[Pipet Devel] Re: LOCI documentation

J.W. Bizzaro bizzaro at bc.edu
Sat Oct 9 20:44:19 EDT 1999

Gary Van Domselaar wrote:
> Great news!  I  have just completed the new web pages for TOL/Loci and
> the DocBook documentation is a perfect fit-- I had planned on using
> docbook to document loci as well-- lets get the documentation source
> onto the cvs tree so we can work on it together!

The module is already on the CVS, and it's called 'loci-doc'.  Below is a copy
of the instructions for using CVS at TOL.  Anyone with a shell account can
access and modify it.

> BTW I think I will
> begin putting up the new pages onto the bioinformatics.org today.  Feel
> free to preview them at
> http://gvd.v-wave.com

Shaggedelic!  And I see PyORBit got a new Web page out of this :-)  Do you think
we'll need a CVS module for the Web pages?  I think Gnome uses CVS for their

 (1) Set the environment variable.  <username> is your shell account
      user name.  For bash, use

        $ export CVSROOT=':pserver:<username>@bioinformatics.org:/home/cvs'

      For csh, use

        $ setenv CVSROOT ':pserver:<username>@bioinformatics.org:/home/cvs'

  (2) Login.

        $ cvs login

      CVS will ask for your password.  This will be your shell account pw.

  (3) To "checkout" a module, use the command by the same name.

        $ cvs checkout <modulename>

      This will create a directory called ./<modulename> (within the pwd)
      with everything in it.

  (4) You can cd to the new directory and make whatever changes you want.

  (5) When you add or remove a file, you need to notify CVS.  Let's say you
      created a README file.

        $ cvs add README

  (6) Once you have finished working in the directory, commit the changes.

        $ cvs commit

      This will commit everything in the pwd, since no specific file was
      specified.  You can also specify a file.

  (7) Newer versions of CVS support logouts.

        $ cvs logout

  (8) You can start all over again at a later time, but it is likely
      the module will have been changed by someone else.  In the
      directory where you created the <modulename> directory, rename
      <modulename> to something else (say "<modulename>-old") if you
      want to keep it.  Otherwise typing "cvs checkout <modulename>"
      may change some things.  If you want to update the copies of the
      files you have, you can use the "update" command.

        $ cvs update <filename>

      Remember that the checkout command is used in the parent directory
      to the <modulename> directory.  The other commands are used within
      the <modulename> directory itself.

  (9) You can also make a new module with the "import" command.

        $ cvs import -m "<message about import>" <modulename> <branchname>

      Note that the -m option lets you put in a message without starting
      an editor.  Otherwise CVS will start up $EDITOR.

  (10) If you would like to see a list of the cvs commands, you can use the
       "help" command.

         $ cvs help

                         |        J.W. Bizzaro        |
                         |  jeff at bioinformatics.org   |
                         |                            |
                         |        THE OPEN LAB        |
                         | Open Source Bioinformatics |
                         |                            |
                         | http://bioinformatics.org/ |

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