3.5 years ago by
United States
Hi -
To let anyone else trying this know, the tool Convert delimiters to TAB executes on a different cluster than tools that require more resource (sequence mapping tools and such). This effectively means that it runs pretty quick once started and there shouldn't be much of a wait time, if this is your only job. If you have other jobs queued, those will run first. Most text/data manipulation tools are the same.
Another great alternative for manipulation operations is to set up your own local Galaxy server (the set-up is very simple for a basic install). Many of these simple manipulation tools are installed by default. Then you can add in anything else you want from the Tool Shed. Be aware that a tool will only execute successfully if the computer/server and associated cluster (if running in production mode) has the resources needed by the tools, tool options selected, and size of the inputs. The general rule is that if it will run line-command, it will run in Galaxy, given the same resources.
To get an idea of the resources any particular tool needs to execute, see that tool's source documentation. In general terms, the minimum system memory needed to run tools in Galaxy is 8 GB, but at least 16 GB for computationally intensive tools (and sometimes more). The available disk memory (size) required depends on the data sizes and can vary. For example, if you have a fastq dataset that is 30 GB (uncompressed), then at least that much free disk needs to available to the Galaxy instance just to load the file one time. In short, the same resource rules required by any stand-alone application running on your computer.
Hope this helps! Jen, Galaxy team
