I am seeing a problem where the tools FreeBayes and BamLeftAlign (under the NGS: Variant Analysis group) appear/disappear from the the left-hand tool panel when usegalaxy.org is refreshed. That is, upon refreshing the usegalaxy.org page FreeBayes and BamLeftAlign are missing from the tool panel when previously they were present. A few minutes later, refreshing will cause FreeBayes and BamLeftAlign to reappear. And so on and so forth.
I am fairly certain this is a server-side (not client-side) issue. I have replicated this issue on Firefox and Chrome. Moreover, when loading a personal workflow that uses FreeBayes during a "down" period, Galaxy fails to load the FreeBayes step properly and returns the error "Unrecognized Tool: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/0.4". (Tools other than FreeBayes and BamLeftAlign may also be affected; these two are the only ones I noticed).
Is this a known issue? Is the disappearance of the FreeBayes and BamLeftAlign tool due to the fact that they fall under the NGS Toolbox Beta umbrella?