diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 84 |
1 files changed, 29 insertions, 55 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 77150e0dce..bb97b2d313 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -14923,32 +14923,44 @@ library automatically handles index file generation and use.") (define-public vcflib (package (name "vcflib") - (version "1.0.1") + (version "1.0.2") (source (origin - (method url-fetch) - (uri (string-append "https://github.com/vcflib/vcflib/releases/" - "download/v" version - "/vcflib-" version "-src.tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/vcflib/vcflib") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 - (base32 "14zzrg8hg8cq9cvq2wdvp21j7nmxxkjrbagw2apd2yqv2kyx42lm")) - (patches (search-patches "vcflib-use-shared-libraries.patch")) + (base32 "1k1z3876kbzifj1sqfzsf3lgb4rw779hvkg6ryxbyq5bc2paj9kh")) (modules '((guix build utils))) (snippet - `(begin + '(begin + (substitute* "CMakeLists.txt" + ((".*fastahack.*") "") + ((".*smithwaterman.*") "") + (("(pkg_check_modules\\(TABIXPP)" text) + (string-append + "pkg_check_modules(FASTAHACK REQUIRED fastahack)\n" + "pkg_check_modules(SMITHWATERMAN REQUIRED smithwaterman)\n" + text)) + (("\\$\\{TABIXPP_LIBRARIES\\}" text) + (string-append "${FASTAHACK_LIBRARIES} " + "${SMITHWATERMAN_LIBRARIES} " + text))) (substitute* (find-files "." "\\.(h|c)(pp)?$") (("\"SmithWatermanGotoh.h\"") "<smithwaterman/SmithWatermanGotoh.h>") (("\"convert.h\"") "<smithwaterman/convert.h>") (("\"disorder.h\"") "<smithwaterman/disorder.h>") - (("\"tabix.hpp\"") "<tabix.hpp>") - (("\"Fasta.h\"") "<fastahack/Fasta.h>")) + (("Fasta.h") "fastahack/Fasta.h")) (for-each delete-file-recursively '("fastahack" "filevercmp" "fsom" "googletest" "intervaltree" - "libVCFH" "multichoose" "smithwaterman" "tabixpp")) + "libVCFH" "multichoose" "smithwaterman")) #t)))) - (build-system gnu-build-system) + (build-system cmake-build-system) (inputs - `(("htslib" ,htslib) + `(("bzip2" ,bzip2) + ("htslib" ,htslib) ("fastahack" ,fastahack) ("perl" ,perl) ("python" ,python) @@ -14961,22 +14973,13 @@ library automatically handles index file generation and use.") ;; Submodules. ;; This package builds against the .o files so we need to extract the source. ("filevercmp-src" ,(package-source filevercmp)) + ("fsom-src" ,(package-source fsom)) ("intervaltree-src" ,(package-source intervaltree)) ("multichoose-src" ,(package-source multichoose)))) (arguments `(#:tests? #f ; no tests #:phases (modify-phases %standard-phases - (add-after 'unpack 'set-flags - (lambda* (#:key outputs #:allow-other-keys) - (substitute* "Makefile" - (("LDFLAGS =") - (string-append "LDFLAGS = -Wl,-rpath=" - (assoc-ref outputs "out") "/lib "))) - (substitute* "filevercmp/Makefile" - (("-c") "-c -fPIC")) - #t)) - (delete 'configure) (add-after 'unpack 'unpack-submodule-sources (lambda* (#:key inputs #:allow-other-keys) (let ((unpack (lambda (source target) @@ -14989,39 +14992,10 @@ library automatically handles index file generation and use.") "--strip-components=1")))))) (and (unpack "filevercmp-src" "filevercmp") + (unpack "fsom-src" "fsom") (unpack "intervaltree-src" "intervaltree") - (unpack "multichoose-src" "multichoose"))))) - (replace 'install - (lambda* (#:key outputs #:allow-other-keys) - (let* ((out (assoc-ref outputs "out")) - (bin (string-append out "/bin")) - (lib (string-append out "/lib"))) - (for-each (lambda (file) - (install-file file bin)) - (find-files "bin" ".*")) - (install-file "libvcflib.so" lib) - (install-file "libvcflib.a" lib) - (for-each - (lambda (file) - (install-file file (string-append out "/include"))) - (find-files "include" "\\.h(pp)?$")) - (mkdir-p (string-append lib "/pkgconfig")) - (with-output-to-file (string-append lib "/pkgconfig/vcflib.pc") - (lambda _ - (format #t "prefix=~a~@ - exec_prefix=${prefix}~@ - libdir=${exec_prefix}/lib~@ - includedir=${prefix}/include~@ - ~@ - ~@ - Name: libvcflib~@ - Version: ~a~@ - Requires: smithwaterman, fastahack~@ - Description: C++ library for parsing and manipulating VCF files~@ - Libs: -L${libdir} -lvcflib~@ - Cflags: -I${includedir}~%" - out ,version)))) - #t))))) + (unpack "multichoose-src" "multichoose")) + #t)))))) (home-page "https://github.com/vcflib/vcflib/") (synopsis "Library for parsing and manipulating VCF files") (description "Vcflib provides methods to manipulate and interpret |