diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 882 |
1 files changed, 682 insertions, 200 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index f6a7a83fe3..d684e4249b 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -4,7 +4,7 @@ ;;; Copyright © 2015, 2016, 2018, 2019, 2020 Pjotr Prins <pjotr.guix@thebird.nl> ;;; Copyright © 2015 Andreas Enge <andreas@enge.fr> ;;; Copyright © 2016, 2020, 2021 Roel Janssen <roel@gnu.org> -;;; Copyright © 2016, 2017, 2018, 2019, 2020, 2021, 2022 Efraim Flashner <efraim@flashner.co.il> +;;; Copyright © 2016-2023 Efraim Flashner <efraim@flashner.co.il> ;;; Copyright © 2016, 2020, 2022 Marius Bakke <marius@gnu.org> ;;; Copyright © 2016, 2018 Raoul Bonnal <ilpuccio.febo@gmail.com> ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr> @@ -56,7 +56,6 @@ #:use-module (guix build-system go) #:use-module (guix build-system haskell) #:use-module (guix build-system meson) - #:use-module (guix build-system ocaml) #:use-module (guix build-system perl) #:use-module (guix build-system pyproject) #:use-module (guix build-system python) @@ -512,6 +511,63 @@ BED, GFF/GTF, VCF.") (inputs (list samtools zlib)))) +(define-public bitmapperbs + (package + (name "bitmapperbs") + (version "1.0.2.3") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/chhylp123/BitMapperBS/") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "02ksssfnvmpskld0a2016smfz5nrzm3d90v8974f3cpzywckvp8v")) + (modules '((guix build utils))) + ;; This package bundles a modified copy of htslib, so we cannot + ;; unbundle it. + (snippet + '(begin + (delete-file-recursively "libdivsufsort-2.0.1") + (delete-file-recursively "pSAscan-0.1.0"))))) + (build-system gnu-build-system) + (arguments + (list + #:tests? #false + #:make-flags '(list "bitmapperBS") + ;; The build system checks for CPU features. For this reason, we want + ;; users to build it locally instead of using substitutes. + #:substitutable? #false + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'fix-build-system + (lambda _ + (substitute* "Makefile" + (("make prefix=../htslib_aim install") + (string-append "make prefix=" #$output " install-so")) + (("htslib_aim/include") "htslib") + (("htslib_aim/lib") + (string-append #$output "/lib"))))) + (add-after 'unpack 'patch-references-to-psascan + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "Makefile" + (("\"(./)?psascan" pre all) + (string-append "\"" pre (search-input-file inputs "/bin/psascan")))))) + (delete 'configure) + (replace 'install + (lambda _ + (install-file "bitmapperBS" + (string-append #$output "/bin/"))))))) + (inputs + (list libdivsufsort psascan zlib)) + (home-page "https://github.com/chhylp123/BitMapperBS/") + (synopsis "Read aligner for whole-genome bisulfite sequencing") + (description + "BitMapperBS is memory-efficient aligner that is designed for +whole-genome bisulfite sequencing (WGBS) reads from directional protocol.") + (license license:asl2.0))) + (define-public cellsnp-lite ;; Last release is from November 2021 and does not contain fixes. (let ((commit "0885d746b0b1ea65c8ef92f8943ca7669ca9734a") @@ -663,6 +719,53 @@ suite native in R.") for all types of microbial diversity analyses.") (license license:expat)))) +(define-public r-conospanel + (let ((commit "39e76b201a783b4e92fd615010a735a61746fbb9") + (revision "1")) + (package + (name "r-conospanel") + (version (git-version "1.0.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/kharchenkolab/conosPanel") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1zf0aj5d4iaxc3ghvjnaja5qby1avlmljzh94bpyvxbd359z9snn")))) + (properties `((upstream-name . "conosPanel"))) + (build-system r-build-system) + (home-page "https://github.com/kharchenkolab/conosPanel") + (synopsis "Data for the conos package") + (description "The data within this package is a panel of four samples, +each with 3000 cells. There are two samples which are bone marrow (BM), and +two samples which are cord blood (CB).") + (license license:gpl3)))) + +(define-public r-p2data + (let ((commit "7d4c0e17d7899f9d9b08ab2bf455abe150912f4c") + (revision "1")) + (package + (name "r-p2data") + (version (git-version "1.0.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/kharchenkolab/p2data") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1hadrldldxvhqs43aqs3c88bqfgql3wcfkbll3jz7fh6z7p3x324")))) + (properties `((upstream-name . "p2data"))) + (build-system r-build-system) + (home-page "https://github.com/kharchenkolab/p2data") + (synopsis "Data for pagoda2") + (description "This package contains data used by pagoda2. The data +within this package are the 3000 bone marrow cells used for vignettes.") + (license license:gpl3)))) + (define-public r-rhtslib12 (let ((commit "ee186daf04876969c7f31c16a0e0fda8e7c16a30") (revision "1")) @@ -690,6 +793,41 @@ high-throughput sequence analysis. The package is primarily useful to developers of other R packages who wish to make use of HTSlib.") (license license:lgpl2.0+)))) +(define-public r-streamgraph + (let ((commit "76f7173ec89d456ace5943a512e20b1f6810bbcb") + (revision "1")) + (package + (name "r-streamgraph") + (version (git-version "0.9.0" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/hrbrmstr/streamgraph") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "010rhnby5a9dg08jvlkr65b3p9iipdxi2f5m1k6j53s80p25yvig")))) + (properties `((upstream-name . "streamgraph"))) + (build-system r-build-system) + (propagated-inputs + (list r-dplyr + r-htmltools + r-htmlwidgets + r-magrittr + r-tidyr + r-xts)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/hrbrmstr/streamgraph") + (synopsis "Htmlwidget for building streamgraph visualizations") + (description + "A streamgraph is a type of stacked area chart. It represents the +evolution of a numeric variable for several groups. Areas are usually +displayed around a central axis, and edges are rounded to give a flowing +shape. This package provides an @code{htmlwidget} for building streamgraph +visualizations.") + (license license:expat)))) + (define-public pbbam (package (name "pbbam") @@ -1057,6 +1195,83 @@ from high-throughput single-cell RNA sequencing (scRNA-seq) data.") and sequence consensus.") (license license:expat))) +(define-public python-demuxem + (package + (name "python-demuxem") + (version "0.1.7") + (source (origin + (method url-fetch) + (uri (pypi-uri "demuxEM" version)) + (sha256 + (base32 + "1bhyxqjk44bmyd26m1smapf68wyf7252kk65i27k50dd3kswgnd6")))) + (build-system pyproject-build-system) + (propagated-inputs + (list python-docopt + python-importlib-metadata + python-numpy + python-pandas + python-pegasusio + python-scikit-learn + python-scipy + python-seaborn)) + (native-inputs (list python-cython python-setuptools-scm)) + (home-page "https://github.com/lilab-bcb/demuxEM") + (synopsis "Analyze cell-hashing/nucleus-hashing data") + (description + "This is a Python module for analyzing cell-hashing/nucleus-hashing data. +It is the demultiplexing module of Pegasus, which is used by Cumulus in the +demultiplexing step.") + (license license:bsd-3))) + +(define-public python-doubletdetection + (package + (name "python-doubletdetection") + (version "4.2") + (source (origin + (method url-fetch) + (uri (pypi-uri "doubletdetection" version)) + (sha256 + (base32 + "0v0a19014h4p6x8pyz1s78xn3q5w5166cysvg574z6vw79a3s9vp")))) + (build-system pyproject-build-system) + (arguments + (list + #:tests? #false ;there are none + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'use-poetry-core + (lambda _ + ;; Patch to use the core poetry API. + (substitute* "pyproject.toml" + (("poetry.masonry.api") + "poetry.core.masonry.api"))))))) + (propagated-inputs + (list python-anndata + python-ipywidgets + python-leidenalg + python-vtraag-louvain + python-matplotlib + python-numpy + python-pandas + python-phenograph + python-scanpy + python-scipy + python-tqdm)) + (native-inputs + (list python-black + python-flake8 + python-poetry-core + python-pytest + python-pre-commit)) + (home-page "https://github.com/JonathanShor/DoubletDetection") + (synopsis + "This is a package to detect doublets in single-cell RNA-seq count matrices") + (description + "This package provides a method to detect and enable removal of doublets +from single-cell RNA-sequencing.") + (license license:expat))) + (define-public python-hclust2 (package (name "python-hclust2") @@ -1103,6 +1318,97 @@ protocol. It provides a simple and reliable way to retrieve genomic data from servers supporting the protocol.") (license license:asl2.0))) +(define-public python-pegasusio + (package + (name "python-pegasusio") + (version "0.7.1") + (source (origin + (method url-fetch) + (uri (pypi-uri "pegasusio" version)) + (sha256 + (base32 + "0gqygspdy398vjymdy6756jmk99s7fhwav9rivdx59kpqjcdxaz9")))) + (build-system pyproject-build-system) + (propagated-inputs + (list python-anndata + python-docopt + python-h5py + python-importlib-metadata + python-loompy + python-natsort + python-numpy + python-pandas + python-pillow + python-scipy + python-zarr)) + (native-inputs (list python-cython python-setuptools-scm)) + (home-page "https://github.com/lilab-bcb/pegasusio") + (synopsis "Read or write single-cell genomics data") + (description + "Pegasusio is a Python package for reading or writing single-cell +genomics data.") + (license license:bsd-3))) + +(define-public python-phenograph + (package + (name "python-phenograph") + (version "1.5.7") + (source (origin + (method url-fetch) + (uri (pypi-uri "PhenoGraph" version)) + (sha256 + (base32 + "0nji449mzwgp1f87iknl5fmnjdkrhkfkapxvafxdw01s0jg8zcj6")) + (modules '((guix build utils))) + ;; Remove bundled binaries + (snippet + '(delete-file-recursively "phenograph/louvain")))) + (build-system pyproject-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + ;; This test can never succeed because Q_leiden is never set to + ;; anything other than None. + (add-after 'unpack 'disable-leiden-test + (lambda _ + (substitute* "tests/test_cluster.py" + (("def test_run_leiden") "def _test_run_leiden")))) + (add-after 'unpack 'patch-louvain + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "phenograph/core.py" + (("lpath = os.path.*") + (string-append "lpath = \"" + (dirname (search-input-file inputs "/bin/community")) + "\"\n")) + (("linux-(community|hierarchy|convert)" _ thing) thing) + ;; Do not write binaries, because the unmodified "convert" + ;; from louvain only knows how to process plain text files. + (("with open\\(filename \\+ \".bin\", \"w\\+b\"\\) as f:") + "with open(filename + \".bin\", \"w+\") as f:") + (("f.writelines\\(\\[e for t in zip\\(ij, s\\) for e in t\\]\\)") + "for [src, dest], weight in zip(ij, s): \ +f.write(src.astype(\"str\") + ' ' + \ +dest.astype(\"str\") + ' ' + \ +weight.astype(\"str\") + '\\n')"))))))) + (inputs + (list louvain)) + (propagated-inputs + (list python-leidenalg + python-numpy + python-psutil + python-scikit-learn + python-scipy)) + (native-inputs + (list python-pytest)) + (home-page "https://github.com/dpeerlab/PhenoGraph.git") + (synopsis "Graph-based clustering for high-dimensional single-cell data") + (description + "PhenoGraph is a clustering method designed for high-dimensional +single-cell data. It works by creating a graph representing phenotypic +similarities between cells and then identifying communities in this graph.") + (license license:expat))) + (define-public python-phylophlan (package (name "python-phylophlan") @@ -1317,7 +1623,7 @@ use-case, we encourage users to compose functions to achieve their goals.") python-scipy)) (native-inputs (list python-cython python-pytest python-pytest-cov python-nose)) - (home-page "http://www.biom-format.org") + (home-page "https://www.biom-format.org") (synopsis "Biological Observation Matrix (BIOM) format utilities") (description "The BIOM file format is designed to be a general-use format for @@ -2244,7 +2550,7 @@ errors at the end of reads.") ("python" ,python-wrapper))) (native-inputs (list perl perl-clone perl-test-deep perl-test-simple)) - (home-page "http://bowtie-bio.sourceforge.net/bowtie2/index.shtml") + (home-page "https://bowtie-bio.sourceforge.net/bowtie2/index.shtml") (synopsis "Fast and sensitive nucleotide sequence read aligner") (description "Bowtie 2 is a fast and memory-efficient tool for aligning sequencing @@ -2286,7 +2592,7 @@ gapped, local, and paired-end alignment modes.") (inputs (list python-wrapper tbb-2020 zlib)) (supported-systems '("x86_64-linux")) - (home-page "http://bowtie-bio.sourceforge.net/index.shtml") + (home-page "https://bowtie-bio.sourceforge.net/index.shtml") (synopsis "Fast aligner for short nucleotide sequence reads") (description "Bowtie is a fast, memory-efficient short read aligner. It aligns short @@ -2407,7 +2713,7 @@ splice junctions between exons.") ;; Non-portable SSE instructions are used so building fails on platforms ;; other than x86_64. (supported-systems '("x86_64-linux")) - (home-page "http://bio-bwa.sourceforge.net/") + (home-page "https://bio-bwa.sourceforge.net/") (synopsis "Burrows-Wheeler sequence aligner") (description "BWA is a software package for mapping low-divergent sequences against a @@ -3000,7 +3306,7 @@ time.") zlib)) (native-inputs (list python-cython python-nose)) - (home-page "http://crossmap.sourceforge.net/") + (home-page "https://crossmap.sourceforge.net/") (synopsis "Convert genome coordinates between assemblies") (description "CrossMap is a program for conversion of genome coordinates or annotation @@ -3307,6 +3613,35 @@ and record oriented data modeling and the Semantic Web.") resources for bioinformatics.") (license license:bsd-3))) +(define-public python-scrublet + (package + (name "python-scrublet") + (version "0.2.3") + (source (origin + (method url-fetch) + (uri (pypi-uri "scrublet" version)) + (sha256 + (base32 + "0fk5pwk12yz9wpvwkl6j2l2g28f3x35b9r9n5bw6f0i9f0qgd191")))) + (build-system pyproject-build-system) + (arguments '(#:tests? #false)) ;there are none + (propagated-inputs + (list python-annoy + python-cython + python-matplotlib + python-numba + python-numpy + python-pandas + python-scikit-image + python-scikit-learn + python-scipy + python-umap-learn)) + (home-page "https://github.com/swolock/scrublet") + (synopsis "Tool to indentify and remove doublets in single-cell data") + (description "This package provides a tool for identifying and removing +doublets in single-cell RNA-seq data.") + (license license:expat))) + (define-public cwltool (package (name "cwltool") @@ -4595,7 +4930,7 @@ high-throughput sequencing (HTS) assays") ("java-xz" ,java-xz))) (native-inputs (list java-testng)) - (home-page "http://samtools.github.io/htsjdk/") + (home-page "https://samtools.github.io/htsjdk/") (synopsis "Java API for high-throughput sequencing data (HTS) formats") (description "HTSJDK is an implementation of a unified Java library for accessing @@ -4638,7 +4973,7 @@ manipulating HTS data.") ("java-xz" ,java-xz))) (native-inputs (list java-junit)) - (home-page "http://samtools.github.io/htsjdk/") + (home-page "https://samtools.github.io/htsjdk/") (synopsis "Java API for high-throughput sequencing data (HTS) formats") (description "HTSJDK is an implementation of a unified Java library for accessing @@ -4743,7 +5078,7 @@ manipulating HTS data.") (list java-htsjdk java-guava)) (native-inputs (list java-testng)) - (home-page "http://broadinstitute.github.io/picard/") + (home-page "https://broadinstitute.github.io/picard/") (synopsis "Tools for manipulating high-throughput sequencing data and formats") (description "Picard is a set of Java command line tools for manipulating high-throughput sequencing (HTS) data and formats. Picard is implemented @@ -4832,7 +5167,7 @@ Class-Path: /~a \ (list java-htsjdk-2.10.1)) (native-inputs (list java-testng java-guava)) - (home-page "http://broadinstitute.github.io/picard/") + (home-page "https://broadinstitute.github.io/picard/") (synopsis "Tools for manipulating high-throughput sequencing data and formats") (description "Picard is a set of Java command line tools for manipulating high-throughput sequencing (HTS) data and formats. Picard is implemented @@ -4961,56 +5296,70 @@ VCF.") (define-public fastqc (package (name "fastqc") - (version "0.11.5") + (version "0.11.9") (source (origin - (method url-fetch) - (uri (string-append "http://www.bioinformatics.babraham.ac.uk/" - "projects/fastqc/fastqc_v" - version "_source.zip")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/s-andrews/FastQC") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "18rrlkhcrxvvvlapch4dpj6xc6mpayzys8qfppybi8jrpgx5cc5f")))) + "00y9drm0bkpxw8xfl8ysss18jmnhj8blgqgr6fpa58rkpfcbg8qk")) + (snippet + '(for-each delete-file + '("cisd-jhdf5.jar" + "sam-1.103.jar" + "jbzip2-0.9.jar"))))) (build-system ant-build-system) (arguments - `(#:tests? #f ; there are no tests - #:build-target "build" - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'fix-dependencies - (lambda* (#:key inputs #:allow-other-keys) - (substitute* "build.xml" - (("jbzip2-0.9.jar") - (search-input-file inputs "/share/java/jbzip2.jar")) - (("sam-1.103.jar") - (search-input-file inputs - "/share/java/sam-1.112.jar")) - (("cisd-jhdf5.jar") - (search-input-file inputs - "/share/java/sis-jhdf5.jar"))))) - ;; There is no installation target - (replace 'install - (lambda* (#:key inputs outputs #:allow-other-keys) - (let* ((out (assoc-ref outputs "out")) - (bin (string-append out "/bin")) - (share (string-append out "/share/fastqc/")) - (exe (string-append share "/fastqc"))) - (for-each mkdir-p (list bin share)) - (copy-recursively "bin" share) - (substitute* exe - (("my \\$java_bin = 'java';") - (string-append "my $java_bin = '" - (assoc-ref inputs "java") - "/bin/java';"))) - (chmod exe #o555) - (symlink exe (string-append bin "/fastqc")) - #t)))))) + (list + #:tests? #f ;there are no tests + #:build-target "build" + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'fix-dependencies + (lambda* (#:key inputs #:allow-other-keys) + (substitute* '("build.xml" ".classpath") + (("jbzip2-0.9.jar") + (search-input-file inputs "/share/java/jbzip2.jar")) + (("sam-1.103.jar") + (search-input-file inputs "/share/java/sam-1.112.jar")) + (("cisd-jhdf5.jar") + (search-input-file inputs "/share/java/sis-jhdf5.jar"))))) + ;; There is no installation target + (replace 'install + (lambda* (#:key inputs #:allow-other-keys) + (let* ((bin (string-append #$output "/bin")) + (share (string-append #$output "/share/fastqc/")) + (exe (string-append share "/fastqc"))) + (for-each mkdir-p (list bin share)) + (copy-recursively "bin" share) + (substitute* exe + (("my \\$java_bin = \"java\";") + (string-append "my $java_bin = \"" + ;; Use java from the JRE, not the JDK + #$(this-package-input "icedtea") "/bin/java" + "\";")) + (("\\$RealBin\\$delimiter\\$RealBin.*") + (string-append + (string-join + (list + share + (search-input-file inputs "/share/java/sam-1.112.jar") + (search-input-file inputs "/share/java/jbzip2.jar") + (search-input-file inputs "/share/java/sis-jhdf5.jar")) + "$delimiter") + "\";\n"))) + (chmod exe #o555) + (symlink exe (string-append bin "/fastqc")))))))) (inputs - `(("java" ,icedtea) - ("perl" ,perl) ; needed for the wrapper script - ("java-cisd-jhdf5" ,java-cisd-jhdf5) - ("java-picard-1.113" ,java-picard-1.113) - ("java-jbzip2" ,java-jbzip2))) + (list icedtea + java-cisd-jhdf5 + java-picard-1.113 + java-jbzip2 + perl)) ;needed for the wrapper script (native-inputs (list unzip)) (home-page "https://www.bioinformatics.babraham.ac.uk/projects/fastqc/") @@ -5038,7 +5387,7 @@ The main functions of FastQC are: (define-public fastp (package (name "fastp") - (version "0.20.1") + (version "0.23.2") (source (origin (method git-fetch) @@ -5048,20 +5397,21 @@ The main functions of FastQC are: (file-name (git-file-name name version)) (sha256 (base32 - "0ly8mxdvrcy23jwxyppysx3dhb1lwsqhfbgpyvargxhfk6k700x4")))) + "04nmrqpjc3qni0cbazlwvpg8rk1mkfmfma0n4q3zivs3zi6rfnav")))) (build-system gnu-build-system) (arguments - `(#:tests? #f ; there are none - #:make-flags - ,#~(list (string-append "PREFIX=" #$output)) - #:phases - (modify-phases %standard-phases - (delete 'configure) - (add-before 'install 'create-target-dir - (lambda* (#:key outputs #:allow-other-keys) - (mkdir-p (string-append (assoc-ref outputs "out") "/bin"))))))) + (list + #:tests? #false ;there are none + #:make-flags + #~(list (string-append "PREFIX=" #$output)) + #:phases + #~(modify-phases %standard-phases + (delete 'configure) + (add-before 'install 'create-target-dir + (lambda _ + (mkdir-p (string-append #$output "/bin"))))))) (inputs - (list zlib)) + (list isa-l libdeflate)) (home-page "https://github.com/OpenGene/fastp/") (synopsis "All-in-one FastQ preprocessor") (description @@ -5252,21 +5602,22 @@ experiments and provide highly stable thresholds based on reproducibility.") (outputs '("out" ;for library "python")) ;for Python bindings (arguments - `(#:configure-flags - ,#~(list "--without-sse" ; configure script probes for CPU features when SSE is enabled. - (string-append "--enable-python-binding=" #$output:python)) - #:phases - (modify-phases %standard-phases + (list + #:configure-flags + #~(list "--without-sse" ; configure script probes for CPU features when SSE is enabled. + (string-append "--enable-python-binding=" #$output:python)) + #:phases + '(modify-phases %standard-phases (add-before 'check 'set-SHELL-variable (lambda _ ;; generator_manager.hpp either uses /bin/sh or $SHELL ;; to run tests. (setenv "SHELL" (which "bash"))))))) (native-inputs - `(("bc" ,bc) - ("time" ,time) - ("python" ,python-wrapper) - ("pkg-config" ,pkg-config))) + (list bc + time + python-wrapper + pkg-config)) (inputs (list htslib)) (synopsis "Tool for fast counting of k-mers in DNA") @@ -5415,7 +5766,7 @@ data.") tar wget zlib)) - (home-page "http://kaiju.binf.ku.dk/") + (home-page "https://kaiju.binf.ku.dk/") (synopsis "Fast and sensitive taxonomic classification for metagenomics") (description "Kaiju is a program for sensitive taxonomic classification of high-throughput sequencing reads from metagenomic whole genome sequencing @@ -5931,7 +6282,7 @@ predicts the locations of structural units in the sequences.") ("openblas" ,openblas))) (native-inputs (list which)) - (home-page "http://www.bioinf.uni-leipzig.de/Software/proteinortho") + (home-page "https://www.bioinf.uni-leipzig.de/Software/proteinortho") (synopsis "Detect orthologous genes across species") (description "Proteinortho is a tool to detect orthologous genes across different @@ -6206,7 +6557,7 @@ phylogenies.") "rsem-run-prsem-testing-procedure")))))))) (inputs (list boost r-minimal perl htslib-1.3 zlib)) - (home-page "http://deweylab.biostat.wisc.edu/rsem/") + (home-page "https://deweylab.biostat.wisc.edu/rsem/") (synopsis "Estimate gene expression levels from RNA-Seq data") (description "RSEM is a software package for estimating gene and isoform expression @@ -6241,7 +6592,7 @@ BAM and Wiggle files in both transcript-coordinate and genomic-coordinate.") zlib)) (native-inputs (list python-nose)) - (home-page "http://rseqc.sourceforge.net/") + (home-page "https://rseqc.sourceforge.net/") (synopsis "RNA-seq quality control package") (description "RSeQC provides a number of modules that can comprehensively evaluate @@ -6301,7 +6652,7 @@ distribution, coverage uniformity, strand specificity, etc.") ("readline" ,readline))) (native-inputs (list pkg-config)) - (home-page "http://seek.princeton.edu") + (home-page "https://seek.princeton.edu") (synopsis "Gene co-expression search engine") (description "SEEK is a computational gene co-expression search engine. SEEK provides @@ -6342,7 +6693,7 @@ to the user's query of interest.") (native-inputs (list pkg-config)) (inputs (list htslib ncurses perl python zlib)) - (home-page "http://samtools.sourceforge.net") + (home-page "https://samtools.sourceforge.net") (synopsis "Utilities to efficiently manipulate nucleotide sequence alignments") (description "Samtools implements various utilities for post-processing nucleotide @@ -7420,7 +7771,7 @@ optionally compressed by gzip.") (install-file "SNAPCommand" bin))))))) (native-inputs (list zlib)) - (home-page "http://snap.cs.berkeley.edu/") + (home-page "https://snap.cs.berkeley.edu/") (synopsis "Short read DNA sequence aligner") (description "SNAP is a fast and accurate aligner for short DNA reads. It is @@ -7687,7 +8038,7 @@ sequences.") ;; no "configure" script (delete 'configure)))) (inputs (list zlib)) - (home-page "http://subread.sourceforge.net/") + (home-page "https://subread.sourceforge.net/") (synopsis "Tool kit for processing next-gen sequencing data") (description "The subread package contains the following tools: subread aligner, a @@ -7734,7 +8085,7 @@ against local background noises.") (install-file "stringtie" bin))))))) (inputs (list bzip2 htslib-for-stringtie libdeflate zlib)) - (home-page "http://ccb.jhu.edu/software/stringtie/") + (home-page "https://ccb.jhu.edu/software/stringtie/") (synopsis "Transcript assembly and quantification for RNA-Seq data") (description "StringTie is a fast and efficient assembler of RNA-Seq sequence @@ -7900,6 +8251,36 @@ sequence.") 3D perspective axes, 3D perspective annotations, and wireframe plots.") (license license:gpl3+)))) +(define-public r-ggsankey + (let ((commit "be08dd0f86eaee9f9ff9e7ff95d47930660a3c36") + (revision "1")) + (package + (name "r-ggsankey") + (version (git-version "0.0.99999" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/davidsjoberg/ggsankey") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0acpmydqqc91pq5p9wpkpmgqp3nhiljabd7d3i00kwhjxgm2bvba")))) + (properties `((upstream-name . "ggsankey"))) + (build-system r-build-system) + (propagated-inputs (list r-dplyr + r-ggplot2 + r-magrittr + r-purrr + r-stringr + r-tidyr)) + (home-page "https://github.com/davidsjoberg/ggsankey") + (synopsis "Sankey, Alluvial and Sankey bump plots") + (description + "This package provides a package that makes it easy to implement +sankey, alluvial and sankey bump plots in @code{ggplot2}.") + (license license:expat)))) + (define-public r-gutils (let ((commit "10e36c7b580aacb2d952140a3fdd82418aaddea6") (revision "1")) @@ -8163,6 +8544,52 @@ doublet-detection methods. In addition, this tool is used for execution and benchmark of those eight mentioned methods.") (license license:gpl3+)))) +(define-public r-psupertime + (let ((commit "73825a28d3bd9bc881c15ee0c4c218eec1c9c207") + (revision "1")) + (package + (name "r-psupertime") + (version (git-version "0.2.6" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/wmacnair/psupertime") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "00h1r3ffz6m9dwcgkvyki8405b059qn6mnjsd8d76a1rabaf2vfh")))) + (properties `((upstream-name . "psupertime"))) + (build-system r-build-system) + (propagated-inputs + (list r-cowplot + r-data-table + r-fastcluster + r-forcats + r-ggplot2 + r-glmnet + r-knitr + r-matrix + r-rcolorbrewer + r-scales + r-scran + r-singlecellexperiment + r-stringr + r-summarizedexperiment + r-topgo)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/wmacnair/psupertime") + (synopsis + "Psupertime is supervised pseudotime for single cell RNAseq data") + (description + "Psupertime is supervised pseudotime for single cell RNAseq data. It +uses single cell RNAseq data, where the cells have a known ordering. This +ordering helps to identify a small number of genes which place cells in that +known order. It can be used for discovery of relevant genes, for +identification of subpopulations, and characterization of further unknown or +differently labelled data.") + (license license:gpl3)))) + (define-public r-pando (package (name "r-pando") @@ -8772,7 +9199,7 @@ of contact distributions around selected landmarks.") (base32 "1hsx6qgwr0i67fhy9257zj7s0ppncph2hjgbia5nn6nfmj0ax6l9")))) (build-system r-build-system) - (home-page "http://centipede.uchicago.edu/") + (home-page "https://centipede.uchicago.edu/") (synopsis "Predict transcription factor binding sites") (description "CENTIPEDE applies a hierarchical Bayesian mixture model to infer regions @@ -9010,7 +9437,7 @@ experience substantial biological insertions and deletions.") perl-getopt-long perl-json perl-statistics-pca)) - (home-page "http://prinseq.sourceforge.net/") + (home-page "https://prinseq.sourceforge.net/") (synopsis "Preprocess sequence data in FASTA or FASTQ formats") (description "PRINSEQ is a bioinformatics tool to help you preprocess your genomic or @@ -9495,7 +9922,7 @@ AM_CONDITIONAL(AMPNG, true)")) zlib)) (native-inputs (list autoconf automake libtool pkg-config)) - (home-page "http://emboss.sourceforge.net") + (home-page "https://emboss.sourceforge.net") (synopsis "Molecular biology analysis suite") (description "EMBOSS is the \"European Molecular Biology Open Software Suite\". EMBOSS is an analysis package specially developed for the needs of @@ -10172,7 +10599,7 @@ remove biased methylation positions for RRBS sequence files.") (for-each (lambda (file) (install-file file target)) (find-files "../exe" ".*")))))))) - (home-page "http://evolution.genetics.washington.edu/phylip/") + (home-page "https://evolution.genetics.washington.edu/phylip/") (synopsis "Tools for inferring phylogenies") (description "PHYLIP (the PHYLogeny Inference Package) is a package of programs for inferring phylogenies (evolutionary trees).") @@ -14443,110 +14870,125 @@ datasets.") (define-public ngless (package (name "ngless") - (version "1.3.0") - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/ngless-toolkit/ngless.git") - (commit (string-append "v" version)))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "0pb9f6b0yk9p4cdwiym8r190q1bcdiwvc7i2s6rw54qgi8r3g6pj")) - (patches (search-patches "ngless-unliftio.patch")))) + (version "1.5.0") + (source (origin + (method url-fetch) + (uri (hackage-uri "NGLess" version)) + (sha256 + (base32 + "0pljyrlpr9r3cl5311dhgxdl8y40szyi4vprn34i3piy0qrldymi")))) (build-system haskell-build-system) (arguments - (list - #:haddock? #f ;The haddock phase fails with: NGLess/CmdArgs.hs:20:1: - ;error: parse error on input import - ;import Options.Applicative - #:phases - #~(modify-phases %standard-phases - (add-after 'unpack 'create-Versions.hs - (lambda _ - (substitute* "Makefile" - (("BWA_VERSION = .*") - (string-append "BWA_VERSION = " - #$(package-version bwa) "\n")) - (("SAM_VERSION = .*") - (string-append "SAM_VERSION = " - #$(package-version samtools) "\n")) - (("PRODIGAL_VERSION = .*") - (string-append "PRODIGAL_VERSION = " - #$(package-version prodigal) "\n")) - (("MINIMAP2_VERSION = .*") - (string-append "MINIMAP2_VERSION = " - #$(package-version minimap2) "\n"))) - (invoke "make" "NGLess/Dependencies/Versions.hs"))) - (add-after 'create-Versions.hs 'create-cabal-file - (lambda _ (invoke "hpack"))) - ;; These tools are expected to be installed alongside ngless. - (add-after 'install 'link-tools - (lambda* (#:key inputs #:allow-other-keys) - (let ((bin (string-append #$output "/bin/"))) - (symlink (search-input-file inputs "/bin/prodigal") - (string-append bin "ngless-" #$version "-prodigal")) - (symlink (search-input-file inputs "/bin/minimap2") - (string-append bin "ngless-" #$version "-minimap2")) - (symlink (search-input-file inputs "/bin/samtools") - (string-append bin "ngless-" #$version "-samtools")) - (symlink (search-input-file inputs "/bin/bwa") - (string-append bin "ngless-" #$version "-bwa")))))))) - (inputs - (list prodigal - bwa - samtools - minimap2 - ghc-aeson - ghc-ansi-terminal - ghc-async - ghc-atomic-write - ghc-bytestring-lexing - ghc-conduit - ghc-conduit-algorithms - ghc-conduit-extra - ghc-configurator - ghc-convertible - ghc-data-default - ghc-diagrams-core - ghc-diagrams-lib - ghc-diagrams-svg - ghc-double-conversion - ghc-edit-distance - ghc-either - ghc-errors - ghc-extra - ghc-filemanip - ghc-file-embed - ghc-gitrev - ghc-hashtables - ghc-http-conduit - ghc-inline-c - ghc-inline-c-cpp - ghc-int-interval-map - ghc-missingh - ghc-optparse-applicative - ghc-regex - ghc-safe - ghc-safeio - ghc-strict - ghc-tar - ghc-tar-conduit - ghc-unliftio - ghc-unliftio-core - ghc-vector - ghc-yaml - ghc-zlib)) + `(#:haddock? #f + #:phases + (modify-phases %standard-phases + (add-before 'configure 'update-constraints + (lambda _ + (substitute* "NGLess.cabal" + (("\\b(base)\\s+[^,]+" all dep) + dep)))) + (add-after 'unpack 'create-Versions.hs + (lambda _ + (substitute* "NGLess/Dependencies/Versions.hs" + (("bwaVersion = .+") + (string-append "bwaVersion = \"" + ,(package-version bwa) "\"")) + (("samtoolsVersion = .+") + (string-append "samtoolsVersion = \"" + ,(package-version samtools) "\"")) + (("prodigalVersion = .+") + (string-append "prodigalVersion = \"" + ,(package-version prodigal) "\"")) + (("megahitVersion = .+") + (string-append "megahitVersion = \"" + ,(package-version megahit) "\"")) + (("minimap2Version = .+") + (string-append "minimap2Version = \"" + ,(package-version minimap2) "\""))))) + ;; See NGLess/FileManagement.hs. + (add-after 'install 'wrap-program + (lambda* (#:key inputs outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (bwa (search-input-file inputs "/bin/bwa")) + (samtools (search-input-file inputs "/bin/samtools")) + (prodigal (search-input-file inputs "/bin/prodigal")) + (minimap2 (search-input-file inputs "/bin/minimap2")) + (megahit (search-input-file inputs "/bin/megahit"))) + (wrap-program (string-append out "/bin/ngless") + `("NGLESS_BWA_BIN" " " = (,bwa)) + `("NGLESS_SAMTOOLS_BIN" " " = (,samtools)) + `("NGLESS_PRODIGAL_BIN" " " = (,prodigal)) + `("NGLESS_MINIMAP2_BIN" " " = (,minimap2)) + `("NGLESS_MEGAHIT_BIN" " " = (,megahit)))))) + ;; Sanity check. + (add-after 'wrap-program 'check-install + (lambda* (#:key outputs #:allow-other-keys) + (let* ((ngless (string-append (assoc-ref outputs "out") "/bin/ngless"))) + (invoke ngless "--check-install")))) + (add-after 'register 'remove-libraries + (lambda* (#:key outputs #:allow-other-keys) + (delete-file-recursively (string-append (assoc-ref outputs "out") "/lib"))))))) + (inputs (list prodigal + bwa + samtools + minimap2 + megahit + ghc-missingh + ghc-aeson + ghc-ansi-terminal + ghc-async + ghc-atomic-write + ghc-bytestring-lexing + ghc-conduit + ghc-conduit-algorithms + ghc-conduit-extra + ghc-configurator + ghc-convertible + ghc-data-default + ghc-edit-distance + ghc-either + ghc-errors + ghc-extra + ghc-file-embed + ghc-filemanip + ghc-hashable + ghc-hashtables + ghc-hostname + ghc-http-client + ghc-http-conduit + ghc-inline-c + ghc-inline-c-cpp + ghc-int-interval-map + ghc-network + ghc-optparse-applicative + ghc-primitive + ghc-random-shuffle + ghc-regex + ghc-resourcet + ghc-safe + ghc-stm-chans + ghc-stm-conduit + ghc-strict + ghc-tar + ghc-tar-conduit + ghc-unix-compat + ghc-unliftio + ghc-unliftio-core + ghc-vector + ghc-vector-algorithms + ghc-yaml + ghc-zlib + ghc-bzlib-conduit + ghc-double-conversion + ghc-safeio)) (propagated-inputs (list r-r6 r-hdf5r r-iterators r-itertools r-matrix)) - (native-inputs - (list ghc-hpack - ghc-quickcheck - ghc-test-framework - ghc-test-framework-hunit - ghc-test-framework-quickcheck2 - ghc-test-framework-th)) + (native-inputs (list ghc-hunit + ghc-quickcheck + ghc-tasty + ghc-tasty-hunit + ghc-tasty-quickcheck + ghc-tasty-th)) (home-page "https://ngless.embl.de/") (synopsis "DSL for processing next-generation sequencing data") (description "Ngless is a domain-specific language for @@ -16451,7 +16893,7 @@ The output is in SAM format.") (list libxml2)) (native-inputs (list check swig)) - (home-page "http://sbml.org/Software/libSBML") + (home-page "https://sbml.org/Software/libSBML") (synopsis "Process SBML files and data streams") (description "LibSBML is a library to help you read, write, manipulate, translate, and validate SBML files and data streams. The @dfn{Systems Biology @@ -16582,6 +17024,40 @@ sequencing (e.g. mapping or base/indel alignment uncertainty), which are usually ignored by other methods or only used for filtering.") (license license:expat))) +(define-public louvain + (package + (name "louvain") + (version "0.2") + (source (origin + (method url-fetch) + (uri "mirror://sourceforge/louvain/louvain_latest.tar.gz") + (sha256 + (base32 + "0hqlv5jqc889nbv7j1bchrx4zhh69hgr2mqvfdygc7kwrywn22lb")))) + (build-system gnu-build-system) + (arguments + (list + #:tests? #false ;there are none + #:phases + #~(modify-phases %standard-phases + (delete 'configure) + (add-after 'unpack 'patch-includes + (lambda _ + (substitute* "main_community.cpp" + (("using namespace std;" m) + (string-append "#include <unistd.h> /* for getpid */\n" m))))) + (replace 'install + (lambda _ + (for-each + (lambda (exe) + (install-file exe (string-append #$output "/bin"))) + '("convert" "community" "hierarchy"))))))) + (home-page "https://sourceforge.net/projects/louvain/") + (synopsis "Multi-criteria community detection") + (description "This package offers a set of functions to use in order to +compute communities on graphs weighted or unweighted.") + (license license:gpl3+))) + (define-public ivar (package (name "ivar") @@ -17388,7 +17864,7 @@ populations.") (define-public scregseg (package (name "scregseg") - (version "0.1.1") + (version "0.1.3") (source (origin (method git-fetch) (uri (git-reference @@ -17397,16 +17873,22 @@ populations.") (file-name (git-file-name name version)) (sha256 (base32 - "1k8hllr5if6k2mm2zj391fv40sfc008cjm04l9vgfsdppb80i112")) + "07g2barywa1wi8mggbxkbxqjw1fzd0a0l9cjdbkx4s40imb1dbxb")) (snippet - #~(begin - (use-modules ((guix build utils))) - (delete-file "src/scregseg/_utils.c"))))) - (build-system python-build-system) + '(delete-file "src/scregseg/_utils.c")))) + (build-system pyproject-build-system) (arguments - `(#:tests? #false ; tests require network access - #:phases - (modify-phases %standard-phases + (list + #: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"))) + ;; Cython extensions have to be built before running the tests. + (add-before 'check 'build-extensions + (lambda _ + (invoke "python" "setup.py" "build_ext" "--inplace"))) (add-after 'unpack 'do-not-fail-to-find-sklearn (lambda _ ;; XXX: I have no idea why it cannot seem to find sklearn. @@ -18324,7 +18806,7 @@ useful for bioinformatic analysis.") (define-public go-github-com-biogo-hts-bam (package (name "go-github-com-biogo-hts-bam") - (version "1.4.3") + (version "1.4.4") (source (origin (method git-fetch) (uri (git-reference @@ -18333,7 +18815,7 @@ useful for bioinformatic analysis.") (file-name (git-file-name name version)) (sha256 (base32 - "013ga6ilc4m3hyfr3yyiva9g4vs81afhj73v2sy7r75b5zxw7lx1")))) + "1vkcqxyajghx5p5j7g2i376nbsxh8q2smk0smlv8mi34yr7hlw5b")))) (build-system go-build-system) (arguments '(#:import-path "github.com/biogo/hts/bam" |