From 3338a28e1ef035372c3a134cb91fe64815446ca1 Mon Sep 17 00:00:00 2001 From: Anthony Bretaudeau Date: Fri, 4 Oct 2019 15:16:09 +0200 Subject: [PATCH] fix command not found --- galaxy/startup.sh | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/galaxy/startup.sh b/galaxy/startup.sh index d6a7dfff3..9ebeb2787 100755 --- a/galaxy/startup.sh +++ b/galaxy/startup.sh @@ -425,7 +425,7 @@ if [[ ! -z $GALAXY_DEFAULT_ADMIN_USER ]] if [ -x /export/post-start-actions.sh ] then # uses ephemeris, present in docker-galaxy-stable, to wait for the local instance - galaxy-wait -g http://127.0.0.1 -v --timeout 120 > $GALAXY_LOGS_DIR/post-start-actions.log && + /tool_deps/_conda/bin/galaxy-wait -g http://127.0.0.1 -v --timeout 120 > $GALAXY_LOGS_DIR/post-start-actions.log && /export/post-start-actions.sh >> $GALAXY_LOGS_DIR/post-start-actions.log & fi fi @@ -433,13 +433,13 @@ fi # Reinstall tools if the user want to if [[ ! -z $GALAXY_AUTO_UPDATE_TOOLS ]] then - galaxy-wait -g http://127.0.0.1 -v --timeout 120 > /home/galaxy/logs/post-start-actions.log && + /tool_deps/_conda/bin/galaxy-wait -g http://127.0.0.1 -v --timeout 120 > /home/galaxy/logs/post-start-actions.log && OLDIFS=$IFS IFS=',' for TOOL_YML in `echo "$GALAXY_AUTO_UPDATE_TOOLS"` do echo "Installing tools from $TOOL_YML" - shed-tools install -g "http://127.0.0.1" -a "$GALAXY_DEFAULT_ADMIN_KEY" -t "$TOOL_YML" + /tool_deps/_conda/bin/shed-tools install -g "http://127.0.0.1" -a "$GALAXY_DEFAULT_ADMIN_KEY" -t "$TOOL_YML" /tool_deps/_conda/bin/conda clean --tarballs --yes done IFS=$OLDIFS