gnu: Add umi-tools.

* gnu/packages/bioinformatics.scm (umi-tools): New variable.
This commit is contained in:
Ricardo Wurmus 2019-04-26 14:57:29 +02:00
parent 8caa458953
commit 7f55904558
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2 changed files with 37 additions and 0 deletions

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@ -14739,3 +14739,38 @@ tools for identifying genome bins that are likely candidates for merging based
on marker set compatibility, similarity in genomic characteristics, and on marker set compatibility, similarity in genomic characteristics, and
proximity within a reference genome.") proximity within a reference genome.")
(license license:gpl3+))) (license license:gpl3+)))
(define-public umi-tools
(package
(name "umi-tools")
(version "1.0.0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "umi_tools" version))
(sha256
(base32
"08y3vz1vcx09whmbsn722lcs6jl9wyrh9i4p3k8j4cb1i32bij4a"))))
(build-system python-build-system)
(inputs
`(("python-setuptools" ,python-setuptools)
("python-pandas" ,python-pandas)
("python-future" ,python-future)
("python-scipy" ,python-scipy)
("python-matplotlib" ,python-matplotlib)
("python-regex" ,python-regex)
("python-pysam" ,python-pysam)))
(native-inputs
`(("python-setuptools" ,python-setuptools)
("python-cython" ,python-cython)))
(home-page "https://github.com/CGATOxford/UMI-tools")
(synopsis "Tools for analyzing unique modular identifiers")
(description "This package provides tools for dealing with @dfn{Unique
Molecular Identifiers} (UMIs) and @dfn{Random Molecular Tags} (RMTs) in
genetic sequences. There are six tools: the @code{extract} and
@code{whitelist} commands are used to prepare a fastq containg UMIs @code{+/-}
cell barcodes for alignment. The remaining commands, @code{group},
@code{dedup}, and @{count}/@code{count_tab}, are used to identify PCR
duplicates using the UMIs and perform different levels of analysis depending
on the needs of the user.")
(license license:expat)))

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@ -54,6 +54,7 @@
#:use-module (guix build-system trivial) #:use-module (guix build-system trivial)
#:use-module (guix build-system go) #:use-module (guix build-system go)
#:use-module (gnu packages) #:use-module (gnu packages)
#:use-module (gnu packages admin)
#:use-module (gnu packages algebra) #:use-module (gnu packages algebra)
#:use-module (gnu packages apr) #:use-module (gnu packages apr)
#:use-module (gnu packages audio) #:use-module (gnu packages audio)
@ -94,6 +95,7 @@
#:use-module (gnu packages gstreamer) #:use-module (gnu packages gstreamer)
#:use-module (gnu packages gtk) #:use-module (gnu packages gtk)
#:use-module (gnu packages guile) #:use-module (gnu packages guile)
#:use-module (gnu packages haskell)
#:use-module (gnu packages image) #:use-module (gnu packages image)
#:use-module (gnu packages imagemagick) #:use-module (gnu packages imagemagick)
#:use-module (gnu packages java) #:use-module (gnu packages java)