diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 295 |
1 files changed, 284 insertions, 11 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 325c159df1..801c9e1642 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -11,7 +11,7 @@ ;;; Copyright © 2017, 2021, 2022 Arun Isaac <arunisaac@systemreboot.net> ;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com> ;;; Copyright © 2018 Gábor Boskovits <boskovits@gmail.com> -;;; Copyright © 2018, 2019, 2020, 2021 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> +;;; Copyright © 2018, 2019, 2020, 2021, 2022 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> ;;; Copyright © 2019, 2020, 2021 Maxim Cournoyer <maxim.cournoyer@gmail.com> ;;; Copyright © 2019 Brian Leung <bkleung89@gmail.com> ;;; Copyright © 2019 Brett Gilio <brettg@gnu.org> @@ -6264,7 +6264,7 @@ subsequent visualization, annotation and storage of results.") (define-public plink-ng (package (inherit plink) (name "plink-ng") - (version "2.00a3-20220315") + (version "2.00a3.3") (source (origin (method git-fetch) @@ -6273,12 +6273,14 @@ subsequent visualization, annotation and storage of results.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "19inr47jwddkjb9kfb14yxc7xb16c73lkhgxj9sncb0fsiskb4x8")))) + (base32 "0m8wkyvbgvcr5kzc284w8fbhpxwglh2c1xq0yc3yv00a53gs7rv0")))) (build-system gnu-build-system) (arguments `(#:make-flags ,#~(list "BLASFLAGS=-llapack -lopenblas" - "CFLAGS=-Wall -O2 -DDYNAMIC_ZLIB=1" + (string-append "CFLAGS=-Wall -O2 -DDYNAMIC_ZLIB=1" + " -I" (search-input-directory + %build-inputs "include/simde")) "ZLIB=-lz" "BIN=plink prettify" (string-append "CC=" #$(cc-for-target)) @@ -6305,7 +6307,7 @@ subsequent visualization, annotation and storage of results.") (inputs (list lapack openblas zlib)) (native-inputs - (list diffutils plink python)) ; for tests + (list diffutils plink python simde)) ; for tests (home-page "https://www.cog-genomics.org/plink/") (license license:gpl3+))) @@ -7523,6 +7525,41 @@ of transcriptional heterogeneity among single cells.") ;; See https://github.com/hms-dbmi/scde/issues/38 (license license:gpl2))) +(define-public r-millefy + (package + (name "r-millefy") + (version "0.1.9-beta") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/yuifu/millefy") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0z2y0x99f761pxvg6n37cmnyrnj699jhjk43pvk05sa86iykgizl")))) + (properties `((upstream-name . "millefy"))) + (build-system r-build-system) + (propagated-inputs + (list r-data-table + r-destiny + r-dplyr + r-genomicranges + r-iranges + r-magrittr + r-rsamtools + r-rtracklayer + r-tidyr)) + (home-page "https://github.com/yuifu/millefy") + (synopsis "Make millefy plot with single-cell RNA-seq data") + (description "@code{Millefy} is a tool for visualizing read coverage of +@dfn{scRNA-seq}(single-cell RNA sequencing) datasets in genomic contexts. By +dynamically and automatically reorder single cells based on locus-specific +pseudo time, @code{Millefy} highlights cell-to-cell heterogeneity in read coverage +of scRNA-seq data.") + (license license:expat))) + (define-public r-misha (package (name "r-misha") @@ -9031,6 +9068,91 @@ remove biased methylation positions for RRBS sequence files.") programs for inferring phylogenies (evolutionary trees).") (license license:bsd-2))) +(define-public phyml + (package + (name "phyml") + (version "3.3.20220408") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/stephaneguindon/phyml") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "03hdqmnsgnzkcrp9r9ajdfkj33jgq4b86kra8ssjlrph65y344sa")) + (snippet + '(delete-file "doc/phyml-manual.pdf")))) + (build-system gnu-build-system) + (supported-systems '("x86_64-linux")) + (arguments + (let ((default-flags (list "--disable-native"))) + `(#:phases + (let ((build (lambda (what) + (lambda args + (apply (assoc-ref %standard-phases 'configure) + (append args + (list #:configure-flags + (cons (format #false "--enable-~a" what) + '() #;,default-flags)))) + (apply (assoc-ref %standard-phases 'build) args) + (apply (assoc-ref %standard-phases 'install) args))))) + (modify-phases %standard-phases + ;; We cannot use --disable-native; see + ;; https://github.com/stephaneguindon/phyml/issues/173 Instead we + ;; patch the code to at least get rid of -march=native. + (add-after 'unpack 'remove-march-native + (lambda _ + (substitute* "configure.ac" + (("DEFAULT_VECTOR_FLAG=\"-march=native\"") + "DEFAULT_VECTOR_FLAG=\"-march=athlon64-sse3\"\n")))) + (add-after 'build 'build-manual + (lambda _ + (with-directory-excursion "doc" + (invoke "make" "phyml-manual.pdf")))) + (add-after 'build-manual 'install-manual + (lambda* (#:key outputs #:allow-other-keys) + (with-directory-excursion "doc" + (install-file "phyml-manual.pdf" + (string-append (assoc-ref outputs "out") + "/share/doc/phyml"))))) + (add-after 'install 'build-phyml-mpi + (build "phyml-mpi")) + (add-after 'build-phyml-mpi 'build-rf + (build "rf")) + (add-after 'build-rf 'build-phyrex + (build "phyrex"))))))) + (native-inputs + (list automake + autoconf + openmpi + (texlive-updmap.cfg (list texlive-amsfonts + texlive-caption + texlive-cite + texlive-fonts-ec + texlive-grfext + texlive-hyperref + texlive-latex-fancyvrb + texlive-latex-graphics + texlive-latex-psfrag + texlive-xcolor)))) + (home-page "https://github.com/stephaneguindon/phyml") + (synopsis "Programs for working on SAM/BAM files") + (description + "@code{PhyML} is a software package that uses modern statistical +approaches to analyse alignments of nucleotide or amino acid sequences in a +phylogenetic framework. The main tool in this package builds phylogenies +under the maximum likelihood criterion. It implements a large number of +substitution models coupled with efficient options to search the space of +phylogenetic tree topologies. code{PhyREX} fits the +spatial-Lambda-Fleming-Viot model to geo-referenced genetic data. This model +is similar to the structured coalescent but assumes that individuals are +distributed along a spatial continuum rather than discrete demes. +@code{PhyREX} can be used to estimate population densities and rates of +dispersal. Its output can be processed by treeannotator (from the +@code{BEAST} package) as well as @code{SPREAD}.") + (license license:gpl3))) + (define-public imp (package (name "imp") @@ -9895,7 +10017,7 @@ The following file formats are supported: (inputs `(("boost" ,boost) ("bzip2" ,bzip2) - ("cereal" ,cereal) + ("cereal" ,cereal-1.3.0) ("curl" ,curl) ("eigen" ,eigen) ("jemalloc" ,jemalloc) @@ -11262,7 +11384,7 @@ Thus the per-base error rate is similar to the raw input reads.") (install-file "Bandage" (string-append out "/bin")) #t)))))) (inputs - (list qtbase-5 qtsvg)) + (list qtbase-5 qtsvg-5)) (native-inputs (list imagemagick)) (home-page "https://rrwick.github.io/Bandage/") @@ -11413,6 +11535,123 @@ including: dynamic cellular processes at single-cell resolution.") (license license:expat)))) +;; Needed for r-liana +(define-public r-omnipathr/devel + (let ((commit "679bb79e319af246a16968d27d64d8d6937a331a") + (revision "1")) + (package + (name "r-omnipathr") + (version (git-version "3.5.5" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/saezlab/omnipathr") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "10h6lyapyx4ik8r4kx5z2dly46jlf2v57caq4g6i0hzifyz2vgjq")))) + (properties `((upstream-name . "OmnipathR"))) + (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'set-HOME + (lambda _ (setenv "HOME" "/tmp")))))) + (propagated-inputs + (list r-checkmate + r-crayon + r-curl + r-digest + r-dplyr + r-httr + r-igraph + r-jsonlite + r-later + r-logger + r-magrittr + r-progress + r-purrr + r-rappdirs + r-readr + r-readxl + r-rlang + r-rvest + r-stringr + r-tibble + r-tidyr + r-tidyselect + r-withr + r-xml2 + r-yaml)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/saezlab/omnipathr") + (synopsis "OmniPath web service client and more") + (description + "This package provides a client for the OmniPath web service and many +other resources. It also includes functions to transform and pretty print +some of the downloaded data, functions to access a number of other resources +such as BioPlex, ConsensusPathDB, EVEX, Gene Ontology, Guide to +Pharmacology (IUPHAR/BPS), Harmonizome, HTRIdb, Human Phenotype Ontology, +InWeb InBioMap, KEGG Pathway, Pathway Commons, Ramilowski et al. 2015, +RegNetwork, ReMap, TF census, TRRUST and Vinayagam et al. 2011. Furthermore, +OmnipathR features a close integration with the NicheNet method for ligand +activity prediction from transcriptomics data, and its R implementation +@code{nichenetr}.") + (license license:expat)))) + +(define-public r-liana + (let ((commit "efb1249af46f576d1d620956053cfa93b2cee961") + (revision "1")) + (package + (name "r-liana") + (version (git-version "0.1.5" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/saezlab/liana/") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0z645k26kqrfj5f1s412vwclw1q47h1zfxxrh9ijr30pxhpv6cv0")))) + (properties `((upstream-name . "liana"))) + (build-system r-build-system) + (arguments + (list + #:phases + `(modify-phases %standard-phases + ;; This is needed to find ~/.config/OmnipathR/omnipathr.yml + (add-after 'unpack 'set-HOME + (lambda _ (setenv "HOME" "/tmp")))))) + (propagated-inputs + (list r-complexheatmap + r-dplyr + r-ggplot2 + r-magrittr + r-omnipathr/devel + r-purrr + r-rcolorbrewer + r-readr + r-reticulate + r-rlang + r-scater + r-scran + r-scuttle + r-seuratobject + r-singlecellexperiment + r-stringr + r-tibble + r-tidyr + r-tidyselect)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/saezlab/liana/") + (synopsis "LIANA: a LIgand-receptor ANalysis frAmework") + (description + "LIANA provides a number of methods and resource for ligand-receptor +interaction inference from scRNA-seq data.") + (license license:gpl3)))) + (define-public r-circus (package (name "r-circus") @@ -11842,19 +12081,23 @@ million cells.") (define-public python-bbknn (package (name "python-bbknn") - (version "1.3.6") + (version "1.5.1") (source (origin (method url-fetch) (uri (pypi-uri "bbknn" version)) (sha256 (base32 - "1jbsh01f57zj4bhvjr3jh4532zznqd6nccmgrl3qi9gnhkf7c4y0")))) + "0q11xdmjr2kf6f179a6kjizj3lllfrq743gslgw67qyzimvrrnhn")))) (build-system python-build-system) (arguments `(#:tests? #f ; no tests are included #: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"))) (add-after 'unpack 'do-not-fail-to-find-sklearn (lambda _ ;; XXX: I have no idea why it cannot seem to find sklearn. @@ -11864,6 +12107,7 @@ million cells.") (list python-annoy python-cython python-numpy + python-pandas python-scikit-learn python-scipy python-umap-learn)) @@ -12060,14 +12304,14 @@ allowing the insertion of arbitrary types into the tree.") (define-public python-intervaltree (package (name "python-intervaltree") - (version "3.0.2") + (version "3.1.0") (source (origin (method url-fetch) (uri (pypi-uri "intervaltree" version)) (sha256 (base32 - "0wz234g6irlm4hivs2qzmnywk0ss06ckagwh15nflkyb3p462kyb")))) + "0bcm6c6r4ck9nfj9xwz4rm2swc5lrjvmw3lyl6rgj639jf41nawh")))) (build-system python-build-system) (arguments `(#:phases @@ -12433,6 +12677,35 @@ cooler). Both @code{hic} and @code{cool} files describe Hi-C contact matrices.") (license license:expat))) +(define-public python-scanorama + (package + (name "python-scanorama") + (version "1.7.2") + (source (origin + (method url-fetch) + (uri (pypi-uri "scanorama" version)) + (sha256 + (base32 + "0il7bf4c7vli2dm2jx7dskh3ymgv8nmk0y90jzgfrnqjzh250x5w")))) + (build-system python-build-system) + (propagated-inputs + (list python-annoy + python-fbpca + python-geosketch + python-intervaltree + python-matplotlib + python-numpy + python-scikit-learn + python-scipy)) + (home-page "https://github.com/brianhie/scanorama") + (synopsis "Panoramic stitching of heterogeneous single cell transcriptomic data") + (description + "Scanorama enables batch-correction and integration of heterogeneous +scRNA-seq datasets, which is described in the paper \"Efficient integration of +heterogeneous single-cell transcriptomes using Scanorama\" by Brian Hie, Bryan +Bryson, and Bonnie Berger.") + (license license:expat))) + (define-public r-pore (package (name "r-pore") |