git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@286 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@285 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

fabfile.py:
- Automatic deployment to remote servers using Fabric.

extras/pre-install.sh:
extras/post-install.sh:
extras/post-upgrade.sh:
INSTALL:
- Refactoring of deployment.
- Better handling of installation vs upgrade.
- Install crontab.
- Install init script links.
- Restart Apache and Mutalyzer batch daemon.

bin/mutalyzer-webservice.wsgi:
bin/mutalyzer-website.wsgi:
- Moved WSGI interfaces from mutalyzer package to bin directory.
- Fixed use of built-in webserver.

extras/apache/mutalyzer.conf:
- Use /var/www/mutalyzer/base symlink for static files.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@284 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@283 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

file.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@282 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

tests/test_wsgi.py:
- Option to skip 'slow' unit tests (decorated by @slow).

tests/test_webservice.py:
- Monkey-patched suds to download xml.xsd from other URL.

mutalyzer/templates/check.html:
- Experimentally colored boxes in namechecker.

mutalyzer/Retriever.py:
- More robust dbSNP API error handling.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@281 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@280 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@279 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@278 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@277 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@276 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

- Warning can also be shown for a roll on the reverse strand.
- Only the roll warning about the selected strand is shown.
- Roll of insertion where the inserted sequence changes now has correct
  description on the reverse strand.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@275 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@274 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

Swapped names (Jeroen <-> Martijn) in NBIC presentation. Fixed text positioning in transcript picture.

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@273 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

Also updated the web interface name checker output:
- Visualised raw variants are now in a separate box with the input form.
- In the case of non-coding transcripts, exon information correctly uses
  n. positioning system.
- Updated message to be non-clickable and have extra info in tooltip.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@272 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@271 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@270 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@269 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@268 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@267 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@266 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@265 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@264 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@263 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@262 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@261 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@260 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@259 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@258 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@257 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@256 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@255 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@254 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@253 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@252 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@251 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

Locations and python paths are correct with respect to the setup.py file.
For development, use
  svn up && python setup.py develop
and for deployment use
  svn up && sudo python setup.py install



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@250 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@249 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@248 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

This is debatable, but makes distribution much easier. Setuptools no longer
ignores the templates this way and stores them along the mutalyzer package,
so they will be globally available.


git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@247 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1