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| -rw-r--r-- | gnu/packages/bioinformatics.scm | 50 |
1 files changed, 50 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index ece59e982e..94d15cc4c0 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -11009,6 +11009,56 @@ and many lower level support classes. ;; license header. (license (list license:gpl2+ license:gpl3+)))) +(define-public biobambam2 + (package + (name "biobambam2") + (version "2.0.182") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://gitlab.com/german.tischler/biobambam2") + (commit (string-append version "-release-20210412001032")))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0b7w7a2a7hpkgrdn0n7hy4pilzrj82zqrh7q4bg1l0cd6bqr60m5")))) + (build-system gnu-build-system) + (arguments + ;; The test suite attempts to execute ../test-driver, which does not exist. + `(#:tests? #false + #:configure-flags + (list (string-append "--with-libmaus2=" + (assoc-ref %build-inputs "libmaus2"))))) + (inputs + `(("libmaus2" ,libmaus2) + ("xerces-c" ,xerces-c))) + (native-inputs + `(("gcc" ,gcc-10) ;Code has C++17 requirements + ("pkg-config" ,pkg-config))) + (home-page "https://gitlab.com/german.tischler/biobambam2") + (synopsis "Tools for processing BAM files") + (description "This package contains some tools for processing BAM files +including: + +@itemize +@item bamsormadup: parallel sorting and duplicate marking +@item bamcollate2: reads BAM and writes BAM reordered such that alignment or + collated by query name +@item bammarkduplicates: reads BAM and writes BAM with duplicate alignments + marked using the BAM flags field +@item bammaskflags: reads BAM and writes BAM while masking (removing) bits + from the flags column +@item bamrecompress: reads BAM and writes BAM with a defined compression + setting. This tool is capable of multi-threading. +@item bamsort: reads BAM and writes BAM resorted by coordinates or query name +@item bamtofastq: reads BAM and writes FastQ; output can be collated or + uncollated by query name. +@end itemize +") + ;; The COPYING file states that the code is distributed under version 3 of + ;; the GPL, but the license headers include the "or later" clause. + (license license:gpl3+))) + (define-public r-circus (package (name "r-circus") |