From 204c51cac44809dc352c86bb33332fc75e2b0056 Mon Sep 17 00:00:00 2001
From: Navid Afkhami <navid.afkhami@mdc-berlin.de>
Date: Tue, 14 Mar 2023 15:01:29 +0000
Subject: gnu: Add r-premessa.

* gnu/packages/bioinformatics.scm (r-premessa): New variable.

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>.
---
 gnu/packages/bioinformatics.scm | 56 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 56 insertions(+)

(limited to 'gnu')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 4de546e1f8..a9c62ab8b1 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -8940,6 +8940,62 @@ target genes, Pando simultaneously infers gene modules and sets of regulatory
 regions for each transcription factor.")
     (license license:expat)))
 
+(define-public r-premessa
+  (let ((commit "68b42bb984637d0f3ad6a0ecc83e9278994afc85")
+        (revision "1"))
+    (package
+      (name "r-premessa")
+      (version (git-version "0.3.4" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/ParkerICI/premessa")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "1l0q431zk0lvg22130nx84gdqi7cpl05yah4am63lbx6m4c769pb"))
+                (snippet
+                 '(delete-file "inst/normalizer_shinyGUI/www/d3.min.js"))))
+      (properties `((upstream-name . "premessa")))
+      (build-system r-build-system)
+      (arguments
+       (list
+        #:phases
+        '(modify-phases %standard-phases
+           (add-after 'unpack 'process-javascript
+             (lambda* (#:key inputs #:allow-other-keys)
+               (with-directory-excursion "inst/normalizer_shinyGUI/www/"
+                 (invoke "esbuild" (assoc-ref inputs "d3.v4.js")
+                         "--minify" "--outfile=d3.min.js")))))))
+      (propagated-inputs
+       (list r-data-table
+             r-flowcore
+             r-ggplot2
+             r-gridextra
+             r-hexbin
+             r-jsonlite
+             r-reshape
+             r-rhandsontable
+             r-shiny
+             r-shinyjqui))
+      (native-inputs
+       `(("esbuild" ,esbuild)
+         ("d3.v4.js"
+          ,(origin
+             (method url-fetch)
+             (uri "https://d3js.org/d3.v4.js")
+             (sha256
+              (base32
+               "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))))
+      (home-page "https://github.com/ParkerICI/premessa")
+      (synopsis "Pre-processing of flow and mass cytometry data")
+      (description
+       "This is an R package for pre-processing of flow and mass cytometry
+data.  This package includes panel editing or renaming for FCS files,
+bead-based normalization and debarcoding.")
+      (license license:gpl3))))
+
 (define-public r-presto
   (let ((commit "052085db9c88aa70a28d11cc58ebc807999bf0ad")
         (revision "0"))
-- 
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