How To Run Tmhmm In Interproscan 5 Standalone Version

Question

[Xingyu Yang]

I'm try to use interproscan 5 standalone version follow the instruction below https://code.google.com/p/interproscan/wiki/HowToRun

I want to run SingnalP and TMHMM module with the annotation, but they are deactivated for license reason.

It say "These analyses use licensed code and data provided by third parties. If you wish to run these analyses it will be necessary for you to obtain a licence from the vendor and configure your local InterProScan 5 installation to use these"

What does it mean by "configure you local interProScan 5 installation"? The software I have(downloaded following this page https://code.google.com/p/interproscan/wiki/HowToDownload) is binary version, I don't even need to install them. How to configure my interproscan to run TMHMM?

Can anyone give me some detailed instruction on how to run TMHMM and SingnalP in interproscan?

Thanks!!!

[Michael]

Btw, if you get hold of SignalP could you give me feedback, I am still waiting for "shipment" after several attempts (received TMHMM just fine).

[David Westergaard]

When did you submit the form? There has been construction work over the weekend at CBS/DTU, so all non-critical servers have been shut down. If it's still a problem next week, try to contact either of the persons listed on the online submission site for SignalP (there should be two emails at the bottom of the site, one for scientific questions and one for technical.) If that does not help let me know, and I'll go poke them with a stick.

[Michael]

Thank you for your reply. I saw the servers were down temporarily from time to time today, I submitted requests on friday trying to start an InterproScan over the weekend, received TMHMM immediately, but not SignalP, I suspected a problem on my side first (max attachment size, SignalP is about 7Mb, but could rule that out), so tried several times using different addresses. No problem waiting a few days if I know it is going to work in the future in principle.

[Michael]

It worked, I have received a copy now.

Answer 1

[Michael]

You can obtain TMHMM and SignalP by submitting the "academic order form" from CBS/DTU

• http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?tmhmm
• http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?signalp

You need an academic email address, ".com" won't work, if you are lucky, the software will "ship" to your email address and you will receive a binary version of the software in an email with an attachment containing the binary. (Politely, one can call this process "suboptimal", it is the only application I know that ships this way). Then you can save and extract the binaries and configure the full path to the binary in interproscan.properties (in the home folder of interproscan), search for "TMHMM" and SignalP to find the lines where to set the paths. There is also a path to set for the TMHMM models, the models are contained in the tar-ball of TMHMM.

Run intersproscan without any options to see if they are enabled.

Run interproscan.sh -i test_proteins.fasta for a test of the tool configuration.

excerpt from the properties file:

# Note: SignalP binary not distributed with InterProScan 5, please install separately e.g. in bin/signalp/4.0/signalp
binary.signalp.4.0.path=/home/michaeld/bin/signalp
# Note: TMHMM binary not distributed with InterProScan 5, please install separately e.g. in bin/tmhmm/2.0c/decodeanhmm
binary.tmhmm.path=/home/michaeld/bin/decodeanhmm.Linux_x86_64
[...a bit further down...]
signalp.4.0.perl.library.dir=/home/michaeld/signalp-4.0/lib

Note that you have to configure the path to decodeanhmm not to the tmhmm wrapper script! It says signalp version 4.0 here, it should still work with 4.1 though.

# Note: TMHMM model files not distributed with InterProScan 5, please install separately e.g. in data/tmhmm/2.0/TMHMM2.0.model
tmhmm.model.path=data/tmhmm/2.0/TMHMM2.0.model # copied them into interproscan's data directory