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-rw-r--r--gn/packages/bioinformatics.scm48
1 files changed, 48 insertions, 0 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index 8141ada..b5fac4d 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -4571,3 +4571,51 @@ and VCF files.")
interface to the basic htslib. It can be easily included in a C++
program for scripting high-performance genomic analyses.")
(license license:asl2.0)))
+
+(define-public r-stitch
+ (package
+ (name "r-stitch")
+ (version "1.6.10")
+ (source
+ ;; The release tarball bundles dependencies. So, use git-fetch.
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/rwdavies/STITCH")
+ (commit version)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "0iy5fq2l5a35xdxqaf9ypj56da57qmwppwqmh9nflbvmbc7kgbkf"))))
+ (build-system r-build-system)
+ (arguments
+ (list
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'unpack 'chdir
+ (lambda _
+ (chdir "STITCH")))
+ (add-after 'chdir 'patch-build-system
+ (lambda _
+ (substitute* "src/Makevars"
+ (("\\$\\(SEQLIB_ROOT\\)/src/libseqlib.a") "-lseqlib")
+ (("\\$\\(SEQLIB_ROOT\\)/htslib/libhts.a") "-lhts")
+ ((": SeqLib") ":")))))))
+ (inputs
+ (list curl htslib seqlib zlib))
+ (native-inputs
+ (list autoconf automake vcfpp))
+ (propagated-inputs
+ (list r-data-table r-rrbgen
+ ;; FIXME: These should be inputs that are substituted into
+ ;; the source. But, for some reason, the reference scanner
+ ;; does not pick them up that way.
+ coreutils findutils htslib rsync))
+ (home-page "https://github.com/rwdavies/STITCH")
+ (synopsis "Sequencing to imputation through constructing haplotypes")
+ (description "@code{r-stitch} is an R program for reference panel free,
+read aware, low coverage sequencing genotype imputation. STITCH runs
+on a set of samples with sequencing reads in BAM format, as well as a
+list of positions to genotype, and outputs imputed genotypes in VCF
+format.")
+ (license license:gpl3)))