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What all different ways available to deploy any custom solution in moss. Which is the best practice to follow while deploying solution?

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Best way is to deploy solution is to make a WSP file that will have all required components in it.

You can deploy it using STSADM statements.

You can also manually copy files to 12 hive folder but ITS NOT RECOMMENDED AT ALL. There are few tools there you can use for deployment as well. For manual you need to copy files to all WFEs.

What I particullary do for moss is to create a solution file add it using STSADM and then deploy it using Central Admin.

Best Practice

Best Practice for Moss is to use STSADM statements to deploy solution files as sometimes Central Admin (UI) times out and if you have multiple WFEs then solution won't going to be installed on all of them.

Useful Links

Manual Deployment

Creating a Solution Package in Windows SharePoint Services 3.0

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