diff options
Diffstat (limited to 'gn/packages/bioinformatics.scm')
| -rw-r--r-- | gn/packages/bioinformatics.scm | 125 |
1 files changed, 115 insertions, 10 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index 02c979d..f7b70e2 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -41,9 +41,7 @@ #:use-module (gnu packages compression) #:use-module (gnu packages cpp) #:use-module (gnu packages cran) - #:use-module (gnu packages crates-compression) - #:use-module (gnu packages crates-io) - #:use-module (gnu packages crates-graphics) + #:use-module (past-crates packages crates-io) #:use-module (gnu packages curl) #:use-module (gnu packages databases) #:use-module (gnu packages datastructures) @@ -56,6 +54,7 @@ #:use-module (gnu packages graph) #:use-module (gnu packages gtk) #:use-module (gnu packages guile) + #:use-module (gnu packages haskell-xyz) #:use-module (gnu packages image) #:use-module (gnu packages imagemagick) #:use-module (gnu packages java) @@ -73,13 +72,16 @@ #:use-module (gnu packages protobuf) #:use-module (gnu packages python) #:use-module (gnu packages python-build) + #:use-module (gnu packages python-compression) #:use-module (gnu packages python-science) #:use-module (gnu packages python-web) - #:use-module ((gnu packages python-xyz) #:hide (python2-six)) + #:use-module (gnu packages python-xyz) + #:use-module (gnu packages python-check) #:use-module (gnu packages rdf) #:use-module (gnu packages readline) #:use-module (gnu packages rsync) #:use-module (gnu packages ruby) + #:use-module (gnu packages ruby-xyz) #:use-module (gnu packages rust) #:use-module (gnu packages serialization) #:use-module (gnu packages shells) @@ -1812,14 +1814,14 @@ dictionaries to record a queryable version of the graph.") (define-public smoothxg (package (name "smoothxg") - (version "0.8.0") + (version "0.8.2") (source (origin (method url-fetch) (uri (string-append "https://github.com/pangenome/smoothxg" "/releases/download/v" version "/smoothxg-v" version ".tar.gz")) (sha256 - (base32 "1gl4dskj81hlma7wsjrwwg77hgzk7dc9iaqqnf2wzrf2f4ll1cdj")) + (base32 "1hqaa6l904zl01rsmw5vzx2kvcncl97i5kln850snywyv33skxp6")) (snippet #~(begin (use-modules (guix build utils)) @@ -2339,14 +2341,14 @@ in-memory footprint at the cost of packing and unpacking.") (define-public vg (package (name "vg") - (version "1.61.0") + (version "1.65.0") (source (origin (method url-fetch) (uri (string-append "https://github.com/vgteam/vg/releases/download/v" version "/vg-v" version ".tar.gz")) (sha256 - (base32 "1yb8ffqq65ma5di42qlj483x42viq5j4xyyg3vpww60gm15n1yxx")) + (base32 "022wiz0rs1x90nk9zaxcf8szhma8kzygnbfhciq9166kjysd0pc6")) (snippet #~(begin (use-modules (guix build utils)) @@ -2506,8 +2508,11 @@ in-memory footprint at the cost of packing and unpacking.") (substitute* "Makefile" ((".*test-docs.*") ""))))) (add-after 'build 'build-manpages - (lambda* (#:key inputs #:allow-other-keys) - (invoke "make" "man"))) + (lambda* (#:key make-flags #:allow-other-keys) + ;; vg is not in PATH. Replace it with full path. + (substitute* "doc/vgmanmd.py" + (("'vg'") "'./bin/vg'")) + (apply invoke "make" "man" make-flags))) (replace 'install (lambda* (#:key outputs #:allow-other-keys) (let ((out (assoc-ref outputs "out"))) @@ -2527,9 +2532,11 @@ in-memory footprint at the cost of packing and unpacking.") bash-tap bc cmake-minimal + ghc-pandoc jq perl pkg-config + python samtools util-linux which @@ -2974,6 +2981,76 @@ to the user.") "http://www.kentinformatics.com/index.html" "Free for universities and non-profit institutions."))))) +(define htslib-1.14 + (package/inherit htslib + (version "1.14") + (source (origin + (method url-fetch) + (uri (string-append + "https://github.com/samtools/htslib/releases/download/" + version "/htslib-" version ".tar.bz2")) + (sha256 + (base32 + "0pwk8yhhvb85mi1d2qhwsb4samc3rmbcrq7b1s0jz0glaa7in8pd")))) + (arguments + (substitute-keyword-arguments (package-arguments htslib) + ((#:configure-flags cf #~'()) + #~(delete "--with-external-htscodecs" #$cf)))) + (propagated-inputs + (modify-inputs (package-propagated-inputs htslib) + (delete "htscodecs"))))) + +(define-public pbbam + (package + (name "pbbam") + (version "2.1.0") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/PacificBiosciences/pbbam") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1iyazi3l7dswpfxh39k5j7ydi0ywja0579xz3r6l9kkwz2n1z6dc")))) + (build-system meson-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'patch-tests + (lambda* (#:key inputs #:allow-other-keys) + ;; Disable this test. I tried fixing it by including + ;; optional_io.hpp, but there's a type error. + (substitute* "tests/src/meson.build" + (("'test_ReadGroupInfo.cpp',") "")) + #; + (substitute* "include/pbbam/ReadGroupInfo.h" + (("#include <boost/optional.hpp>" m) + (string-append m "\n#include <boost/optional/optional_io.hpp>"))) + (substitute* '("tests/scripts/cram/_test.py" + "tests/scripts/cram/_main.py") + (("'/bin/sh'") + (string-append "'" (which "sh") "'")))))))) + ;; These libraries are listed as "Required" in the pkg-config file. + (propagated-inputs + (list htslib-1.14 pbcopper zlib)) + (inputs + (list boost samtools)) + (native-inputs + (list googletest + pkg-config + python-wrapper)) ;for tests + (home-page "https://github.com/PacificBiosciences/pbbam") + (synopsis "Work with PacBio BAM files") + (description + "The pbbam software package provides components to create, query, and +edit PacBio BAM files and associated indices. These components include a core +C++ library, bindings for additional languages, and command-line utilities. +This library is not intended to be used as a general-purpose BAM utility - all +input and output BAMs must adhere to the PacBio BAM format specification. +Non-PacBio BAMs will cause exceptions to be thrown.") + (license license:bsd-3))) + (define-public bam2fastx (package (name "bam2fastx") @@ -4496,6 +4573,8 @@ automatically vectorize for different architectures without adapting the code.") (base32 "1vhqy8licl2pkzar4aag0q5fhnb3fdch8acyjh9445ia42z01z9c")))) (build-system r-build-system) + (arguments + (list #:tests? #f)) ;; tests fail and seem to require data (propagated-inputs (list r-rcpp r-rcpparmadillo)) @@ -4594,6 +4673,32 @@ interface to the basic htslib. It can be easily included in a C++ program for scripting high-performance genomic analyses.") (license license:asl2.0))) +(define-public r-genio + (package + (name "r-genio") + (version "1.1.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "genio" version)) + (sha256 + (base32 "0izx8yv8mvnfxdqnqpnp2ldw1hzs6ggxi7jgmjlgxkgmm4vngbgl")))) + (properties `((upstream-name . "genio"))) + (build-system r-build-system) + (propagated-inputs (list r-dplyr r-rcpp r-readr r-tibble)) + (native-inputs (list r-knitr r-testthat)) + (home-page "https://github.com/OchoaLab/genio") + (synopsis "Genetics Input/Output Functions") + (description "@code{r-genio} implements readers and writers for file formats +associated with genetics data. Reading and writing Plink BED/BIM/FAM +and GCTA binary GRM formats is fully supported, including a +lightning-fast BED reader and writer implementations. Other functions +are readr wrappers that are more constrained, user-friendly, and +efficient for these particular applications; handles Plink and +Eigenstrat tables (FAM, BIM, IND, and SNP files). There are also make +functions for FAM and BIM tables with default values to go with +simulated genotype data.") + (license license:gpl3))) (define-public r-stitch (package |