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gn: Update vg

wip-tensorflow
Efraim Flashner 3 months ago
parent
commit
e889b266c8
Signed by: efraim GPG Key ID: 41AAE7DCCA3D8351
  1. 61
      gn/packages/bioinformatics.scm

61
gn/packages/bioinformatics.scm

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

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