+TODO write some help on the executable.properties within this file! \r
+check that after binaries relocation build tasks point to correct locations!\r
+GET rid of binaries/help directory!\r
+update binaries\r
+ + muscle binary version 3.8.31 for win/lin32/lin64 and sources, docs in website/prog_docs\r
+ - test Muscle on the cluster\r
+ - test Muscle compilation\r
+ + probcons up-to-date\r
+ + clustal up-to-date \r
+ - update tcoffee (8.99 latest)\r
+ - update Mafft (6.857 latest)\r
++ make sure conf files are optional!\r
+\r
TODO: \r
+Registry 1 week\r
+webservices - 1 week\r
+client - 1 week\r
+docs - 1 week\r
+\r
+Cluster stats: \r
+ +cancelled should not be reported as incomplete!\r
+ -Remove hyperlinks from tasks which workdirs were removed \r
+ -graph generation \r
+ -user documentation (do not forget how to enable follow symlinks!)\r
+ -use the same name for output for different executables\r
+ +ant task to clean up clean stat db task before packing web app\r
+ +pack web apps with stat db (NOT TESTED!)\r
+ +change input size bites\r
+ +add help info for each column in the detailed job list table\r
+ +replace default -1 with ? \r
+ +delete and re-import the database to fix clustal input staff \r
+\r
+add to help text: To disable a web service remove it from WEB-INF/sun-jaxws.xml descriptor\r
+\r
+add to help: VirtualBox 4.0.4 works fine with JABAWS update links \r
+\r
+rename jaba.war to jabaws.war and make sure jabaws context path is used throughout. \r
+\r
+Current stat collector has to rely on file dates! \r
+\r
+Test all WS as names from Executables were removed\r
+\r
+Add default names for input and output in every executable and use them consistently\r
+throughts (e.g. in all WS). Best of all use the same name from SceletalExectuable \r
+For statistics. \r
+\r
+FIXME: \r
+Conecting to JABAWS version 2 service\r
+09-Feb-2011 15:27:53 compbio.ws.client.Jws2Client connect\r
+INFO: Connected successfully!\r
+Exception in thread "main" java.lang.NullPointerException\r
+ at compbio.ws.client.MetadataHelper.getParametersList(MetadataHelper.java:30)\r
+ at compbio.ws.client.Jws2Client.<init>(Jws2Client.java:179)\r
+ at compbio.ws.client.Jws2Client.main(Jws2Client.java:483)\r
+ \r
+ScoreManager should output scores properly \r
+\r
+Allow empty Parameters and Preset files! \r
+\r
+Check the WS input and reject it on submission rather then of access with error message\r
+\r
+Globprot need a proper reference to bio python and sav_gol binaries -> they should be \r
+somehow taken from disembl. \r
+\r
++Add registry service to query services status\r
+\r
++Refactor web services checker to enable a programmatic access to its methods.\r
++Finish the client\r
+\r
+Add interface for Jalview annotation \r
+Add the method to return Jalview Annotation to SequenceAnnotation IF \r
+\r
+Develop generic Interface to return Jalview annotation for easy to add new \r
+services (?) \r
+\r
+Replace conservation.Method with server.ws.Method \r
+and try building WS. If this does not work - get rid of Method\r
+\r
+Output file parsing for stat reporting\r
+cluster engine stat of www-jws2 user\r
+\r
+integrate the above to tweak the size of the local job\r
\r
+Add AACon ws\r
Add iupred ws http://iupred.enzim.hu/\r
-Add globprot ws \r
+Add globprot ws - does not report raw scores, just regions\r
Add ronn ws\r
\r
+Philogeny Mrbayes + Philip\r
+ \r
USE CASE - TURN ALIGNMENT INTO PROFILE AND SEARCH SEQUENCE DATABASE USECASE\r
- Receive user alignment \r
- use hmmerbuild to turn it to profile\r
\r
Think hard on what to do with large output files? \r
e.g. serve the hits table in full, but retrieve alignments on demand.\r
-What actually neeeds to be sent? \r
+What actually needs to be sent? \r
\r
Add facility to distribute other results of the calculations like the trees and \r
annotation file for probcons. \r
git://source.jalview.org / jabaws.git / blobdiff