                            Installing  GotCloud

The complete installation consists of these packages

  gotcloud-test      - test files
  hs37-db132.tar.gz  - reference files of possible interest
  gotcloud-bin       - aligner and umake executables

Packages exist for Ubuntu (lucid and precise compatible) and in time
packages will be made available for Redhat/CentOS. These packages 
require root authority to install everything in /usr/local/gotcloud.
In time a large compressed tar file will be provided so non-root
users can install GotCloud in their HOME directories.



You may find it convenient to provide a symlink for your users so the keys scripts
are in the normal user's PATH.  E.g.

 ln -s /usr/local/gotcloud/bin/gen_biopipeline.pl /usr/local/bin/gen_biopipeline.pl
 ln -s /usr/local/gotcloud/bin/umake.pl /usr/local/bin/umake.pl



These tools have been developed and tested extensively on Ubuntu
installations, although we expect they will run on other Unix distributions 
as long as the binaries are compiled for the target system.


Dependencies - not forced by the packages, but actually required for a successful run.

  Ubuntu Lucid or Precise
    java-common default-jre make libssl0.9.8

  RedHat / CentOS
    to be provided



A complete test is available and you are encouraged to run it once,
just to prove everything is correct. Run the test case with

  /usr/local/gotcloud/bin/gen_biopipeline.pl --test /your/testdir/path
  /usr/local/gotcloud/bin/umake.pl           --test /your/testdir/path

The first will take about 2 minutes, the second about 15 minutes. Both
are self checking. Errors will be reported and it will be obvious that
the test failed or was successful.
