diff options
| author | Efraim Flashner | 2019-09-02 09:29:10 -0500 |
|---|---|---|
| committer | Efraim Flashner | 2019-09-02 09:40:12 -0500 |
| commit | 77456aa56b3199ad076f3fa3de7bc1115dd0ae00 (patch) | |
| tree | 41efcac34cf2e051954a33b3685da53cc89e5b37 /gn | |
| parent | fc7de7d90e780f6e9ac3154460dbc8fdeea873e4 (diff) | |
| download | guix-bioinformatics-77456aa56b3199ad076f3fa3de7bc1115dd0ae00.tar.gz | |
gn: Add sniffles.
* gn/packages/bioinformatics.scm (sniffles): New variable.
Diffstat (limited to 'gn')
| -rw-r--r-- | gn/packages/bioinformatics.scm | 41 |
1 files changed, 41 insertions, 0 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index a219025..8b9bef3 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -7,6 +7,7 @@ #:use-module (guix download) #:use-module (guix git-download) #:use-module (guix build-system ant) + #:use-module (guix build-system cmake) #:use-module (guix build-system gnu) #:use-module (gnu packages) #:use-module (gnu packages bioinformatics) @@ -487,3 +488,43 @@ reads.") (files '("/etc/ssl/certs/ca-certificates.crt"))))) ;; Due to the precompiled binaries we download: (supported-systems '("x86_64-linux")))) + +;; TODO: Unbundle zlib, bamtools, tclap +(define-public sniffles + (package + (name "sniffles") + (version "1.0.11") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/fritzsedlazeck/Sniffles.git") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0rkwqn1ycckfzrg2wdid4cqahq8q2jmmgi7vvl8qxgpsihqfbq0j")))) + (build-system cmake-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + (install-file (string-append "../source/bin/sniffles-core-" + ,version "/sniffles") + (string-append out "/bin"))) + #t)) + (replace 'check + (lambda _ + (with-directory-excursion "../source/test_set" + (for-each make-file-writable (find-files ".")) + (invoke (string-append "../bin/sniffles-core-" ,version "/sniffles") + "-m" "reads_region.bam" "-v" "test.vcf"))))))) + (native-inputs + `(("zlib" ,zlib))) + (home-page "https://github.com/fritzsedlazeck/Sniffles") + (synopsis "Structural variation caller using third generation sequencing") + (description + "Sniffles is a structural variation caller using third generation sequencing +(PacBio or Oxford Nanopore). It detects all types of SVs (10bp+) using evidence +from split-read alignments, high-mismatch regions, and coverage analysis.") + (license license:expat))) |