Question: Running TopHat locally
1
Suzanne Gomes • 120 wrote:
Hi,
I'm trying to run Tophat2 on a local instance of galaxy. Tophat2 and Bowtie 2 have been installed from the toolshed. I'm using a custom genome, which has been uploaded to the history. I've also uploaded the read files into the history (using the data library function - and we tried both just linking to the files, and copying the data into galaxy.) When I run Tophat2, it just immediately changes to complete, and all the resulting files are empty.
Any ideas on what may be going wrong? Are we missing some necessary tool?
Thanks
Suzanne
No error is displayed? Bowtie2 is working?
The job completes (i.e. they turn green), so there's no actual error message. But it said something about 'TopHat2 not found' in the details of the run. I'm not sure why, because it says TopHat2 is installed.
So, for anyone else trying to install a local galaxy instance: apparently installing tools from the toolshed is not sufficient - they actually need to be separately installed on your computer in addition to being added from the toolshed. Basically, it seems that installing from the toolshed just makes the tool available on your galaxy interface, and allows the galaxy interface to then go ask your computer to run the tool for you.
That's not always true - it depends on the specific tool repository. Some specify all dependencies and how to install them automatically. Some don't, yet. The goal for the main toolshed is that eventually, all tools there should automagically install all the specific versions of the required dependencies too. Some existing popular tools (eg FastQC) are totally automatic. Others are not yet. In general the devteam or iuc owned tools should be automatic and not rely on external system dependencies. If they don't, that's probably a bug.
I asked the guy who installed the tools for me, and this is what he said:
- I used the default Tool Shed (the one listed by Martin)
- I did select install dependencies
- I set tool_dependency_dir = dep_dir
- I did not see an error message during the installation.
From an admin view please open 'Manage installed tool shed repositories' and click on tophat2. The site you will see should look like this:
https://www.dropbox.com/s/89raoqteer1b17r/Screenshot%202014-07-16%2016.14.03.png
Does it look the same?
Unfortunately, looks like we can't check this out. Apparently galaxy has been uninstalled from the computer on which we were having this problem. We actually ended up getting it working on a computer with biolinux installed as the sole OS, as opposed to the original computer where we were running it as biolinux on a linux OS. Not sure if that might have had something to do with it?
It might have. Well, I am glad it works now. Good luck!