| 1 | Requirements:
|
|---|
| 2 | =============
|
|---|
| 3 |
|
|---|
| 4 | 1. PIL (aka python-imaging in most unix systems).
|
|---|
| 5 |
|
|---|
| 6 | 2. python development files (it could be python-dev in unix systems).
|
|---|
| 7 |
|
|---|
| 8 | 3. gcc and usual tools for compiling and installing.
|
|---|
| 9 |
|
|---|
| 10 | 4. BioPerl (optional) see BIOPERL.txt
|
|---|
| 11 |
|
|---|
| 12 | 5. postgres and/or mysql development files (optional) for plone4bio.biosql support.
|
|---|
| 13 |
|
|---|
| 14 | Installing a BioPlone site:
|
|---|
| 15 | ===========================
|
|---|
| 16 |
|
|---|
| 17 | 1. Make a symbolic link buildout.cfg to select the profile you want to
|
|---|
| 18 | use; production, staging or development. For example:
|
|---|
| 19 |
|
|---|
| 20 | $ rm buildout.cfg
|
|---|
| 21 | $ ln -s demo.cfg buildout.cfg
|
|---|
| 22 |
|
|---|
| 23 | 2. Run bootstrap.py with the python interpreter you want to use. This
|
|---|
| 24 | will install Buildout.
|
|---|
| 25 |
|
|---|
| 26 | $ python2.4 bootstrap.py
|
|---|
| 27 |
|
|---|
| 28 | or if you've used MacPorts for MacOSX to install your python 2.6:
|
|---|
| 29 |
|
|---|
| 30 | $ /opt/local/bin/python2.6 bootstrap.py
|
|---|
| 31 |
|
|---|
| 32 | or if you've used Fink for MacOSX to install your python 2.6:
|
|---|
| 33 |
|
|---|
| 34 | $ /sw/bin/python2.6 bootstrap.py
|
|---|
| 35 |
|
|---|
| 36 | 3. Run buildout
|
|---|
| 37 |
|
|---|
| 38 | $ bin/buildout -v
|
|---|
| 39 |
|
|---|
| 40 | note: it may take some time ...
|
|---|
| 41 |
|
|---|
| 42 | 4. Start up the instance
|
|---|
| 43 |
|
|---|
| 44 | $ bin/instance fg
|
|---|
| 45 |
|
|---|
| 46 | 5. If you selected demo.cfg or postgresql.cfg on step 1 then you can stop here and open
|
|---|
| 47 | your browser at http://localhost:8080/plone4bio you can also login as manager (admin/admin)
|
|---|
| 48 |
|
|---|
| 49 | 6. Log into the ZMI at http://localhost:8080/manage as (admin/admin).
|
|---|
| 50 | Create a Plone site and then go to the quickinstaller and install the
|
|---|
| 51 | following products:
|
|---|
| 52 |
|
|---|
| 53 | plone4bio.base
|
|---|
| 54 | plone4bio.pscoils
|
|---|
| 55 |
|
|---|
| 56 | Now you should be able to add new Sequence types to your Plone site and
|
|---|
| 57 | to run the pscoils (http://www.plone4bio.org/pscoils/) code
|
|---|
| 58 | against it.
|
|---|
| 59 |
|
|---|
| 60 | 7. To extend the BioPlone site with new predictors, refer to the
|
|---|
| 61 | skeleton code in plone4bio.pscoils: you should be able to create a set
|
|---|
| 62 | of tools to run against your sequences.
|
|---|
