I was looking at various flavors of Galaxy on public servers, and came across a few that have Trinity installed. In what I noted of both instances, you are forced to select 'Paired' or 'Single', and for each, only one file can be utilized. I actually have both paired AND single, and I have two files for each. Can I set up Trinity for myself and use both data types, for multiple files each?
Thanks!
M
Hi,
I don't have a recent version of Trinity but the Galaxy wrapper I have for version r2013_08_14, roughly one year old.
https://github.com/vipints/oqtans/blob/master/oqtans_tools/Trinity/r2013_08_14/galaxy/trinity.xml
Please let me know if you have any issue to set up. Also you can access the same version of Trinity here https://galaxy.cbio.mskcc.org/tool_runner?tool_id=trinity on our public instance.
Hope that helps, Vipin
My issue with the version on your website is that it allows for only one file for merged OR one of each pair, unmerged. I have multiple files for both data types that I intend to put into the alignment. Do you know if the Trinity wrapper will allow for this? Also, how do I select for number of cores and RAM when setting up? I'm thinking I'll need at least 32 cores and 250 GB RAM, per the Pittsburgh Supercomputing website for Trinity usage.
Thanks! M
From: vipin on Galaxy Biostar [notifications@biostars.org] Sent: Tuesday, August 05, 2014 4:07 PM To: mjmv Subject: [galaxy-biostar] A: Trinity on Galaxy
Activity on a post you are following on Galaxy Biostar<http: biostar.usegalaxy.org="">
User vipin<http: biostar.usegalaxy.org="" u="" 2812=""/> wrote Answer: Trinity on Galaxy<http: biostar.usegalaxy.org="" p="" 8530="" #8541="">:
Hi,
I don't have a recent version of Trinity but the Galaxy wrapper I have for version r2013_08_14, roughly one year old.
https://github.com/vipints/oqtans/blob/master/oqtans_tools/Trinity/r2013_08_14/galaxy/trinity.xml
Please let me know if you have any issue to set up. Also you can access the same version of Trinity here https://galaxy.cbio.mskcc.org/tool_runner?tool_id=trinity on our public instance.
Hope that helps, Vipin
I believe you have different chunks of input read files and you need to generate the single alignment/assembly file, is that right? On our public instance we are only providing 50G and by default it will use 2 cores. Of course you can adjust these parameters when you set up and local instance of trinity using the wrapper script which I provided in my oqtans package.
Add an option field in XML file (below the file and line number) with the amount of RAM, something like <option value="250G">250G</option>
CPU number you can specify in the input box and which will set minimum 1 and by default it will be using 2 cores.
Here is the line: https://github.com/vipints/oqtans/blob/master/oqtans_tools/Trinity/r2013_08_14/galaxy/trinity.xml#L49
Do let me know if you still have any issues to set up.
Do you know if the source of the wrapper is available somewhere? If so, I can guide you through the process of enhancing the wrapper.
There is only one file for Trinity that I have seen on your toolshed, and I am not really sure what a 'wrapper' is, but figure it makes Trinity work with Galaxy. This has to be available somewhere, though I am not sure where. Also, this instance of Galaxy has an updated version, as compared to what is in the toolshed:
https://galaxy.cbio.mskcc.org/
Thanks, M
Ha! I know one of these guys. I will ask him to update the wrappers and point him to your question!