Subject: [PATCH] gnu: Add r-rphyloxml.
From: "Afkhami, Navid" <[email-masked]>
To: <[email-masked]>
Cc: "Afkhami, Navid" <[email-masked]>
Date: Mon, 10 Jun 2024 15:41:37 +0000
List-Id: <debbugs-submit.debbugs.gnu.org>

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

Change-Id: I5b799986064f2af5fe74454f2e78fea7d9947260
---
 gnu/packages/bioinformatics.scm | 43 +++++++++++++++++++++++++++++++++
 1 file changed, 43 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index cecd94bbb7..3282258b48 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -14096,6 +14096,49 @@ (define-public sambamba
 sort, markdup, and depth.")
     (license license:gpl2+)))
 
+(define-public r-rphyloxml
+  (let ((commit "a30e39249239b2de01d6964ae2a2205a6c48b475")
+        (revision "1"))
+    (package
+      (name "r-rphyloxml")
+      (version (git-version "0.0-9000" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/USCbiostats/rphyloxml")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "15ijzqvjxx6vqyqlg5asdbqlhw1g0ix6palf1rism3si0qapddgw"))))
+      (properties `((upstream-name . "rphyloxml")))
+      (build-system r-build-system)
+      (arguments
+       (list
+        #:modules '((guix build r-build-system)
+                    (guix build minify-build-system)
+                    (guix build utils)
+                    (ice-9 match))
+        #:imported-modules `(,@%r-build-system-modules (guix build
+                                                        minify-build-system))
+        #:phases '(modify-phases %standard-phases
+                    (add-after 'unpack 'process-javascript
+                      (lambda* (#:key inputs #:allow-other-keys)
+                        (with-directory-excursion "inst/"
+                          (for-each (match-lambda
+                                      ((source . target) (minify source
+                                                                 #:target
+                                                                 target)))
+                                    '())))))))
+      (propagated-inputs (list r-ape r-xml2))
+      (native-inputs (list esbuild))
+      (home-page "https://github.com/USCbiostats/rphyloxml")
+      (synopsis "Read and write phyloXML files in R")
+      (description
+       "The package reads phylogenetic data in the @code{phyloXML} format.
+It also includes functions for writing data in this format.")
+      (license license:expat))))
+
 (define-public ritornello
   (package
     (name "ritornello")

base-commit: 2b2337f275a6421a0d0964c54987df4ac74162e6
-- 
2.34.1