diff options
| author | Roel Janssen <roel@gnu.org> | 2018-03-29 14:58:15 +0200 |
|---|---|---|
| committer | Leo Famulari <leo@famulari.name> | 2018-03-30 10:48:01 -0400 |
| commit | fdc306879b388b08be63ead6209473c184daa1e0 (patch) | |
| tree | a7e7e2e8f0fadaf0b49993d550416157af11c4a6 /gnu/packages/bioinformatics.scm | |
| parent | 183ce9884924794677eefca78cf445ada5551260 (diff) | |
gnu: Add delly.
* gnu/packages/bioinformatics.scm (delly): New variable.
* gnu/packages/patches/delly-use-system-libraries.patch: New file.
* gnu/local.mk: Include delly-use-system-libraries.patch.
Signed-off-by: Leo Famulari <leo@famulari.name>
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 47 |
1 files changed, 47 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index af515c026e..66d5bd3707 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2030,6 +2030,53 @@ normalized and standardized files, multiple visualizations can be created to identify enrichments with functional annotations of the genome.") (license license:gpl3+))) +(define-public delly + (package + (name "delly") + (version "0.7.7") + (source (origin + (method url-fetch) + (uri (string-append + "https://github.com/tobiasrausch/delly/archive/v" + version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "0dkwy3pyxmi6dhh1lpsr3698ri5sslw9qz67hfys0bz8dgrqwabj")) + (patches (search-patches "delly-use-system-libraries.patch")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ; There are no tests to run. + #:make-flags '("PARALLEL=1") ; Allow parallel execution at run-time. + #:phases + (modify-phases %standard-phases + (delete 'configure) ; There is no configure phase. + (replace 'install + (lambda _ + (let ((bin (string-append (assoc-ref %outputs "out") "/bin")) + (templates (string-append (assoc-ref %outputs "out") + "/share/delly/templates"))) + (mkdir-p bin) + (mkdir-p templates) + (copy-recursively "excludeTemplates" templates) + (install-file "src/cov" bin) + (install-file "src/delly" bin) + (install-file "src/dpe" bin))))))) + (native-inputs + `(("python" ,python-2))) + (inputs + `(("boost" ,boost) + ("htslib" ,htslib) + ("zlib" ,zlib) + ("bzip2" ,bzip2))) + (home-page "https://github.com/tobiasrausch/delly") + (synopsis "Integrated structural variant prediction method") + (description "Delly is an integrated structural variant prediction method +that can discover and genotype deletions, tandem duplications, inversions and +translocations at single-nucleotide resolution in short-read massively parallel +sequencing data. It uses paired-ends and split-reads to sensitively and +accurately delineate genomic rearrangements throughout the genome.") + (license license:gpl3+))) + (define-public diamond (package (name "diamond") |