diff options
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 57 |
1 files changed, 57 insertions, 0 deletions
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") |