From e1888bca8136a05438fcf33bc995531514e6cde0 Mon Sep 17 00:00:00 2001 From: Arun Isaac Date: Fri, 23 Feb 2024 21:28:22 +0000 Subject: gn: Add r-stitch. * gn/packages/bioinformatics.scm (r-stitch): New variable. --- gn/packages/bioinformatics.scm | 48 ++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 48 insertions(+) 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))) -- cgit v1.2.3