# HG changeset patch
# User genouest
# Date 1707734295 0
# Node ID 3452c806c478b832de7f61d29966ef712c159d36
# Parent  96ad8f880755f09f97273d8136b0c0003be6972a
planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit 5bcf6a26284965f4fbf04be67ae7c186bb7e908f

diff -r 96ad8f880755 -r 3452c806c478 braker3.xml
--- a/braker3.xml	Wed Jan 31 06:49:47 2024 +0000
+++ b/braker3.xml	Mon Feb 12 10:38:15 2024 +0000
@@ -16,6 +16,10 @@
 
 export PATH="\$GENEMARK_PATH/../tools/:\$PATH" &&
 
+## Copy Augustus config dir to work dir, to make sure it's writable when running with containers
+cp -r "\$AUGUSTUS_CONFIG_PATH/" augustus_dir/ &&
+export AUGUSTUS_CONFIG_PATH=`pwd`/augustus_dir/ &&
+
 braker.pl
 --genome '${genome}'
 $softmasking
@@ -133,7 +137,7 @@
             <filter>output_format == 'gff3'</filter>
         </data>
     </outputs>
-    
+
     <tests>
         <test expect_failure="true">
             <param name="genome" value="genome_masked.fa"/>
@@ -183,7 +187,7 @@
             <output name="output_gff" file="out_genome/braker.gff3"/>
         </test> -->
 
-    
+
     <help><![CDATA[
 
 Braker3_ allows for fully automated training of the gene prediction tools GeneMark-EX and AUGUSTUS from RNA-Seq and/or protein homology information, and that integrates the extrinsic evidence from RNA-Seq and protein homology information into the prediction.
diff -r 96ad8f880755 -r 3452c806c478 macros.xml
--- a/macros.xml	Wed Jan 31 06:49:47 2024 +0000
+++ b/macros.xml	Mon Feb 12 10:38:15 2024 +0000
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <macros>
     <token name="@TOOL_VERSION@">3.0.7</token>
-    <token name="@VERSION_SUFFIX@">2</token>
+    <token name="@VERSION_SUFFIX@">3</token>
 
     <xml name="requirements">
         <requirement type="package" version="@TOOL_VERSION@">braker3</requirement>