From 9098a88f3dc68ca90fa2f8e952c2dc7497dca863 Mon Sep 17 00:00:00 2001 From: John Chilton Date: Tue, 14 Jan 2014 16:02:11 -0600 Subject: [PATCH] Fix R env handling in fabric_util broken with 864f8f4. Thanks BjoernGruening. --- lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py b/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py index 5a0ae9eca40..21fc7e4535e 100755 --- a/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py @@ -409,7 +409,7 @@ def install_and_build_package( app, tool_dependency, actions_dict ): with lcd( current_dir ): with settings( warn_only=True ): for tarball_name in tarball_names: - cmd = '''PATH=$PATH:$R_HOME/bin; export PATH; R_LIBS=$INSTALL_DIR; export R_LIBS; && + cmd = '''PATH=$PATH:$R_HOME/bin; export PATH; R_LIBS=$INSTALL_DIR; export R_LIBS; Rscript -e "install.packages(c('%s'),lib='$INSTALL_DIR', repos=NULL, dependencies=FALSE)"''' % ( str( tarball_name ) ) cmd = install_environment.build_command( td_common_util.evaluate_template( cmd, install_dir ) ) return_code = handle_command( app, tool_dependency, install_dir, cmd )