FileStructure

/projects/sysbio filesystem

 

If you're perplexed by trying to figure out where files are in our /projects/sysbio section of the filesystem, here is a maybe-helpful organizational chart.

 

alexgw/ Alex's files.

 

apps/ Applications (executables) for the whole lab.

  • i386/ Programs that run on all the Intel (x86) machines. Install new i386 software here.
  • java/ Java programs
  • groovy/ Groovy interpreter.
    • lib/ Java libraries (yours or 3rd parties) to be globally accessible from Groovy. 
  • man/ Manpages. It's unclear if this actually works.
  • perl/ Some perl programs, but not the main repository of Josh's scripts.
  • src/ Source code for certain programs and libraries. Sometimes needed to compile other things.
  • windows/ Programs for running in Windows.
  • x86_64/ Programs that only run on x86_64 (64-bit) machines. Type "arch" to see if your computer is x86_64. These will not run on 386 or 686 machines. Install new x86_64 software here.

 

bin@ This is a symlink to apps

.

 

cchen/ Chad Chen's files.

 

cluegene/ The ClueGene project.

 

conodera/ Courtney Onodera's files. Did a rotation in Josh's lab, now works for David Haussler.

 

cpowell/ Corey Powell's files. Graduated in 2005.

 

cvaske/ Charlie Vaske's files.

 

cvsroot/ A different cvsroot than the normal one we use. I don't know if any files here are actively updated.

  • Our main CVSROOT is located in /projects/compbio3/cvsroot/stuartlab . So don't use the one here unless you really know what you're doing.

 

dev/

  • perl/ System-wide copy of perl scripts from the repository at /projects/compbio3/cvsroot/stuartlab . Do not edit these files directly--edit your own checked-out copy. Note that if you update a script here, it might still be overridden by your local repository. (That is, you may have also checked out a copy of /projects/compbio3/cvsroot/stuartlab into a different location.) If you want to update the dev/ repository to the latest version run the command: cd /projects/sysbio/dev/ ; cvs up ; cd -

 

dmng/ David Ng's files.

 

etc/

  • stuartlab-init.csh In your own .cshrc file, you should "source" this file. It contains all the lab-wide settings for environment variables that everyone uses (like $MAPDIR). This is the file to use if you use csh, tcsh, or a similar program (not bash). Type echo $SHELL to figure out which shell you are using.
  • stuartlab-init.sh In your own bash init file, you should "source" this file. It's like the .csh file above, but it's for bash and sh. It will not work with csh or tcsh. Type echo $SHELL to figure out which shell you are using.

 

jstuart/ Josh Stuart's files.

 

 

lib/ Files for inclusion.

  • cpp/ C++ files that you can include
  • perl5/ Perl files. Note that this is NOT the main repository of Josh's scripts. (That is in /projects/compbio3/cvsroot/stuartlab/perl)
  • x86_64/

 

lmlui/ Lauren Lui's files. Summer student, 2004 (I think).

 

man/ Manpages? It is unclear if this works.

 

map/ Project files

 

marcosw/ Marcos's files.

 

martina/ Martina's files.

 

msgr/ Multi-species gene recommender files.

 

pinal/ Pinal's files.

 

share/ A few odd files.

 

system-is-now-apps A reminder that the "system" folder is no more--it is "apps" now.

 

tmp/ A sysbio temporary items folder. Items subject to deletion without notice.

 

weirauch/ Matt Weirauch's files.

 

www/

  • htdocs/ Project web pages (not the wiki).