diff options
Diffstat (limited to 'gn/packages')
| -rw-r--r-- | gn/packages/bioinformatics.scm | 61 |
1 files changed, 44 insertions, 17 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index a264423..9d65d6f 100644 --- a/gn/packages/bioinformatics.scm +++ b/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") |