diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 430 |
1 files changed, 407 insertions, 23 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 430551887d..d91ff13b46 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -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+)))) |