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01/13: gnu: Add bitmapperbs.
From: |
guix-commits |
Subject: |
01/13: gnu: Add bitmapperbs. |
Date: |
Tue, 7 Feb 2023 14:06:28 -0500 (EST) |
rekado pushed a commit to branch master
in repository guix.
commit 532dace22d2f1312a53ca91efffdee72e4f3a737
Author: Navid Afkhami <navid.afkhami@mdc-berlin.de>
AuthorDate: Tue Feb 7 16:08:49 2023 +0100
gnu: Add bitmapperbs.
* gnu/packages/bioinformatics.scm (bitmapperbs): New variable.
Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
---
gnu/packages/bioinformatics.scm | 57 +++++++++++++++++++++++++++++++++++++++++
1 file changed, 57 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index ef1e7ae988..055c8ca47b 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -512,6 +512,63 @@ 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)))
+ ;; This package bundles a modified copy of htslib, so we cannot
+ ;; unbundle it.
+ (snippet
+ '(begin
+ (delete-file-recursively "libdivsufsort-2.0.1")
+ (delete-file-recursively "pSAscan-0.1.0")))))
+ (build-system gnu-build-system)
+ (arguments
+ (list
+ #:tests? #false
+ #:make-flags '(list "bitmapperBS")
+ ;; The build system checks for CPU features. For this reason, we want
+ ;; users to build it locally instead of using substitutes.
+ #:substitutable? #false
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'unpack 'fix-build-system
+ (lambda _
+ (substitute* "Makefile"
+ (("make prefix=../htslib_aim install")
+ (string-append "make prefix=" #$output " install-so"))
+ (("htslib_aim/include") "htslib")
+ (("htslib_aim/lib")
+ (string-append #$output "/lib")))))
+ (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)
+ (replace 'install
+ (lambda _
+ (install-file "bitmapperBS"
+ (string-append #$output "/bin/")))))))
+ (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
+whole-genome bisulfite sequencing (WGBS) reads from directional protocol.")
+ (license license:asl2.0)))
+
(define-public cellsnp-lite
;; Last release is from November 2021 and does not contain fixes.
(let ((commit "0885d746b0b1ea65c8ef92f8943ca7669ca9734a")
- branch master updated (31b707cf5d -> 09c6de4412), guix-commits, 2023/02/07
- 04/13: gnu: bristol: Use JACK 2., guix-commits, 2023/02/07
- 05/13: gnu: jack-select: Drop input labels., guix-commits, 2023/02/07
- 01/13: gnu: Add bitmapperbs.,
guix-commits <=
- 03/13: gnu: bristol: Pass -fcommon., guix-commits, 2023/02/07
- 06/13: gnu: jack-keyboard: Use JACK 2., guix-commits, 2023/02/07
- 09/13: gnu: milkytracker: Drop input labels., guix-commits, 2023/02/07
- 02/13: gnu: bristol: Remove trailing #T., guix-commits, 2023/02/07
- 07/13: gnu: jack-capture: Use JACK 2., guix-commits, 2023/02/07
- 12/13: gnu: milkytracker: Use JACK 2., guix-commits, 2023/02/07
- 08/13: gnu: seq24: Use JACK 2., guix-commits, 2023/02/07
- 10/13: gnu: milkytracker: Drop trailing #T from snippet., guix-commits, 2023/02/07
- 11/13: gnu: milkytracker: Reformat description., guix-commits, 2023/02/07
- 13/13: gnu: rtmidi: Use JACK 2., guix-commits, 2023/02/07