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| author | Ricardo Wurmus <rekado@elephly.net> | 2019-04-26 14:57:29 +0200 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2019-04-26 21:00:37 +0200 |
| commit | 7f55904558e0f481d2f60ab52510c7e126c73fd0 (patch) | |
| tree | 2bdb13cac016db6585f966e504eaa806fe36da55 | |
| parent | 8caa458953eeac783c73a0e5aaa72842fe3914c9 (diff) | |
| download | patches-7f55904558e0f481d2f60ab52510c7e126c73fd0.tar patches-7f55904558e0f481d2f60ab52510c7e126c73fd0.tar.gz | |
gnu: Add umi-tools.
* gnu/packages/bioinformatics.scm (umi-tools): New variable.
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 35 | ||||
| -rw-r--r-- | gnu/packages/music.scm | 2 |
2 files changed, 37 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 4cf6900498..4891bb15af 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 29b448fc9a..aafe420d04 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) |