4.9 years ago by
You can obtain TMHMM and SignalP by submitting the "academic order form" from CBS/DTU
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.
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
# Note: TMHMM binary not distributed with InterProScan 5, please install separately e.g. in bin/tmhmm/2.0c/decodeanhmm
[...a bit further down...]
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