From e31d46f821048cbde3ab1cefb09cc9d734123d82 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 11 Sep 2019 04:09:08 -0500 Subject: gnu: Add bamaddrg. * gn/packages/bioinformatics.scm (bamaddrg): New variable. --- gn/packages/bioinformatics.scm | 49 ++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 49 insertions(+) (limited to 'gn/packages') diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index ad4db7b..a28ceb8 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -609,3 +609,52 @@ variants. Unlike existing methods, SVIM integrates information from across the genome to precisely distinguish similar events, such as tandem and interspersed duplications and novel element insertions.") (license license:gpl3))) + +(define-public bamaddrg + (let ((commit "3fccbf057eef21f6304fade6c306c5bb64158865") ; May 26, 2012 + (revision "1")) + (package + (name "bamaddrg") + (version (git-version "0.0.0" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/ekg/bamaddrg.git") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "14hq66cc7f4cssagb6079fmd2i6hfr9vmpcw5vi5kzsqr3ifc5yk")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ; no tests + #:phases + (modify-phases %standard-phases + (delete 'configure) + ;; The Makefile wants to vendor bamtools' source so we mimic it. + (replace 'build + (lambda* (#:key inputs #:allow-other-keys) + (let ((bam (assoc-ref inputs "bamtools"))) + (apply invoke + `("g++" "-O3" + ,(string-append "-I" bam "/include/bamtools") + ,(string-append "-L" bam "/lib/libbamtools.a") + "bamaddrg.cpp" "-o" "bamaddrg" "-lbamtools" "-lz"))) + #t)) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) + (install-file "bamaddrg" bin) + #t)))))) + (native-inputs + `(("bamtools" ,bamtools))) + (inputs + `(("zlib" ,zlib))) + (home-page "https://github.com/ekg/bamaddrg") + (synopsis "Adds read groups to input BAM files, streams BAM output on stdout") + (description + "This is intended for use \"fixing up\" RG tags on the fly so that they +reflect the source file from which the aligment originated from. This allows +the \"safe\" merging of many files from many individuals into one stream, +suitable for input into downstream processing systems such as freebayes ( +population variant detector).") + (license #f)))) ; no license listed -- cgit v1.2.3