Hi all, Folmer's advice is exactly right. However, just for the curious I'd like to point out a way to run CCP4 programs without having to explicitly source a setup script. For example (and for demonstration purposes, ignoring the fact that $CCP4 is only defined when the environment is sourced) you may directly run a command like
$CCP4/share/python/CCP4Dispatchers/bin/refmac5 What happens here is that a Python dispatcher script is first started. This sets the environment just prior to running the job as a subprocess, to which it passes the command line and stdin. We developed this system a little while back as an approach to avoid exporting the heavyweight environment that CCP4 required. In practice, since then we have cleaned the environment up so much that it is hardly a worry any more. The dispatchers may still be of interest though for people who think it is barbaric to set anything else other than PATH, or for people who regularly swap between different versions of CCP4. There is a side effect of creating the CCP4Dispatchers package that is in fact much more interesting than avoiding explicit environment set up. That is there is now a Python interface for running CCP4 programs that comes free with the suite. This makes development of simple scripts and pipelines very easy in Python. Please see the documentation for details ( http://www.ccp4.ac.uk/html/CCP4Dispatchers.html). Cheers -- David On 16 November 2014 08:43, Folmer Fredslund <[email protected]> wrote: > Dear Peter, > > Put your source command in your ".bashrc" file. > > It's a hidden file (because of the dot in the start) in your home folder > and will be run every time you open a terminal, so any command inside > will be executed. > > You can edit the file by typing > gedit .bashrc > Just after opening a terminal. > > If you just started using Linux and you're interested in an introduction > to how Linux works, I'd recommend the Linux Foundations free online course > > https://www.edx.org/course/linuxfoundationx/linuxfoundationx-lfs101x-2-introduction-5386 > > Especially if you are not working in a lab were people can help you with > questions like the one you just asked. > > Venlig hilsen/Best regards > Folmer Fredslund > Den 16/11/2014 07.34 skrev "陈昂" <[email protected]>: > > Dear all: >> >> I have installed CCP4 suit on my computer. The OS IS fedora 18. Every >> time I open the software, I have to >> >> use the command source. Does anyone else can run it in terminal without >> that command? >> >> Thank u so much! >> >> best regards, >> >> Peter >> >
