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| author | Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> | 2019-05-14 16:13:26 +0200 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2019-05-14 16:15:19 +0200 |
| commit | 44323e63a34f31144b3af9cad900005745d47e87 (patch) | |
| tree | 56eeb365001bc9adf4423043f572034556ee0d10 | |
| parent | 46ca002d1c22dc3570f6e28e20ca024aed1365f7 (diff) | |
gnu: Add ataqv.
* gnu/packages/bioinformatics.scm (ataqv): New variable.
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 42 |
1 files changed, 42 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index ce720f46ed..93418bf705 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -57,6 +57,7 @@ #:use-module (gnu packages bioconductor) #:use-module (gnu packages boost) #:use-module (gnu packages check) + #:use-module (gnu packages code) #:use-module (gnu packages compression) #:use-module (gnu packages cpio) #:use-module (gnu packages cran) @@ -14788,3 +14789,44 @@ cell barcodes for alignment. The remaining commands, @code{group}, duplicates using the UMIs and perform different levels of analysis depending on the needs of the user.") (license license:expat))) + +(define-public ataqv + (package + (name "ataqv") + (version "1.0.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/ParkerLab/ataqv.git") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "031xr6jx1aprh26y5b1lv3gzrlmzg4alfl73vvshymx8cq8asrqi")))) + (build-system gnu-build-system) + (arguments + `(#:make-flags + (list (string-append "prefix=" (assoc-ref %outputs "out")) + (string-append "BOOST_ROOT=" + (assoc-ref %build-inputs "boost")) + (string-append "HTSLIB_ROOT=" + (assoc-ref %build-inputs "htslib"))) + #:test-target "test" + #:phases + (modify-phases %standard-phases + (delete 'configure)))) + (inputs + `(("boost" ,boost) + ("htslib" ,htslib) + ("ncurses" ,ncurses) + ("zlib" ,zlib))) + (native-inputs + `(("lcov" ,lcov))) + (home-page "https://github.com/ParkerLab/ataqv") + (synopsis "Toolkit for quality control and visualization of ATAC-seq data") + (description "This package provides a toolkit for measuring and comparing +ATAC-seq results. It was written to make it easier to spot differences that +might be caused by ATAC-seq library prep or sequencing. The main program, +@code{ataqv}, examines aligned reads and reports some basic metrics.") + (license license:gpl3+))) |