diff options
| -rw-r--r-- | gn/packages/bioinformatics.scm | 81 |
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))) |