diff --git a/files/galaxy/tpv/tools.yml b/files/galaxy/tpv/tools.yml
index dd5919bff..097ae1559 100644
--- a/files/galaxy/tpv/tools.yml
+++ b/files/galaxy/tpv/tools.yml
@@ -1072,6 +1072,9 @@ tools:
         - if: helpers.tool_version_eq(tool, '3.0.6+galaxy2')
           execute: |
             entity.params['singularity_container_id_override']="docker://teambraker/braker3:v1.0.6"
+          env:
+            GENEMARK_PATH: "/usr/local/tools/_conda/envs/__braker3@3.0.6/bin/genemark/bin/"
+            PROTHINT_PATH: "/usr/local/tools/_conda/envs/__braker3@3.0.6/bin/genemark/bin/gmes/ProtHint/bin/"
         - if: helpers.tool_version_eq(tool, '3.0.7+galaxy2')
           execute: |
             entity.params['singularity_container_id_override']="docker://teambraker/braker3:v3.0.7.1"