Thanks Alan, But there is something strange:
I run this command in Taverna using a external tool: echo $SHELL;source /home/susana/.bashrc;echo $PATH; which python The result in STDOUT outport is: /bin/bash /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games /usr/bin/python The second and third line correspond to the values of $PATH and the route to python, and I see the environment is not set properly. The result in STDERR output is: /bin/sh: source: not found It seems Taverna uses the basic shell instead of the Bourne shell, but this does not fit in with the value got in $SHELL (/bin/bash) Susana. 2012/10/9 Alan R Williams <[email protected]>: > 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/ -- Susana Sánchez Expósito Instituto de Astrofísica de Andalucía IAA (CSIC) Camino Bajo de Huétor, 50. Granada E-18008 Tel:(+34) 958 121 311 / (+34) 958 230 618 Fax:(+34) 958 814 530 e-mail: [email protected] ------------------------------------------------------------------------------ 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/
