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| author | Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> | 2016-02-29 15:13:52 +0100 |
|---|---|---|
| committer | Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> | 2016-03-01 10:31:04 +0100 |
| commit | d29150b55d4c0dcc371949d90d74b54d58bae098 (patch) | |
| tree | c7401229cb6b32357bd1b25dc55c92f67ba03783 | |
| parent | b4464d384c7a7b500e611ec257cf092cdc47d977 (diff) | |
| download | patches-d29150b55d4c0dcc371949d90d74b54d58bae098.tar patches-d29150b55d4c0dcc371949d90d74b54d58bae098.tar.gz | |
gnu: Add bwa-pssm.
* gnu/packages/bioinformatics.scm (bwa-pssm): New variable.
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 30 |
1 files changed, 30 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 7b3838d36f..eef33dd42f 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -42,6 +42,7 @@ #:use-module (gnu packages cpio) #:use-module (gnu packages curl) #:use-module (gnu packages doxygen) + #:use-module (gnu packages datastructures) #:use-module (gnu packages file) #:use-module (gnu packages gawk) #:use-module (gnu packages gcc) @@ -774,6 +775,35 @@ and more accurate. BWA-MEM also has better performance than BWA-backtrack for 70-100bp Illumina reads.") (license license:gpl3+))) +(define-public bwa-pssm + (package (inherit bwa) + (name "bwa-pssm") + (version "0.5.11") + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/pkerpedjiev/bwa-pssm/" + "archive/" version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "02p7mpbs4mlxmn84g2x4ghak638vbj4lqix2ipx5g84pz9bhdavg")))) + (build-system gnu-build-system) + (inputs + `(("gdsl" ,gdsl) + ("zlib" ,zlib) + ("perl" ,perl))) + (home-page "http://bwa-pssm.binf.ku.dk/") + (synopsis "Burrows-Wheeler transform-based probabilistic short read mapper") + (description + "BWA-PSSM is a probabilistic short genomic sequence read aligner based on +the use of @dfn{position specific scoring matrices} (PSSM). Like many of the +existing aligners it is fast and sensitive. Unlike most other aligners, +however, it is also adaptible in the sense that one can direct the alignment +based on known biases within the data set. It is coded as a modification of +the original BWA alignment program and shares the genome index structure as +well as many of the command line options.") + (license license:gpl3+))) + (define-public python2-bx-python (package (name "python2-bx-python") |