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-rw-r--r--gnu/packages/bioinformatics.scm197
1 files changed, 196 insertions, 1 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 6580cac531..f6410c3ca4 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -76,7 +76,7 @@
#:use-module (gnu packages imagemagick)
#:use-module (gnu packages java)
#:use-module (gnu packages jemalloc)
- #:use-module (gnu packages ldc)
+ #:use-module (gnu packages dlang)
#:use-module (gnu packages linux)
#:use-module (gnu packages logging)
#:use-module (gnu packages machine-learning)
@@ -13504,3 +13504,198 @@ reference transcripts provided in a annotation file (also in GTF/GFF3 format).
(list
license:expat ;license for gffcompare
license:artistic2.0))))) ;license for gclib
+
+(define-public python-intervaltree
+ (package
+ (name "python-intervaltree")
+ (version "2.1.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "intervaltree" version))
+ (sha256
+ (base32
+ "02w191m9zxkcjqr1kv2slxvhymwhj3jnsyy3a28b837pi15q19dc"))))
+ (build-system python-build-system)
+ ;; FIXME: error when collecting tests
+ (arguments '(#:tests? #f))
+ (propagated-inputs
+ `(("python-sortedcontainers" ,python-sortedcontainers)))
+ (native-inputs
+ `(("python-pytest" ,python-pytest)))
+ (home-page "https://github.com/chaimleib/intervaltree")
+ (synopsis "Editable interval tree data structure")
+ (description
+ "This package provides a mutable, self-balancing interval tree
+implementation for Python. Queries may be by point, by range overlap, or by
+range envelopment. This library was designed to allow tagging text and time
+intervals, where the intervals include the lower bound but not the upper
+bound.")
+ (license license:asl2.0)))
+
+(define-public python-pypairix
+ (package
+ (name "python-pypairix")
+ (version "0.3.6")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "pypairix" version))
+ (sha256
+ (base32
+ "0zs92b74s5v4xy2h16s15f3z6l4nnbw8x8zyif7xx5xpafjn0xss"))))
+ (build-system python-build-system)
+ ;; FIXME: the tests fail because test.support cannot be loaded:
+ ;; ImportError: cannot import name 'support'
+ (arguments '(#:tests? #f))
+ (inputs
+ `(("zlib" ,zlib)))
+ (home-page "https://github.com/4dn-dcic/pairix")
+ (synopsis "Support for querying pairix-indexed bgzipped text files")
+ (description
+ "Pypairix is a Python module for fast querying on a pairix-indexed
+bgzipped text file that contains a pair of genomic coordinates per line.")
+ (license license:expat)))
+
+(define-public python-pyfaidx
+ (package
+ (name "python-pyfaidx")
+ (version "0.5.4.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "pyfaidx" version))
+ (sha256
+ (base32
+ "0y5zyjksj1rdglj601xd2bbni5abhdh622y3ck76chyzxz9z4rx8"))))
+ (build-system python-build-system)
+ (propagated-inputs
+ `(("python-setuptools" ,python-setuptools)
+ ("python-six" ,python-six)))
+ (home-page "http://mattshirley.com")
+ (synopsis "Random access to fasta subsequences")
+ (description
+ "This package provides procedures for efficient pythonic random access to
+fasta subsequences.")
+ (license license:bsd-3)))
+
+(define-public python-cooler
+ (package
+ (name "python-cooler")
+ (version "0.7.11")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "cooler" version))
+ (sha256
+ (base32
+ "08k5nxnxa6qsbk15z5z0q01n28042k87wi4905hh95rzqib15mhx"))))
+ (build-system python-build-system)
+ (propagated-inputs
+ `(("python-biopython" ,python-biopython)
+ ("python-click" ,python-click)
+ ("python-cytoolz" ,python-cytoolz)
+ ("python-dask" ,python-dask)
+ ("python-h5py" ,python-h5py)
+ ("python-multiprocess" ,python-multiprocess)
+ ("python-pandas" ,python-pandas)
+ ("python-pyfaidx" ,python-pyfaidx)
+ ("python-pypairix" ,python-pypairix)
+ ("python-pysam" ,python-pysam)
+ ("python-scipy" ,python-scipy)))
+ (native-inputs
+ `(("python-mock" ,python-mock)
+ ("python-nose" ,python-nose)
+ ("python-numpydoc" ,python-numpydoc)
+ ("python-sphinx" ,python-sphinx)))
+ (home-page "https://github.com/mirnylab/cooler")
+ (synopsis "Sparse binary format for genomic interaction matrices")
+ (description
+ "Cooler is a support library for a sparse, compressed, binary persistent
+storage format, called @code{cool}, used to store genomic interaction data,
+such as Hi-C contact matrices.")
+ (license license:bsd-3)))
+
+(define-public python-hicexplorer
+ (package
+ (name "python-hicexplorer")
+ (version "2.1.4")
+ (source
+ (origin
+ ;; The latest version is not available on Pypi.
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/deeptools/HiCExplorer.git")
+ (commit version)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "0q5gpbzmrkvygqgw524q36b4nrivcmyi5v194vsx0qw7b3gcmq08"))))
+ (build-system python-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'loosen-up-requirements
+ (lambda _
+ (substitute* "setup.py"
+ (("==") ">="))
+ #t)))))
+ (propagated-inputs
+ `(("python-biopython" ,python-biopython)
+ ("python-configparser" ,python-configparser)
+ ("python-cooler" ,python-cooler)
+ ("python-future" ,python-future)
+ ("python-intervaltree" ,python-intervaltree)
+ ("python-jinja2" ,python-jinja2)
+ ("python-matplotlib" ,python-matplotlib)
+ ("python-numpy" ,python-numpy)
+ ("python-pandas" ,python-pandas)
+ ("python-pybigwig" ,python-pybigwig)
+ ("python-pysam" ,python-pysam)
+ ("python-scipy" ,python-scipy)
+ ("python-six" ,python-six)
+ ("python-tables" ,python-tables)
+ ("python-unidecode" ,python-unidecode)))
+ (home-page "http://hicexplorer.readthedocs.io")
+ (synopsis "Process, analyze and visualize Hi-C data")
+ (description
+ "HiCExplorer is a powerful and easy to use set of tools to process,
+normalize and visualize Hi-C data. HiCExplorer facilitates the creation of
+contact matrices, correction of contacts, TAD detection, A/B compartments,
+merging, reordering or chromosomes, conversion from different formats
+including cooler and detection of long-range contacts. Moreover, it allows
+the visualization of multiple contact matrices along with other types of data
+like genes, compartments, ChIP-seq coverage tracks (and in general any type of
+genomic scores), long range contacts and the visualization of viewpoints.")
+ (license license:gpl3)))
+
+(define-public python-pygenometracks
+ (package
+ (name "python-pygenometracks")
+ (version "2.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "pyGenomeTracks" version))
+ (sha256
+ (base32
+ "1fws6bqsyy9kj3qiabhkqx4wd4i775gsxnhszqd3zg7w67sc1ic5"))))
+ (build-system python-build-system)
+ (propagated-inputs
+ `(("python-configparser" ,python-configparser)
+ ("python-future" ,python-future)
+ ("python-hicexplorer" ,python-hicexplorer)
+ ("python-intervaltree" ,python-intervaltree)
+ ("python-matplotlib" ,python-matplotlib)
+ ("python-numpy" ,python-numpy)
+ ("python-pybigwig" ,python-pybigwig)))
+ (native-inputs
+ `(("python-pytest" ,python-pytest)))
+ (home-page "https://pygenometracks.readthedocs.io")
+ (synopsis "Program and library to plot beautiful genome browser tracks")
+ (description
+ "This package aims to produce high-quality genome browser tracks that
+are highly customizable. Currently, it is possible to plot: bigwig, bed (many
+options), bedgraph, links (represented as arcs), and Hi-C matrices.
+pyGenomeTracks can make plots with or without Hi-C data.")
+ (license license:gpl3+)))