Change-Id: I8155083427bef2d4652e32e8b1f6a833bfd7c011
1 files changed, 58 insertions, 0 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index 3734a79..a404c7b 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -4973,3 +4973,61 @@ today's most advanced CPUs.")
(description "This package provides Python bindings for the
parasail C library.")
(license license:bsd-2)))
+
+(define-public liftoff
+ (package
+ (name "liftoff")
+ (version "1.6.3")
+ (source
+ ;; The PyPI tarball is missing the tests.
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/agshumate/Liftoff")
+ (commit version)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "18840vdv75nsq0fw5hzvrp7l0k6ciamlzkhgxxhnjh23ghih71dx"))))
+ (build-system pyproject-build-system)
+ (arguments
+ (list #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'unpack 'relax-version-requirements
+ (lambda _
+ (substitute* "setup.py"
+ (("==") ">=")))))))
+ (inputs
+ (list python-biopython
+ python-gffutils
+ python-interlap
+ python-networkx
+ python-numpy
+ python-parasail
+ python-pyfaidx
+ python-pysam
+ python-ujson))
+ (native-inputs
+ (list minimap2
+ python-pytest
+ python-setuptools
+ python-wheel))
+ (home-page "https://github.com/ashumate/Liftoff")
+ (synopsis "GFF3/GTF lift over pipeline")
+ (description "Liftoff is a tool that accurately maps annotations
+in GFF or GTF between assemblies of the same, or closely-related
+species. Unlike current coordinate lift-over tools which require a
+pre-generated “chain” file as input, Liftoff is a standalone tool that
+takes two genome assemblies and a reference annotation as input and
+outputs an annotation of the target genome. Liftoff uses minimap2 to
+align the gene sequences from a reference genome to the target genome.
+Rather than aligning whole genomes, aligning only the gene sequences
+allows genes to be lifted over even if there are many structural
+differences between the two genomes. For each gene, Liftoff finds the
+alignments of the exons that maximize sequence identity while
+preserving the transcript and gene structure. If two genes incorrectly
+map to overlapping loci, Liftoff determines which gene is most-likely
+mis-mapped, and attempts to re-map it. Liftoff can also find
+additional gene copies present in the target assembly that are not
+annotated in the reference.")
+ (license license:gpl3+)))
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