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authorEfraim Flashner2019-09-02 09:29:10 -0500
committerEfraim Flashner2019-09-02 09:40:12 -0500
commit77456aa56b3199ad076f3fa3de7bc1115dd0ae00 (patch)
tree41efcac34cf2e051954a33b3685da53cc89e5b37 /gn/packages
parentfc7de7d90e780f6e9ac3154460dbc8fdeea873e4 (diff)
downloadguix-bioinformatics-77456aa56b3199ad076f3fa3de7bc1115dd0ae00.tar.gz
gn: Add sniffles.
* gn/packages/bioinformatics.scm (sniffles): New variable.
Diffstat (limited to 'gn/packages')
-rw-r--r--gn/packages/bioinformatics.scm41
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)))