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 folm...@gmail.com 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 angsc...@outlook.com:
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
