From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
To: 32642@debbugs.gnu.org
Cc: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Subject: [bug#32642] [PATCH 15/16] gnu: Add python-hicexplorer.
Date: Wed, 5 Sep 2018 16:07:27 +0200 [thread overview]
Message-ID: <20180905140728.11138-1-ricardo.wurmus@mdc-berlin.de> (raw)
In-Reply-To: <20180905140006.10783-9-ricardo.wurmus@mdc-berlin.de>
* gnu/packages/bioinformatics.scm (python-hicexplorer): New variable.
---
gnu/packages/bioinformatics.scm | 53 +++++++++++++++++++++++++++++++++
1 file changed, 53 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index e555fb009..ccc3ed26a 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -13662,3 +13662,56 @@ 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)))
--
2.18.0
next prev parent reply other threads:[~2018-09-05 14:08 UTC|newest]
Thread overview: 18+ messages / expand[flat|nested] mbox.gz Atom feed top
2018-09-05 13:46 [bug#32642] [PATCH 00/16] gnu: Add python-pygenometracks Ricardo Wurmus
2018-09-05 13:54 ` [bug#32642] [PATCH 01/16] gnu: Add python-dill Ricardo Wurmus
2018-09-05 13:54 ` [bug#32642] [PATCH 02/16] gnu: Add python-multiprocess Ricardo Wurmus
2018-09-05 13:54 ` [bug#32642] [PATCH 03/16] gnu: Add python-toolz Ricardo Wurmus
2018-09-05 13:54 ` [bug#32642] [PATCH 04/16] gnu: Add python-cytoolz Ricardo Wurmus
2018-09-05 13:54 ` [bug#32642] [PATCH 05/16] gnu: Add python-sortedcontainers Ricardo Wurmus
2018-09-05 13:59 ` [bug#32642] [PATCH 06/16] gnu: Add python-cloudpickle Ricardo Wurmus
2018-09-05 13:59 ` [bug#32642] [PATCH 07/16] gnu: Add python-locket Ricardo Wurmus
2018-09-05 13:59 ` [bug#32642] [PATCH 08/16] gnu: Add python-blosc Ricardo Wurmus
2018-09-05 13:59 ` [bug#32642] [PATCH 09/16] gnu: Add python-partd Ricardo Wurmus
2018-09-05 14:00 ` [bug#32642] [PATCH 10/16] gnu: Add python-dask Ricardo Wurmus
2018-09-05 14:00 ` [bug#32642] [PATCH 11/16] gnu: Add python-intervaltree Ricardo Wurmus
2018-09-05 14:00 ` [bug#32642] [PATCH 12/16] gnu: Add python-pypairix Ricardo Wurmus
2018-09-05 14:00 ` [bug#32642] [PATCH 13/16] gnu: Add python-pyfaidx Ricardo Wurmus
2018-09-05 14:00 ` [bug#32642] [PATCH 14/16] gnu: Add python-cooler Ricardo Wurmus
2018-09-05 14:07 ` Ricardo Wurmus [this message]
2018-09-05 14:07 ` [bug#32642] [PATCH 16/16] gnu: Add python-pygenometracks Ricardo Wurmus
2018-09-10 14:52 ` bug#32642: " Ricardo Wurmus
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