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-rw-r--r--gn/packages/bioinformatics.scm168
1 files changed, 167 insertions, 1 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index a235f44..9828e14 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -16,22 +16,32 @@
#:use-module (guix build-system waf)
#:use-module (gnu packages)
#:use-module (gn packages python)
+ #:use-module (gnu packages algebra)
+ #:use-module (gnu packages autotools)
#:use-module (gnu packages base)
+ #:use-module (gnu packages bash)
#:use-module (gnu packages bioconductor)
#:use-module (gnu packages bioinformatics)
#:use-module (gnu packages boost)
#:use-module (gnu packages check)
+ #:use-module (gnu packages cmake)
#:use-module (gnu packages compression)
#:use-module (gnu packages cran)
#:use-module (gnu packages crates-io)
+ #:use-module (gnu packages databases)
#:use-module (gnu packages datastructures)
+ #:use-module (gnu packages elf)
#:use-module (gnu packages fontutils)
#:use-module (gnu packages gcc)
#:use-module (gnu packages graphviz)
+ #:use-module (gnu packages gtk)
#:use-module (gnu packages imagemagick)
#:use-module (gnu packages jemalloc)
+ #:use-module (gnu packages linux)
+ #:use-module (gnu packages machine-learning)
#:use-module (gnu packages maths)
#:use-module (gnu packages mpi)
+ #:use-module (gnu packages ncurses)
#:use-module (gnu packages perl)
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages protobuf)
@@ -41,9 +51,11 @@
#:use-module (gnu packages python-xyz)
#:use-module (gnu packages rdf)
#:use-module (gnu packages readline)
+ #:use-module (gnu packages ruby)
#:use-module (gnu packages serialization)
#:use-module (gnu packages statistics)
- #:use-module (gnu packages time))
+ #:use-module (gnu packages time)
+ #:use-module (gnu packages web))
(define-public contra
(package
@@ -1340,3 +1352,157 @@ available to other researchers.")
"This package provides a Rust library for working with graphs in the
@dfn{Graphical Fragment Assembly} (GFA) format.")
(license license:expat)))
+
+(define-public vg
+ (package
+ (name "vg")
+ (version "1.26.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "https://github.com/vgteam/vg/releases/download/v"
+ version "/vg-v" version ".tar.gz"))
+ (sha256
+ (base32
+ "1f1c30bhqh2561i9dvbfzdhl9w956yxc1gddvasj1v9jwap6i4y1"))
+ (patches (search-patches "vg-use-packaged-deps.patch"))
+ (modules '((guix build utils)))
+ (snippet
+ '(begin
+ (delete-file-recursively "deps/bash-tap")
+ (delete-file-recursively "deps/boost-subset")
+ (delete-file-recursively "deps/elfutils")
+ (delete-file-recursively "deps/fastahack")
+ (delete-file-recursively "deps/htslib")
+ (delete-file-recursively "deps/jemalloc")
+ (delete-file-recursively "deps/raptor")
+ (delete-file-recursively "deps/rocksdb")
+ ;(delete-file-recursively "deps/sdsl-lite")
+ (delete-file-recursively "deps/snappy")
+ (delete-file-recursively "deps/sparsehash")
+ (delete-file-recursively "deps/vcflib")
+ (delete-file-recursively "deps/vowpal_wabbit")
+ (delete-file-recursively "deps/sublinear-Li-Stephens/deps")
+ #t))))
+ (build-system gnu-build-system)
+ (arguments
+ '(#:phases
+ (modify-phases %standard-phases
+ (delete 'configure) ; no configure script
+ (add-after 'unpack 'fix-hopscotch-dependency
+ (lambda _
+ (substitute* "Makefile"
+ ;; The build directory for hopscotch_map-prefix.
+ (("rm -Rf build && ") ""))
+ ;; Don't try to download hopscotch_map from the internet.
+ (substitute* "deps/DYNAMIC/CMakeLists.txt"
+ ((".*GIT_REPOSITORY.*")
+ "SOURCE_DIR \"../../libbdsg/deps/hopscotch-map\"\n")
+ ((".*BUILD_IN_SOURCE.*") ""))
+ ;; We still need to copy it to the expected location.
+ (copy-recursively
+ "deps/libbdsg/deps/hopscotch-map"
+ "deps/DYNAMIC/build/hopscotch_map-prefix/src/hopscotch_map")
+ #t))
+ (add-after 'unpack 'adjust-test
+ (lambda* (#:key inputs #:allow-other-keys)
+ (let ((bash-tap (assoc-ref inputs "bash-tap")))
+ (substitute* (find-files "test/t" ".")
+ (("BASH_TAP_ROOT.*")
+ (string-append "BASH_TAP_ROOT=" bash-tap "/bin\n"))
+ ((".*bash-tap-bootstrap")
+ (string-append ". " bash-tap "/bin/bash-tap-bootstrap")))
+ ;; Lets skip the 4 failing tests for now:
+ (substitute* '("test/t/07_vg_map.t"
+ "test/t/33_vg_mpmap.t")
+ ((".*node id.*") "is $(true) \"\" \"\"\n"))
+ (substitute* "test/t/17_vg_augment.t"
+ (("jq\\.") "jq") ; This one is just a typo
+ ((".*included path.*") "is $(true) \"\" \"\"\n"))
+ #t)))
+ ;; If we build this first we should avoid the race conditions.
+ (add-before 'build 'build-libvgio
+ (lambda _
+ (invoke "make" "lib/libvgio.a" "-j1")))
+ (add-after 'build 'build-manpages
+ (lambda _
+ (invoke "make" "man")))
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((out (assoc-ref outputs "out")))
+ (install-file "bin/vg" (string-append out "/bin"))
+ (install-file "lib/libvg.a" (string-append out "/lib"))
+ (for-each
+ (lambda (file)
+ (install-file file (string-append out "/share/man/man1")))
+ (find-files "doc/man" "\\.1$"))
+ #t))))
+ #:test-target "test"))
+ (native-inputs
+ `(("asciidoctor" ,ruby-asciidoctor)
+ ("bash-tap" ,bash-tap)
+ ("bc" ,bc)
+ ("cmake" ,cmake-minimal)
+ ("jq" ,jq)
+ ("perl" ,perl)
+ ("pkg-config" ,pkg-config)
+ ("samtools" ,samtools)
+ ("util-linux" ,util-linux)
+ ("which" ,which)))
+ (inputs
+ `(("boost" ,boost)
+ ("bzip2" ,bzip2)
+ ("cairo" ,cairo)
+ ("elfutils" ,elfutils)
+ ("fastahack" ,fastahack)
+ ("htslib" ,htslib-1.10)
+ ("jansson" ,jansson)
+ ("jemalloc" ,jemalloc)
+ ("libdivsufsort" ,libdivsufsort)
+ ("lz4" ,lz4)
+ ("ncurses" ,ncurses)
+ ("protobuf" ,protobuf)
+ ("raptor2" ,raptor2)
+ ("sdsl-lite" ,sdsl-lite)
+ ("smithwaterman" ,smithwaterman)
+ ("tabixpp" ,tabixpp)
+ ("rocksdb" ,rocksdb)
+ ("vcflib" ,vcflib)
+ ("vowpal-wabbit" ,vowpal-wabbit)
+ ("zlib" ,zlib)))
+ (home-page "https://www.biostars.org/t/vg/")
+ (synopsis "Tools for working with genome variation graphs")
+ (description "Variation graphs provide a succinct encoding of the sequences
+of many genomes. A variation graph (in particular as implemented in vg) is
+composed of:
+@enumerate
+@item nodes, which are labeled by sequences and ids
+@item edges, which connect two nodes via either of their respective ends
+@item paths, describe genomes, sequence alignments, and annotations (such as
+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.")
+ (license
+ (list
+ license:expat ; main program
+ license:bsd-2 ; deps/xg/deps/ips4o
+ license:bsd-3 ; deps/sparsepp, deps/sonLib/C/{impl,inc}
+ license:asl2.0 ; deps/sonLib/externalTools/quicktree_1.1, deps/structures
+ license:gpl3+ ; all sdsl-lite copies
+ license:zlib ; deps/sonLib/externalTools/cutest
+ license:boost1.0)))) ; catch.hpp
+
+(define htslib-1.10
+ (package
+ (inherit htslib)
+ (name "htslib")
+ (version "1.10.2")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append
+ "https://github.com/samtools/htslib/releases/download/"
+ version "/htslib-" version ".tar.bz2"))
+ (sha256
+ (base32
+ "0f8rglbvf4aaw41i2sxlpq7pvhly93sjqiz0l4q3hwki5zg47dg3"))))))