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-rw-r--r--gn/packages/bioinformatics.scm41
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