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authorEfraim Flashner2019-09-03 02:22:28 -0500
committerEfraim Flashner2019-09-03 02:22:28 -0500
commit53045359b18e247789d90ed00d78c26aa989c389 (patch)
treecca18ea2adebd61330bd8d54d9068d7c1bfd66a6 /gn
parent77456aa56b3199ad076f3fa3de7bc1115dd0ae00 (diff)
downloadguix-bioinformatics-53045359b18e247789d90ed00d78c26aa989c389.tar.gz
gn: Add ngmlr, svim.
* gn/packages/bioinformatics.scm (ngmlr, svim): New variables.
Diffstat (limited to 'gn')
-rw-r--r--gn/packages/bioinformatics.scm81
1 files changed, 81 insertions, 0 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index 8b9bef3..ad4db7b 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -9,6 +9,7 @@
#:use-module (guix build-system ant)
#:use-module (guix build-system cmake)
#:use-module (guix build-system gnu)
+ #:use-module (guix build-system python)
#:use-module (gnu packages)
#:use-module (gnu packages bioinformatics)
#:use-module (gnu packages boost)
@@ -18,6 +19,7 @@
#:use-module (gnu packages maths)
#:use-module (gnu packages perl)
#:use-module (gnu packages python)
+ #:use-module (gnu packages python-xyz)
#:use-module (gnu packages statistics))
(define-public contra
@@ -528,3 +530,82 @@ reads.")
(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)))
+
+;; TODO: Unbundle Complete-Striped-Smith-Waterman-Library
+(define-public ngmlr
+ (package
+ (name "ngmlr")
+ (version "0.2.7")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/philres/ngmlr.git")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "0lmsy8w0kxbyfnrln7lxgmnx3d82sv2b20n2yw5742rvfhq1v31n"))))
+ (build-system cmake-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-after 'patch-source-shebangs 'patch-more-tools
+ (lambda* (#:key inputs #:allow-other-keys)
+ (let ((bed (assoc-ref inputs "bedtools"))
+ (sam (assoc-ref inputs "samtools")))
+ (substitute* (find-files "test" "\\.sh$")
+ (("bedtools") (string-append bed "/bin/bedtools"))
+ (("samtools") (string-append sam "/bin/samtools")))
+ #t)))
+ (replace 'check
+ (lambda _
+ (with-directory-excursion "../source"
+ (invoke "sh" "test/test_travis.sh")))))))
+ (native-inputs
+ `(("bedtools" ,bedtools)
+ ("samtools" ,samtools)))
+ (inputs
+ `(("zlib" ,zlib)))
+ (home-page "https://github.com/philres/ngmlr")
+ (synopsis "Long-read mapper designed to align PacBio or Oxford Nanopore")
+ (description
+ "NGMLR is a long-read mapper designed to align PacBio or Oxford Nanopore
+(standard and ultra-long) to a reference genome with a focus on reads that span
+structural variations.")
+ (license license:expat)))
+
+(define-public svim
+ (package
+ (name "svim")
+ (version "1.2.0")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/eldariont/svim.git")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "08j02in9jbq41b67dna1apnc3y30i37v44d1khml1xlx0iga720s"))))
+ (build-system python-build-system)
+ (arguments
+ '(#:phases
+ (modify-phases %standard-phases
+ (replace 'check
+ (lambda _
+ (invoke "python3" "-m" "unittest" "discover" "-s" "src/"))))))
+ (propagated-inputs
+ `(("python-matplotlib" ,python-matplotlib)
+ ("python-numpy" ,python-numpy)
+ ("python-pysam" ,python-pysam)
+ ("python-scipy" ,python-scipy)
+ ("minimap2" ,minimap2)
+ ("ngmlr" ,ngmlr)
+ ("samtools" ,samtools)))
+ (home-page "https://github.com/eldariont/svim")
+ (synopsis "Structural Variant Identification Method using Long Reads")
+ (description
+ "SVIM (pronounced SWIM) is a structural variant caller for long reads. It
+is able to detect, classify and genotype five different classes of structural
+variants. Unlike existing methods, SVIM integrates information from across the
+genome to precisely distinguish similar events, such as tandem and interspersed
+duplications and novel element insertions.")
+ (license license:gpl3)))