diff options
author | Ricardo Wurmus <rekado@elephly.net> | 2023-02-07 15:36:21 +0100 |
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committer | Ricardo Wurmus <rekado@elephly.net> | 2023-02-07 15:36:21 +0100 |
commit | a083a9b512b695f5a5c7bca7d5a19dda97bd33b9 (patch) | |
tree | 91933e49a8b4fdd5bb12968933211ced770efc7f /gnu | |
parent | 9a0f840b383839bd3d02b7328cf4396783f2fd90 (diff) |
Revert "gnu: Add bitmapperbs."
This reverts commit f55cc9cb0fb6c5dd56196009681e042c1aef415d.
This commit was prematurely pushed.
Diffstat (limited to 'gnu')
-rw-r--r-- | gnu/packages/bioinformatics.scm | 51 |
1 files changed, 0 insertions, 51 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 782dd6bdd8..ef1e7ae988 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -512,57 +512,6 @@ 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") |