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authorEfraim Flashner2022-11-16 14:56:36 +0200
committerEfraim Flashner2022-11-16 14:57:29 +0200
commitcc8ee17a6e63cf20adc9374735a1322dd9c7f88e (patch)
treedd52eb357089ae4c94b66687f716d5bb0bdf6b4a
parentdd9aab67b68cad7f2fa2c15626d73b1e25198dee (diff)
downloadguix-bioinformatics-cc8ee17a6e63cf20adc9374735a1322dd9c7f88e.tar.gz
gn: Add graph-genotyper and dependent packages
-rw-r--r--gn/packages/bioinformatics.scm133
-rw-r--r--gn/packages/crates-io.scm135
2 files changed, 267 insertions, 1 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index 8f98b8e..76b93d9 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -512,6 +512,34 @@ reads.")
collapses them into a non-redundant graph structure.")
(license license:expat)))
+(define-public gafpack
+ (let ((commit "ad31875b6914d964c6fd72d1bf334f0843538fb6") ; November 10, 2022
+ (revision "1"))
+ (package
+ (name "gafpack")
+ (version (git-version "0.0.0" revision commit))
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/ekg/gafpack")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "0di2psh0ls7jlbnqs7k71p55f73pn23a09k1h3ril7gwjcrzr3rk"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:install-source? #f
+ #:cargo-inputs
+ (("rust-clap" ,rust-clap-4)
+ ("rust-gfa" ,rust-gfa-0.10))))
+ (home-page "https://github.com/ekg/gafpack")
+ (synopsis "Convert variation graph alignments to coverage maps over nodes")
+ (description
+ "Gafpack converts alignments to pangenome variation graphs to coverage
+maps useful in haplotype-based genotyping.")
+ (license license:expat))))
+
(define-public agc-for-pgr-tk
(let ((commit "453c0afdc54b4aa00fa8e97a63f196931fdb81c4") ; April 26, 2022
(revision "1"))
@@ -728,6 +756,61 @@ performance.)")
"file:///LICENSE"
"CC-BY-NC-SA 4.0"))))
+(define-public graph-genotyper
+ (let ((commit "e7cc6b43a5b1f389d76bf9aac7f2ee02f92caeaf") ; October 17, 2022
+ (revision "13"))
+ (package
+ (name "graph-genotyper")
+ (version (git-version "0.0.0" revision commit))
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/davidebolo1993/graph_genotyper")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "1l8yjpkqamiqr1q5i7vr5z04aba7skpbcwyc9dx5fiklvljjfhcx"))))
+ (build-system copy-build-system)
+ (arguments
+ `(#:install-plan
+ '(("genotype.py" "bin/")
+ ("genotype.sh" "bin/"))
+ #:phases
+ (modify-phases %standard-phases
+ (add-after 'install 'wrap-genotype
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (let ((out (assoc-ref outputs "out")))
+ (wrap-script (string-append out "/bin/genotype.sh")
+ `("GUIX_PYTHONPATH" ":" prefix (,(getenv "GUIX_PYTHONPATH")))
+ `("PATH" ":" prefix
+ ,(map (lambda (file-name)
+ (string-append (assoc-ref inputs file-name) "/bin"))
+ (list "gafpack"
+ "odgi"
+ "python"
+ "samtools"
+ "vg"))))))))))
+ (inputs
+ (list gafpack
+ guile-3.0
+ odgi
+ python
+ python-numpy
+ python-pandas
+ python-scipy
+ samtools
+ vg))
+ (home-page "https://bitbucket.org/jana_ebler")
+ (synopsis "Genotyping based on k-mers and pangenome graphs")
+ (description
+ "This package provides a genotyper for various types of genetic variants
+(such as SNPs, indels and structural variants). Genotypes are computed based on
+read k-mer counts and a panel of known haplotypes. A description of the method
+can be found @url{https://www.biorxiv.org/content/10.1101/2020.11.11.378133v1,
+here}.")
+ (license (license:non-copyleft
+ "No license listed")))))
+
(define-public pangenie
(let ((commit "e779076827022d1416ab9fabf99a03d8f4725956") ; September 2, 2021 from phasing-tests branch
(revision "2"))
@@ -1811,6 +1894,56 @@ available to other researchers.")
(delete-file "scanpy/tests/test_pca.py")
#t)))))))))
+;; TODO: Unbundle everything
+(define-public odgi
+ (package
+ (name "odgi")
+ (version "0.8.1")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "https://github.com/pangenome/odgi/releases"
+ "/download/v" version
+ "/odgi-v" version ".tar.gz"))
+ (sha256
+ (base32 "175083pb9hp0vn9a00hbxlayyk5a5j8p52yq5qfmbnfvndisbmbv"))
+ (snippet
+ #~(begin
+ (use-modules (guix build utils))
+ (substitute* "CMakeLists.txt"
+ (("-march=native") "")
+ (("-msse4\\.2") ""))
+ (delete-file-recursively "deps/pybind11")
+ (delete-file-recursively "deps/sdsl-lite")))))
+ (build-system cmake-build-system)
+ (native-inputs
+ (list pkg-config))
+ (inputs
+ (list jemalloc
+ libdivsufsort
+ pybind11
+ python
+ sdsl-lite))
+ (home-page "https://github.com/vgteam/odgi")
+ (synopsis "Optimized Dynamic Genome/Graph Implementation")
+ (description "@acronym{Optimized Dynamic Genome/Graph Implementation, odgi}
+provides an efficient and succinct dynamic DNA sequence graph model, as well as
+a host of algorithms that allow the use of such graphs in bioinformatic
+analyses.
+
+Careful encoding of graph entities allows odgi to efficiently compute and
+transform pangenomes with minimal overheads. @command{odgi} implements a
+dynamic data structure that leveraged multi-core CPUs and can be updated on the
+fly.
+
+The edges and path steps are recorded as deltas between the current node id and
+the target node id, where the node id corresponds to the rank in the global
+array of nodes. Graphs built from biological data sets tend to have local
+partial order and, when sorted, the deltas be small. This allows them to be
+compressed with a variable length integer representation, resulting in a small
+in-memory footprint at the cost of packing and unpacking.")
+ (properties '((tunable? . #t)))
+ (license license:expat)))
+
(define-public vg
(package
(name "vg")
diff --git a/gn/packages/crates-io.scm b/gn/packages/crates-io.scm
index 847b2ef..8b7bc4c 100644
--- a/gn/packages/crates-io.scm
+++ b/gn/packages/crates-io.scm
@@ -7,7 +7,8 @@
#:use-module (guix build-system cargo)
#:use-module (gnu packages crates-graphics)
#:use-module (gnu packages crates-io)
- #:use-module (gnu packages maths))
+ #:use-module (gnu packages maths)
+ #:use-module (gnu packages python))
(define-public rust-bgzip-0.2
(package
@@ -65,6 +66,25 @@ for massive key sets}. It generates an @acronym{MPHF, minimal perfect hash
functions} for a collection of hashable objects.")
(license license:expat)))
+(define-public rust-clap-lex-0.3
+ (package
+ (name "rust-clap-lex")
+ (version "0.3.0")
+ (source (origin
+ (method url-fetch)
+ (uri (crate-uri "clap-lex" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "1a4dzbnlxiamfsn0pnkhn7n9bdfjh66j9fxm6mmr7d227vvrhh8d"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:cargo-inputs (("rust-os-str-bytes" ,rust-os-str-bytes-6))))
+ (home-page "https://github.com/clap-rs/clap/tree/master/clap_lex")
+ (synopsis "Minimal, flexible command line parser")
+ (description "Minimal, flexible command line parser")
+ (license (list license:expat license:asl2.0))))
+
(define-public rust-cuckoofilter-0.5
(package
(name "rust-cuckoofilter")
@@ -352,6 +372,51 @@ Python code from a Rust binary is also supported.")
(description "This package provides succinct data structures for Rust.")
(license (list license:expat license:asl2.0))))
+(define-public rust-terminal-size-0.2
+ (package
+ (name "rust-terminal-size")
+ (version "0.2.2")
+ (source (origin
+ (method url-fetch)
+ (uri (crate-uri "terminal-size" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "0yhza8sc6jkka6j0nq5sl749ckx1jagvxp3b38yhh4px6k291jj0"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:skip-build? #t
+ ;#:cargo-inputs
+ ;(("rust-rustix" ,rust-rustix-0.35)
+ ; ("rust-windows-sys" ,rust-windows-sys-0.42))
+ ))
+ (home-page "https://github.com/eminence/terminal-size")
+ (synopsis "Gets the size of your Linux or Windows terminal")
+ (description "Gets the size of your Linux or Windows terminal")
+ (license (list license:expat license:asl2.0))))
+
+(define-public rust-unic-emoji-char-0.9
+ (package
+ (name "rust-unic-emoji-char")
+ (version "0.9.0")
+ (source (origin
+ (method url-fetch)
+ (uri (crate-uri "unic-emoji-char" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "0ka9fr7s6lv0z43r9xphg9injn35pfxf9g9q18ki0wl9d0g241qb"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:cargo-inputs
+ (("rust-unic-char-property" ,rust-unic-char-property-0.9)
+ ("rust-unic-char-range" ,rust-unic-char-range-0.9)
+ ("rust-unic-ucd-version" ,rust-unic-ucd-version-0.9))))
+ (home-page "https://github.com/open-i18n/rust-unic/")
+ (synopsis "UNIC â Unicode Emoji â Emoji Character Properties")
+ (description "UNIC â Unicode Emoji â Emoji Character Properties")
+ (license (list license:expat license:asl2.0))))
+
(define-public rust-clap-for-jrep
(package
(name "rust-clap")
@@ -499,6 +564,48 @@ or any combination.")
Argument Parser")
(license (list license:expat license:asl2.0))))
+(define-public rust-clap-4
+ (package
+ (name "rust-clap")
+ (version "4.0.9")
+ (source (origin
+ (method url-fetch)
+ (uri (crate-uri "clap" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "1w0dxqzrh449s9l2k8g66pdsff02599bwi5mh0gny3227kcpsq1h"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:cargo-inputs
+ (("rust-atty" ,rust-atty-0.2)
+ ("rust-backtrace" ,rust-backtrace-0.3)
+ ("rust-bitflags" ,rust-bitflags-1)
+ ("rust-clap-derive" ,rust-clap-derive-4)
+ ("rust-clap-lex" ,rust-clap-lex-0.3)
+ ("rust-once-cell" ,rust-once-cell-1)
+ ("rust-strsim" ,rust-strsim-0.10)
+ ("rust-termcolor" ,rust-termcolor-1)
+ ("rust-terminal-size" ,rust-terminal-size-0.2)
+ ("rust-unicase" ,rust-unicase-2)
+ ("rust-unicode-width" ,rust-unicode-width-0.1))
+ #:cargo-development-inputs
+ (("rust-humantime" ,rust-humantime-2)
+ ("rust-rustversion" ,rust-rustversion-1)
+ ("rust-shlex" ,rust-shlex-1)
+ ("rust-snapbox" ,rust-snapbox-0.4)
+ ("rust-static-assertions" ,rust-static-assertions-1)
+ ("rust-trybuild" ,rust-trybuild-1)
+ ("rust-trycmd" ,rust-trycmd-0.13)
+ ("rust-unic-emoji-char" ,rust-unic-emoji-char-0.9))))
+ (home-page "https://github.com/clap-rs/clap")
+ (synopsis
+ "A simple to use, efficient, and full-featured Command Line Argument Parser")
+ (description
+ "This package provides a simple to use, efficient, and full-featured Command Line
+ Argument Parser")
+ (license (list license:expat license:asl2.0))))
+
;; ready to upstream, WITH rust-clap-derive
;; replace fields with those from upstream.
(define-public rust-clap-derive-3.1
@@ -527,6 +634,32 @@ or any combination.")
"Parse command line argument by defining a struct, derive crate.")
(license (list license:expat license:asl2.0))))
+(define-public rust-clap-derive-4
+ (package
+ (name "rust-clap-derive")
+ (version "4.0.9")
+ (source (origin
+ (method url-fetch)
+ (uri (crate-uri "clap-derive" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "02zhbbmyz3dpy9ml6xfp7i8p3ffj1djvkdnkg6gr6d0s5r4hg8x4"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:cargo-inputs
+ (("rust-heck" ,rust-heck-0.4)
+ ("rust-proc-macro-error" ,rust-proc-macro-error-1)
+ ("rust-proc-macro2" ,rust-proc-macro2-1)
+ ("rust-quote" ,rust-quote-1)
+ ("rust-syn" ,rust-syn-1))))
+ (home-page "https://github.com/clap-rs/clap/tree/master/clap_derive")
+ (synopsis
+ "Parse command line argument by defining a struct, derive crate.")
+ (description
+ "Parse command line argument by defining a struct, derive crate.")
+ (license (list license:expat license:asl2.0))))
+
(define-public rust-textwrap-0.15
(package
(name "rust-textwrap")