source.jalview.org Git - jabaws.git/log

pvtroshin [Fri, 12 Aug 2011 12:32:00 +0000 (12:32 +0000)]

Services class refactored to get rid of engines and runners dependencies.
Build script has new task to pack client sources

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4500 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Thu, 11 Aug 2011 15:00:41 +0000 (15:00 +0000)]

Change header template for a new version

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4495 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Thu, 11 Aug 2011 15:00:30 +0000 (15:00 +0000)]

Change header template for a new version

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4494 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Thu, 11 Aug 2011 15:00:12 +0000 (15:00 +0000)]

Change header template for a new version

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4493 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Thu, 11 Aug 2011 12:56:46 +0000 (12:56 +0000)]

Adding new web service, getting rid of virtual box in docs

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4491 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Thu, 11 Aug 2011 12:00:20 +0000 (12:00 +0000)]

clustalo x64 from the developer

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4490 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Thu, 11 Aug 2011 11:57:24 +0000 (11:57 +0000)]

x86 and x64 clustalo binaries

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4489 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Thu, 11 Aug 2011 11:56:53 +0000 (11:56 +0000)]

x86 clustalo binary

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4488 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Thu, 11 Aug 2011 10:45:09 +0000 (10:45 +0000)]

Fixes to testcase, take into account the new WS

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4487 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Wed, 10 Aug 2011 16:07:37 +0000 (16:07 +0000)]

Drop support for VirtualBox

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4484 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Thu, 4 Aug 2011 14:44:32 +0000 (14:44 +0000)]

dundee executable conf

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4476 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Thu, 4 Aug 2011 14:38:34 +0000 (14:38 +0000)]

Get rid of v_hmem settings

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4475 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Thu, 4 Aug 2011 14:38:26 +0000 (14:38 +0000)]

Get rid of v_hmem settings

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4474 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Thu, 4 Aug 2011 14:32:46 +0000 (14:32 +0000)]

Comments

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4473 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Thu, 4 Aug 2011 13:22:09 +0000 (13:22 +0000)]

update

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4470 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Thu, 4 Aug 2011 13:21:54 +0000 (13:21 +0000)]

ClustalO servlets

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4469 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Thu, 4 Aug 2011 13:21:26 +0000 (13:21 +0000)]

reverting cluster engine settings (disabled by default)

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4468 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Thu, 4 Aug 2011 13:19:45 +0000 (13:19 +0000)]

ClustalO settings

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4467 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Thu, 4 Aug 2011 13:19:25 +0000 (13:19 +0000)]

ClustalO compile

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4466 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Thu, 4 Aug 2011 13:18:35 +0000 (13:18 +0000)]

clustalo 64x binary

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4465 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Thu, 4 Aug 2011 13:17:10 +0000 (13:17 +0000)]

Clustal Omega web service wrapper and tester

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4464 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Thu, 4 Aug 2011 13:16:38 +0000 (13:16 +0000)]

Clustal Omega web service wrapper and tester

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4463 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Thu, 4 Aug 2011 13:16:16 +0000 (13:16 +0000)]

Clustal Omega web service wrapper and tester

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4462 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Wed, 3 Aug 2011 17:06:32 +0000 (17:06 +0000)]

Wrapper for Clustal Omega.

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4458 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Tue, 2 Aug 2011 16:50:27 +0000 (16:50 +0000)]

Updates to a web site

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4441 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Tue, 2 Aug 2011 16:49:23 +0000 (16:49 +0000)]

fix for a broken link to a static page

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4440 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Wed, 13 Jul 2011 11:31:19 +0000 (11:31 +0000)]

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4412 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Wed, 13 Jul 2011 11:31:08 +0000 (11:31 +0000)]

new web site design and updates to the web pages

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4411 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Wed, 13 Jul 2011 11:30:06 +0000 (11:30 +0000)]

new images for jabaws 2 web site, getting rid of old images

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4410 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Wed, 6 Jul 2011 12:18:53 +0000 (12:18 +0000)]

formatting change

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4396 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Wed, 6 Jul 2011 12:15:05 +0000 (12:15 +0000)]

ia32 iupred

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4395 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Wed, 6 Jul 2011 12:14:49 +0000 (12:14 +0000)]

ia32 iupred

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4394 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Wed, 6 Jul 2011 12:13:54 +0000 (12:13 +0000)]

Pre release Executable.properties, help added, unused properties commented out

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4393 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Wed, 6 Jul 2011 10:56:04 +0000 (10:56 +0000)]

Better method for searching JAVA

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4392 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Fri, 1 Jul 2011 10:59:53 +0000 (10:59 +0000)]

Add servlet for public usage stats display.

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4384 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Fri, 1 Jul 2011 09:42:12 +0000 (09:42 +0000)]

Limits are optional so correct tests

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4379 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Fri, 1 Jul 2011 09:41:27 +0000 (09:41 +0000)]

remove assert

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4378 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Thu, 30 Jun 2011 17:22:57 +0000 (17:22 +0000)]

obtain JAVA executable path from the JAVA_HOME variable. Does not require path to java for jar libraries.

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4376 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Tue, 28 Jun 2011 16:54:59 +0000 (16:54 +0000)]

Stat collector updates to work with JABA 2 input & output files

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4366 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Tue, 28 Jun 2011 15:30:02 +0000 (15:30 +0000)]

Clean database & small changes

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4363 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Mon, 27 Jun 2011 17:11:09 +0000 (17:11 +0000)]

Expose a few methods of Client and WSTester as API for Jim, new distributables.

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4343 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Mon, 27 Jun 2011 16:40:37 +0000 (16:40 +0000)]

Slight refactoring

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4342 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Mon, 27 Jun 2011 15:33:31 +0000 (15:33 +0000)]

Minor tweaks

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4340 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Mon, 27 Jun 2011 14:55:27 +0000 (14:55 +0000)]

Dundee compiled x86 binaries a few fixes for compile script

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4338 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Mon, 27 Jun 2011 13:48:11 +0000 (13:48 +0000)]

Build script improvements & updated util

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4337 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Mon, 27 Jun 2011 13:42:45 +0000 (13:42 +0000)]

Generalizing configuration prior to release.

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4336 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Mon, 27 Jun 2011 13:29:22 +0000 (13:29 +0000)]

remove settings as separate settings no longer required
Add separate conf setting for engines and executables for dundee

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4334 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Fri, 24 Jun 2011 23:32:23 +0000 (23:32 +0000)]

Get rid of unused code

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4329 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Fri, 24 Jun 2011 17:17:29 +0000 (17:17 +0000)]

Further simplification of build tasks
get rid of biojava jar as it's not in use

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4328 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Thu, 23 Jun 2011 14:15:51 +0000 (14:15 +0000)]

update to compbio.utils and a few small changes

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4327 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Thu, 23 Jun 2011 14:11:27 +0000 (14:11 +0000)]

build script updated

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4326 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Thu, 23 Jun 2011 14:10:48 +0000 (14:10 +0000)]

links update (not checked though)

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4325 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Thu, 23 Jun 2011 14:10:02 +0000 (14:10 +0000)]

compbio projects sources

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4324 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Thu, 23 Jun 2011 14:08:55 +0000 (14:08 +0000)]

pack binaries from folders into archives for easy download

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4323 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Thu, 23 Jun 2011 14:04:51 +0000 (14:04 +0000)]

relocated to website/archive folder

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4322 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Thu, 23 Jun 2011 14:04:22 +0000 (14:04 +0000)]

relocate pre-compiled executables from binaries folder

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4321 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Thu, 23 Jun 2011 14:02:01 +0000 (14:02 +0000)]

remove old executables

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4320 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Thu, 23 Jun 2011 12:09:51 +0000 (12:09 +0000)]

rename

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4317 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Thu, 23 Jun 2011 10:56:00 +0000 (10:56 +0000)]

regenerated stubs & TODO

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4314 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Thu, 23 Jun 2011 09:47:41 +0000 (09:47 +0000)]

Adding latest test results

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4313 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Thu, 23 Jun 2011 09:46:17 +0000 (09:46 +0000)]

Remove old test from web site to replace with most recent

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4312 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Thu, 23 Jun 2011 09:34:27 +0000 (09:34 +0000)]

Disable failed tests

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4311 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Thu, 23 Jun 2011 09:16:47 +0000 (09:16 +0000)]

modification to enable globplot run on nanna (PYTHONPATH variable)

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4310 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Thu, 23 Jun 2011 09:15:05 +0000 (09:15 +0000)]

Fixes to test cases

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4309 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Wed, 22 Jun 2011 17:26:22 +0000 (17:26 +0000)]

annotate test with appropriate groups

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4308 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Wed, 22 Jun 2011 17:11:48 +0000 (17:11 +0000)]

Fix for testcases

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4307 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Tue, 21 Jun 2011 17:17:08 +0000 (17:17 +0000)]

Fixes for failed test cases (most was due to the data being used or problems with test cases themselves)

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4303 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Tue, 21 Jun 2011 15:44:23 +0000 (15:44 +0000)]

custom test suit xml

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4302 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Tue, 21 Jun 2011 14:48:37 +0000 (14:48 +0000)]

tcoffee updated docs & todo

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4301 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Tue, 21 Jun 2011 14:47:39 +0000 (14:47 +0000)]

IA32 and x64 tcoffee binaries are added

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4300 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Tue, 21 Jun 2011 14:34:00 +0000 (14:34 +0000)]

getting rid of ambiguous documentation folder. all prog_doc are now stored in website/prog_docs

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4299 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Tue, 21 Jun 2011 14:25:36 +0000 (14:25 +0000)]

new version of tcoffee 8.99 not yet compiled for ia32 linux (currently compiled for dundee cluster)

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4298 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Tue, 21 Jun 2011 14:14:44 +0000 (14:14 +0000)]

removing tcoffee to update

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4297 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Tue, 21 Jun 2011 12:29:25 +0000 (12:29 +0000)]

Revert multithreading support for mafft as it does not seem to work

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4296 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Tue, 21 Jun 2011 12:29:09 +0000 (12:29 +0000)]

Revert multithreading support for mafft as it does not seem to work

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4295 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Tue, 21 Jun 2011 12:06:02 +0000 (12:06 +0000)]

Get rind of NativeClusterJob interface as pretty much every jobs best to use some cluster settings, and they are simply defined in the executable conf file and passed by the SkeletalExecutable.

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4294 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Tue, 21 Jun 2011 11:35:08 +0000 (11:35 +0000)]

mafft new location

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4293 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Tue, 21 Jun 2011 11:34:53 +0000 (11:34 +0000)]

Changes to accomodate new version's of mafft packaging

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4292 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Tue, 21 Jun 2011 11:33:39 +0000 (11:33 +0000)]

add IA32 linux muscle binary

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4291 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Tue, 21 Jun 2011 11:10:02 +0000 (11:10 +0000)]

IA32 mafft executables

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4290 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Tue, 21 Jun 2011 10:58:50 +0000 (10:58 +0000)]

New Mafft binaries for 32 bit linux system

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4289 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Tue, 21 Jun 2011 10:57:18 +0000 (10:57 +0000)]

New Mafft binaries for 64 bit linux system

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4288 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Tue, 21 Jun 2011 10:27:17 +0000 (10:27 +0000)]

remove mafft extensions - we do not support them

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4287 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Tue, 21 Jun 2011 10:02:51 +0000 (10:02 +0000)]

new mafft v 6.857 with extensions

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4286 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Tue, 21 Jun 2011 10:01:52 +0000 (10:01 +0000)]

Removing old version of mafft to replace with the new

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4285 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Mon, 20 Jun 2011 16:43:34 +0000 (16:43 +0000)]

todo update

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4284 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Mon, 20 Jun 2011 16:37:41 +0000 (16:37 +0000)]

new version of muscle 3.8.31
binaries for various systems, sources, help file and configuration is updated

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4283 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Fri, 17 Jun 2011 16:17:57 +0000 (16:17 +0000)]

todos

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4282 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Fri, 17 Jun 2011 15:45:17 +0000 (15:45 +0000)]

Web services refactoring & bug fixing

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4281 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Fri, 17 Jun 2011 14:06:30 +0000 (14:06 +0000)]

Refactoring of all SequenceAnnotation web services
New version of Metro
Definition for IUPred exec
Stubs regenerated

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4280 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Thu, 16 Jun 2011 16:48:52 +0000 (16:48 +0000)]

todos

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4279 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Thu, 16 Jun 2011 16:46:41 +0000 (16:46 +0000)]

Binaries relocation

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4278 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Thu, 16 Jun 2011 16:18:33 +0000 (16:18 +0000)]

IUPred for windows

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4277 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Thu, 16 Jun 2011 14:40:43 +0000 (14:40 +0000)]

Integrating IUPredWS

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4276 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Thu, 16 Jun 2011 14:30:04 +0000 (14:30 +0000)]

A few more tests for IUPred

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4275 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Thu, 16 Jun 2011 14:22:06 +0000 (14:22 +0000)]

IUPred final touches. All test cases pass

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4274 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Thu, 16 Jun 2011 13:35:08 +0000 (13:35 +0000)]

Improvements to the code

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4273 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Thu, 16 Jun 2011 13:13:19 +0000 (13:13 +0000)]

IUpred integration

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4272 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Thu, 16 Jun 2011 13:10:17 +0000 (13:10 +0000)]

Modified IUPred to read multiple fasta as input

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4271 e3abac25-378b-4346-85de-24260fe3988d

commit | commitdiff | tree

pvtroshin [Tue, 14 Jun 2011 17:26:54 +0000 (17:26 +0000)]

Adding XML executable description for IUPred

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4266 e3abac25-378b-4346-85de-24260fe3988d