Question: Torrent Variant Caller (TVC) in local galaxy
0
gravatar for dganiewich
5 months ago by
dganiewich10
dganiewich10 wrote:

Hello everyone!

I have recently created a local galaxy instance, and I would like to run the Torrent Variant Caller (TVC) tool on it, which is part of the Torrent Suite.

I have not been able to find it in the main ToolShed. I have found it though on a public server (https://galaxy-public.curie.fr/) but doesn't seem to have its tools for use in local instances.

Does anyone know how to install TVC (or the whole Torrent Suite) on my local galaxy instance?

Thank you!

Daiana

ADD COMMENTlink modified 5 months ago • written 5 months ago by dganiewich10
1
gravatar for Jennifer Hillman Jackson
5 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

The underlying software is open source so there shouldn't be any licensing problems around that portion: https://github.com/iontorrent/TS/blob/master/LICENSE.txt. However, the Institut Curie public server does restrict usage -- only non-commercial use is allowed and may be why they are not publically sharing tools they have wrapped/developed.

I would suggest contacting the admins of that server and ask if they are willing to add their version (along with their TMAP, which is stated as an upstream dependency) to the ToolShed https://usegalaxy.org/toolshed. Wrapped tools do not necessarily need to be in the ToolShed, but they do need to be wrapped for Galaxy in order to install them in a local. I couldn't locate a public repository that contains a Galaxy wrapped version -- but you could ask them directly. Contact information is on their home page.

The final option is to wrap the tool or complete suite of tools yourself. The versions of TMAP in the ToolShed are several years old. There are two versions, and you could review and contact the original authors if you want to contribute/build on what they have rather than start completely over. Log into the ToolShed, search for the tools, and find the option to contact repository owners under the menu "Repository Actions". Or, you could reach out to the original tool authors and ask if they plan to wrap the tool for Galaxy.

I also asked the IUC team if they had plans to wrap these tools at Gitter, please follow and join in if you would like to: https://gitter.im/galaxy-iuc/iuc?at=5acd172bdf3e0fb547c2f463

Links:

Thanks, Jen, Galaxy team

ADD COMMENTlink written 5 months ago by Jennifer Hillman Jackson25k

Update:

With some help from the IUC team we found this: https://github.com/iontorrent/TS/tree/f2205b61dcf47b69fbef27ec7185a0a4de817106/Analysis/TMAP/scripts/galaxy

No one is sure if it works, but you could test it out, and there is some new discussion at the Gitter channel I linked to about updating/integrating that existing wrapper. Please feel free to join in.

ADD REPLYlink written 5 months ago by Jennifer Hillman Jackson25k
1

I believe it does work, I have installed it with no problem, although I haven't used it yet. So the problem is that the Ion Torrent's mapping tool (TMAP) does have the galaxy wrapper but its variant caller (TVC) does not...

ADD REPLYlink written 5 months ago by dganiewich10

Great that TMAP works, thanks for confirming that for others that may find this post. And correct - the other tools in the suite (including TVC) do not appear to be wrapped yet, or at least not publically, except for the version on the public server.

ADD REPLYlink written 5 months ago by Jennifer Hillman Jackson25k
0
gravatar for dganiewich
5 months ago by
dganiewich10
dganiewich10 wrote:

Hi Jen! Thank you for your prompt response and help! I've been following your conversation in gitter. Also, I have already contacted Institute Curie, still waiting for their answer, so I will let you know when I do.

TMAP wrapper is indeed working fine since it is just the wrapper what's in ToolShed, I could install the latest TMAP release, and wrap it with it (its independent of the TMAP version). I have already this working.

My problem is with TVC, which doesn't have that wrapper nor any available info on how to install it. Guess I will try on do the wrapping myself, although I am far from an expert on how to do this haha. Any help on this matter? Thank you very much! Daiana

ADD COMMENTlink written 5 months ago by dganiewich10
1

Yes, just TMAP is wrapped as far as I can tell. Use Planemo for development (link is above at end of the original post). And you can coordinate with the developers if you run into problems. Community contributions are always welcomed!

ADD REPLYlink written 5 months ago by Jennifer Hillman Jackson25k
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