diff options
| author | Ricardo Wurmus <rekado@elephly.net> | 2025-04-09 15:18:55 +0200 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2025-04-09 15:19:56 +0200 |
| commit | 32e9a1298b59cc4492d682bc963222db2f4e296e (patch) | |
| tree | bd6483ee976eea7cc3459ca76c00c574ad9a68f6 | |
| parent | 90357c6090de8c6befec232996dbc7415112a081 (diff) | |
| download | guix-32e9a1298b59cc4492d682bc963222db2f4e296e.tar.gz guix-32e9a1298b59cc4492d682bc963222db2f4e296e.zip | |
gnu: Add chromap.
* gnu/packages/bioinformatics.scm (chromap): New variable.
Change-Id: I3b477cf793591b5f9f4583cc47c09854bffd9f6d
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 41 |
1 files changed, 41 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 22bceb45d6..180f08ce14 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -21322,6 +21322,47 @@ on marker set compatibility, similarity in genomic characteristics, and proximity within a reference genome.") (license license:gpl3+))) +(define-public chromap + (package + (name "chromap") + (version "0.2.7") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/haowenz/chromap") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "099y3kac6npiqyx5prc9ggigw6248j7kchjznqvd9hxkq24rrsqs")))) + (build-system gnu-build-system) + (arguments + (list + #:tests? #false ;there are none + #:phases + #~(modify-phases %standard-phases + (delete 'configure) + (replace 'install + (lambda _ + (install-file "chromap" (string-append #$output "/bin"))))))) + (inputs (list zlib)) + (home-page "https://github.com/haowenz/chromap") + (synopsis "Fast alignment and preprocessing of chromatin profiles") + (description "Chromap is a fast method for aligning and preprocessing high +throughput chromatin profiles. Typical use cases include: + +@itemize +@item trimming sequencing adapters, mapping bulk ATAC-seq or ChIP-seq genomic + reads to the human genome and removing duplicates; +@item trimming sequencing adapters, mapping single cell ATAC-seq genomic reads + to the human genome, correcting barcodes, removing duplicates and performing + Tn5 shift; +@item split alignment of Hi-C reads against a reference genome. +@end itemize") + (supported-systems '("x86_64-linux")) ;requires CPU with SSE4.1 + (license license:expat))) + (define-public umi-tools (package (name "umi-tools") |