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Merge branch 'master' into core-updates-frozen

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Ludovic Courtès 2021-09-07 11:04:44 +02:00
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gnu/packages/bioinformatics.scm
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@ -104,6 +104,7 @@
#:use-module (gnu packages java)
#:use-module (gnu packages java-compression)
#:use-module (gnu packages jemalloc)
#:use-module (gnu packages jupyter)
#:use-module (gnu packages linux)
#:use-module (gnu packages lisp-xyz)
#:use-module (gnu packages logging)
@ -4534,7 +4535,7 @@ The main functions of FastQC are:
(define-public fastp
(package
(name "fastp")
(version "0.14.1")
(version "0.20.1")
(source
(origin
(method git-fetch)
@ -4544,19 +4545,18 @@ The main functions of FastQC are:
(file-name (git-file-name name version))
(sha256
(base32
"1r6ms5zbf5rps4rgp4z73nczadl00b5rqylw8f684isfz27dp0xh"))))
"0ly8mxdvrcy23jwxyppysx3dhb1lwsqhfbgpyvargxhfk6k700x4"))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f ; there are none
#:make-flags
(list (string-append "BINDIR=" (assoc-ref %outputs "out") "/bin"))
(list (string-append "PREFIX=" (assoc-ref %outputs "out")))
#: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"))
#t)))))
(mkdir-p (string-append (assoc-ref outputs "out") "/bin")))))))
(inputs
`(("zlib" ,zlib)))
(home-page "https://github.com/OpenGene/fastp/")
@ -10381,7 +10381,7 @@ once. This package provides tools to perform Drop-seq analyses.")
(define-public pigx-rnaseq
(package
(name "pigx-rnaseq")
(version "0.0.18")
(version "0.0.19")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/BIMSBbioinfo/pigx_rnaseq/"
@ -10389,7 +10389,7 @@ once. This package provides tools to perform Drop-seq analyses.")
"/pigx_rnaseq-" version ".tar.gz"))
(sha256
(base32
"1622l6grmsk0wm859rvllngx29q3v16jjvzcdq2bmrlamccrj82y"))))
"1ja3bda1appxrzbfy7wp7khy30mm7lic8xbq3gkbpc5bld3as9cm"))))
(build-system gnu-build-system)
(arguments
`(#:parallel-tests? #f ; not supported
@ -11387,38 +11387,53 @@ implementation differs in these ways:
(define-public python-scanpy
(package
(name "python-scanpy")
(version "1.7.2")
(version "1.8.1")
(source
(origin
(method url-fetch)
(uri (pypi-uri "scanpy" version))
(method git-fetch)
(uri (git-reference
(url "https://github.com/theislab/scanpy")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32
"0c66adnfizsyk0h8bv2yhmay876z0klpxwpn4z6m71wly7yplpmd"))))
"0w1qmv3djqi8q0sn5hv34ivzs157fwjjb9nflfnagnhpxmw8vx5g"))))
(build-system python-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(replace 'build
(lambda _
(setenv "SETUPTOOLS_SCM_PRETEND_VERSION" ,version)
;; ZIP does not support timestamps before 1980.
(setenv "SOURCE_DATE_EPOCH" "315532800")
(invoke "flit" "build")))
(replace 'install
(lambda* (#:key inputs outputs #:allow-other-keys)
(add-installed-pythonpath inputs outputs)
(let ((out (assoc-ref outputs "out")))
(for-each (lambda (wheel)
(format #true wheel)
(invoke "python" "-m" "pip" "install"
wheel (string-append "--prefix=" out)))
(find-files "dist" "\\.whl$")))))
(replace 'check
(lambda* (#:key inputs #:allow-other-keys)
;; These tests require Internet access.
(delete-file-recursively "scanpy/tests/notebooks")
(delete-file "scanpy/tests/test_clustering.py")
(delete-file "scanpy/tests/test_datasets.py")
(delete-file "scanpy/tests/test_score_genes.py")
(delete-file "scanpy/tests/test_highly_variable_genes.py")
;; TODO: I can't get the plotting tests to work, even with Xvfb.
(delete-file "scanpy/tests/test_plotting.py")
(delete-file "scanpy/tests/test_embedding_plots.py")
(delete-file "scanpy/tests/test_preprocessing.py")
(delete-file "scanpy/tests/test_read_10x.py")
;; The following tests need anndata.tests, which aren't included
;; in the final python-anndata package.
(delete-file "scanpy/tests/test_combat.py")
(delete-file "scanpy/tests/test_embedding_plots.py")
(delete-file "scanpy/tests/test_normalization.py")
(delete-file "scanpy/tests/test_pca.py")
(delete-file "scanpy/tests/external/test_scrublet.py")
;; TODO: these fail with TypingError and "Use of unsupported
;; NumPy function 'numpy.split'".
(delete-file "scanpy/tests/test_metrics.py")
;; The following tests requires 'scanorama', which isn't
;; packaged yet.
@ -11426,8 +11441,24 @@ implementation differs in these ways:
(setenv "PYTHONPATH"
(string-append (getcwd) ":"
(assoc-ref inputs "python-anndata:source") ":"
(getenv "PYTHONPATH")))
(invoke "pytest"))))))
(invoke "pytest" "-vv"
"-k"
;; Plot tests that fail.
(string-append "not test_dotplot_matrixplot_stacked_violin"
" and not test_violin_without_raw"
" and not test_correlation"
" and not test_scatterplots"
" and not test_scatter_embedding_add_outline_vmin_vmax_norm"
" and not test_paga"
" and not test_paga_compare"
;; These try to connect to the network
" and not test_plot_rank_genes_groups_gene_symbols"
" and not test_pca_chunked"
" and not test_pca_sparse"
" and not test_pca_reproducible")))))))
(propagated-inputs
`(("python-anndata" ,python-anndata)
("python-h5py" ,python-h5py)
@ -11445,16 +11476,19 @@ implementation differs in these ways:
("python-scikit-learn" ,python-scikit-learn)
("python-scipy" ,python-scipy)
("python-seaborn" ,python-seaborn)
("python-sinfo" ,python-sinfo)
("python-statsmodels" ,python-statsmodels)
("python-tables" ,python-tables)
("python-pytoml" ,python-pytoml)
("python-tqdm" ,python-tqdm)
("python-umap-learn" ,python-umap-learn)))
(native-inputs
`(("python-leidenalg" ,python-leidenalg)
`(;; This package needs anndata.tests, which is not installed.
("python-anndata:source" ,(package-source python-anndata))
("python-flit" ,python-flit)
("python-leidenalg" ,python-leidenalg)
("python-pytest" ,python-pytest)
("python-setuptools-scm" ,python-setuptools-scm)
("python-sinfo" ,python-sinfo)))
("python-setuptools-scm" ,python-setuptools-scm)))
(home-page "https://github.com/theislab/scanpy")
(synopsis "Single-Cell Analysis in Python.")
(description "Scanpy is a scalable toolkit for analyzing single-cell gene
@ -14203,6 +14237,32 @@ 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 ivar
(package
(name "ivar")
(version "1.3.1")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/andersen-lab/ivar")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
"044xa0hm3b8fga64csrdx05ih8w7kwmvcdrdrhkg8j11ml4bi4xv"))))
(build-system gnu-build-system)
(inputs
`(("htslib" ,htslib)
("zlib" ,zlib)))
(native-inputs
`(("autoconf" ,autoconf)
("automake" ,automake)))
(home-page "https://andersen-lab.github.io/ivar/html/")
(synopsis "Tools for amplicon-based sequencing")
(description "iVar is a computational package that contains functions
broadly useful for viral amplicon-based sequencing. ")
(license license:gpl3+)))
(define-public python-pyliftover
(package
(name "python-pyliftover")
@ -14678,6 +14738,263 @@ produced by Oxford Nanopore Technologies’ MinION, GridION or PromethION
instruments, or Pacific Biosciences RSII or Sequel sequencers.")
(license license:expat)))
(define-public python-strawc
(package
(name "python-strawc")
(version "0.0.2.1")
(source
(origin
(method url-fetch)
(uri (pypi-uri "strawC" version))
(sha256
(base32
"1z1gy8n56lhriy6hdkh9r82ndikndipq2cy2wh8q185qig4rimr6"))))
(build-system python-build-system)
(inputs
`(("curl" ,curl)
("zlib" ,zlib)))
(propagated-inputs
`(("pybind11" ,pybind11)))
(home-page "https://github.com/aidenlab/straw")
(synopsis "Stream data from .hic files")
(description "Straw is library which allows rapid streaming of contact
data from @file{.hic} files. This package provides Python bindings.")
(license license:expat)))
(define-public python-pybbi
(package
(name "python-pybbi")
(version "0.3.0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "pybbi" version))
(sha256
(base32
"1hvy2f28i2b41l1pq15vciqbj538n0lichp8yr6413jmgg06xdsk"))))
(build-system python-build-system)
(arguments
`(#:tests? #false ; tests require network access
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'set-cc
(lambda _ (setenv "CC" "gcc")))
(replace 'check
(lambda* (#:key inputs outputs tests? #:allow-other-keys)
(when tests?
(add-installed-pythonpath inputs outputs)
(copy-recursively "tests" "/tmp/tests")
(with-directory-excursion "/tmp/tests"
(invoke "python" "-m" "pytest" "-v"))))))))
(native-inputs
`(("pkg-config" ,pkg-config)
("python-pkgconfig" ,python-pkgconfig)
("python-pytest" ,python-pytest)))
(inputs
`(("libpng" ,libpng)
("openssl" ,openssl)
("zlib" ,zlib)))
(propagated-inputs
`(("python-cython" ,python-cython)
("python-numpy" ,python-numpy)
("python-pandas" ,python-pandas)
("python-six" ,python-six)))
(home-page "https://github.com/nvictus/pybbi")
(synopsis "Python bindings to UCSC Big Binary file library")
(description
"This package provides Python bindings to the UCSC Big
Binary (bigWig/bigBed) file library. This provides read-level access to local
and remote bigWig and bigBed files but no write capabilitites. The main
feature is fast retrieval of range queries into numpy arrays.")
(license license:expat)))
(define-public python-dna-features-viewer
(package
(name "python-dna-features-viewer")
(version "3.0.3")
(source
(origin
(method url-fetch)
(uri (pypi-uri "dna_features_viewer" version))
(sha256
(base32
"0vci6kg2id6r6rh3cifq7ccnh7j0mb8iqg3hji6rva0ayrdqzafc"))))
(build-system python-build-system)
(arguments '(#:tests? #false)) ; there are none
(propagated-inputs
`(("python-biopython" ,python-biopython)
("python-matplotlib" ,python-matplotlib)))
(home-page
"https://github.com/Edinburgh-Genome-Foundry/DnaFeaturesViewer")
(synopsis "Plot features from DNA sequences")
(description
"DNA Features Viewer is a Python library to visualize DNA features,
e.g. from GenBank or Gff files, or Biopython SeqRecords.")
(license license:expat)))
(define-public python-coolbox
(package
(name "python-coolbox")
(version "0.3.8")
(source
(origin
(method url-fetch)
(uri (pypi-uri "coolbox" version))
(sha256
(base32
"0gqp76285w9klswr47y6kxbzwhv033b26jfa179kccfhiaq5p2xa"))))
(build-system python-build-system)
(arguments '(#:tests? #false)) ; there are none
(inputs
`(("pybind11" ,pybind11)))
(propagated-inputs
`(("python-cooler" ,python-cooler)
("python-dna-features-viewer" ,python-dna-features-viewer)
("python-fire" ,python-fire)
("python-h5py" ,python-h5py)
("python-intervaltree" ,python-intervaltree)
("python-ipywidgets" ,python-ipywidgets)
("jupyter" ,jupyter)
("python-matplotlib" ,python-matplotlib)
("python-nbformat" ,python-nbformat)
("python-numpy" ,python-numpy)
("python-numpydoc" ,python-numpydoc)
("python-pandas" ,python-pandas)
("python-pybbi" ,python-pybbi)
("python-pytest" ,python-pytest)
("python-scipy" ,python-scipy)
("python-statsmodels" ,python-statsmodels)
("python-strawc" ,python-strawc)
("python-svgutils" ,python-svgutils)
("python-termcolor" ,python-termcolor)
("python-voila" ,python-voila)))
(home-page "https://github.com/GangCaoLab/CoolBox")
(synopsis "Genomic data visualization toolkit")
(description
"CoolBox is a toolkit for visual analysis of genomics data. It aims to
be highly compatible with the Python ecosystem, easy to use and highly
customizable with a well-designed user interface. It can be used in various
visualization situations, for example, to produce high-quality genome track
plots or fetch common used genomic data files with a Python script or command
line, interactively explore genomic data within Jupyter environment or web
browser.")
(license license:gpl3+)))
(define-public scregseg
(package
(name "scregseg")
(version "0.1.1")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/BIMSBbioinfo/scregseg")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
"1k8hllr5if6k2mm2zj391fv40sfc008cjm04l9vgfsdppb80i112"))))
(build-system python-build-system)
(arguments
`(#:tests? #false ; tests require network access
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'do-not-fail-to-find-sklearn
(lambda _
;; XXX: I have no idea why it cannot seem to find sklearn.
(substitute* "setup.py"
(("'sklearn',") "")))))))
(native-inputs
`(("python-cython" ,python-cython)))
(propagated-inputs
`(("python-scikit-learn" ,python-scikit-learn)
("python-scipy" ,python-scipy)
("python-numpy" ,python-numpy)
("python-hmmlearn" ,python-hmmlearn)
("python-pandas" ,python-pandas)
("python-numba" ,python-numba)
("python-anndata" ,python-anndata)
("python-scanpy" ,python-scanpy)
("python-pybedtools" ,python-pybedtools)
("python-pysam" ,python-pysam)
("python-matplotlib" ,python-matplotlib)
("python-seaborn" ,python-seaborn)
("python-coolbox" ,python-coolbox)))
(home-page "https://github.com/BIMSBbioinfo/scregseg")
(synopsis "Single-cell regulatory landscape segmentation")
(description "Scregseg (Single-Cell REGulatory landscape SEGmentation) is a
tool that facilitates the analysis of single cell ATAC-seq data by an
HMM-based segmentation algorithm. Scregseg uses an HMM with
Dirichlet-Multinomial emission probabilities to segment the genome either
according to distinct relative cross-cell accessibility profiles or (after
collapsing the single-cell tracks to pseudo-bulk tracks) to capture distinct
cross-cluster accessibility profiles.")
(license license:gpl3+)))
(define-public megadepth
(package
(name "megadepth")
(version "1.1.1")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/ChristopherWilks/megadepth")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32
"0hj69d2dgmk2zwgazik7xzc04fxxlk93p888kpgc52fmhd95qph7"))))
(build-system cmake-build-system)
(arguments
`(#:tests? #false ; some tests seem to require connection to
; www.ebi.ac.uk; this may be caused by htslib.
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'prepare-CMakeLists.txt
(lambda _
(rename-file "CMakeLists.txt.ci" "CMakeLists.txt")
(substitute* "CMakeLists.txt"
(("`cat ../VERSION`") ,version)
(("target_link_libraries\\(megadepth_static") "#")
(("target_link_libraries\\(megadepth_statlib") "#")
(("add_executable\\(megadepth_static") "#")
(("add_executable\\(megadepth_statlib") "#"))
(substitute* "tests/test.sh"
;; Disable remote test
(("./megadepth http://stingray.cs.jhu.edu/data/temp/test.bam") "#")
;; Prior to installation the binary's name differs from what
;; the test script assumes.
(("./megadepth") "../build/megadepth_dynamic"))))
(replace 'check
(lambda* (#:key tests? #:allow-other-keys)
(when tests?
(with-directory-excursion "../source"
(invoke "bash" "tests/test.sh" "use-local-test-data")))))
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let ((bin (string-append (assoc-ref outputs "out") "/bin")))
(mkdir-p bin)
(copy-file "megadepth_dynamic"
(string-append bin "/megadepth"))))))))
(native-inputs
`(("diffutils" ,diffutils)
("perl" ,perl)
("grep" ,grep)))
(inputs
`(("curl" ,curl)
("htslib" ,htslib)
("libdeflate" ,libdeflate)
("libbigwig" ,libbigwig)
("zlib" ,zlib)))
(home-page "https://github.com/ChristopherWilks/megadepth")
(synopsis "BigWig and BAM/CRAM related utilities")
(description "Megadepth is an efficient tool for extracting coverage
related information from RNA and DNA-seq BAM and BigWig files. It supports
reading whole-genome coverage from BAM files and writing either indexed TSV or
BigWig files, as well as efficient region coverage summary over intervals from
both types of files.")
(license license:expat)))
(define-public r-ascat
(package
(name "r-ascat")
@ -14737,6 +15054,34 @@ copy number estimation, as described by
@url{doi:10.1016/j.cell.2012.04.023,Nik-Zainal et al.}")
(license license:gpl3)))
(define-public r-catch
(let ((commit "196ddd5a51b1a5f5daa01de53fdaad9b7505e084")
(revision "1"))
(package
(name "r-catch")
(version (git-version "1.0" revision commit))
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/zhanyinx/CaTCH")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32
"11c7f1fc8f57wnwk1hrgr5y814m80zj8gkz5021vxyxy2v02cqgd"))))
(build-system r-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'chdir
(lambda _ (chdir "CaTCH"))))))
(home-page "https://github.com/zhanyinx/CaTCH_R")
(synopsis "Call a hierarchy of domains based on Hi-C data")
(description "This package allows building the hierarchy of domains
starting from Hi-C data. Each hierarchical level is identified by a minimum
value of physical insulation between neighboring domains.")
(license license:gpl2+))))
(define-public r-spectre
(let ((commit "f6648ab3eb9499300d86502b5d60ec370ae9b61a")
(revision "1"))
@ -14808,3 +15153,42 @@ copy number estimation, as described by
integration, exploration, and analysis of high-dimensional single-cell
cytometry and imaging data.")
(license license:expat))))
(define-public r-cytonorm
(let ((commit "e4b9d343ee65db3c422800f1db3e77c25abde987")
(revision "1"))
(package
(name "r-cytonorm")
(version (git-version "0.0.7" revision commit))
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/saeyslab/CytoNorm")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32
"0h2rdy15i4zymd4dv60n5w0frbsdbmzpv99dgm0l2dn041qv7fah"))))
(properties `((upstream-name . "CytoNorm")))
(build-system r-build-system)
(propagated-inputs
`(("r-cytoml" ,r-cytoml)
("r-dplyr" ,r-dplyr)
("r-emdist" ,r-emdist)
("r-flowcore" ,r-flowcore)
("r-flowsom" ,r-flowsom)
("r-flowworkspace" ,r-flowworkspace)
("r-ggplot2" ,r-ggplot2)
("r-gridextra" ,r-gridextra)
("r-pheatmap" ,r-pheatmap)
("r-stringr" ,r-stringr)))
(home-page "https://github.com/saeyslab/CytoNorm")
(synopsis "Normalize cytometry data measured across multiple batches")
(description
"This package can be used to normalize cytometry samples when a control
sample is taken along in each of the batches. This is done by first
identifying multiple clusters/cell types, learning the batch effects from the
control samples and applying quantile normalization on all markers of
interest.")
(license license:gpl2+))))