From b8c9f061e100949f081157eb4c9a7a2299ce9187 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 11 Nov 2021 13:53:59 +0000 Subject: gnu: Add bioparser. * gnu/packages/bioinformatics.scm (bioparser): New variable. --- gnu/packages/bioinformatics.scm | 36 ++++++++++++++++++++++++++++++++++++ 1 file changed, 36 insertions(+) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 8139ce43de..ae3cf01c87 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1354,6 +1354,42 @@ relying on a complex dependency tree.") used for storage and logging in bioinformatics tools.") (license license:expat))) +(define-public bioparser + (package + (name "bioparser") + (version "3.0.13") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/rvaser/bioparser") + ;; Corresponds to tag 3.0.13 + (commit "13341e6e0855c6b358ffcea6dad216e1009e1287"))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0c5p2dl8jb12ci9f427jzrmmm9cgvc1k4fxsn2ggkfsin6r1r82i")))) + (build-system cmake-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "./bin/bioparser_test"))))))) + (inputs + `(("biosoup" ,biosoup))) + (propagated-inputs + `(("zlib" ,zlib))) + (native-inputs + `(("googletest" ,googletest))) + (home-page "https://github.com/rvaser/bioparser") + (synopsis "C++ library for parsing several formats in bioinformatics") + (description "Bioparser is a C++ header only parsing library for several +bioinformatics formats (FASTA/Q, MHAP/PAF/SAM), with support for zlib +compressed files.") + (license license:expat))) + (define-public ciri-long (package (name "ciri-long") -- cgit v1.2.3