I have 40 fastq RNA-seq libraries uploaded in the galaxy mirror at UNC, however the tophat and cufflinks version in that server has not been updated for a while and I will like to use the main server at PSU. Do I have to upload the 40 files one by one again in the main galaxy or there any less painful way to share files and histories between different Galaxies?

Here are some suggestions for moving many files between Galaxy instances: (a) use the history export function to compress a history into an archive file; this is likely to take a while and the resulting archive may be very large; (b) find the 'download' URL for each dataset and paste those URLs into the upload form's box one after the other; this will upload multiple datasets at once.

In addition, today I have been all day trying to connect with the main galaxy server (https://main.g2.bx.psu.edu/) and either do not responde or if the site is loaded then every time I try to submit a task it stop to respond

The server is very busy right now, and we're working to improve its performance. Please let us know if you continue to have problems over the next week or so. Good luck, J.