diff --git a/tools/ruvseq/ruvseq.xml b/tools/ruvseq/ruvseq.xml
index 1adf171d0c0..75eae9c9471 100644
--- a/tools/ruvseq/ruvseq.xml
+++ b/tools/ruvseq/ruvseq.xml
@@ -4,16 +4,16 @@
         <xref type="bio.tools">ruvseq</xref>
     </xrefs>
     <macros>
-        <token name="@TOOL_VERSION@">1.34.0</token>
+        <token name="@TOOL_VERSION@">1.36.0</token>
         <token name="@WRAPPER_VERSION@">0</token>
     </macros>
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">bioconductor-ruvseq</requirement>
-        <requirement type="package" version="1.40.2">bioconductor-deseq2</requirement>
-        <requirement type="package" version="1.28.0">bioconductor-tximport</requirement>
-        <requirement type="package" version="1.52.1">bioconductor-genomicfeatures</requirement>
-        <requirement type="package" version="0.9.3">r-ggrepel</requirement>
-        <requirement type="package" version="1.20.3">r-getopt</requirement>
+        <requirement type="package" version="1.42.0">bioconductor-deseq2</requirement>
+        <requirement type="package" version="1.30.0">bioconductor-tximport</requirement>
+        <requirement type="package" version="1.54.1">bioconductor-genomicfeatures</requirement>
+        <requirement type="package" version="0.9.4">r-ggrepel</requirement>
+        <requirement type="package" version="1.20.4">r-getopt</requirement>
         <requirement type="package" version="1.4.4">r-reshape2</requirement>
     </requirements>
     <stdio>