diff options
| -rw-r--r-- | gn/packages/bioinformatics.scm | 41 |
1 files changed, 21 insertions, 20 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index e8df572..4c2f8cf 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -1579,15 +1579,14 @@ available to other researchers.") (define-public vg (package (name "vg") - (version "1.33.0") + (version "1.39.0") (source (origin (method url-fetch) (uri (string-append "https://github.com/vgteam/vg/releases/download/v" version "/vg-v" version ".tar.gz")) (sha256 - (base32 - "1pd4gdqb3ar0r1igzhf730kh9x0wj5l4shmjxz0j2mj78wy8y2sg")) + (base32 "0cj575qr2jkingrm6r4ki7f89s7glrf18d4pvaa69smxh2vbajv3")) (modules '((guix build utils))) (snippet '(begin @@ -1600,12 +1599,10 @@ available to other researchers.") (delete-file-recursively "deps/bash-tap") ;(delete-file-recursively "deps/dozeu") (delete-file-recursively "deps/elfutils") - ;(delete-file-recursively "deps/fastahack") ; Fasta.o + (delete-file-recursively "deps/fastahack") ;(delete-file-recursively "deps/fermi-lite") ;(delete-file-recursively "deps/gbwt") - (delete-file-recursively "deps/gbwt/deps") ;(delete-file-recursively "deps/gbwtgraph") - (delete-file-recursively "deps/gbwtgraph/deps") ;(delete-file-recursively "deps/gcsa2") ;(delete-file-recursively "deps/gfakluge") ;(delete-file-recursively "deps/gssw") @@ -1617,13 +1614,16 @@ available to other researchers.") ;(delete-file-recursively "deps/libbdsg/bdsg/deps") (delete-file-recursively "deps/libbdsg/bdsg/deps/BBHash") (delete-file-recursively "deps/libbdsg/bdsg/deps/DYNAMIC") + ;(delete-file-recursively "deps/libbdsg/bdsg/deps/DYNAMIC/deps/hopscotch-map") ;(delete-file-recursively "deps/libbdsg/bdsg/deps/hopscotch-map") (delete-file-recursively "deps/libbdsg/bdsg/deps/libhandlegraph") + ;(delete-file-recursively "deps/libbdsg/bdsg/deps/mio") (delete-file-recursively "deps/libbdsg/bdsg/deps/pybind11") (delete-file-recursively "deps/libbdsg/bdsg/deps/sdsl-lite") (delete-file-recursively "deps/libbdsg/bdsg/deps/sparsepp") ;(delete-file-recursively "deps/libdeflate") ;(delete-file-recursively "deps/libhandlegraph") + ;(delete-file-recursively "deps/libVCFH") ;(delete-file-recursively "deps/libvgio") ;(delete-file-recursively "deps/libvgio/deps") ; libhandlegraph ;(delete-file-recursively "deps/lru_cache") @@ -1641,6 +1641,7 @@ available to other researchers.") ;(delete-file-recursively "deps/progress_bar") (delete-file-recursively "deps/raptor") ;(delete-file-recursively "deps/sdsl-lite") + ;(delete-file-recursively "deps/sha1") (delete-file-recursively "deps/snappy") ;(delete-file-recursively "deps/sonLib") (delete-file-recursively "deps/sparsehash") @@ -1655,8 +1656,7 @@ available to other researchers.") (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") - #t)))) + "deps/libvgio/include/handlegraph"))))) (build-system gnu-build-system) (arguments '(#:phases @@ -1695,6 +1695,8 @@ available to other researchers.") (string-append " " (assoc-ref inputs "fastahack") "/bin/fastahack")) ((" \\$\\(FASTAHACK_DIR\\)/bin/fastahack") (string-append " " (assoc-ref inputs "fastahack") "/bin/fastahack")) + (("\\+= \\$\\(OBJ_DIR\\)/Fasta\\.o") + (string-append "+= " (assoc-ref inputs "fastahack") "/lib/libfastahack.so")) ((" \\$\\(LIB_DIR\\)/libsnappy.a") (string-append " " (assoc-ref inputs "snappy") "/lib/libsnappy.so")) @@ -1716,7 +1718,7 @@ available to other researchers.") (string-append " " (assoc-ref inputs "libdivsufsort") "/lib/libdivsufsort64.so")) ((" \\$\\(LIB_DIR\\)/libjemalloc.a") - (string-append " " (assoc-ref inputs "jemalloc") "/lib/libjemalloc.so")) + (string-append " " (assoc-ref inputs "jemalloc") "/lib/libjemalloc.a")) ((" \\$\\(INC_DIR\\)/sparsehash") (string-append " " (assoc-ref inputs "sparsehash") "/include/sparsehash")) @@ -1729,13 +1731,11 @@ available to other researchers.") (string-append " " (assoc-ref inputs "raptor2") "/bin/rapper"))) ;; vcf2tsv shows up in a couple of other places (substitute* "test/t/02_vg_construct.t" - (("../deps/vcflib/bin/vcf2tsv") (which "vcf2tsv"))) - #t)) + (("../deps/vcflib/bin/vcf2tsv") (which "vcf2tsv"))))) (add-after 'unpack 'fix-fastahack-dependency (lambda _ (substitute* "src/aligner.hpp" - (("Fasta.h") "fastahack/Fasta.h")) - #t)) + (("Fasta.h") "fastahack/Fasta.h")))) (add-after 'unpack 'fix-hopscotch-dependency (lambda _ (substitute* "Makefile" @@ -1749,8 +1749,7 @@ available to other researchers.") ;; We still need to copy it to the expected location. (copy-recursively "deps/libbdsg/bdsg/deps/hopscotch-map" - "deps/DYNAMIC/build/hopscotch_map-prefix/src/hopscotch_map") - #t)) + "deps/DYNAMIC/build/hopscotch_map-prefix/src/hopscotch_map"))) (add-after 'unpack 'adjust-tests (lambda* (#:key inputs #:allow-other-keys) (let ((bash-tap (assoc-ref inputs "bash-tap"))) @@ -1768,8 +1767,7 @@ available to other researchers.") ((".*node id.*") "is $(true) \"\" \"\"\n")) ;; Don't test the docs, we're not providing npm (substitute* "Makefile" - ((".*test-docs.*") "")) - #t))) + ((".*test-docs.*") ""))))) (add-after 'build 'build-manpages (lambda _ (invoke "make" "man"))) @@ -1781,11 +1779,13 @@ available to other researchers.") (for-each (lambda (file) (install-file file (string-append out "/share/man/man1"))) - (find-files "doc/man" "\\.1$")) - #t)))) + (find-files "doc/man" "\\.1$")))))) #:test-target "test")) (native-inputs - `(("asciidoctor" ,ruby-asciidoctor) + `(,@(if (member (%current-system) + (package-transitive-supported-systems ruby-asciidoctor)) + `(("asciidoctor" ,ruby-asciidoctor)) + '()) ("bash-tap" ,bash-tap) ("bc" ,bc) ("cmake" ,cmake-minimal) @@ -1829,6 +1829,7 @@ gene models and transcripts) as walks through nodes connected by edges @end enumerate This model is similar to sequence graphs that have been used in assembly and multiple sequence alignment.") + (properties `((release-monitoring-url . "https://github.com/vgteam/vg/releases"))) (license (list license:expat ; main program |