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

[jabaws.git] / TODO.txt

diff --git a/TODO.txt b/TODO.txt
index e08270c..1c907cf 100644 (file)
--- a/TODO.txt
+++ b/TODO.txt
@@ -1,4 +1,40 @@
+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
@@ -26,12 +62,10 @@ Check the WS input and reject it on submission rather then of access with error
 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
-Rename it to avoid confusion with jabaws client\r
++Add registry service to query services status\r
 \r
-Finish the client\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