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-rw-r--r--gnu/packages/bioinformatics.scm805
1 files changed, 668 insertions, 137 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 77bc2eba14..41cdcc1de6 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -131,6 +131,7 @@
#:use-module (gnu packages pdf)
#:use-module (gnu packages perl)
#:use-module (gnu packages perl-check)
+ #:use-module (gnu packages perl-web)
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages popt)
#:use-module (gnu packages protobuf)
@@ -162,6 +163,7 @@
#:use-module (gnu packages time)
#:use-module (gnu packages tls)
#:use-module (gnu packages uglifyjs)
+ #:use-module (gnu packages video)
#:use-module (gnu packages vim)
#:use-module (gnu packages web)
#:use-module (gnu packages wget)
@@ -574,6 +576,30 @@ BED, GFF/GTF, VCF.")
whole-genome bisulfite sequencing (WGBS) reads from directional protocol.")
(license license:asl2.0)))
+(define-public bustools
+ (package
+ (name "bustools")
+ (version "0.43.2")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/BUStools/bustools")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "068kjlc4d528269nl5mc3j8h2c95r1v545d3fi1iw1ckg8rba0hg"))))
+ (build-system cmake-build-system)
+ (arguments (list #:tests? #f)) ;no test target
+ (inputs (list zlib))
+ (home-page "https://bustools.github.io")
+ (synopsis "Tools for working with BUS files")
+ (description "bustools is a program for manipulating BUS files for single
+cell RNA-Seq datasets. It can be used to error correct barcodes, collapse
+UMIs, produce gene count or transcript compatibility count matrices, and is useful
+for many other tasks.")
+ (license license:bsd-2)))
+
(define-public cellsnp-lite
;; Last release is from November 2021 and does not contain fixes.
(let ((commit "0885d746b0b1ea65c8ef92f8943ca7669ca9734a")
@@ -617,6 +643,50 @@ Compared to cellSNP, this package is more efficient with higher speed and less
memory usage.")
(license license:asl2.0))))
+(define-public cpat
+ (package
+ (name "cpat")
+ (version "3.0.4")
+ (source (origin
+ (method url-fetch)
+ (uri (pypi-uri "CPAT" version))
+ (sha256
+ (base32
+ "0dfrwwbhv1n4nh2a903d1qfb30fgxgya89sa70aci3wzf8h2z0vd"))
+ (modules '((guix build utils)))
+ (snippet
+ '(for-each delete-file-recursively
+ (list ".eggs"
+ "lib/__pycache__/"
+ "lib/cpmodule/__pycache__/")))))
+ (build-system pyproject-build-system)
+ (arguments
+ (list
+ #:phases
+ '(modify-phases %standard-phases
+ (replace 'check
+ (lambda* (#:key tests? #:allow-other-keys)
+ (when tests?
+ (with-directory-excursion "test"
+ ;; There is no test4.fa
+ (substitute* "test.sh"
+ ((".*-g test4.fa.*") ""))
+ (invoke "bash" "test.sh"))))))))
+ (propagated-inputs
+ (list python-numpy python-pysam))
+ (inputs
+ (list r-minimal))
+ (home-page "https://wlcb.oit.uci.edu/cpat/")
+ (synopsis "Alignment-free distinction between coding and noncoding RNA")
+ (description
+ "CPAT is a method to distinguish coding and noncoding RNA by using a
+logistic regression model based on four pure sequence-based, linguistic
+features: ORF size, ORF coverage, Ficket TESTCODE, and Hexamer usage bias.
+Linguistic features based method does not require other genomes or protein
+databases to perform alignment and is more robust. Because it is
+alignment-free, it runs much faster and also easier to use.")
+ (license license:gpl2+)))
+
(define-public pbcopper
(package
(name "pbcopper")
@@ -1070,12 +1140,48 @@ of single-cell data using Seurat, RcppML nmf, SingleCellExperiments and
similar.")
(license license:gpl2+))))
+(define-public r-stacas
+ (package
+ (name "r-stacas")
+ (version "2.2.0")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/carmonalab/STACAS")
+ (commit version)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "13i0h5i6vlbrb8ndq9gr81560z9d74b2c7m3rjfzls01irjza9hm"))))
+ (properties `((upstream-name . "STACAS")))
+ (build-system r-build-system)
+ (propagated-inputs
+ (list r-biocneighbors
+ r-biocparallel
+ r-ggplot2
+ r-ggridges
+ r-pbapply
+ r-r-utils
+ r-seurat))
+ (home-page "https://github.com/carmonalab/STACAS")
+ (synopsis "Sub-type anchoring correction for alignment in Seurat")
+ (description
+ "This package implements methods for batch correction and integration of
+scRNA-seq datasets, based on the Seurat anchor-based integration framework.
+In particular, STACAS is optimized for the integration of heterogenous
+datasets with only limited overlap between cell sub-types (e.g. TIL sets of
+CD8 from tumor with CD8/CD4 T cells from lymphnode), for which the default
+Seurat alignment methods would tend to over-correct biological differences.
+The 2.0 version of the package allows the users to incorporate explicit
+information about cell-types in order to assist the integration process.")
+ (license license:gpl3)))
+
(define-public r-stringendo
- (let ((commit "83b8f2d82a09b33b9e895438bb523a021138be01")
+ (let ((commit "15594b1bba11048a812874bafec0eea1dcc8618a")
(revision "1"))
(package
(name "r-stringendo")
- (version (git-version "0.3.4" revision commit))
+ (version (git-version "0.6.0" revision commit))
(source (origin
(method git-fetch)
(uri (git-reference
@@ -1084,10 +1190,10 @@ similar.")
(file-name (git-file-name name version))
(sha256
(base32
- "1ap0nhbyd6xx0yl2vgmwk38p22yrkv4k9hw13r35z4wf343rry6v"))))
+ "15ij4zf2j9c8m9n4bqhmxkchjh2bhddwjfxngfpwv7c5wjqyi6ir"))))
(properties `((upstream-name . "Stringendo")))
(build-system r-build-system)
- (propagated-inputs (list r-devtools r-usethis))
+ (propagated-inputs (list r-clipr))
(home-page "https://github.com/vertesy/Stringendo")
(synopsis "Stringendo is a string parsing library")
(description
@@ -1096,11 +1202,11 @@ plotnames, filenames and paths.")
(license license:gpl3))))
(define-public r-readwriter
- (let ((commit "12d32cb6533ef4b9eab4d707d1502525c2034aee")
+ (let ((commit "91373c44641014a1ce8e1c3e928747608aae8f54")
(revision "1"))
(package
(name "r-readwriter")
- (version (git-version "0.3.2" revision commit))
+ (version (git-version "1.5.3" revision commit))
(source (origin
(method git-fetch)
(uri (git-reference
@@ -1109,11 +1215,11 @@ plotnames, filenames and paths.")
(file-name (git-file-name name version))
(sha256
(base32
- "1hy47g8d7zppr2i9zlkwl2yb0ii8x710hqk07h089ldx9171qxab"))))
+ "156kvmplrip0w1zhs9yl5r0ayjipa0blhy614l65hbsjn1lwbskr"))))
(properties `((upstream-name . "ReadWriter")))
(build-system r-build-system)
(propagated-inputs
- (list r-gdata r-gtools r-openxlsx r-readr r-stringendo))
+ (list r-gtools r-openxlsx r-readr r-stringendo))
(home-page "https://github.com/vertesy/ReadWriter")
(synopsis "Functions to read and write files conveniently")
(description
@@ -1156,6 +1262,32 @@ shape. This package provides an @code{htmlwidget} for building streamgraph
visualizations.")
(license license:expat))))
+(define-public r-wasabi
+ (let ((commit "8c33cabde8d18c2657cd6e38e7cb834f87cf9846")
+ (revision "1"))
+ (package
+ (name "r-wasabi")
+ (version (git-version "1.0.1" revision commit))
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/COMBINE-lab/wasabi")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "0rpdj6n4cnx8n2zl60dzgl638474sg49dknwi9x3qb4g56dpphfa"))))
+ (properties `((upstream-name . "wasabi")))
+ (build-system r-build-system)
+ (propagated-inputs (list r-data-table r-rhdf5 r-rjson))
+ (home-page "https://github.com/COMBINE-lab/wasabi")
+ (synopsis "Use Sailfish and Salmon with Sleuth")
+ (description
+ "This package converts the output of the Sailfish and Salmon RNA-seq
+quantification tools so that it can be used with the Sleuth differential
+analysis package.")
+ (license license:bsd-3))))
+
(define-public pbbam
(package
(name "pbbam")
@@ -2260,6 +2392,40 @@ sequencing data and the end result are tables of UMI-unique DamID and CEL-Seq
counts.")
(license license:expat)))
+(define-public python-snaptools
+ (package
+ (name "python-snaptools")
+ (version "1.4.8")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "snaptools" version))
+ (sha256
+ (base32
+ "1s5373g5jjbshh3q39zy7dlxr7nda6ksxq9d1gw46h82c4fsmfbn"))))
+ (build-system pyproject-build-system)
+ (propagated-inputs
+ (list python-future
+ python-h5py
+ python-louvain
+ python-numpy
+ python-pybedtools
+ python-pysam))
+ (home-page "https://github.com/r3fang/SnapTools")
+ (synopsis "Tools for processing snap files" )
+ (description
+ "@code{SnapTools} can operate on snap files the following types of
+operations:
+
+@itemize
+@item index the reference genome before alignment;
+@item align reads to the corresponding reference genome;
+@item pre-process by convert pair-end reads into fragments, checking the
+ mapping quality score, alingment and filtration;
+@item create the cell-by-bin matrix.
+@end itemize")
+ (license license:asl2.0)))
+
(define-public python-bioframe
(package
(name "python-bioframe")
@@ -4289,6 +4455,107 @@ annotations of the genome.")
other types of unwanted sequence from high-throughput sequencing reads.")
(license license:expat)))
+(define-public lammps
+ (let ((commit "stable_2Aug2023_update2"))
+ (package
+ (name "lammps")
+ (version (string-append "0." commit))
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/lammps/lammps.git")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "11xagacgxgldkx34qdzyjrjvn8x3hpl0kgzhh9zh7skpq79pwycz"))))
+ (build-system gnu-build-system)
+ (arguments
+ (list
+ #:tests? #f ; no check target
+ #:make-flags
+ '(list "CC=mpicc" "mpi"
+ "LMP_INC=-DLAMMPS_GZIP \
+-DLAMMPS_JPEG -DLAMMPS_PNG -DLAMMPS_FFMPEG -DLAMMPS_MEMALIGN=64"
+ "LIB=-gz -ljpeg -lpng -lavcodec")
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'unpack 'chdir
+ (lambda _ (chdir "src")))
+ (replace 'configure
+ (lambda _
+ (substitute* "MAKE/Makefile.mpi"
+ (("SHELL =.*")
+ (string-append "SHELL=" (which "bash") "\n"))
+ (("cc ") "mpicc "))
+ (substitute* "Makefile"
+ (("SHELL =.*")
+ (string-append "SHELL=" (which "bash") "\n")))))
+ (add-after 'configure 'configure-modules
+ (lambda _
+ (invoke "make"
+ "yes-molecule"
+ "yes-misc"
+ "yes-granular"
+ (string-append "HDF5_PATH="
+ #$(this-package-input "hdf5")))))
+ (replace 'install
+ (lambda _
+ (let ((bin (string-append #$output "/bin")))
+ (mkdir-p bin)
+ (install-file "lmp_mpi" bin)))))))
+ (inputs
+ (list ffmpeg
+ gfortran
+ gzip
+ hdf5
+ libjpeg-turbo
+ libpng
+ openmpi
+ python-wrapper))
+ (native-inputs (list bc))
+ (home-page "https://www.lammps.org/")
+ (synopsis "Classical molecular dynamics simulator")
+ (description "LAMMPS is a classical molecular dynamics simulator
+designed to run efficiently on parallel computers. LAMMPS has potentials for
+solid-state materials (metals, semiconductors), soft matter (biomolecules,
+polymers), and coarse-grained or mesoscopic systems. It can be used to model
+atoms or, more generically, as a parallel particle simulator at the atomic,
+meso, or continuum scale.")
+ (license license:gpl2+))))
+
+(define-public lammps-serial
+ (package
+ (inherit lammps)
+ (name "lammps-serial")
+ (arguments
+ (substitute-keyword-arguments (package-arguments lammps)
+ ((#:make-flags flags)
+ '(list "CC=gcc" "serial"
+ "LMP_INC=-DLAMMPS_GZIP \
+-DLAMMPS_JPEG -DLAMMPS_PNG -DLAMMPS_FFMPEG -DLAMMPS_MEMALIGN=64"
+ "LIB=-gz -ljpeg -lpng -lavcodec"))
+ ((#:phases phases)
+ #~(modify-phases #$phases
+ (replace 'configure
+ (lambda _
+ (substitute* "MAKE/Makefile.serial"
+ (("SHELL =.*")
+ (string-append "SHELL=" (which "bash") "\n"))
+ (("cc ") "gcc "))
+ (substitute* "Makefile"
+ (("SHELL =.*")
+ (string-append "SHELL=" (which "bash") "\n")))))
+ (replace 'install
+ (lambda _
+ (let ((bin (string-append #$output "/bin")))
+ (mkdir-p bin)
+ (install-file "lmp_serial" bin))))))))
+ (inputs
+ (modify-inputs (package-inputs lammps)
+ (delete "openmpi")))))
+
(define-public libbigwig
(package
(name "libbigwig")
@@ -4793,6 +5060,126 @@ be of arbitrary length. Repeats with pattern size in the range from 1 to 2000
bases are detected.")
(license license:agpl3+)))
+(define-public trinityrnaseq
+ (package
+ (name "trinityrnaseq")
+ (version "2.13.2")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/trinityrnaseq/trinityrnaseq.git")
+ (commit (string-append "Trinity-v" version))
+ (recursive? #true)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "1qszrxqbx4q5pavpgm4rkrh1z1v1mf7qx83vv3fnlqdmncnsf1gv"))))
+ (build-system gnu-build-system)
+ (arguments
+ (list
+ #:test-target "test"
+ #:modules
+ '((guix build gnu-build-system)
+ (guix build utils)
+ (ice-9 match)
+ (srfi srfi-1))
+ #:make-flags
+ #~(list (string-append "CC=" #$(cc-for-target)))
+ #:phases
+ #~(modify-phases %standard-phases
+ (replace 'configure
+ (lambda _
+ (setenv "SHELL" (which "sh"))
+ (setenv "CONFIG_SHELL" (which "sh"))
+ ;; Do not require version.h, which triggers a local build of a
+ ;; vendored htslib.
+ (substitute* "trinity-plugins/bamsifter/Makefile"
+ (("sift_bam_max_cov.cpp htslib/version.h")
+ "sift_bam_max_cov.cpp"))))
+ (add-after 'build 'build-plugins
+ (lambda _
+ ;; Run this in the subdirectory to avoid running the
+ ;; tests right here.
+ (with-directory-excursion "trinity-plugins"
+ (invoke "make" "plugins"))))
+ ;; The install script uses rsync, provides no overrides for the
+ ;; default location at /usr/local/bin, and patching it would change
+ ;; all lines that do something.
+ (replace 'install
+ (lambda* (#:key inputs #:allow-other-keys)
+ (let ((share (string-append #$output "/share/trinity/"))
+ (bin (string-append #$output "/bin/")))
+ (mkdir-p bin)
+ (copy-recursively "." share)
+ (delete-file (string-append share "/Chrysalis/build/CMakeFiles/CMakeOutput.log"))
+ (delete-file (string-append share "/Inchworm/build/CMakeFiles/CMakeOutput.log"))
+
+ (wrap-program (string-append share "Trinity")
+ `("R_LIBS_SITE" ":" = (,(getenv "R_LIBS_SITE")))
+ `("PERL5LIB" ":" = (,(getenv "PERL5LIB")))
+ `("PYTHONPATH" ":" = (,(getenv "GUIX_PYTHONPATH")))
+ `("PATH" ":" =
+ ,(cons (string-append share "/trinity-plugins/BIN")
+ (filter-map (match-lambda
+ ((name . dir)
+ (string-append dir "/bin")))
+ inputs))))
+ (symlink (string-append share "Trinity")
+ (string-append bin "Trinity"))))))))
+ (inputs
+ (list blast+
+ bowtie
+ fastqc
+ hisat
+ htslib
+ icedtea-8
+ jellyfish
+ kallisto
+ multiqc
+ perl
+ perl-uri-escape
+ python-numpy
+ python-wrapper
+ r-ape
+ r-argparse
+ r-biobase
+ r-ctc
+ r-deseq2
+ r-edger
+ r-fastcluster
+ r-glimma
+ r-goplot
+ r-goseq
+ r-gplots
+ r-minimal
+ r-qvalue
+ r-rots
+ r-sm
+ r-tidyverse
+ rsem
+ salmon
+ samtools
+ sra-tools
+ star
+ zlib))
+ (propagated-inputs
+ (list coreutils
+ gzip
+ which))
+ (native-inputs (list cmake))
+ (home-page "https://github.com/trinityrnaseq/trinityrnaseq/wiki")
+ (synopsis "Trinity RNA-Seq de novo transcriptome assembly")
+ (description "Trinity assembles transcript sequences from Illumina RNA-Seq
+data. Trinity represents a novel method for the efficient and robust de novo
+reconstruction of transcriptomes from RNA-seq data. Trinity combines three
+independent software modules: Inchworm, Chrysalis, and Butterfly, applied
+sequentially to process large volumes of RNA-seq reads. Trinity partitions
+the sequence data into many individual de Bruijn graphs, each representing the
+transcriptional complexity at a given gene or locus, and then processes each
+graph independently to extract full-length splicing isoforms and to tease
+apart transcripts derived from paralogous genes.")
+ (license license:bsd-3)))
+
(define-public repeat-masker
(package
(name "repeat-masker")
@@ -10203,6 +10590,51 @@ data. This package includes panel editing or renaming for FCS files,
bead-based normalization and debarcoding.")
(license license:gpl3))))
+(define-public r-projectils
+ (let ((commit "cc73b97471b4b6eea11ce779b5c4a7dc5c3e1709")
+ (revision "1"))
+ (package
+ (name "r-projectils")
+ (version (git-version "3.0.0" revision commit))
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/carmonalab/ProjecTILs")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "0dpzvbhhb9andnj7angpj32cgkwd6rs6qgpl6i21pqzcn6vqqhqw"))))
+ (properties `((upstream-name . "ProjecTILs")))
+ (build-system r-build-system)
+ (propagated-inputs
+ (list r-biocneighbors
+ r-biocparallel
+ r-dplyr
+ r-ggplot2
+ r-matrix
+ r-patchwork
+ r-pheatmap
+ r-pracma
+ r-purrr
+ r-rcolorbrewer
+ r-reshape2
+ r-scales
+ r-scgate
+ r-seurat
+ r-seuratobject
+ r-stacas
+ r-ucell
+ r-umap
+ r-uwot))
+ (home-page "https://github.com/carmonalab/ProjecTILs")
+ (synopsis "Reference-based analysis of scRNA-seq data")
+ (description
+ "This package implements methods to project single-cell RNA-seq data
+onto a reference atlas, enabling interpretation of unknown cell transcriptomic
+states in the the context of known, reference states.")
+ (license license:gpl3))))
+
(define-public r-presto
(let ((commit "052085db9c88aa70a28d11cc58ebc807999bf0ad")
(revision "0"))
@@ -10237,55 +10669,54 @@ auROC analysis.")
(license license:gpl3))))
(define-public r-sccustomize
- (let ((commit "8414d1f5fb32277855b0619191a568932b7baeb0")
+ (let ((commit "397374590dae2ccc0c560897dcd1ce4382c18798")
(revision "1"))
(package
(name "r-sccustomize")
- (version (git-version "0.7.0" revision commit))
- (source (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/samuel-marsh/scCustomize")
- (commit commit)))
- (file-name (git-file-name name version))
- (sha256
- (base32
- "1wcgfq7lx83a2kf8pjbw524gdvxf351n08cwd5wzmmy57kf4knbj"))))
+ (version (git-version "2.0.1" revision commit))
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/samuel-marsh/scCustomize")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "11bafm0mlck27fqd8brz80pxb8dc5q0aqbp8zv0s9sx97njp7wsl"))))
(properties `((upstream-name . "scCustomize")))
(build-system r-build-system)
- (propagated-inputs
- (list r-circlize
- r-colorway
- r-cowplot
- r-data-table
- r-dittoseq
- r-dplyr
- r-forcats
- r-ggbeeswarm
- r-ggplot2
- r-ggprism
- r-ggpubr
- r-ggrastr
- r-ggrepel
- r-glue
- r-janitor
- r-magrittr
- r-matrix
- r-paletteer
- r-patchwork
- r-pbapply
- r-purrr
- r-remotes
- r-scales
- r-scattermore
- r-seurat
- r-seuratobject
- r-stringi
- r-stringr
- r-tibble
- r-tidyr
- r-tidyselect
- r-viridis))
+ (propagated-inputs (list r-circlize
+ r-colorway
+ r-cowplot
+ r-data-table
+ r-dittoseq
+ r-dplyr
+ r-forcats
+ r-ggbeeswarm
+ r-ggplot2
+ r-ggprism
+ r-ggpubr
+ r-ggrastr
+ r-ggrepel
+ r-glue
+ r-janitor
+ r-magrittr
+ r-matrix
+ r-paletteer
+ r-patchwork
+ r-pbapply
+ r-purrr
+ r-remotes
+ r-scales
+ r-scattermore
+ r-seurat
+ r-seuratobject
+ r-stringi
+ r-stringr
+ r-tibble
+ r-tidyr
+ r-tidyselect
+ r-viridis))
(native-inputs (list r-knitr))
(home-page "https://github.com/samuel-marsh/scCustomize")
(synopsis "Custom visualization and analyses of single-cell sequencing")
@@ -10418,6 +10849,43 @@ analysis of cell types, subtypes, transcriptional gradients,cell-cycle
variation, gene modules and their regulatory models and more.")
(license license:expat))))
+(define-public r-sleuth
+ (package
+ (name "r-sleuth")
+ (version "0.30.1")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/pachterlab/sleuth")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "09xgc7r6iisjkk0c0wn0q56zy0aph386kphwixfzq4422y7vlqci"))))
+ (properties `((upstream-name . "sleuth")))
+ (build-system r-build-system)
+ (propagated-inputs (list r-aggregation
+ r-data-table
+ r-dplyr
+ r-ggplot2
+ r-lazyeval
+ r-matrixstats
+ r-pheatmap
+ r-reshape2
+ r-rhdf5
+ r-shiny
+ r-tidyr))
+ (native-inputs (list r-knitr))
+ (home-page "https://github.com/pachterlab/sleuth")
+ (synopsis "Tools for investigating RNA-Seq")
+ (description
+ "Sleuth is a program for differential analysis of RNA-Seq data.
+It makes use of quantification uncertainty estimates obtained via Kallisto for
+accurate differential analysis of isoforms or genes, allows testing in the
+context of experiments with complex designs, and supports interactive
+exploratory data analysis via sleuth live.")
+ (license license:gpl3)))
+
(define-public r-snapatac
(package
(name "r-snapatac")
@@ -15341,7 +15809,9 @@ activity prediction from transcriptomics data, and its R implementation
(add-after 'unpack 'set-HOME
(lambda _ (setenv "HOME" "/tmp"))))))
(propagated-inputs
- (list r-complexheatmap
+ (list r-basilisk
+ r-basilisk-utils
+ r-complexheatmap
r-dplyr
r-ggplot2
r-magrittr
@@ -16491,7 +16961,16 @@ the HiCExplorer and pyGenomeTracks packages.")
(file-name (git-file-name name version))
(sha256
(base32
- "1yavgxry38g326z10bclvdf8glmma05fxj5m73h15m1r2l9xmw3v"))))
+ "1yavgxry38g326z10bclvdf8glmma05fxj5m73h15m1r2l9xmw3v"))
+ (modules '((guix build utils)))
+ ;; setup.py is malformed. The requirements are defined using a catchall
+ ;; pattern for the patch version number. This has been fixed in version
+ ;; 3.7.3, but we cannot upgrade to this version yet, since some Guix
+ ;; packages are not new enough. (See upstream commit
+ ;; 4845c715ec7b105e938d0c2426e27d0181690bfe for the fix).
+ (snippet '(substitute* "setup.py"
+ (("\\.\\*")
+ "")))))
(build-system pyproject-build-system)
(arguments
(list
@@ -17889,12 +18368,40 @@ The tool enables the de novo search for new structural elements and
facilitates comparative analysis of known RNA families.")
(license license:bsd-3)))
+(define-public r-databaselinke-r
+ (let ((commit "cf3d6cc3d36f2e1c9a557390232e9a8ed5abb7fd")
+ (revision "1"))
+ (package
+ (name "r-databaselinke-r")
+ (version (git-version "1.7.0" revision commit))
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/vertesy/DatabaseLinke.R")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "0hk76sb3w1v8a7c1knpc572ypsbgqlrv0p49c9y55a0dr12n16s1"))))
+ (properties `((upstream-name . "DatabaseLinke.R")))
+ (build-system r-build-system)
+ (propagated-inputs (list r-readwriter))
+ (home-page "https://github.com/vertesy/DatabaseLinke.R")
+ (synopsis
+ "Parse links to databases from your list of gene symbols")
+ (description
+ "This package provides a set of functions to parse and open (search
+query) links to genomics related and other websites for R. Useful when you
+want to explore e.g.: the function of a set of differentially expressed
+genes.")
+ (license license:gpl3))))
+
(define-public r-seurat-utils
- (let ((commit "0b6f5b548a49148cfbeaa654e8a618c0a020afa5")
+ (let ((commit "c0374cc9e25ce391ba8013fda0f8c7babbb9201d")
(revision "1"))
(package
(name "r-seurat-utils")
- (version (git-version "1.6.5" revision commit))
+ (version (git-version "2.5.0" revision commit))
(source (origin
(method git-fetch)
(uri (git-reference
@@ -17903,12 +18410,15 @@ facilitates comparative analysis of known RNA families.")
(file-name (git-file-name name version))
(sha256
(base32
- "1mn64h375mkj6x4ix5493z32gqg96yc507j5jr0lx9g5wk1bf762"))))
+ "15l86b43q245gzz7gsr5rhs4sir74lc14d64yqxfqcb0zrb2bzzd"))))
(properties `((upstream-name . "Seurat.utils")))
(build-system r-build-system)
(propagated-inputs (list r-codeandroll2
r-cowplot
+ r-databaselinke-r
r-dplyr
+ r-enhancedvolcano
+ r-foreach
r-ggcorrplot
r-ggexpress
r-ggplot2
@@ -17916,15 +18426,21 @@ facilitates comparative analysis of known RNA families.")
r-ggrepel
r-hgnchelper
r-htmlwidgets
+ r-job
+ r-magrittr
r-markdownhelpers
r-markdownreports
r-matrix
r-matrixstats
+ r-pheatmap
+ r-plotly
r-princurve
+ r-qs
r-r-utils
r-readr
r-readwriter
r-reshape2
+ r-rstudioapi
r-scales
r-seurat
r-soupx
@@ -17933,6 +18449,7 @@ facilitates comparative analysis of known RNA families.")
r-stringr
r-tibble
r-tictoc
+ r-tidyverse
r-vroom))
(home-page "https://github.com/vertesy/Seurat.utils")
(synopsis "Collection of utility functions for Seurat")
@@ -17984,7 +18501,7 @@ updated much more frequently.")
(define-public python-ctxcore
(package
(name "python-ctxcore")
- (version "0.1.1")
+ (version "0.2.0")
(source
(origin
(method git-fetch)
@@ -17994,8 +18511,8 @@ updated much more frequently.")
(file-name (git-file-name name version))
(sha256
(base32
- "16nlj7z8pirgjad7vlgm7226b3hpw4a7n967vyfg26dsf5n8k70d"))))
- (build-system python-build-system)
+ "0nv4lc46cnzpg5gcdxrsv7b4srmkq55zl3rcadw5pn3yyz5fzd2k"))))
+ (build-system pyproject-build-system)
(arguments
(list
#:phases
@@ -18007,12 +18524,12 @@ updated much more frequently.")
(setenv "SETUPTOOLS_SCM_PRETEND_VERSION" #$version))))))
(propagated-inputs
(list python-cytoolz
- python-numba
python-frozendict
+ python-numba
python-numpy
python-pandas
+ python-pyarrow
python-pyyaml
- python-pyarrow-0.16
python-tqdm))
(native-inputs
(list python-pytest
@@ -18060,67 +18577,77 @@ tree-based ensemble regressors.")
(license license:bsd-3)))
(define-public pyscenic
- (package
- (name "pyscenic")
- (version "0.11.2")
- (source
- (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/aertslab/pySCENIC")
- (commit version)))
- (file-name (git-file-name name version))
- (sha256
- (base32
- "0pbmmr1zdb1vbbs6wx357s59d13pna6x03wq8blj6ckjws8bbq73"))))
- (build-system python-build-system)
- (arguments
- `(#:phases
- (modify-phases %standard-phases
- ;; Numba needs a writable dir to cache functions.
- (add-before 'check 'set-numba-cache-dir
- (lambda _
- (setenv "NUMBA_CACHE_DIR" "/tmp")))
- (replace 'check
- (lambda _
- (invoke "pytest" "-v"))))))
- (propagated-inputs
- (list python-ctxcore
- python-cytoolz
- python-multiprocessing-on-dill
- python-llvmlite
- python-numba
- python-attrs
- python-frozendict
- python-numpy
- python-pandas
- python-cloudpickle
- python-dask
- python-distributed
- python-arboreto
- python-boltons
- python-setuptools
- python-pyyaml
- python-tqdm
- python-interlap
- python-umap-learn
- python-loompy
- python-networkx
- python-scipy
- python-fsspec
- python-requests
- python-aiohttp
- python-scikit-learn))
- (native-inputs
- (list python-pytest))
- (home-page "https://scenic.aertslab.org/")
- (synopsis "Single-Cell regulatory network inference and clustering")
- (description
- "pySCENIC is a Python implementation of the SCENIC pipeline (Single-Cell
+ ;; Latest commit from the update-pyarrow branch
+ (let ((commit "5f170fdf474548c37ab381d1849c662820d658ee")
+ (revision "1"))
+ (package
+ (name "pyscenic")
+ (version (git-version "0.11.2" revision commit))
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/aertslab/pySCENIC")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "03qkvy400rjndg2ds6bhcaprir71mqr2v3yv9vd77lcnzxgw3s0z"))))
+ (build-system pyproject-build-system)
+ (arguments
+ (list
+ #:phases
+ '(modify-phases %standard-phases
+ ;; The cli modules referenced here have been removed, so this
+ ;; breaks the sanity check.
+ (add-after 'unpack 'do-not-reference-deleted-modules
+ (lambda _
+ (substitute* "setup.py"
+ (("'db2feather = .*',") "")
+ (("'invertdb = .*',") "")
+ (("'gmt2regions = pyscenic.cli.gmt2regions:main'") ""))))
+ ;; Numba needs a writable dir to cache functions.
+ (add-before 'check 'set-numba-cache-dir
+ (lambda _
+ (setenv "NUMBA_CACHE_DIR" "/tmp"))))))
+ (propagated-inputs
+ (list python-ctxcore
+ python-cytoolz
+ python-multiprocessing-on-dill
+ python-llvmlite
+ python-numba
+ python-attrs
+ python-frozendict
+ python-numpy
+ python-pandas
+ python-cloudpickle
+ python-dask
+ python-pyarrow ;XXX for dask
+ python-distributed
+ python-arboreto
+ python-boltons
+ python-setuptools
+ python-pyyaml
+ python-tqdm
+ python-interlap
+ python-umap-learn
+ python-loompy
+ python-networkx
+ python-scipy
+ python-fsspec
+ python-requests
+ python-aiohttp
+ python-scikit-learn))
+ (native-inputs
+ (list python-pytest))
+ (home-page "https://scenic.aertslab.org/")
+ (synopsis "Single-Cell regulatory network inference and clustering")
+ (description
+ "pySCENIC is a Python implementation of the SCENIC pipeline (Single-Cell
rEgulatory Network Inference and Clustering) which enables biologists to infer
transcription factors, gene regulatory networks and cell types from
single-cell RNA-seq data.")
- (license license:gpl3+)))
+ (license license:gpl3+))))
(define-public python-ikarus
(package
@@ -20169,24 +20696,28 @@ aligner.")
(uri (pypi-uri "scvelo" version))
(sha256
(base32 "0h5ha1459ljs0qgpnlfsw592i8dxqn6p9bl08l1ikpwk36baxb7z"))))
- (build-system python-build-system)
+ (build-system pyproject-build-system)
(arguments
- `(#:phases
- (modify-phases %standard-phases
- ;; Numba needs a writable dir to cache functions.
- (add-before 'check 'set-numba-cache-dir
- (lambda _
- (setenv "NUMBA_CACHE_DIR" "/tmp")))
- (replace 'check
- (lambda* (#:key outputs tests? #:allow-other-keys)
- (when tests?
- ;; The discovered test file names must match the names of the
- ;; compiled files, so we cannot run the tests from
- ;; /tmp/guix-build-*.
- (with-directory-excursion
- (string-append (assoc-ref outputs "out")
- "/lib/python3.10/site-packages/scvelo/core/tests/")
- (invoke "pytest" "-v"))))))))
+ (list
+ #:test-flags
+ ;; XXX: these two tests fail for unknown reasons
+ '(list "-k" "not test_perfect_fit and not test_perfect_fit_2d")
+ #:phases
+ #~(modify-phases %standard-phases
+ ;; Numba needs a writable dir to cache functions.
+ (add-before 'check 'set-numba-cache-dir
+ (lambda _
+ (setenv "NUMBA_CACHE_DIR" "/tmp")))
+ (replace 'check
+ (lambda* (#:key tests? test-flags #:allow-other-keys)
+ (when tests?
+ ;; The discovered test file names must match the names of the
+ ;; compiled files, so we cannot run the tests from
+ ;; /tmp/guix-build-*.
+ (with-directory-excursion
+ (string-append #$output
+ "/lib/python3.10/site-packages/scvelo/core/tests/")
+ (apply invoke "pytest" "-v" test-flags))))))))
(propagated-inputs
(list python-anndata
python-hnswlib
generated by cgit v1.2.3 (git 2.46.0) at 2024-08-13 14:26:34 +0000