From: "Mădălin Ionel Patrașcu" <madalinionel.patrascu@mdc-berlin.de>
To: <46946@debbugs.gnu.org>
Cc: rekado@elephly.net,
"Mădălin Ionel Patrașcu" <madalinionel.patrascu@mdc-berlin.de>
Subject: [bug#46946] [PATCH 1/2] gnu: Add python-bioframe.
Date: Fri, 5 Mar 2021 15:19:29 +0100 [thread overview]
Message-ID: <20210305141930.28787-1-madalinionel.patrascu@mdc-berlin.de> (raw)
In-Reply-To: <a2e7d423-e124-af29-6367-33a2b478008d@mdc-berlin.de>
* gnu/packages/bioinformatics.scm (python-bioframe): New variable.
---
gnu/packages/bioinformatics.scm | 46 +++++++++++++++++++++++++++++++++
1 file changed, 46 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index d617736e57..fb357b8b6c 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -120,6 +120,7 @@
#:use-module (gnu packages popt)
#:use-module (gnu packages protobuf)
#:use-module (gnu packages python)
+ #:use-module (gnu packages python-build)
#:use-module (gnu packages python-check)
#:use-module (gnu packages python-compression)
#:use-module (gnu packages python-science)
@@ -923,6 +924,51 @@ Python.")
`(("python2-pathlib" ,python2-pathlib)
,@(package-native-inputs pybedtools))))))
+(define-public python-bioframe
+ (package
+ (name "python-bioframe")
+ (version "0.2.0")
+ ;;pypi sources does not contain requirements.txt
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/open2c/bioframe")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "0w5xrb93cf3hx3d1lw48a0l1ranghpj260b05b1rpk58wwwcsqfh"))))
+ (build-system python-build-system)
+ (propagated-inputs
+ `(("python-click" ,python-click)
+ ("python-numpy" ,python-numpy)
+ ("python-pandas" ,python-pandas)
+ ("python-requests" ,python-requests)))
+ (native-inputs
+ `(("python-dask" ,python-dask) ;;for unittest.loader
+ ("python-matplotlib" ,python-matplotlib) ;;for unittest.loader
+ ("python-numba" ,python-numba) ;;for unittest.loader
+ ("python-pypairix" ,python-pypairix) ;;for unittest.loader
+ ("python-pytest" ,python-pytest)
+ ("python-wheel" ,python-wheel)))
+ (home-page "https://github.com/open2c/bioframe")
+ (synopsis
+ "Framework for genomic data analysis using Pandas dataframes")
+ (description
+ "This package is a library to enable flexible and scalable operations on
+genomic interval dataframes in python. @code{python-bioframe} enables access
+to a rich set of dataframe operations. Working in python enables rapid
+visualization (e.g. matplotlib, seaborn) and iteration of genomic analyses.
+The philosophy underlying @code{python-bioframe} is to enable flexible
+operations: instead of creating a function for every possible use-case, we
+instead encourage users to compose functions to achieve their goals. As a
+rough rule of thumb, if a function requires three steps and is crucial for
+genomic interval arithmetic we have included it; conversely if it can be
+performed in a single line by composing two of the core functions, we have not
+included it.")
+ (license license:expat)))
+
(define-public python-biom-format
(package
(name "python-biom-format")
--
2.30.1
next prev parent reply other threads:[~2021-03-05 14:20 UTC|newest]
Thread overview: 8+ messages / expand[flat|nested] mbox.gz Atom feed top
2021-03-05 13:50 [bug#46946] (no subject) Mădălin Ionel Patrașcu
2021-03-05 14:19 ` Mădălin Ionel Patrașcu [this message]
2021-03-05 14:19 ` [bug#46946] [PATCH 2/2] gnu: Add python-cooltools Mădălin Ionel Patrașcu
2021-04-01 15:38 ` [bug#46946] [PATCH 1/2] gnu: Add python-bioframe Ricardo Wurmus
2022-10-14 22:49 ` [bug#46946] [ext] " MadalinIonel.Patrascu
2022-10-14 22:52 ` [bug#46946] " Mădălin Ionel Patrașcu
2022-10-14 22:52 ` [bug#46946] [PATCH 2/2] gnu: Add python-cooltools Mădălin Ionel Patrașcu
2022-11-04 12:53 ` bug#46946: Add python-bioframe, python-cooltools Ricardo Wurmus
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