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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.
master
Ricardo Wurmus 2023-05-12 21:54:01 +02:00
parent 8ba3bf6564
commit 0e20ed322d
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GPG Key ID: 197A5888235FACAC
1 changed files with 77 additions and 75 deletions
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@ -8013,86 +8013,88 @@ unique transcripts.")
"1cr2mijkfs5sm35ffjs6861qsd1qkgnhnbavdv65zg5d655abbjf"))))
(build-system gnu-build-system)
(arguments
`(#:parallel-build? #f ; not supported
#:tests? #f ; no "check" target
#:make-flags
,#~(list (string-append "DEFAULT_CRT="
#$(this-package-input "ncbi-vdb")
"/kfg/certs.kfg")
(string-append "DEFAULT_KFG="
#$(this-package-input "ncbi-vdb")
"/kfg/default.kfg")
(string-append "VDB_LIBDIR="
#$(this-package-input "ncbi-vdb")
#$(if (string-prefix? "x86_64"
(or (%current-target-system)
(%current-system)))
"/lib64"
"/lib32")))
(list
#:parallel-build? #f ; not supported
#:tests? #f ; no "check" target
#:make-flags
#~(list (string-append "DEFAULT_CRT="
#$(this-package-input "ncbi-vdb")
"/kfg/certs.kfg")
(string-append "DEFAULT_KFG="
#$(this-package-input "ncbi-vdb")
"/kfg/default.kfg")
(string-append "VDB_LIBDIR="
#$(this-package-input "ncbi-vdb")
#$(if (string-prefix? "x86_64"
(or (%current-target-system)
(%current-system)))
"/lib64"
"/lib32")))
#:phases
(modify-phases %standard-phases
(add-before 'configure 'set-perl-search-path
(lambda _
;; Work around "dotless @INC" build failure.
(setenv "PERL5LIB"
(string-append (getcwd) "/setup:"
(getenv "PERL5LIB")))
#t))
(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');"))
#~(modify-phases %standard-phases
(add-before 'configure 'set-perl-search-path
(lambda _
;; Work around "dotless @INC" build failure.
(setenv "PERL5LIB"
(string-append (getcwd) "/setup:"
(getenv "PERL5LIB")))))
(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"))
(substitute* "tools/driver-tool/utf8proc/Makefile"
(("CC\\?=gcc") "myCC=gcc")
(("\\(CC\\)") "(myCC)"))
;; Dynamic linking
(substitute* "tools/copycat/Makefile"
(("smagic-static") "lmagic"))
(substitute* "tools/driver-tool/utf8proc/Makefile"
(("CC\\?=gcc") "myCC=gcc")
(("\\(CC\\)") "(myCC)"))
;; 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-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")))
#t)))))
;; Don't link libxml2 statically
(substitute* "build/ld.linux.exe.sh"
(("grep -q 'OS_DISTRIBUTOR = Ubuntu.*") "true\n"))
;; The 'configure' script doesn't recognize things like
;; '--enable-fast-install'.
(invoke "./configure"
(string-append "--build-prefix=" (getcwd) "/build")
(string-append "--prefix=" #$output)
(string-append "--debug")
(string-append "--with-fuse-prefix="
#$(this-package-input "fuse"))
(string-append "--with-magic-prefix="
#$(this-package-input "file"))
(string-append "--with-xml2-prefix="
#$(this-package-input "libxml2"))
(string-append "--with-ncbi-vdb-sources="
#$(this-package-input "ncbi-vdb"))
(string-append "--with-ncbi-vdb-build="
#$(this-package-input "ncbi-vdb"))
(string-append "--with-ngs-sdk-prefix="
#$(this-package-input "ngs-sdk"))
(string-append "--with-hdf5-prefix="
#$(this-package-input "hdf5"))))))))
(native-inputs (list perl))
(inputs
`(("ngs-sdk" ,ngs-sdk)
("ncbi-vdb" ,ncbi-vdb)
("libmagic" ,file)
("fuse" ,fuse)
("hdf5" ,hdf5-1.10)
("zlib" ,zlib)
("python" ,python-wrapper)))
(list ngs-sdk
ncbi-vdb
file
fuse
hdf5-1.10
libxml2
zlib
python-wrapper))
(home-page
"https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software")
(synopsis "Tools and libraries for reading and writing sequencing data")