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author | Navid Afkhami <navid.afkhami@mdc-berlin.de> | 2023-01-26 17:37:18 +0100 |
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committer | Ricardo Wurmus <rekado@elephly.net> | 2023-02-07 15:04:12 +0100 |
commit | f55cc9cb0fb6c5dd56196009681e042c1aef415d (patch) | |
tree | b5ed46a27b9f08766939bfc472edd738b6221339 /gnu/packages/bioinformatics.scm | |
parent | 08751bcebb5dfd38d0deea9f096e8e97f6774441 (diff) | |
download | guix-f55cc9cb0fb6c5dd56196009681e042c1aef415d.tar.gz guix-f55cc9cb0fb6c5dd56196009681e042c1aef415d.zip |
gnu: Add bitmapperbs.
* gnu/packages/bioinformatics.scm (bitmapperbs): New variable.
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
-rw-r--r-- | gnu/packages/bioinformatics.scm | 51 |
1 files changed, 51 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index ef1e7ae988..782dd6bdd8 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -512,6 +512,57 @@ BED, GFF/GTF, VCF.") (inputs (list samtools zlib)))) +(define-public bitmapperbs + (package + (name "bitmapperbs") + (version "1.0.2.3") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/chhylp123/BitMapperBS/") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "02ksssfnvmpskld0a2016smfz5nrzm3d90v8974f3cpzywckvp8v")) + (modules '((guix build utils))) + (snippet '(begin + (delete-file-recursively "libdivsufsort-2.0.1") + (delete-file-recursively "pSAscan-0.1.0"))))) + ;;this package bundles a modified copy of htslib, so we cannot unbundle it + (build-system gnu-build-system) + (arguments + (list + #:tests? #false + #:make-flags '(list "bitmapperBS") + #:phases + #~(modify-phases %standard-phases + (replace 'install + (lambda _ + (install-file "bitmapperBS" + (string-append #$output "/bin/")))) + #;(add-after 'unpack 'fix-build-system + (lambda _ + (substitute* "Makefile" + (("-Wl,-rpath=htslib_aim/lib") "") + #;(("^HTSLIB_INFO.*") "")))) + (add-after 'unpack 'patch-references-to-psascan + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "Makefile" + (("\"(./)?psascan" pre all) + (string-append "\"" pre (search-input-file inputs "/bin/psascan")))))) + (delete 'configure)))) + (inputs + (list libdivsufsort + psascan + zlib)) + (home-page "https://github.com/chhylp123/BitMapperBS/") + (synopsis "read aligner for whole-genome bisulfite sequencing") + (description + "BitMapperBS is memory-efficient aligner that +is designed for WGBS reads from directional protocol.") + (license license:gpl3+))) + (define-public cellsnp-lite ;; Last release is from November 2021 and does not contain fixes. (let ((commit "0885d746b0b1ea65c8ef92f8943ca7669ca9734a") |