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authorNavid Afkhami <navid.afkhami@mdc-berlin.de>2023-01-26 17:37:18 +0100
committerRicardo Wurmus <rekado@elephly.net>2023-02-07 15:04:12 +0100
commitf55cc9cb0fb6c5dd56196009681e042c1aef415d (patch)
treeb5ed46a27b9f08766939bfc472edd738b6221339 /gnu
parent08751bcebb5dfd38d0deea9f096e8e97f6774441 (diff)
gnu: Add bitmapperbs.
* gnu/packages/bioinformatics.scm (bitmapperbs): New variable.
Diffstat (limited to 'gnu')
-rw-r--r--gnu/packages/bioinformatics.scm51
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")