open wsadmin shell
ksh ./wsadmin.sh -lang jython -conntype SOAP -host yourhost.com -port 8879 -user userid -password password
print AdminApp.update('MyAppName', 'file', '[-operation update -contents /home/users/sg/1.xml -contenturi MyEJB.jar/META-INF/ejb-jar.xml]')
where
NOTE that -contenturi is
MyEJB.jar/META-INF/ejb-jar.xml
NOT
MyEJB.jar,META-INF/ejb-jar.xml
if you put , instead of / you will get
com.ibm.websphere.management.exception.AdminException: ERROR: File does not exist for update operation
P.S always look in dmgr logs for errors in deployment.