HowToInstall

How to install software

 

Perl programs written by you:

 

Probably these should go into /projects/sysbio/dev/perl/(some subdirectory). This is the lab-wide dev directory. Note that it is CVS controlled (more information about CVS), so you should also do cvs add (your file) and cvs commit once you add it.

 

Old instructions: This is the trickiest. Check these into $CVSROOT/perl/Tools somewhere, and make sure it is part of the path. You can edit your own $PATH variable, or edit $PATH in /projects/sysbio/etc/stuartlab-init.csh (but make sure you know what you're doing if you edit the latter, since it is lab-wide). Note: stuartlab-init.csh REALLY needs to be CVS-controlled! Someone should do that.

 

Shell Scripts written by you:

 

Check these into $CVSROOT/shell_scripts/ using CVS. Easy!

 

C / other compiled source (but NOT your own code):

 

When you run ./configure (before make, make install), run with ./configure --prefix=/projects/sysbio/apps/$MACHTYPE/ and everything will be installed system-wide. Otherwise it will only be installed to the particular computer you are working on.

 

Perl from the internet (but NOT your own code):

 

This goes into /projects/sysbio/apps/perl/ . You can copy it directly, there's no CVS involved.

 

Java programs from the internet (but NOT your own code):

 

These go into /projects/sysbio/apps/java/ . You can copy it directly, there's no CVS involved. Note that you may have to create a "something.runjar" script to run the Java jar file from the command line with the proper options. Check out the other examples in this directory to see how to do this.

 

R Packages (yours or others)

 

If you have either an unpacked directory or a tarball of the library, use the following command: R CMD INSTALL --library=/projects/sysbio/apps/$MACHTYPE/Rlib <dir_or_tarball>

 

How to use the lab CVS repositories