[bug#65689] [PATCH 1/2] gnu: Add r-strawr.

[bug#65689] [PATCH 1/2] gnu: Add r-strawr.

[Navid Afkhami]

* gnu/packages/cran.scm (r-strawr): New variable.
---
 gnu/packages/cran.scm | 22 ++++++++++++++++++++++
 1 file changed, 22 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 4ec6b802ff..adf2d4c32a 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -8287,6 +8287,28 @@ (define-public r-statsexpressions
 for ggstatsplot.")
     (license license:gpl3)))
 
+(define-public r-strawr
+  (package
+    (name "r-strawr")
+    (version "0.0.91")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "strawr" version))
+              (sha256
+               (base32
+                "1nbcn20g3f3f5x9sscj3020n5h4iaphr70s90n2fz31vc4snzq2m"))))
+    (properties `((upstream-name . "strawr")))
+    (build-system r-build-system)
+    (inputs (list curl openssh openssl zlib))
+    (propagated-inputs (list r-rcpp))
+    (home-page "https://github.com/aidenlab/straw/tree/master/R")
+    (synopsis "Fast Implementation of Reading/Dump for .hic Files")
+    (description
+     "API for efficient .hic file data extraction with programmatic matrix access.
+It doesn't store the pointer data for all the matrices, only theone
+queried, and currently we are only supporting matrices.")
+    (license license:expat)))
+
 (define-public r-stringdist
   (package
     (name "r-stringdist")

base-commit: 7309da3ba64a191f074807275d8c5661a25c035c
prerequisite-patch-id: 70b98dde8ca4056fb8bd1b731716853ac2c9f0a1
-- 
2.34.1

[bug#65688] [PATCH 2/2] gnu: Add r-trackviewer.

[Navid Afkhami]

* gnu/packages/bioconductor.scm (r-trackviewer): New variable.
---
 gnu/packages/bioconductor.scm | 42 +++++++++++++++++++++++++++++++++++
 1 file changed, 42 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 88592c4f71..0070d7777c 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -9931,6 +9931,48 @@ (define-public r-tkwidgets
      "This package implements widgets to provide user interfaces.")
     (license license:artistic2.0)))
 
+(define-public r-trackviewer
+  (package
+    (name "r-trackviewer")
+    (version "1.36.2")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "trackViewer" version))
+              (sha256
+               (base32
+                "1ngfpd308y8i3vgv07cggk2azs64lsyyc9zfi3pz0gapr33ha6a1"))))
+    (properties `((upstream-name . "trackViewer")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-annotationdbi
+                             r-biocgenerics
+                             r-genomeinfodb
+                             r-genomicalignments
+                             r-genomicfeatures
+                             r-genomicranges
+                             r-graph
+                             r-grimport
+                             r-gviz
+                             r-htmlwidgets
+                             r-interactionset
+                             r-iranges
+                             r-plotrix
+                             r-rgraphviz
+                             r-rhdf5
+                             r-rsamtools
+                             r-rtracklayer
+                             r-s4vectors
+                             r-scales
+                             r-strawr))
+    (native-inputs (list esbuild r-knitr))
+    (home-page "https://bioconductor.org/packages/trackViewer")
+    (synopsis "Web interface for interactive multi-omics data analysis")
+    (description
+     "TrackViewer offers multi-omics analysis with web based  tracks and lollipops.
+Visualize mapped reads along with annotation as track layers for NGS dataset
+such as @code{ChIP-seq,} RNA-seq, @code{miRNA-seq,} DNA-seq, SNPs and
+methylation data.")
+    (license license:gpl2+)))
+
 (define-public r-transcriptr
   (package
     (name "r-transcriptr")
-- 
2.34.1

bug#65689: [PATCH 1/2] gnu: Add r-strawr.

[Ricardo Wurmus]

Applied with minor changes.  Thank you!

-- 
Ricardo

bug#65688: [PATCH 2/2] gnu: Add r-trackviewer.

[Ricardo Wurmus]

Thanks for the patch!

This one needed a little more work.  The “esbuild” in the native inputs
was added by the importer because the package includes minified
JavaScript files.

Luckily it’s just one file and we can replace it easily.  I’ve made the
necessary changes and pushed it with commit
8c0c94bf9f70a9252cd6f4261d2bce6bdba2bd0b to the “master” branch.

-- 
Ricardo