv "PERL5LIB"
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(string-append (getcwd) "/setup:"
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(getenv "PERL5LIB")))))
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(replace 'configure
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(lambda* (#:key inputs outputs #:allow-other-keys)
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;; The build system expects a directory containing the sources and
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;; raw build output of ncbi-vdb, including files that are not
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;; installed. Since we are building against an installed version of
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;; ncbi-vdb, the following modifications are needed.
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(substitute* "setup/konfigure.perl"
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;; Make the configure script look for the "ilib" directory of
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;; "ncbi-vdb" without first checking for the existence of a
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;; matching library in its "lib" directory.
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(("^ my \\$f = File::Spec->catdir\\(\\$libdir, \\$lib\\);")
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"my $f = File::Spec->catdir($ilibdir, $ilib);")
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;; Look for interface libraries in ncbi-vdb's "ilib" directory.
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(("my \\$ilibdir = File::Spec->catdir\\(\\$builddir, 'ilib'\\);")
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"my $ilibdir = File::Spec->catdir($dir, 'ilib');"))
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;; Dynamic linking
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(substitute* "tools/copycat/Makefile"
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(("smagic-static") "lmagic"))
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(substitute* "tools/driver-tool/utf8proc/Makefile"
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(("CC\\?=gcc") "myCC=gcc")
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(("\\(CC\\)") "(myCC)"))
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;; Dynamic linking
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(substitute* "tools/copycat/Makefile"
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(("smagic-static") "lmagic"))
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(substitute* "tools/driver-tool/utf8proc/Makefile"
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(("CC\\?=gcc") "myCC=gcc")
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(("\\(CC\\)") "(myCC)"))
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;; The 'configure' script doesn't recognize things like
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;; '--enable-fast-install'.
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(invoke "./configure"
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(string-append "--build-prefix=" (getcwd) "/build")
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(string-append "--prefix=" (assoc-ref outputs "out"))
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(string-append "--debug")
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(string-append "--with-fuse-prefix="
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(assoc-ref inputs "fuse"))
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(string-append "--with-magic-prefix="
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(assoc-ref inputs "libmagic"))
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;; TODO: building with libxml2 fails with linker errors
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#;
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(string-append "--with-xml2-prefix="
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(assoc-ref inputs "libxml2"))
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(string-append "--with-ncbi-vdb-sources="
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(assoc-ref inputs "ncbi-vdb"))
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(string-append "--with-ncbi-vdb-build="
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(assoc-ref inputs "ncbi-vdb"))
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(string-append "--with-ngs-sdk-prefix="
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(assoc-ref inputs "ngs-sdk"))
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(string-append "--with-hdf5-prefix="
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(assoc-ref inputs "hdf5")))
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#t)))))
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;; Don't link libxml2 statically
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(substitute* "build/ld.linux.exe.sh"
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(("grep -q 'OS_DISTRIBUTOR = Ubuntu.*") "true\n"))
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;; The 'configure' script doesn't recognize things like
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;; '--enable-fast-install'.
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(invoke "./configure"
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(string-append "--build-prefix=" (getcwd) "/build")
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(string-append "--prefix=" #$output)
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(string-append "--debug")
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(string-append "--with-fuse-prefix="
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#$(this-package-input "fuse"))
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(string-append "--with-magic-prefix="
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#$(this-package-input "file"))
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(string-append "--with-xml2-prefix="
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#$(this-package-input "libxml2"))
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(string-append "--with-ncbi-vdb-sources="
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#$(this-package-input "ncbi-vdb"))
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(string-append "--with-ncbi-vdb-build="
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#$(this-package-input "ncbi-vdb"))
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(string-append "--with-ngs-sdk-prefix="
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#$(this-package-input "ngs-sdk"))
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(string-append "--with-hdf5-prefix="
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#$(this-package-input "hdf5"))))))))
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(native-inputs (list perl))
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(inputs
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`(("ngs-sdk" ,ngs-sdk)
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("ncbi-vdb" ,ncbi-vdb)
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("libmagic" ,file)
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("fuse" ,fuse)
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("hdf5" ,hdf5-1.10)
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("zlib" ,zlib)
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("python" ,python-wrapper)))
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(list ngs-sdk
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ncbi-vdb
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file
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fuse
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hdf5-1.10
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libxml2
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zlib
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python-wrapper))
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(home-page
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"https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software")
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(synopsis "Tools and libraries for reading and writing sequencing data")
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