How to install gap4/gap5 on linux server

[54016565]

Hi,
I download staden-2.0.0b9.x86_64, but when I try to run files in bin folder like "./gap4" mistake jump out - "no display name and no $DISPLAY environment variable". And I did not find any installation manual either. How can I install the gap4/gap5 on linux server without root privilege and run it by command line?

[jkbonfield]

Are you running X Windows? This error typically occurs when you don't have X windows running, or it is but you've connected to a remote unix server without tunneling X11 traffic. Try "xeyes" or something to test if X11 is working first.

If this is your own local system, then I'd expect it to be working fine. (Although it's still the case that ssh to localhost can remove X11 support.) Most systems have X11 forwarding enabled by default in ssh, but some vendors have different setups. If in doubt try "ssh -Y hostname" (or -X if -Y doesn't work).

As to installing it, you do not need root. Basically just untar the tarball wherever you like and then run the programs from the bin directory. The main GUI programs (gap4, gap5, trev, spin, pregap4) are little wrapper scripts that setup the environment for you and then relaunch themselves. If you want to run the various command line tools directly (eg makeSCF, init_exp, extract_seq, etc) then you'll need to set the STADENROOT environment variable and source $STADENROOT/share/staden/staden.profile.

Eg, for bash users, if you unpacked it in ~/opt

export STADENROOT=$HOME/opt/staden-2.0.0b9.x86_64
. $STADENROOT/share/staden/staden.profile

That will add $STADENROOT/bin to your path along with setting LD_LIBRARY_PATH, MANPATH and a few other variables.

There should be a nearly 700 page manual in $STADENROOT/share/doc/staden/manual.pdf, but I acknowledge the installation notes aren't clear so my apologies for that. I will update the README file in the home directory for future releases.

[archie.chauhan]

Hi 54016565,
I am having the same problem in finding how to install staden-2.0.0b9.x86_64 on my cluster.
@jkbonfield i tried the options mentioned by you but did not succeed. i am not a computer specialist but tried hard to fix the problem.
i did the following:
export STADENROOT=/data/achauah1/staden-2.0.0b9.x86_64/
followed by
. $STADENROOT/share/staden/staden.profile
it always comes up with this error:
-bash: /data/achauah1/staden-2.0.0b9.x86_64/share/staden/staden.profile: No such file or directory
I made staden.profile executable by using the following command:
chmod 777 staden.profile
but was useless the error was same. I am very much sure the directories are there.

@jkbonfield
since i am new to gap4, i would appreciate if you could write from scratch he steps/commands required to install/get staden running