[bug#54856] [PATCH] gnu: Add r-xcir.

[bug#54856] [PATCH] gnu: Add r-xcir.

[Mădălin Ionel Patrașcu]

* gnu/packages/bioconductor.scm (r-xcir): New variable.
---
 gnu/packages/bioconductor.scm | 37 ++++++++++++++++++++++++++++++++++-
 1 file changed, 36 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index ce1e23f0bf..d78fcdce32 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -7,7 +7,7 @@
 ;;; Copyright © 2017, 2018, 2019, 2020, 2021 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2019, 2020, 2021, 2022 Simon Tournier <zimon.toutoune@gmail.com>
 ;;; Copyright © 2020 Peter Lo <peterloleungyau@gmail.com>
-;;; Copyright © 2020, 2021 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
+;;; Copyright © 2020, 2021, 2022 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
 ;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net>
 ;;; Copyright © 2021 Hong Li <hli@mdc-berlin.de>
 ;;; Copyright © 2021 Tim Howes <timhowes@lavabit.com>
@@ -5100,6 +5100,41 @@ (define-public r-vsn
 and specific in detecting differential transcription.")
     (license license:artistic2.0)))
 
+;; This package doesn't have a release yet.
+(define-public r-xcir
+  (let ((commit "4e51efe9980056e7fe274224da0173fcfaf2edd7") (revision "1"))
+    (package
+      (name "r-xcir")
+      (version (git-version "1.7.2" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/SRenan/XCIR")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "0pb2fnpwlimw2p43ygy56pwj90h1l7yz2npqm3ypzp3bgld9b8n5"))))
+      (properties `((upstream-name . "XCIR")))
+      (build-system r-build-system)
+      (propagated-inputs (list r-biomart
+                               r-biostrings
+                               r-data-table
+                               r-ggplot2
+                               r-iranges
+                               r-readxl
+                               r-s4vectors
+                               r-seqminer
+                               r-variantannotation))
+      (native-inputs (list r-knitr))
+      (home-page "https://github.com/SRenan/XCIR")
+      (synopsis "Analysis of X chromosome inactivation")
+      (description
+       "This package @code{XCIR} is a R package that offers models and tools
+for subject level analysis of X chromosome inactivation (XCI) and XCI-escape
+inference.")
+      (license license:gpl2))))
+
 (define-public r-xina
   (package
     (name "r-xina")
-- 
2.34.0

bug#54856: [PATCH] gnu: Add r-xcir.

[Ricardo Wurmus]

Thanks for the patch!

I changed this a little: it’s better to fetch the code from the official
Bioconductor git repository.  I took the latest commit from the
RELEASE_3_14 branch.  This corresponded to version 1.8.0.

I also changed the description a little.

-- 
Ricardo