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authorRicardo Wurmus <rekado@elephly.net>2019-04-26 14:57:29 +0200
committerRicardo Wurmus <rekado@elephly.net>2019-04-26 21:00:37 +0200
commit7f55904558e0f481d2f60ab52510c7e126c73fd0 (patch)
tree2bdb13cac016db6585f966e504eaa806fe36da55
parent8caa458953eeac783c73a0e5aaa72842fe3914c9 (diff)
downloadguix-7f55904558e0f481d2f60ab52510c7e126c73fd0.tar.gz
gnu: Add umi-tools.
* gnu/packages/bioinformatics.scm (umi-tools): New variable.
-rw-r--r--gnu/packages/bioinformatics.scm35
-rw-r--r--gnu/packages/music.scm2
2 files changed, 37 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 4cf690049..4891bb15a 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -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
proximity within a reference genome.")
(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)))
diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm
index 29b448fc9..aafe420d0 100644
--- a/gnu/packages/music.scm
+++ b/gnu/packages/music.scm
@@ -54,6 +54,7 @@
#:use-module (guix build-system trivial)
#:use-module (guix build-system go)
#:use-module (gnu packages)
+ #:use-module (gnu packages admin)
#:use-module (gnu packages algebra)
#:use-module (gnu packages apr)
#:use-module (gnu packages audio)
@@ -94,6 +95,7 @@
#:use-module (gnu packages gstreamer)
#:use-module (gnu packages gtk)
#:use-module (gnu packages guile)
+ #:use-module (gnu packages haskell)
#:use-module (gnu packages image)
#:use-module (gnu packages imagemagick)
#:use-module (gnu packages java)