1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/b6138d0f8a75/ Changeset: b6138d0f8a75 User: davebgx Date: 2014-03-03 21:35:26 Summary: Update setup_r_environment to work with the elimination of fabric. Affected #: 1 file
diff -r 957e0c7548626c2532af6fd00387ec1568b7dce0 -r b6138d0f8a753cfcc76881d18c0e4cac6298a921 lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py @@ -296,7 +296,7 @@ retain control over the process. This method is named "complex" because it uses queues and threads to execute a command while capturing and displaying the output. """ - wrapped_command = shlex.split( "/bin/sh -c '%s'" % str( command ) ) + wrapped_command = shlex.split( '/bin/sh -c "%s"' % str( command ) ) # Launch the command as subprocess. A bufsize of 1 means line buffered. process_handle = subprocess.Popen( wrapped_command, stdout=subprocess.PIPE, @@ -607,7 +607,7 @@ with settings( warn_only=True ): for tarball_name in tarball_names: cmd = '''PATH=$PATH:$R_HOME/bin; export PATH; R_LIBS=$INSTALL_DIR; export R_LIBS; - Rscript -e "install.packages(c('%s'),lib='$INSTALL_DIR', repos=NULL, dependencies=FALSE)"''' % ( str( tarball_name ) ) + 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 ) if return_code:
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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