From mboxrd@z Thu Jan 1 00:00:00 1970 Received: from eggs.gnu.org ([2001:4830:134:3::10]:57660) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1fxYTW-0006PV-AT for guix-patches@gnu.org; Wed, 05 Sep 2018 10:08:11 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1fxYTT-0004Yx-3B for guix-patches@gnu.org; Wed, 05 Sep 2018 10:08:06 -0400 Received: from debbugs.gnu.org ([208.118.235.43]:42283) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1fxYTS-0004XD-Nq for guix-patches@gnu.org; Wed, 05 Sep 2018 10:08:03 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1fxYTS-0005M4-CA for guix-patches@gnu.org; Wed, 05 Sep 2018 10:08:02 -0400 Subject: [bug#32642] [PATCH 15/16] gnu: Add python-hicexplorer. Resent-Message-ID: From: Ricardo Wurmus Date: Wed, 5 Sep 2018 16:07:27 +0200 Message-ID: <20180905140728.11138-1-ricardo.wurmus@mdc-berlin.de> In-Reply-To: <20180905140006.10783-9-ricardo.wurmus@mdc-berlin.de> References: <20180905140006.10783-9-ricardo.wurmus@mdc-berlin.de> MIME-Version: 1.0 Content-Type: text/plain List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+kyle=kyleam.com@gnu.org Sender: "Guix-patches" To: 32642@debbugs.gnu.org Cc: Ricardo Wurmus * 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