FAQ

Table of Contents

• Set python3 as default
• Error with SignalP
• Error with COILS2
• More

Set python3 as default

[For Ubuntu only] As Python2 will soon not being supported anymore, we should move to Python3. To make Python3 as default Python for your system, just add this line at the beginning of your ~/.bashrc (or ~/.bash_profile) file

alias python=python3

Together with Python3, pip3 should also be set as default to replace pip

sudo update-alternatives --install /usr/bin/pip pip /usr/bin/pip3 1

Error with SignalP

If you encounter this error message after running setupFAS

vinh@vinh-desktop:~$ setupFAS -t /home/vinh/annotation_tools
Annotation tools will be installed in
/home/vinh/annotation_tools
----------------------------------
Do you want to use TMHMM (v2.0c) and SignalP (v4.1g)? (y/n)
y
Please download TMHMM 2.0c and SignalP 4.1g at https://services.healthtech.dtu.dk/ and enter path to the downloaded tar files:/home/vinh/dtu_tools
----------------------------------
...
...
...
Checking if annotation tools are excutable...
Error with SignalP. You can reinstall it by running setupFAS with --force!

You can check if you have this line in the /path/to/your/annotation_tools/SignalP/signalp file:

$ENV{SIGNALP} = '/usr/opt/www/pub/CBS/services/SignalP-4.1/signalp-4.1';

If so, you should replace it with

$ENV{SIGNALP} = "/path/to/your/annotation_fas/SignalP";

and rerun setupFAS with option --checkExecutable

setupFAS -t /home/vinh/annotation_tools --checkExecutable

Error with COILS2

In case you have issue with COILS2 while doing FAS setup, please check if the COILSDIR variable can be found in /path/to/your/FAS/annotation_tools/fas.profile, (or ~/.bashrc, ~/.bash_profile for FAS older than v1.14) file? This should point to the path of the installed COILS2 within the FAS annotation tool directory, e.g. export COILSDIR=/home/vinh/annotation_fas/COILS2/coils. If not, you can manually put that into the corresponding file (see how to set COILSDIR variable). If it is there, you should source the file (source /path/to/your/FAS/annotation_tools/fas.profile or source ~/.bashrc) and rerun setupFAS with the option --checkExecutable

setupFAS -t /path/to/your/FAS/annotation_tools --checkExecutable

More

If you have any more questions, please open an issue on GitHub or get in touch via email.