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gnu: vcflib: Use libwfa2.pc. 

* gnu/packages/bioinformatics.scm (vcflib)[source]: Use pkg-config to look for
libwfa2.
[inputs]: Move wfa2-lib from here...
[propagated-inputs]: ...to here.
[arguments]: Drop WFA_LINK_LIBRARIES option; fix typo in build phase name;
patch IntervalTree.h includes; add libwfa2 to pkg-config file.
master
Ricardo Wurmus 2023-04-27 11:38:16 +02:00
parent 479f2558fe
commit 133957f7bb
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GPG Key ID: 197A5888235FACAC
1 changed files with 14 additions and 5 deletions
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gnu/packages/bioinformatics.scm
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@ -17220,11 +17220,13 @@ sequences to accelerate the alignment process.")
((".*smithwaterman.*") "") ((".*smithwaterman.*") "")
(("(pkg_check_modules\\(TABIXPP)" text) (("(pkg_check_modules\\(TABIXPP)" text)
(string-append (string-append
"pkg_check_modules(WFA2 REQUIRED libwfa2)\n"
"pkg_check_modules(FASTAHACK REQUIRED fastahack)\n" "pkg_check_modules(FASTAHACK REQUIRED fastahack)\n"
"pkg_check_modules(SMITHWATERMAN REQUIRED smithwaterman)\n" "pkg_check_modules(SMITHWATERMAN REQUIRED smithwaterman)\n"
text)) text))
(("\\$\\{TABIXPP_LIBRARIES\\}" text) (("\\$\\{TABIXPP_LIBRARIES\\}" text)
(string-append "${FASTAHACK_LIBRARIES} " (string-append "${FASTAHACK_LIBRARIES} "
"${WFA2_LIBRARIES} "
"${SMITHWATERMAN_LIBRARIES} " "${SMITHWATERMAN_LIBRARIES} "
text))) text)))
(substitute* (find-files "." "\\.(h|c)(pp)?$") (substitute* (find-files "." "\\.(h|c)(pp)?$")
@ -17244,9 +17246,10 @@ sequences to accelerate the alignment process.")
pybind11 pybind11
smithwaterman smithwaterman
tabixpp tabixpp
wfa2-lib
xz xz
zlib)) zlib))
(propagated-inputs
(list wfa2-lib))
(native-inputs (native-inputs
`(("pkg-config" ,pkg-config) `(("pkg-config" ,pkg-config)
;; Submodules. ;; Submodules.
@ -17262,7 +17265,6 @@ sequences to accelerate the alignment process.")
"-DTABIXPP_LOCAL=OFF" "-DTABIXPP_LOCAL=OFF"
"-DTABIX_FOUND=ON" "-DTABIX_FOUND=ON"
"-DWFA_GITMODULE=OFF" "-DWFA_GITMODULE=OFF"
"-DWFA_LINK_LIBRARIES=-lwfa2cpp"
(string-append "-DPKG_CONFIG_EXECUTABLE=" (string-append "-DPKG_CONFIG_EXECUTABLE="
(search-input-file (search-input-file
%build-inputs (string-append %build-inputs (string-append
@ -17270,7 +17272,7 @@ sequences to accelerate the alignment process.")
#:tests? #f ; no tests #:tests? #f ; no tests
#:phases #:phases
#~(modify-phases %standard-phases #~(modify-phases %standard-phases
(add-after 'unpack 'find-wf2lib-headers (add-after 'unpack 'find-wfa2lib-headers
(lambda _ (lambda _
(setenv "CPLUS_INCLUDE_PATH" (setenv "CPLUS_INCLUDE_PATH"
(string-append (string-append
@ -17297,7 +17299,14 @@ sequences to accelerate the alignment process.")
(unpack "filevercmp-src" "contrib/filevercmp") (unpack "filevercmp-src" "contrib/filevercmp")
(unpack "fsom-src" "contrib/fsom") (unpack "fsom-src" "contrib/fsom")
(unpack "intervaltree-src" "contrib/intervaltree") (unpack "intervaltree-src" "contrib/intervaltree")
(unpack "multichoose-src" "contrib/multichoose"))))) (unpack "multichoose-src" "contrib/multichoose"))
;; This is needed for downstream packages to allow building
;; with GCC 11+.
(substitute* "contrib/intervaltree/IntervalTree.h"
(("#include <vector>" m)
(string-append m "
#include <limits> /* std::numeric_limits */"))))))
;; This pkg-config file is provided by other distributions. ;; This pkg-config file is provided by other distributions.
(add-after 'install 'install-pkg-config-file (add-after 'install 'install-pkg-config-file
(lambda _ (lambda _
@ -17313,7 +17322,7 @@ includedir=${prefix}/include~@
~@ ~@
Name: vcflib~@ Name: vcflib~@
Version: ~a~@ Version: ~a~@
Requires: smithwaterman, fastahack, tabixpp~@ Requires: libwfa2, smithwaterman, fastahack, tabixpp~@
Description: C++ library for parsing and manipulating VCF files~@ Description: C++ library for parsing and manipulating VCF files~@
Libs: -L${libdir} -lvcflib~@ Libs: -L${libdir} -lvcflib~@
Cflags: -I${includedir}~%" Cflags: -I${includedir}~%"