diff options
Diffstat (limited to 'gnu')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 35 |
1 files changed, 35 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 6f835b3875..f3e0e41e4d 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -15570,6 +15570,41 @@ manipulation of hierarchical features (e.g., genes, transcripts, and exons) than is possible with plain-text methods alone.") (license license:expat)))) +(define-public indelfixer + (package + (name "indelfixer") + (version "1.1") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/cbg-ethz/InDelFixer/") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "10ak05x8i1bx2p7rriv2rglqg1wr7c8wrhjrqlq1wm7ka99w8i79")))) + (build-system ant-build-system) + (arguments + `(#:jar-name "InDelFixer.jar" + #:source-dir "src/main/java" + #:test-dir "src/test")) + (inputs + `(("java-commons-lang2" ,java-commons-lang) + ("java-args4j" ,java-args4j))) + (native-inputs + `(("java-junit" ,java-junit))) + (home-page "https://github.com/cbg-ethz/InDelFixer/") + (synopsis "Iterative and sensitive NGS sequence aligner") + (description "InDelFixer is a sensitive aligner for 454, Illumina and +PacBio data, employing a full Smith-Waterman alignment against a reference. +This Java command line application aligns Next-Generation Sequencing (NGS) and +third-generation reads to a set of reference sequences, by a prior fast k-mer +matching and removes indels, causing frame shifts. In addition, only a +specific region can be considered. An iterative refinement of the alignment +can be performed, by alignment against the consensus sequence with wobbles. +The output is in SAM format.") + (license license:gpl3+))) + (define-public libsbml (package (name "libsbml") |