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@ -1338,7 +1338,7 @@ available to other researchers.") |
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(define-public vg |
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(package |
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(name "vg") |
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(version "1.32.0") |
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(version "1.33.0") |
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(source |
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(origin |
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(method url-fetch) |
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@ -1346,7 +1346,7 @@ available to other researchers.") |
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version "/vg-v" version ".tar.gz")) |
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(sha256 |
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(base32 |
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"0sqk2ymd5p1mpvsxaaz5vz3fdc8m9vd2l9307bd59603nijm8yzf")) |
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"1pd4gdqb3ar0r1igzhf730kh9x0wj5l4shmjxz0j2mj78wy8y2sg")) |
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(modules '((guix build utils))) |
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(snippet |
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'(begin |
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@ -1354,11 +1354,12 @@ available to other researchers.") |
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;(delete-file-recursively "deps/BBHash") |
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;(delete-file-recursively "deps/DYNAMIC") |
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;(delete-file-recursively "deps/FlameGraph") |
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;(delete-file-recursively "deps/atomic_queue") |
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;(delete-file-recursively "deps/backward-cpp") |
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(delete-file-recursively "deps/bash-tap") |
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;(delete-file-recursively "deps/dozeu") |
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(delete-file-recursively "deps/elfutils") |
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;(delete-file-recursively "deps/fastahack") |
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;(delete-file-recursively "deps/fastahack") ; Fasta.o |
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;(delete-file-recursively "deps/fermi-lite") |
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;(delete-file-recursively "deps/gbwt") |
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(delete-file-recursively "deps/gbwt/deps") |
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@ -1367,7 +1368,8 @@ available to other researchers.") |
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;(delete-file-recursively "deps/gcsa2") |
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;(delete-file-recursively "deps/gfakluge") |
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;(delete-file-recursively "deps/gssw") |
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;(delete-file-recursively "deps/ipso") |
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(delete-file-recursively "deps/htslib") |
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;(delete-file-recursively "deps/ips4o") |
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(delete-file-recursively "deps/jemalloc") |
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;(delete-file-recursively "deps/libVCFH") |
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;(delete-file-recursively "deps/libbdsg") |
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@ -1382,19 +1384,34 @@ available to other researchers.") |
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;(delete-file-recursively "deps/libdeflate") |
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;(delete-file-recursively "deps/libhandlegraph") |
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;(delete-file-recursively "deps/libvgio") |
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;(delete-file-recursively "deps/libvgio/deps") |
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;(delete-file-recursively "deps/libvgio/deps") ; libhandlegraph |
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;(delete-file-recursively "deps/lru_cache") |
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;(delete-file-recursively "deps/mio") |
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;(delete-file-recursively "deps/mmmultimap") |
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(delete-file-recursively "deps/mmmultimap/deps/DYNAMIC") |
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(delete-file-recursively "deps/mmmultimap/deps/args") |
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(delete-file-recursively "deps/mmmultimap/deps/atomic_queue") |
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;(delete-file-recursively "deps/mmmultimap/deps/hopscotch-map") |
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(delete-file-recursively "deps/mmmultimap/deps/ips4o") |
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(delete-file-recursively "deps/mmmultimap/deps/mio") |
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;(delete-file-recursively "deps/mmmultimap/deps/paryfor") |
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(delete-file-recursively "deps/mmmultimap/deps/sdsl-lite") |
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;(delete-file-recursively "deps/pinchesAndCacti") |
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;(delete-file-recursively "deps/progress_bar") |
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(delete-file-recursively "deps/raptor") |
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;(delete-file-recursively "deps/sdsl-lite") |
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(delete-file-recursively "deps/snappy") |
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;(delete-file-recursively "deps/sonLib") |
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(delete-file-recursively "deps/sparsehash") |
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;(delete-file-recursively "deps/sparsepp") |
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;(delete-file-recursively "deps/ssw") |
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;(delete-file-recursively "deps/structures") |
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;(delete-file-recursively "deps/sublinear-Li-Stephens") |
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(delete-file-recursively "deps/sublinear-Li-Stephens/deps") |
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(delete-file-recursively "deps/tabixpp") |
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(delete-file-recursively "deps/vcflib") |
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(delete-file-recursively "deps/vowpal_wabbit") |
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;(delete-file-recursively "deps/xg") |
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;; Removing causes segfaults in the test suite |
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;(delete-file-recursively "deps/xg/deps") |
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(delete-file-recursively "deps/xg/deps") |
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;; libvgio doesn't search the correct include directory. |
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(copy-recursively "deps/libhandlegraph/src/include/handlegraph" |
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"deps/libvgio/include/handlegraph") |
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@ -1409,32 +1426,38 @@ available to other researchers.") |
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(substitute* "Makefile" |
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;; PKG_CONFIG_DEPS needs to be substituted to actually link to everything. |
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(("cairo jansson") |
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"cairo jansson vcflib htslib sdsl-lite libvw raptor2 protobuf libelf libdw") |
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"cairo htslib jansson libdw libelf protobuf raptor2 sdsl-lite tabixpp vcflib") |
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;; Skip the part where we link static libraries special. It doesn't like the changes we make |
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(("-Wl,-B.*") "\n") |
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(("\\$\\(CWD\\)/\\$\\(LIB_DIR\\)/libtabixpp\\.a") "$(LIB_DIR)/libtabixpp.a") |
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((" \\$\\(LIB_DIR\\)/libtabixpp\\.a") |
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(string-append " " (assoc-ref inputs "tabixpp") "/lib/libtabixpp.so")) |
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(("\\$\\(LIB_DIR\\)/pkgconfig/tabixpp\\.pc") |
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(string-append " " (assoc-ref inputs "tabixpp") "/lib/pkgconfig/tabixpp.pc")) |
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(("\\$\\(CWD\\)/\\$\\(LIB_DIR\\)/libhts\\.a") "$(LIB_DIR)/libhts.a") |
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((" \\$\\(LIB_DIR\\)/libhts\\.a") |
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(string-append " " (assoc-ref inputs "htslib") "/lib/libhts.so")) |
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(("\\$\\(LIB_DIR\\)/pkgconfig/htslib\\.pc") "") |
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(("\\$\\(LIB_DIR\\)/pkgconfig/htslib\\.pc") |
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(string-append " " (assoc-ref inputs "htslib") "/lib/pkgconfig/htslib.pc")) |
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((" \\$\\(LIB_DIR\\)/libvcflib.a") |
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(string-append " " (assoc-ref inputs "vcflib") "/lib/libvcflib.so")) |
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((" \\$\\(BIN_DIR\\)/vcf2tsv") |
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(string-append " " (assoc-ref inputs "vcflib") "/bin/vcf2tsv")) |
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((" \\$\\(VCFLIB_DIR\\)/bin/vcf2tsv") |
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(string-append " " (assoc-ref inputs "vcflib") "/bin/vcf2tsv")) |
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((" \\$\\(FASTAHACK_DIR\\)/fastahack") |
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(string-append " " (assoc-ref inputs "fastahack") "/bin/fastahack")) |
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((" \\$\\(FASTAHACK_DIR\\)/bin/fastahack") |
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(string-append " " (assoc-ref inputs "fastahack") "/bin/fastahack")) |
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((" \\$\\(LIB_DIR\\)/libsnappy.a") |
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(string-append " " (assoc-ref inputs "snappy") "/lib/libsnappy.so")) |
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((" \\$\\(LIB_DIR\\)/libvw.a") |
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(string-append " " (assoc-ref inputs "vowpal-wabbit") "/lib/libvw.so")) |
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((" \\$\\(LIB_DIR\\)/liballreduce.a") |
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(string-append " " (assoc-ref inputs "vowpal-wabbit") "/lib/liballreduce.so")) |
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;; Only link against the libraries in the elfutils package. |
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(("-ldwfl -ldw -ldwelf -lelf -lebl") "-ldw -lelf") |
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((" \\$\\(LIB_DIR\\)/libelf.a") |
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@ -1467,6 +1490,11 @@ available to other researchers.") |
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(substitute* "test/t/02_vg_construct.t" |
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(("../deps/vcflib/bin/vcf2tsv") (which "vcf2tsv"))) |
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#t)) |
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(add-after 'unpack 'fix-fastahack-dependency |
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(lambda _ |
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(substitute* "src/aligner.hpp" |
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(("Fasta.h") "fastahack/Fasta.h")) |
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#t)) |
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(add-after 'unpack 'fix-hopscotch-dependency |
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(lambda _ |
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(substitute* "Makefile" |
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@ -1485,7 +1513,7 @@ available to other researchers.") |
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(add-after 'unpack 'adjust-tests |
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(lambda* (#:key inputs #:allow-other-keys) |
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(let ((bash-tap (assoc-ref inputs "bash-tap"))) |
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(substitute* (find-files "test/t" ".") |
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(substitute* (find-files "test/t") |
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(("BASH_TAP_ROOT.*") |
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(string-append "BASH_TAP_ROOT=" bash-tap "/bin\n")) |
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((".*bash-tap-bootstrap") |
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@ -1546,7 +1574,6 @@ available to other researchers.") |
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("sparsehash" ,sparsehash) |
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("tabixpp" ,tabixpp) |
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("vcflib" ,vcflib) |
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("vowpal-wabbit" ,vowpal-wabbit) |
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("zlib" ,zlib))) |
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(home-page "https://www.biostars.org/t/vg/") |
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(synopsis "Tools for working with genome variation graphs") |
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