diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 81 |
1 files changed, 60 insertions, 21 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 14fcd0119d..dde7ef151a 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1814,7 +1814,8 @@ intended to behave exactly the same as the original BWK awk.") (base32 "1pm1szyxabhn8jismrj9cjhf88ajgcmm39f0cgf36iagw5qakprl")))) (build-system pyproject-build-system) - (propagated-inputs (list python-biopython python-six)) + (propagated-inputs (list python-biopython python-six python-setuptools + python-wheel)) (native-inputs (list python-pytest)) (home-page "https://github.com/chapmanb/bcbb/tree/master/gff") (synopsis "Read and write GFF files with Biopython integration") @@ -1939,7 +1940,7 @@ from bokeh.util.dataclasses import entries\n")) python-tornado-6 python-tqdm python-umap-learn)) - (native-inputs (list python-pytest)) + (native-inputs (list python-pytest python-setuptools python-wheel)) (home-page "https://github.com/LooseLab/bulkVis") (synopsis "Interactive visualization of bulk RNA-seq data") (description @@ -2270,7 +2271,8 @@ biological activities from omics data within a unified framework.") python-scikit-learn python-scipy python-seaborn)) - (native-inputs (list python-cython python-setuptools-scm)) + (native-inputs (list python-cython python-setuptools-scm + python-setuptools python-wheel)) (home-page "https://github.com/lilab-bcb/demuxEM") (synopsis "Analyze cell-hashing/nucleus-hashing data") (description @@ -2343,6 +2345,7 @@ from single-cell RNA-sequencing.") python-numpy python-pandas python-scipy)) + (native-inputs (list python-setuptools python-wheel)) (home-page "https://github.com/SegataLab/hclust2/") (synopsis "Plotting heat-maps for publications") (description @@ -2362,7 +2365,7 @@ to produce high quality figures that can be used in publications.") "111q4pzkav26aa3hkgh948wqlyrq7dq6sjml9z63n3blw8s6b0c4")))) (build-system pyproject-build-system) (native-inputs - (list python-setuptools-scm)) + (list python-setuptools-scm python-setuptools python-wheel)) (propagated-inputs (list python-humanize python-requests python-six)) (home-page "https://pypi.org/project/htsget/") @@ -2462,6 +2465,7 @@ framework enables the use of any LR method with any resources.") (build-system pyproject-build-system) (propagated-inputs (list python-matplotlib python-numpy python-pandas)) + (native-inputs (list python-setuptools python-wheel)) (home-page "https://logomaker.readthedocs.io") (synopsis "Package for making Sequence Logos") (description "Logomaker is a Python package for generating @@ -2696,7 +2700,8 @@ three prime UTR.") python-pillow python-scipy python-zarr)) - (native-inputs (list python-cython python-setuptools-scm)) + (native-inputs (list python-cython python-setuptools-scm + python-setuptools python-wheel)) (home-page "https://github.com/lilab-bcb/pegasusio") (synopsis "Read or write single-cell genomics data") (description @@ -2755,7 +2760,7 @@ weight.astype(\"str\") + '\\n')"))))))) python-scikit-learn python-scipy)) (native-inputs - (list python-pytest)) + (list python-pytest python-setuptools python-wheel)) (home-page "https://github.com/dpeerlab/PhenoGraph.git") (synopsis "Graph-based clustering for high-dimensional single-cell data") (description @@ -2786,6 +2791,7 @@ similarities between cells and then identifying communities in this graph.") python-numpy python-pandas python-seaborn)) + (native-inputs (list python-setuptools python-wheel)) (home-page "https://github.com/biobakery/phylophlan") (synopsis "Phylogenetic analysis of microbial isolates and genomes from metagenomes") @@ -2865,6 +2871,8 @@ phylogenetic markers, and can also scale to very large phylogenies comprising python-cython kentutils ; for bedGraphToBigWig python-six + python-setuptools + python-wheel ;; For the test suite. python-pytest python-psutil)) @@ -3245,6 +3253,7 @@ alignments and perform the following operations: (build-system pyproject-build-system) (arguments (list #:tests? #false)) ;there are none (propagated-inputs (list python-pandas)) + (native-inputs (list python-setuptools python-wheel)) (home-page "https://github.com/alexomics/read-paf") (synopsis "Minimap2 PAF file reader") (description @@ -3357,6 +3366,7 @@ sequencing.") (lambda _ (setenv "HOME" "/tmp")))))) (propagated-inputs (list python-numpy)) + (native-inputs (list python-setuptools python-wheel)) (home-page "https://biopython.org/") (synopsis "Tools for biological computation in Python") (description @@ -4416,7 +4426,8 @@ off-target reads for a capture method that targets CpG-rich region.") (inputs (list zlib)) (native-inputs - (list python-cython python-lzo python-pytest)) + (list python-cython python-lzo python-pytest python-setuptools + python-wheel)) (home-page "https://github.com/bxlab/bx-python") (synopsis "Tools for manipulating biological data") (description @@ -4642,6 +4653,8 @@ subgroups.") (native-inputs (list python-cython python-pytest + python-setuptools + python-wheel ;; Dependencies below are are for tests only. samtools bcftools)) @@ -4735,6 +4748,8 @@ UCSC genome browser.") (native-inputs `(("python-cython" ,python-cython) ("python-pytest" ,python-pytest) + ("python-setuptools" ,python-setuptools) + ("python-wheel" ,python-wheel) ("test-data" ,(origin (method url-fetch) @@ -5062,7 +5077,8 @@ file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF.") (arguments (list #:tests? #false)) ;there are none (native-inputs - (list python-cython python-pytest python-setuptools-scm)) + (list python-cython python-pytest python-setuptools-scm + python-setuptools python-wheel)) (propagated-inputs (list python-xopen)) (home-page "https://github.com/marcelm/dnaio/") @@ -5414,6 +5430,7 @@ gkm-SVM.") (list python-numpy)) (inputs (list libbigwig zlib curl)) + (native-inputs (list python-setuptools python-wheel)) (home-page "https://github.com/dpryan79/pyBigWig") (synopsis "Access bigWig files in Python using libBigWig") (description @@ -5539,9 +5556,12 @@ Note that this package has been deprecated in favor of @code{pyfaidx}.") python-mypy-extensions python-rdflib python-requests - python-ruamel.yaml)) + python-ruamel.yaml + python-setuptools ; For pkg_resources. + python-typing-extensions)) (native-inputs - (list python-black python-pytest python-pytest-runner python-pytest-xdist)) + (list python-black python-pytest python-pytest-runner + python-wheel)) (home-page "https://github.com/common-workflow-language/schema_salad") (synopsis "Schema Annotations for Linked Avro Data (SALAD)") (description @@ -5625,6 +5645,7 @@ resources for bioinformatics.") python-scikit-learn python-scipy python-umap-learn)) + (native-inputs (list python-setuptools python-wheel)) (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 @@ -5790,6 +5811,7 @@ documents.") python-requests python-ruamel.yaml python-schema-salad + python-setuptools ; For pkg_resources. python-shellescape python-spython python-typing-extensions @@ -5803,7 +5825,7 @@ documents.") python-pytest-cov python-pytest-mock python-pytest-runner - python-pytest-xdist)) + python-wheel)) (home-page "https://github.com/common-workflow-language/common-workflow-language") (synopsis "Common Workflow Language reference implementation") @@ -5857,7 +5879,8 @@ CWL descriptions.") (substitute* "tests/test_datamodel_taxon.py" (("collections.Iterable") "collections.abc.Iterable"))))))) - (native-inputs (list python-pytest)) + (native-inputs (list python-pytest python-wheel)) + (propagated-inputs (list python-setuptools)) (home-page "https://dendropy.org/") (synopsis "Library for phylogenetics and phylogenetic computing") (description @@ -6676,7 +6699,8 @@ multiple DJU methods.") (base32 "0cjpzyqz6r4lmiwry2gcxdczwpkhl3lyyjg4s8addln17691ysxk")))) (build-system pyproject-build-system) - (propagated-inputs (list python-pytest)) + (propagated-inputs (list python-pytest python-setuptools)) + (native-inputs (list python-wheel)) (home-page "https://github.com/betteridiot/bamnostic/") (synopsis "Tool for binary alignment map, random access and parsing") (description @@ -6774,7 +6798,7 @@ analysis tool Scanpy (Genome Biology, 2018).") python-pyqt python-scipy)) (native-inputs - (list python-pytest)) + (list python-pytest python-setuptools python-wheel)) (home-page "http://etetoolkit.org") (synopsis "Python environment for phylogenetic tree exploration") (description @@ -6795,6 +6819,7 @@ exploration.") (build-system pyproject-build-system) (arguments (list #:tests? #false)) ;there are none (propagated-inputs (list python-matplotlib python-numpy python-levenshtein)) + (native-inputs (list python-setuptools python-wheel python-pip)) (home-page "https://github.com/meren/illumina-utils") (synopsis "Library and scripts to work with Illumina paired-end data") (description @@ -6818,6 +6843,7 @@ Illumina paired-end data (for CASAVA 1.8+).") (propagated-inputs (list python-biopython python-matplotlib python-pandas python-scipy python-seaborn)) + (native-inputs (list python-setuptools python-wheel)) (home-page "https://widdowquinn.github.io/pyani/") (synopsis "Calculate genome-scale average nucleotide identity") (description @@ -10489,7 +10515,9 @@ complexity samples.") (build-system pyproject-build-system) (native-inputs (list python-pytest-cov - python-pytest-runner)) + python-pytest-runner + python-setuptools + python-wheel)) (home-page "https://github.com/dib-lab/screed/") (synopsis "Short read sequence database utilities") (description "Screed parses FASTA and FASTQ files and generates databases. @@ -10831,7 +10859,7 @@ bioinformatics file formats, sequence alignment, and more.") (inputs (list python-biopython python-pygtrie)) (native-inputs - (list python-pytest)) + (list python-pytest python-setuptools python-wheel)) (home-page "https://github.com/fhcrc/seqmagick") (synopsis "Tools for converting and modifying sequence files") (description @@ -14026,10 +14054,12 @@ replacement for strverscmp.") python-requests python-rich python-rich-click + python-setuptools ; For pkg_resources. python-simplejson python-spectra)) (native-inputs `(("python-pytest" ,python-pytest) + ("python-wheel" ,python-wheel) ("tests" ,(let ((commit "c3e7400affe3f3ca996973805797af61b93070ba")) (origin @@ -15764,9 +15794,10 @@ using the same syntax.") python-pydot python-requests python-scipy + python-setuptools python-statsmodels python-xlsxwriter)) - (native-inputs (list python-pytest)) + (native-inputs (list python-pytest python-wheel)) (home-page "https://github.com/tanghaibao/goatools") (synopsis "Python scripts to find enrichment of GO terms") (description "Python scripts to find enrichment of GO terms. In addition, @@ -15882,9 +15913,10 @@ API services.") python-pysam python-regex python-ruamel.yaml + python-setuptools snakemake)) (native-inputs - (list python-pytest)) + (list python-pytest python-wheel)) (home-page "https://github.com/caleblareau/mgatk") (synopsis "Mitochondrial genome analysis toolkit.") (description "This package is a Python-based command line interface for @@ -18125,6 +18157,7 @@ implementation differs in these ways: python-patsy python-scikit-learn python-scipy + python-setuptools ; For pkg_resources. python-seaborn python-session-info python-sinfo @@ -18518,7 +18551,9 @@ bgzipped text file that contains a pair of genomic coordinates per line.") python-mock python-numpy python-pytest - python-pytest-cov)) + python-pytest-cov + python-wheel)) + (propagated-inputs (list python-setuptools)) (home-page "http://mattshirley.com") (synopsis "Random access to fasta subsequences") (description @@ -18640,7 +18675,7 @@ includes operations like compartment, insulation or peak calling.") python-scipy python-tables)) (native-inputs - (list python-pytest)) + (list python-pytest python-setuptools python-wheel)) (home-page "https://github.com/deeptools/HiCMatrix/") (synopsis "HiCMatrix class for HiCExplorer and pyGenomeTracks") (description @@ -19503,6 +19538,7 @@ polymorphisms) and indels with respect to a reference genome and more.") ;; R packages r-dnacopy)) (inputs (list r-minimal)) ;for tests + (native-inputs (list python-setuptools python-wheel)) (home-page "https://cnvkit.readthedocs.org/") (synopsis "Copy number variant detection from targeted DNA sequencing") (description @@ -21730,7 +21766,9 @@ coordinates between different assemblies.") (list python-pytest lsof inetutils - openssl)) + openssl + python-setuptools + python-wheel)) (inputs (list time)) (propagated-inputs (list python-apsw @@ -22234,6 +22272,7 @@ feature is fast retrieval of range queries into numpy arrays.") (list python-biopython python-matplotlib python-packaging)) + (native-inputs (list python-setuptools python-wheel)) (home-page "https://github.com/Edinburgh-Genome-Foundry/DnaFeaturesViewer") (synopsis "Plot features from DNA sequences") |