On 09/10/2012 17:37, Susana Sanchez Exposito wrote: > Hi all, Hello
> I have a doubt about the shell environment used by taverna: when > Taverna runs an external tool (orange box), Does it take into account > the .bashrc? Probably not. The rules about what login scripts are run when you do an ssh (which is what the tool service does) are complicated. See http://www.linuxquestions.org/questions/linux-software-2/bashrc-doesnt-execute-on-ssh-login-329009/ > In my .bashrc I set some specific variables in order to use a specific > version of python and other things, but it seems Taverna does not take > into account this. > > Can you say something about how Taverna runs in a terminal the external tools? It uses an ssh connection (which is where the issue is). The parameters to the call of the service are used to create the actual command to be run. It can also upload some files. The actual command is then run over the ssh connection. The results are then downloaded (or kept on the remote machine and a remote reference used). One possible solution is to add "source BLAH/.bashrc" where BLAH is your home directory to the script. Alternatively, you can change or create other bash login scripts such as your .bash_profile. > Thanks in advance, > Susana. Alan ------------------------------------------------------------------------------ Don't let slow site performance ruin your business. Deploy New Relic APM Deploy New Relic app performance management and know exactly what is happening inside your Ruby, Python, PHP, Java, and .NET app Try New Relic at no cost today and get our sweet Data Nerd shirt too! http://p.sf.net/sfu/newrelic-dev2dev _______________________________________________ taverna-users mailing list [email protected] [email protected] Web site: http://www.taverna.org.uk Mailing lists: http://www.taverna.org.uk/about/contact-us/
