Commits · 08fab97d81d2068b140b60f507d858aaa2085d86 · Mirrors / mutalyzer

May 16, 2011

Merging r274 through r277 from trunk. · 08fab97d

Vermaat authored 13 years ago

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

08fab97d

Apr 21, 2011

Fixed bug in previous commit: summary with number of warnings was incorrect. · 5b08e3e0

Vermaat authored 13 years ago

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

5b08e3e0

Fixes for roll on reverse strand. · 8c350459

Vermaat authored 13 years ago

- 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

8c350459

Apr 18, 2011

Merged r269 r270 r271 r273 from trunk. · 38bf9c11

Vermaat authored 13 years ago

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

38bf9c11

Swapped names (Jeroen <-> Martijn) in NBIC presentation. Fixed text... · 74c5623b

Vermaat authored 13 years ago

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

74c5623b

Several small fixes and comments. · e61ddd5e

Vermaat authored 13 years ago

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

e61ddd5e

Apr 13, 2011

Made some final alterations to the NBIC poster. · 2e48dcef

Laros authored 13 years ago


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

2e48dcef

Apr 12, 2011

Added a picture in one of the presentations, added a poster presentation. · c37509b0
Laros authored 13 years ago
```
git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@270 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1
```
c37509b0
Added a presentation that Martijn will give on the NBIC conference. · 191632fd
Laros authored 13 years ago
```
git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@269 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1
```
191632fd

Small fixes. · abcc9460

Vermaat authored 13 years ago

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

abcc9460

Apr 11, 2011

Fixes for whole-exon deletions. · 38e90d0b

Vermaat authored 13 years ago

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

38e90d0b

Quick fix for navigation menu highlighting (Fixes Trac #47). · 95eaea9b

Vermaat authored 13 years ago

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

95eaea9b

Batch interface now accepts new-style input with multiple columns. · 4911ffb7

Vermaat authored 13 years ago

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

4911ffb7

Apr 08, 2011

Moved GBparser and LRGparser to parsers/genbank and parsers/lrg. · 65f8f996

Vermaat authored 14 years ago

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

65f8f996

Fixed VarInfo. · 9bc19e07

Vermaat authored 14 years ago

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

9bc19e07

Moved Serializers.py to models.py. · 23fca441

Vermaat authored 14 years ago

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

23fca441

Removed dead configuration options. · d9a5d0a8

Vermaat authored 14 years ago

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

d9a5d0a8

Fixed UCSC update. · 2e68c7fa

Vermaat authored 14 years ago

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

2e68c7fa

Apr 07, 2011

Updated README and INSTALL files. · aa863451

Vermaat authored 14 years ago

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

aa863451

Updated installation instructions. · 95d76894

Vermaat authored 14 years ago

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

95d76894

Fixed installation scripts. · 25f0d9c1

Vermaat authored 14 years ago

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

25f0d9c1

Revised installation instructions. Added pre-install script. · ddffc86a

Vermaat authored 14 years ago

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

ddffc86a

Fixed batch daemon init script. · 20196ccb

Vermaat authored 14 years ago

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

20196ccb

Use environment variable MUTALYZER_ENV=test to use testing settings. · d2c3743f

Vermaat authored 14 years ago

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

d2c3743f

Completed post-install script. Related fixes. · 9289bd3f

Vermaat authored 14 years ago

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

9289bd3f

Apr 06, 2011

Some reorganisation. Added post-install script. · 6c4f4bdd

Vermaat authored 14 years ago

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

6c4f4bdd

Apr 05, 2011

Merging r249 from trunk. · 65b9196f

Vermaat authored 14 years ago

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

65b9196f

Sort of working version with setuptools. · b70090c6

Vermaat authored 14 years ago

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

b70090c6

Added a line about logging in the disclaimer. · 83431124

Laros authored 14 years ago

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

83431124

Further changes to setup.py. · 0c3e89d1

Vermaat authored 14 years ago

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

0c3e89d1

Moved templates/ to mutalyzer/templates/. · 835de4de

Vermaat authored 14 years ago

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

835de4de

Renamed ./examples to ./extras. · bccd091a

Vermaat authored 14 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@246 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

bccd091a

Apr 04, 2011

Added setuptools setup.py file. · a4bf5e55

Vermaat authored 14 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@245 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

a4bf5e55

- Moved tests from ./mutalyzer/tests/ to ./tests/. · e2b51a1f

Vermaat authored 14 years ago

- Added error recovery to batch daemon.
- Added example init script for batch daemon.


git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@244 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

e2b51a1f

The bin/find_log_bugs script is now executable. · 98a55a55

Vermaat authored 14 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@243 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

98a55a55

Merged 236 from trunk. · 352e2026

Vermaat authored 14 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@242 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

352e2026

Merge 235 from trunk. · 85b1a786

Vermaat authored 14 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@241 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

85b1a786

Added SOAP example clients. · 2595121b

Vermaat authored 14 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@240 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

2595121b

Apr 01, 2011

Added detection for running batch daemon. · 528bd312

Vermaat authored 14 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@239 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

528bd312

Rewrote the batch job processing daemon. · c31da7f7

Vermaat authored 14 years ago

It now shuts down gracefully, completing the current job item. General
daemon handling code is now also better, including PID file handling.

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@238 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

c31da7f7