Re: [galaxy-user] Can't seem to stop or restart the Galaxy in server

I have had it happen occasionally, but didn't pay attention to the details. Perhaps I forget to put --reload sometimes. Also, it seems that sometimes the Galaxy processes do not all stop with --stop-daemon. I wrote the text below as a recipe for people in my lab to restart in those situation

Re: [galaxy-user] More help neeeded

Hello Kshama, I went into your account and examined your data. Starting with "Saved Histories", the default view is all active histories in the center panel. In your case right now, none of these have hidden or deleted datasets. Next, I clicked on "Advanced Search" in this same view in the m

Re: [galaxy-user] Can't seem to stop or restart the Galaxy in server

On Oct 18, 2012, at 1:43 AM, Todd Oakley wrote: > Yes, daemon/stop-daemon is the best way. However, to stop a process that was > not started with --daemon, this is what I do: > > ps aux | grep galaxy > > Identify the process numbers for 3 Galaxy processes, which will change every > time Gala

Re: [galaxy-user] using our own reference genome ?

Hello Didier, A custom reference genome can be used with the RNA-seq tools. In short, you load a fasta file (your custom reference genome) using FTP to the public Galaxy server, then select it for use with the tools (genome "from the history"). Help is in our wiki: http://wiki.g2.bx.psu.edu/S

[galaxy-user] More help neeeded

Hello , I tried everything possible according to the reply I got from Jen , helping me fix my problem but is not working.Please see below . Is it possible that because the usage shows 91% I am not able to retrieve anything back to display? Might sound ridiculous but have no clue !! I still have no

Re: [galaxy-user] Data table named 'bowtie2_indexes' is required by tool but not configured

Thanks but after adding those lines when I stop and started the server using --daemon mode, the server is not working? What might be the problem? On Fri, Oct 19, 2012 at 9:01 AM, Jeremy Goecks wrote: > You'll need to update the tool_data_table_conf.xml file in your Galaxy > home directory. > > If

Re: [galaxy-user] Data table named 'bowtie2_indexes' is required by tool but not configured

You'll need to update the tool_data_table_conf.xml file in your Galaxy home directory. If you haven't made changes to the file, you can copy tool_data_table_conf.xml.sample to tool_data_table_conf.xml If you have made changes, add these entries to the file: -- value, dbkey, name, path