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| -rw-r--r-- | gn/packages/bioinformatics.scm | 65 |
1 files changed, 65 insertions, 0 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index c3e5020..b0590ca 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -4485,3 +4485,68 @@ and writing using 8, 16, 24 or 32 bits per probability, using Layout = ploidy 2. Any other format specification may crash unexpectedly without a properly defined error.") (license license:gpl3))) + +(define-public seqlib + (package + (name "seqlib") + (version "0.1.4") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/Zilong-Li/SeqLib") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1hczg1swghnxm6af74l09crdgf7l282jabmyck9mi5bk6vg9s1pn")))) + (build-system gnu-build-system) + (arguments + (list #:phases + #~(modify-phases %standard-phases + ;; Patch build scripts to unbundle htslib and build a + ;; seqlib shared library using libtool. + (add-after 'unpack 'patch-build-scripts + (lambda _ + ;; Initialize libtool. + (substitute* "configure.ac" + (("AM_INIT_AUTOMAKE\\(foreign\\)\n" all) + (string-append all "LT_INIT\n"))) + (substitute* "Makefile.am" + ;; Install headers + (("^SUBDIRS" all) + (string-append "nobase_include_HEADERS = " + (string-join (find-files "SeqLib")) + "\n" all)) + ;; Do not recurse into htslib submodule. + (("htslib") "") + ;; Remove install target override. + (("^install:") "") + (("^\tmkdir -p lib && cp src/libseqlib.a /libhts.a lib") "")) + (substitute* "src/Makefile.am" + ;; Build libtool library. + (("noinst_LIBRARIES = libseqlib\\.a") + "lib_LTLIBRARIES = libseqlib.la\nlibseqlib_la_LIBADD = -ljsoncpp") + (("libseqlib\\.a") "libseqlib.la") + (("libseqlib_a") "libseqlib_la")) + (substitute* (list "SeqLib/BamHeader.h" + "SeqLib/BamRecord.h" + "SeqLib/RefGenome.h" + "src/ReadFilter.cpp") + ;; Patch path to htslib headers. + (("\"htslib/htslib/([^\"]*)\"" all header) + (string-append "<htslib/" header ">")))))))) + (inputs + (list zlib)) + (native-inputs + (list autoconf automake libtool)) + ;; seqlib headers include headers from htslib and jsoncpp. So, + ;; they are propagated inputs. + (propagated-inputs + (list htslib jsoncpp)) + (home-page "https://github.com/Zilong-Li/SeqLib") + (synopsis "C++ htslib interface for manipulating sequence data and VCF") + (description "@code{seqlib} is a C++ htslib interface for manipulating sequence data +and VCF files.") + (license (list license:expat ; SeqLib/IntervalTree.h, SeqLib/aho_corasick.hpp, + ; json/json-forwards.h, json/json.h, src/jsoncpp.cpp, src/ssw.c, + license:asl2.0)))) ; main license |