From a9d496b353e71f22e5ace5bff9319fc74dfb6643 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 16:00:01 +0200 Subject: gnu: Add python-intervaltree. * gnu/packages/bioinformatics.scm (python-intervaltree): New variable. --- gnu/packages/bioinformatics.scm | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 6580cac531..dd8ed725d8 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -13504,3 +13504,31 @@ 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))) -- cgit v1.2.3 From 1f41f01c1499fb0aa5933b9b60d2a18c2bef9d5c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 16:00:02 +0200 Subject: gnu: Add python-pypairix. * gnu/packages/bioinformatics.scm (python-pypairix): New variable. --- gnu/packages/bioinformatics.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index dd8ed725d8..9b047c21b8 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -13532,3 +13532,27 @@ 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))) -- cgit v1.2.3 From 80f4db91b17ff5d82260c9194ec09a408f854455 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 16:00:03 +0200 Subject: gnu: Add python-pyfaidx. * gnu/packages/bioinformatics.scm (python-pyfaidx): New variable. --- gnu/packages/bioinformatics.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 9b047c21b8..d66d9ef40e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -13556,3 +13556,25 @@ bound.") "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))) -- cgit v1.2.3 From 5bb9e0af8dce2d4a9e66c9f673daa3af8fbae99b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 16:00:04 +0200 Subject: gnu: Add python-cooler. * gnu/packages/bioinformatics.scm (python-cooler): New variable. --- gnu/packages/bioinformatics.scm | 37 +++++++++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index d66d9ef40e..65da049c79 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -13578,3 +13578,40 @@ bgzipped text file that contains a pair of genomic coordinates per line.") "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))) -- cgit v1.2.3 From 1189c7f1b050aa495b0ec6d9436c644ee308695f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 16:07:27 +0200 Subject: gnu: Add python-hicexplorer. * gnu/packages/bioinformatics.scm (python-hicexplorer): New variable. --- gnu/packages/bioinformatics.scm | 53 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 53 insertions(+) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 65da049c79..7e6d76e022 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -13615,3 +13615,56 @@ fasta subsequences.") 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))) -- cgit v1.2.3 From 5bfa7510d144c3a35bc9022d79fdf4192d4aa1f8 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 16:07:28 +0200 Subject: gnu: Add python-pygenometracks. * gnu/packages/bioinformatics.scm (python-pygenometracks): New variable. --- gnu/packages/bioinformatics.scm | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 7e6d76e022..fc8be4d7db 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -13668,3 +13668,34 @@ 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+))) -- cgit v1.2.3 From 875d0681768408997cda108457aaf10116da3732 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Mon, 10 Sep 2018 15:42:07 -0400 Subject: Adjust all users of (gnu packages ldc) to use (gnu packages dlang). This is a followup to commit 98d6543f86d01486c2f6e808eedd97c601ba3e7a. * gnu/packages/bioinformatics.scm, guix/build-system/dub.scm: Adjust accordingly. --- gnu/packages/bioinformatics.scm | 2 +- guix/build-system/dub.scm | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index fc8be4d7db..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) diff --git a/guix/build-system/dub.scm b/guix/build-system/dub.scm index 13c89e8648..5a31a2f51a 100644 --- a/guix/build-system/dub.scm +++ b/guix/build-system/dub.scm @@ -35,13 +35,13 @@ (define (default-ldc) "Return the default ldc package." ;; Lazily resolve the binding to avoid a circular dependency. - (let ((ldc (resolve-interface '(gnu packages ldc)))) + (let ((ldc (resolve-interface '(gnu packages dlang)))) (module-ref ldc 'ldc))) (define (default-dub) "Return the default dub package." ;; Lazily resolve the binding to avoid a circular dependency. - (let ((ldc (resolve-interface '(gnu packages ldc)))) + (let ((ldc (resolve-interface '(gnu packages dlang)))) (module-ref ldc 'dub))) (define (default-pkg-config) -- cgit v1.2.3