Moved remote_resources directory from scigap repo to here. This is the version history (svn log --verbose) from the scigap repo, of remote_resources, just before making the move. The history prior to the creation of the scigap repo had already been lost (though, I suppose it can be found in the old cipres location). ------------------------------------------------------------------------ r321 | terri | 2015-02-21 06:46:38 -0800 (Sat, 21 Feb 2015) | 3 lines Changed paths: M /trunk/sdk/scripts/remote_resource/trestles/beast2onlywrapper M /trunk/sdk/scripts/remote_resource/trestles/beast2wrapper Mark says these are changes that david made for him. ------------------------------------------------------------------------ r315 | mmiller | 2015-02-18 12:33:48 -0800 (Wed, 18 Feb 2015) | 1 line Changed paths: M /trunk/sdk/scripts/remote_resource/trestles/mbmpiwrapper_3.2.4 fix version ------------------------------------------------------------------------ r314 | mmiller | 2015-02-18 12:33:11 -0800 (Wed, 18 Feb 2015) | 1 line Changed paths: A /trunk/sdk/scripts/remote_resource/trestles/mbmpiwrapper_3.2.4 first versioned mbmpiwrapper 3.2.4 ------------------------------------------------------------------------ r313 | mmiller | 2015-02-18 12:32:44 -0800 (Wed, 18 Feb 2015) | 1 line Changed paths: A /trunk/sdk/scripts/remote_resource/trestles/mbmpiwrapper_3.2.3 first versioned mbmpiwrapper for 3.2.3 ------------------------------------------------------------------------ r312 | mmiller | 2015-02-18 12:30:58 -0800 (Wed, 18 Feb 2015) | 1 line Changed paths: M /trunk/sdk/scripts/remote_resource/trestles/mbmpiwrapper final version of mbmpirwrapper for production ------------------------------------------------------------------------ r311 | mmiller | 2015-02-18 12:29:46 -0800 (Wed, 18 Feb 2015) | 1 line Changed paths: M /trunk/sdk/scripts/remote_resource/trestles/mbmpiwrapper ------------------------------------------------------------------------ r310 | mmiller | 2015-02-18 12:28:15 -0800 (Wed, 18 Feb 2015) | 1 line Changed paths: M /trunk/sdk/scripts/remote_resource/trestles/mbmpiwrapper make it mb 3.2.3 for production ------------------------------------------------------------------------ r309 | mmiller | 2015-02-18 10:48:36 -0800 (Wed, 18 Feb 2015) | 1 line Changed paths: M /trunk/sdk/scripts/remote_resource/trestles/mbmpiwrapper return to original version ------------------------------------------------------------------------ r308 | mmiller | 2015-02-18 10:17:24 -0800 (Wed, 18 Feb 2015) | 1 line Changed paths: M /trunk/sdk/scripts/remote_resource/trestles/mbmpiwrapper ------------------------------------------------------------------------ r307 | mmiller | 2015-02-18 09:58:45 -0800 (Wed, 18 Feb 2015) | 1 line Changed paths: M /trunk/sdk/scripts/remote_resource/trestles/mbmpiwrapper ------------------------------------------------------------------------ r306 | mmiller | 2015-02-18 09:11:17 -0800 (Wed, 18 Feb 2015) | 1 line Changed paths: M /trunk/sdk/scripts/remote_resource/trestles/mbmpiwrapper change module load string ------------------------------------------------------------------------ r237 | terri | 2014-12-30 14:49:28 -0800 (Tue, 30 Dec 2014) | 4 lines Changed paths: M /trunk/sdk/scripts/remote_resource/trestles/workbench.rc Terri committing David's fix for ulimit setting. Should really be close to 8 gig now: 8,000,000,000. I believe 8 gig is actually 8589934592 bytes, but I think this is close enough for what we care about. ------------------------------------------------------------------------ r115 | terri | 2014-11-21 06:18:33 -0800 (Fri, 21 Nov 2014) | 2 lines Changed paths: M /trunk/sdk/scripts/remote_resource/trestles/beastwrapper Not sure who made this change, I'm (terri) just committing it. ------------------------------------------------------------------------ r114 | terri | 2014-11-21 06:18:09 -0800 (Fri, 21 Nov 2014) | 3 lines Changed paths: M /trunk/sdk/scripts/remote_resource/trestles/beast2onlywrapper M /trunk/sdk/scripts/remote_resource/trestles/beast2wrapper David Wang changes: Edited the beast2wrappers to include the paths to the > following packages: BDSKY, SA, SubstBMA ------------------------------------------------------------------------ r41 | phoover | 2014-10-01 10:13:30 -0700 (Wed, 01 Oct 2014) | 3 lines Changed paths: M /trunk/default/build.properties.template M /trunk/portal/src/main/java/org/ngbw/web/actions/SessionManager.java M /trunk/portal/src/main/java/org/ngbw/web/controllers/FolderController.java M /trunk/portal/src/main/java/org/ngbw/web/controllers/SessionController.java M /trunk/portal/src/main/webapp/pages/user/login.jsp A /trunk/rest/cipresrest/ReleaseNotes.txt M /trunk/rest/cipresrest/alltests.sh M /trunk/rest/cipresrest/concurrencytests.sh M /trunk/rest/cipresrest/createapp.template A /trunk/rest/cipresrest/createapp_insects.sh A /trunk/rest/cipresrest/createapp_test.sh M /trunk/rest/cipresrest/job.sh A /trunk/rest/cipresrest/job2.sh M /trunk/rest/cipresrest/limit.sh A /trunk/rest/cipresrest/mary.sh A /trunk/rest/cipresrest/sample1_in.fasta A /trunk/rest/cipresrest/sample2_in.fasta M /trunk/rest/cipresrest/src/main/java/org/ngbw/cipresrest/Readme.txt M /trunk/rest/cipresrest/src/main/java/org/ngbw/cipresrest/auth/AuthenticationExceptionMapper.java M /trunk/rest/cipresrest/src/main/java/org/ngbw/cipresrest/auth/AuthorizationExceptionMapper.java M /trunk/rest/cipresrest/src/main/java/org/ngbw/cipresrest/auth/SecurityFilter.java M /trunk/rest/cipresrest/src/main/java/org/ngbw/cipresrest/webresource/BaseResource.java M /trunk/rest/cipresrest/src/main/java/org/ngbw/cipresrest/webresource/CipresAdmin.java M /trunk/rest/cipresrest/src/main/java/org/ngbw/cipresrest/webresource/CipresApplication.java M /trunk/rest/cipresrest/src/main/java/org/ngbw/cipresrest/webresource/CipresJob.java M /trunk/rest/cipresrest/src/main/java/org/ngbw/cipresrest/webresource/CipresRestAdmin.java M /trunk/rest/cipresrest/src/main/java/org/ngbw/cipresrest/webresource/CipresUser.java M /trunk/rest/cipresrest/src/main/java/org/ngbw/cipresrest/webresource/JobFormParser.java M /trunk/rest/cipresrest/src/main/java/org/ngbw/cipresrest/webresource/UserMismatchExceptionMapper.java M /trunk/rest/cipresrest/submit.sh M /trunk/rest/cipresrest/testAndDemoAccounts M /trunk/rest/cipresrest/testfw.sh A /trunk/rest/cipresrest/tom.sh A /trunk/rest/cipresrest/url.sh A /trunk/rest/cipresrest/url2.sh M /trunk/rest/cipresrest/user.sh M /trunk/rest/cipresrest/user2.sh M /trunk/rest/datatypes/src/main/java/org/ngbw/restdatatypes/ApplicationData.java M /trunk/rest/datatypes/src/main/java/org/ngbw/restdatatypes/UserData.java M /trunk/rest/pom.xml M /trunk/rest/pycipres/conf/pycipres.conf M /trunk/rest/pycipres/setup.py A /trunk/rest/pycipres/testdata/tooltests/variants/pauprat A /trunk/rest/pycipres/testdata/tooltests/variants/pauprat/Readme.txt A /trunk/rest/pycipres/testdata/tooltests/variants/pauprat/documentation.txt A /trunk/rest/pycipres/testdata/tooltests/variants/pauprat/infile_.txt A /trunk/rest/pycipres/testdata/tooltests/variants/pauprat/seth_paup_rat.nex A /trunk/rest/pycipres/testdata/tooltests/variants/pauprat/testInput.properties A /trunk/rest/pycipres/testdata/tooltests/variants/pauprat/testParam.properties A 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/trunk/rest/restclient/src/main/webapp/taskList.jsp M /trunk/rest/restclient/src/main/webapp/taskStatus.jsp M /trunk/rest/restusers/.settings/org.eclipse.m2e.core.prefs M /trunk/rest/restusers/pom.xml M /trunk/rest/restusers/src/main/java/org/ngbw/restusers/Application.java A /trunk/rest/restusers/src/main/java/org/ngbw/restusers/actions/Apps.java M /trunk/rest/restusers/src/main/java/org/ngbw/restusers/actions/BaseAction.java M /trunk/rest/restusers/src/main/java/org/ngbw/restusers/actions/Login.java M /trunk/rest/restusers/src/main/java/org/ngbw/restusers/actions/Profile.java M /trunk/rest/restusers/src/main/java/org/ngbw/restusers/actions/Register.java A /trunk/rest/restusers/src/main/java/org/ngbw/restusers/actions/admin A /trunk/rest/restusers/src/main/java/org/ngbw/restusers/actions/admin/ManageApplications.java A /trunk/rest/restusers/src/main/java/org/ngbw/restusers/actions/admin/ManageUsers.java M /trunk/rest/restusers/src/main/java/org/ngbw/restusers/rest/WorkbenchMethods.java A /trunk/rest/restusers/src/main/resources/app.properties A /trunk/rest/restusers/src/main/resources/newApp-html.ftl A /trunk/rest/restusers/src/main/resources/newApp-text.ftl A /trunk/rest/restusers/src/main/resources/resetPassword-html.ftl A /trunk/rest/restusers/src/main/resources/resetPassword-text.ftl A /trunk/rest/restusers/src/main/resources/spring-mail.xml M /trunk/rest/restusers/src/main/resources/struts.xml A /trunk/rest/restusers/src/main/webapp/WEB-INF/admin A /trunk/rest/restusers/src/main/webapp/WEB-INF/admin/applicationList.jsp A /trunk/rest/restusers/src/main/webapp/WEB-INF/admin/applicationManagement.jsp A /trunk/rest/restusers/src/main/webapp/WEB-INF/admin/regenID.jsp A /trunk/rest/restusers/src/main/webapp/WEB-INF/admin/updateApplicationInformation.jsp A /trunk/rest/restusers/src/main/webapp/WEB-INF/admin/updateUserInformation.jsp A /trunk/rest/restusers/src/main/webapp/WEB-INF/admin/userList.jsp A /trunk/rest/restusers/src/main/webapp/WEB-INF/admin/userManagement.jsp M /trunk/rest/restusers/src/main/webapp/WEB-INF/decorators.xml A /trunk/rest/restusers/src/main/webapp/WEB-INF/docs A /trunk/rest/restusers/src/main/webapp/WEB-INF/enduser A /trunk/rest/restusers/src/main/webapp/WEB-INF/enduser/almostDone.jsp A /trunk/rest/restusers/src/main/webapp/WEB-INF/enduser/applicationList.jsp A /trunk/rest/restusers/src/main/webapp/WEB-INF/enduser/applicationManagement.jsp A /trunk/rest/restusers/src/main/webapp/WEB-INF/enduser/changeAuthentication.jsp A /trunk/rest/restusers/src/main/webapp/WEB-INF/enduser/confirmActivation.jsp A /trunk/rest/restusers/src/main/webapp/WEB-INF/enduser/createApplication.jsp A /trunk/rest/restusers/src/main/webapp/WEB-INF/enduser/errorActivation.jsp A /trunk/rest/restusers/src/main/webapp/WEB-INF/enduser/forgotPassword.jsp A /trunk/rest/restusers/src/main/webapp/WEB-INF/enduser/home.jsp A /trunk/rest/restusers/src/main/webapp/WEB-INF/enduser/login.jsp A /trunk/rest/restusers/src/main/webapp/WEB-INF/enduser/profile.jsp A /trunk/rest/restusers/src/main/webapp/WEB-INF/enduser/regenID.jsp A /trunk/rest/restusers/src/main/webapp/WEB-INF/enduser/register.jsp A /trunk/rest/restusers/src/main/webapp/WEB-INF/enduser/register.jsp.save A /trunk/rest/restusers/src/main/webapp/WEB-INF/enduser/status.jsp A /trunk/rest/restusers/src/main/webapp/WEB-INF/enduser/updateApplicationInformation.jsp A /trunk/rest/restusers/src/main/webapp/WEB-INF/enduser/updatePassword.jsp A /trunk/rest/restusers/src/main/webapp/WEB-INF/enduser/updateProfile.jsp M /trunk/rest/restusers/src/main/webapp/WEB-INF/web.xml A /trunk/rest/restusers/src/main/webapp/bootstrap-form-helpers A /trunk/rest/restusers/src/main/webapp/bootstrap-form-helpers/dist A /trunk/rest/restusers/src/main/webapp/bootstrap-form-helpers/dist/css A 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/trunk/rest/restusers/src/main/webapp/css/cipres.css A /trunk/rest/restusers/src/main/webapp/css/cipres_toc.css A /trunk/rest/restusers/src/main/webapp/css/jquery.dataTables.css A /trunk/rest/restusers/src/main/webapp/css/jquery.tocify.css M /trunk/rest/restusers/src/main/webapp/decorators/default.jsp A /trunk/rest/restusers/src/main/webapp/decorators/doc.jsp D /trunk/rest/restusers/src/main/webapp/decorators/index.jsp A /trunk/rest/restusers/src/main/webapp/decorators/rawdoc.jsp A /trunk/rest/restusers/src/main/webapp/docs A /trunk/rest/restusers/src/main/webapp/docs/faq.html A /trunk/rest/restusers/src/main/webapp/docs/guide.html A /trunk/rest/restusers/src/main/webapp/docs/index.jsp D /trunk/rest/restusers/src/main/webapp/enduser M /trunk/rest/restusers/src/main/webapp/error.jsp A /trunk/rest/restusers/src/main/webapp/images/Sorting icons.psd A /trunk/rest/restusers/src/main/webapp/images/back_disabled.png A /trunk/rest/restusers/src/main/webapp/images/back_enabled.png A 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/trunk/sdk/src/main/java/org/ngbw/sdk/database/StreamColumn.java M /trunk/sdk/src/main/java/org/ngbw/sdk/database/StringColumn.java M /trunk/sdk/src/main/java/org/ngbw/sdk/database/StringCriterion.java M /trunk/sdk/src/main/java/org/ngbw/sdk/database/Task.java M /trunk/sdk/src/main/java/org/ngbw/sdk/database/TaskInputParameter.java M /trunk/sdk/src/main/java/org/ngbw/sdk/database/TaskInputSourceDocument.java M /trunk/sdk/src/main/java/org/ngbw/sdk/database/TaskLogMessage.java M /trunk/sdk/src/main/java/org/ngbw/sdk/database/TaskOutputParameter.java M /trunk/sdk/src/main/java/org/ngbw/sdk/database/TaskOutputSourceDocument.java M /trunk/sdk/src/main/java/org/ngbw/sdk/database/TextColumn.java M /trunk/sdk/src/main/java/org/ngbw/sdk/database/Tgusage.java M /trunk/sdk/src/main/java/org/ngbw/sdk/database/TomcatConnectionSource.java A /trunk/sdk/src/main/java/org/ngbw/sdk/database/UpdateOp.java M /trunk/sdk/src/main/java/org/ngbw/sdk/database/User.java M /trunk/sdk/src/main/java/org/ngbw/sdk/database/UserDataItem.java M /trunk/sdk/src/main/java/org/ngbw/sdk/database/UserItemDataRecord.java M /trunk/sdk/src/main/java/org/ngbw/sdk/database/VersionedRow.java M /trunk/sdk/src/main/java/org/ngbw/sdk/jobs/Job.java M /trunk/sdk/src/main/java/org/ngbw/sdk/jobs/JobStatus.java M /trunk/sdk/src/main/java/org/ngbw/sdk/jobs/UsageLimit.java A /trunk/sdk/src/main/java/org/ngbw/sdk/jobs/UsageLimitSetter.java M /trunk/sdk/src/main/java/org/ngbw/sdk/tool/BaseProcessWorker.java M /trunk/sdk/src/main/java/org/ngbw/sdk/tool/JobCompleteEvent.java M /trunk/sdk/src/main/java/org/ngbw/sdk/tool/SFTPInputStream.java M /trunk/sdk/src/main/java/org/ngbw/sdk/tool/SSHExecProcessWorker.java M /trunk/sdk/src/main/java/org/ngbw/sdk/tool/TaskMonitor.java M /trunk/sdk/src/main/java/org/ngbw/sdk/tool/TaskValidator.java M /trunk/sdk/src/main/java/org/ngbw/sdk/tool/Tool.java A /trunk/sdk/src/main/java/org/ngbw/utils/CreateTables.java M /trunk/sdk/src/main/java/org/ngbw/utils/DeleteTasks.java M /trunk/sdk/src/main/java/org/ngbw/utils/UserTgAllocation.java M /trunk/sdk/src/main/resources/pisexml/beast2_xsede.xml A /trunk/sdk/src/main/resources/pisexml/jmodeltest2_xsede.xml M /trunk/sdk/src/main/resources/pisexml/mafft_tg.xml A /trunk/sdk/src/main/resources/pisexml/paup_2.xml M /trunk/sdk/src/main/resources/pisexml/pauprat.xml M /trunk/sdk/src/main/resources/pisexml/raxmlhpc2_tgb.xml M /trunk/sdk/src/main/resources/pisexml/raxmlhpc2bb.xml M /trunk/sdk/src/main/resources/submitJob_log4j.xml A /trunk/sdk/src/main/resources/tool/activation-html.ftl A /trunk/sdk/src/main/resources/tool/activation-text.ftl M /trunk/sdk/src/main/resources/tool/spring-mail.xml merged in revision 8781 of the cipres trunk ------------------------------------------------------------------------ r30 | phoover | 2014-07-03 12:58:37 -0700 (Thu, 03 Jul 2014) | 3 lines Changed paths: M /trunk/sdk/scripts/remote_resource/trestles/beast2wrapper more updates from the cipres trunk ------------------------------------------------------------------------ r24 | phoover | 2014-06-11 12:55:31 -0700 (Wed, 11 Jun 2014) | 3 lines Changed paths: M /trunk/default/build.properties.template M /trunk/portal/src/main/java/org/ngbw/web/controllers/SessionController.java M /trunk/rest/build.py M /trunk/rest/cipresrest/alltests.sh A /trunk/rest/cipresrest/app.sh A /trunk/rest/cipresrest/concurrencytests.sh M /trunk/rest/cipresrest/job.sh A /trunk/rest/cipresrest/limit.sh M /trunk/rest/cipresrest/src/main/java/org/ngbw/cipresrest/auth/SecurityFilter.java M /trunk/rest/cipresrest/src/main/java/org/ngbw/cipresrest/webresource/CipresAdmin.java M /trunk/rest/cipresrest/src/main/java/org/ngbw/cipresrest/webresource/CipresJob.java M /trunk/rest/cipresrest/src/main/java/org/ngbw/cipresrest/webresource/CipresRestAdmin.java M /trunk/rest/cipresrest/src/main/java/org/ngbw/cipresrest/webresource/CipresUser.java M /trunk/rest/cipresrest/src/main/java/org/ngbw/cipresrest/webresource/JStatus.java M /trunk/rest/cipresrest/src/main/java/org/ngbw/cipresrest/webresource/JobNotFoundExceptionMapper.java M /trunk/rest/cipresrest/src/main/java/org/ngbw/cipresrest/webresource/ThisApplication.java A /trunk/rest/cipresrest/src/main/java/org/ngbw/cipresrest/webresource/UsageFilter.java A /trunk/rest/cipresrest/src/main/java/org/ngbw/cipresrest/webresource/UsageLimitExceptionMapper.java M /trunk/rest/cipresrest/src/main/java/org/ngbw/cipresrest/webresource/UserMismatchExceptionMapper.java M /trunk/rest/cipresrest/src/main/java/org/ngbw/cipresrest/webresource/ValidationExceptionMapper.java M /trunk/rest/cipresrest/src/main/java/org/ngbw/cipresrest/webresource/WebApplicationExceptionMapper.java M /trunk/rest/cipresrest/src/main/resources/log4j.xml M /trunk/rest/cipresrest/testAndDemoAccounts M /trunk/rest/cipresrest/testfw.sh M /trunk/rest/cipresrest/user.sh M /trunk/rest/cipresrest/user2.sh M /trunk/rest/datatypes/src/main/java/org/ngbw/restdatatypes/ErrorData.java M /trunk/rest/datatypes/src/main/java/org/ngbw/restdatatypes/UserData.java M /trunk/rest/pycipres/conf/pycipres.conf M /trunk/rest/restclient/src/main/java/org/ngbw/restclient/TaskCreate.java M /trunk/rest/restclient/src/main/webapp/taskCreate.jsp M /trunk/rest/restusers/src/main/java/org/ngbw/restusers/Application.java M /trunk/rest/restusers/src/main/java/org/ngbw/restusers/actions/BaseAction.java M /trunk/rest/restusers/src/main/java/org/ngbw/restusers/actions/Login.java M /trunk/rest/restusers/src/main/java/org/ngbw/restusers/actions/Profile.java M /trunk/rest/restusers/src/main/java/org/ngbw/restusers/actions/Register.java M /trunk/rest/restusers/src/main/java/org/ngbw/restusers/rest/WorkbenchMethods.java M /trunk/rest/restusers/src/main/resources/struts.xml M /trunk/rest/restusers/src/main/webapp/css/cipres.css M /trunk/rest/restusers/src/main/webapp/decorators/default.jsp M /trunk/rest/restusers/src/main/webapp/decorators/index.jsp M /trunk/rest/restusers/src/main/webapp/enduser/home.jsp M /trunk/rest/restusers/src/main/webapp/enduser/login.jsp M /trunk/rest/restusers/src/main/webapp/enduser/profile.jsp M /trunk/rest/restusers/src/main/webapp/enduser/register.jsp M /trunk/rest/restusers/src/main/webapp/enduser/updateProfile.jsp M /trunk/sdk/build.py M /trunk/sdk/scripts/remote_resource/trestles/RAxML-Light-1.0.9.sh M /trunk/sdk/scripts/remote_resource/trestles/beast2wrapper M /trunk/sdk/scripts/remote_resource/trestles/fasttreewrappper M /trunk/sdk/scripts/remote_resource/trestles/mb_3.2.1_mpiwrapper M /trunk/sdk/scripts/remote_resource/trestles/mbhwrapper M /trunk/sdk/scripts/remote_resource/trestles/mbmpiwrapper M /trunk/sdk/scripts/remote_resource/trestles/snappwrapper M /trunk/sdk/scripts/usage.py M /trunk/sdk/src/main/java/org/ngbw/examples/LoadTest1.java M /trunk/sdk/src/main/java/org/ngbw/examples/TestJob.java A /trunk/sdk/src/main/java/org/ngbw/sdk/UsageLimitException.java M /trunk/sdk/src/main/java/org/ngbw/sdk/Workbench.java M /trunk/sdk/src/main/java/org/ngbw/sdk/api/tool/ToolResource.java M /trunk/sdk/src/main/java/org/ngbw/sdk/clients/Client.java M /trunk/sdk/src/main/java/org/ngbw/sdk/clients/UmbrellaUser.java M /trunk/sdk/src/main/java/org/ngbw/sdk/common/util/FileUtils.java M /trunk/sdk/src/main/java/org/ngbw/sdk/common/util/StringUtils.java M /trunk/sdk/src/main/java/org/ngbw/sdk/database/Application.java A /trunk/sdk/src/main/java/org/ngbw/sdk/database/ConstraintException.java M /trunk/sdk/src/main/java/org/ngbw/sdk/database/FileColumn.java M /trunk/sdk/src/main/java/org/ngbw/sdk/database/Row.java M /trunk/sdk/src/main/java/org/ngbw/sdk/database/RunningTask.java M /trunk/sdk/src/main/java/org/ngbw/sdk/database/Statistics.java M /trunk/sdk/src/main/java/org/ngbw/sdk/database/Task.java M /trunk/sdk/src/main/java/org/ngbw/sdk/database/User.java M /trunk/sdk/src/main/java/org/ngbw/sdk/database/VersionedRow.java M /trunk/sdk/src/main/java/org/ngbw/sdk/jobs/Job.java M /trunk/sdk/src/main/java/org/ngbw/sdk/jobs/JobMetadata.java M /trunk/sdk/src/main/java/org/ngbw/sdk/jobs/JobOutput.java M /trunk/sdk/src/main/java/org/ngbw/sdk/jobs/JobStatus.java M /trunk/sdk/src/main/java/org/ngbw/sdk/jobs/JobWorkingDir.java A /trunk/sdk/src/main/java/org/ngbw/sdk/jobs/UsageLimit.java M /trunk/sdk/src/main/java/org/ngbw/sdk/tool/BaseProcessWorker.java M /trunk/sdk/src/main/java/org/ngbw/sdk/tool/DefaultToolResource.java M /trunk/sdk/src/main/java/org/ngbw/sdk/tool/JobCharge.java M /trunk/sdk/src/main/java/org/ngbw/sdk/tool/JobCompleteEvent.java M /trunk/sdk/src/main/java/org/ngbw/sdk/tool/RenderedCommand.java M /trunk/sdk/src/main/java/org/ngbw/sdk/tool/SSHProcessWorker.java M /trunk/sdk/src/main/java/org/ngbw/sdk/tool/SchedulerProperties.java M /trunk/sdk/src/main/java/org/ngbw/sdk/tool/TaskInitiate.java M /trunk/sdk/src/main/java/org/ngbw/sdk/tool/TaskMonitor.java M /trunk/sdk/src/main/java/org/ngbw/sdk/tool/Tool.java M /trunk/sdk/src/main/java/org/ngbw/sdk/tool/WorkQueue.java M /trunk/sdk/src/main/java/org/ngbw/utils/CancelUsersJobs.java M /trunk/sdk/src/main/java/org/ngbw/utils/RunTasks.java M /trunk/sdk/src/main/java/org/ngbw/utils/UserDelete.java M /trunk/sdk/src/main/resources/database/database.properties M /trunk/sdk/src/main/resources/pisexml/raxmlhpc2_tgb.xml A /trunk/sdk/src/main/resources/triton_run_time.xml M /trunk/sdk/src/main/resources/workbench.properties merged revision 8323 of the trunk ------------------------------------------------------------------------ r14 | phoover | 2014-04-01 15:23:36 -0700 (Tue, 01 Apr 2014) | 3 lines Changed paths: M /trunk/default/build.properties.template M /trunk/portal/pom.xml M /trunk/sdk/pom.xml M /trunk/sdk/scripts/deleteUserData.py M /trunk/sdk/scripts/deleteWarning1.txt M /trunk/sdk/scripts/mailer.py M /trunk/sdk/scripts/portal_allocation_message.txt M /trunk/sdk/scripts/remote_resource/lib.py M /trunk/sdk/scripts/remote_resource/trestles/gordon_lib.py M /trunk/sdk/scripts/remote_resource/trestles/gordon_lib_v2.py M /trunk/sdk/scripts/remote_resource/trestles/lib.py M /trunk/sdk/scripts/remote_resource/trestles/lib_v2.py M /trunk/sdk/scripts/remote_resource/trestles/test_gordon_lib.py M /trunk/sdk/scripts/remote_resource/trestles/test_lib.py M /trunk/sdk/scripts/remote_resource/triton/lib.py M /trunk/sdk/scripts/remote_resource/triton/lib_v2.py M /trunk/sdk/scripts/rest_allocation_message.txt D /trunk/sdk/src/main/codeGeneration/build.xml.save M /trunk/sdk/src/main/java/org/ngbw/sdk/clients/UmbrellaUser.java M /trunk/sdk/src/main/java/org/ngbw/sdk/jobs/JobStatus.java M /trunk/sdk/src/main/java/org/ngbw/sdk/tool/BaseProcessWorker.java M /trunk/sdk/src/main/java/org/ngbw/sdk/tool/JobCharge.java M /trunk/sdk/src/main/java/org/ngbw/sdk/tool/TaskMonitor.java M /trunk/sdk/src/main/resources/tool/job-html.ftl M /trunk/sdk/src/main/resources/tool/spring-mail.xml more resource filtering ------------------------------------------------------------------------ r11 | phoover | 2014-03-19 14:54:36 -0700 (Wed, 19 Mar 2014) | 3 lines Changed paths: M /trunk/build.py M /trunk/portal/src/main/codeGeneration/build.xml M /trunk/portal/src/main/java/org/ngbw/web/actions/NgbwSupport.java M /trunk/portal/src/main/webapp/css/cipres.css M /trunk/portal/src/main/webapp/decorators/default.jsp M /trunk/portal/src/main/webapp/decorators/index.jsp M /trunk/portal/src/main/webapp/js/site/core.js M /trunk/portal/src/main/webapp/js/themes/apple/style.css M /trunk/portal/src/main/webapp/pages/common/dataUploadLists.jsp M /trunk/portal/src/main/webapp/pages/common/footer.jsp M /trunk/portal/src/main/webapp/pages/common/menu.jsp M /trunk/portal/src/main/webapp/pages/user/data/displayData.jsp M /trunk/portal/src/main/webapp/pages/user/data/pasteForm.jsp M /trunk/portal/src/main/webapp/pages/user/folder/displayFolder.jsp M /trunk/portal/src/main/webapp/pages/user/folder/folderForm.jsp M /trunk/portal/src/main/webapp/pages/user/forgotPassword.jsp M /trunk/portal/src/main/webapp/pages/user/login.jsp M /trunk/portal/src/main/webapp/pages/user/profile.jsp M /trunk/portal/src/main/webapp/pages/user/register.jsp M /trunk/portal/src/main/webapp/pages/user/task/displayOutput.jsp M /trunk/portal/src/main/webapp/pages/user/task/displayTask.jsp M /trunk/portal/src/main/webapp/pages/user/task/displayTransformedRecord.jsp M /trunk/portal/src/main/webapp/pages/user/task/outputForm.jsp M /trunk/portal/src/main/webapp/pages/user/task/taskList.jsp M /trunk/portal/src/main/webapp/pages/user/task/taskSummary.jsp M /trunk/portal/src/main/webapp/pages/user/updatePassword.jsp M /trunk/portal/src/main/webapp/pages/user/updateProfile.jsp D /trunk/sdk/scripts/allocation_message1.txt D /trunk/sdk/scripts/allocation_message2.txt D /trunk/sdk/scripts/allocation_message3.txt D /trunk/sdk/scripts/allocation_message4.txt D /trunk/sdk/scripts/allocation_message5.txt A /trunk/sdk/scripts/deleteTasksD M /trunk/sdk/scripts/deleteUserData.py M /trunk/sdk/scripts/mailer.py A /trunk/sdk/scripts/portal_allocation_message.txt A /trunk/sdk/scripts/remote_resource/trestles/PBMultiRun.bash A /trunk/sdk/scripts/remote_resource/trestles/PBterminator.bash A /trunk/sdk/scripts/remote_resource/trestles/SDSC-gateway-submit-attributes A /trunk/sdk/scripts/remote_resource/trestles/beast2onlywrapper A /trunk/sdk/scripts/remote_resource/trestles/beast2wrapper A /trunk/sdk/scripts/remote_resource/trestles/fasttreewrappper M /trunk/sdk/scripts/remote_resource/trestles/garli2.0_wrap.sh M /trunk/sdk/scripts/remote_resource/trestles/gordon_submit_v2.py M /trunk/sdk/scripts/remote_resource/trestles/raxmlHPC-HYBRID M /trunk/sdk/scripts/remote_resource/trestles/raxmlHPC-PTHREADS A /trunk/sdk/scripts/remote_resource/trestles/snappwrapper M /trunk/sdk/scripts/remote_resource/trestles/submit_v2.py M /trunk/sdk/scripts/remote_resource/trestles/test_gordon_submit.py M /trunk/sdk/scripts/remote_resource/trestles/test_submit.py M /trunk/sdk/scripts/remote_resource/triton/submit_v2.py A /trunk/sdk/scripts/rest_allocation_message.txt M /trunk/sdk/scripts/tgusage.sh M /trunk/sdk/scripts/usage.py M /trunk/sdk/scripts/usage.sh M /trunk/sdk/src/main/codeGeneration/build.xml A /trunk/sdk/src/main/codeGeneration/lib/jar/resolver.jar A /trunk/sdk/src/main/codeGeneration/lib/jar/serializer.jar A /trunk/sdk/src/main/codeGeneration/lib/jar/xalan.jar A /trunk/sdk/src/main/codeGeneration/lib/jar/xercesImpl.jar A /trunk/sdk/src/main/codeGeneration/lib/jar/xml-apis.jar M /trunk/sdk/src/main/java/org/ngbw/sdk/api/tool/ToolRegistry.java M /trunk/sdk/src/main/java/org/ngbw/sdk/api/tool/ToolResource.java M /trunk/sdk/src/main/java/org/ngbw/sdk/api/tool/ToolResourceType.java M /trunk/sdk/src/main/java/org/ngbw/sdk/common/util/FileUtils.java M /trunk/sdk/src/main/java/org/ngbw/sdk/database/Column.java A /trunk/sdk/src/main/java/org/ngbw/sdk/database/DatabaseTools.java M /trunk/sdk/src/main/java/org/ngbw/sdk/database/ExampleRow.java M /trunk/sdk/src/main/java/org/ngbw/sdk/database/FileColumn.java M /trunk/sdk/src/main/java/org/ngbw/sdk/database/LongColumn.java M /trunk/sdk/src/main/java/org/ngbw/sdk/database/MemoryValue.java M /trunk/sdk/src/main/java/org/ngbw/sdk/database/SourceDocumentRow.java M /trunk/sdk/src/main/java/org/ngbw/sdk/database/Statistics.java M /trunk/sdk/src/main/java/org/ngbw/sdk/database/StreamColumn.java M /trunk/sdk/src/main/java/org/ngbw/sdk/database/TextColumn.java M /trunk/sdk/src/main/java/org/ngbw/sdk/database/User.java M /trunk/sdk/src/main/java/org/ngbw/sdk/database/Value.java M /trunk/sdk/src/main/java/org/ngbw/sdk/tool/BaseProcessWorker.java M /trunk/sdk/src/main/java/org/ngbw/sdk/tool/DefaultToolRegistry.java M /trunk/sdk/src/main/java/org/ngbw/sdk/tool/DefaultToolResource.java A /trunk/sdk/src/main/java/org/ngbw/sdk/tool/JobCharge.java M /trunk/sdk/src/main/java/org/ngbw/sdk/tool/SFTPFileHandler.java M /trunk/sdk/src/main/java/org/ngbw/sdk/tool/SSHExecProcessWorker.java M /trunk/sdk/src/main/java/org/ngbw/sdk/tool/Tool.java A /trunk/sdk/src/main/java/org/ngbw/utils/MigrateDbFiles.java M /trunk/sdk/src/main/java/org/ngbw/utils/UserDelete.java A /trunk/sdk/src/main/resources/pisexml/fasttree_tg.xml M /trunk/sdk/src/main/resources/pisexml/raxmlhpc2_tgb.xml M /trunk/sdk/src/main/resources/pisexml/raxmlhpc2bb.xml M /trunk/sdk/src/main/resources/workbench.properties merged in changes from the trunk ------------------------------------------------------------------------ r1 | phoover | 2014-02-10 12:51:07 -0800 (Mon, 10 Feb 2014) | 3 lines Changed paths: A /branches A /tags A /trunk A /trunk/build.py A /trunk/defaults A /trunk/defaults/build.properties.template A /trunk/defaults/portal A /trunk/defaults/portal/src A /trunk/defaults/portal/src/main A /trunk/defaults/portal/src/main/webapp A /trunk/defaults/portal/src/main/webapp/css A /trunk/defaults/sdk A /trunk/defaults/sdk/src A /trunk/defaults/sdk/src/main A /trunk/defaults/sdk/src/main/resources A /trunk/defaults/sdk/src/main/resources/ssl.properties A /trunk/defaults/sdk/src/main/resources/tool A /trunk/defaults/sdk/src/main/resources/tool/tool-registry.cfg.xml A /trunk/lib A /trunk/lib/python A /trunk/lib/python/cipres A /trunk/lib/python/cipres/BuildError.py A /trunk/lib/python/cipres/Cipres.py A /trunk/lib/python/cipres/Properties.py A /trunk/lib/python/cipres/__init__.py A /trunk/pom.xml A /trunk/portal A /trunk/portal/build.py A /trunk/portal/pom.xml A /trunk/portal/src A /trunk/portal/src/main A /trunk/portal/src/main/codeGeneration A /trunk/portal/src/main/codeGeneration/FreemarkerTemplate A /trunk/portal/src/main/codeGeneration/FreemarkerTemplate/pise2JSP.ftl A /trunk/portal/src/main/codeGeneration/FreemarkerTemplate/pise2JSPAdvanced.ftl A /trunk/portal/src/main/codeGeneration/FreemarkerTemplate/pise2JSPSimple.ftl A /trunk/portal/src/main/codeGeneration/FreemarkerTemplate/pise2JavaScript.ftl A /trunk/portal/src/main/codeGeneration/FreemarkerTemplate/pise2JavaScriptControl.ftl A /trunk/portal/src/main/codeGeneration/FreemarkerTemplate/pise2JavaScriptWarning.ftl A /trunk/portal/src/main/codeGeneration/FreemarkerTemplate/pise2Logic.ftl A /trunk/portal/src/main/codeGeneration/FreemarkerTemplate/pise2action.ftl A /trunk/portal/src/main/codeGeneration/FreemarkerTemplate/pise2action_defaultValues.ftl A /trunk/portal/src/main/codeGeneration/FreemarkerTemplate/pise2action_old.ftl A /trunk/portal/src/main/codeGeneration/FreemarkerTemplate/pise2help.ftl A /trunk/portal/src/main/codeGeneration/FreemarkerTemplate/pise2outputProperties.ftl A /trunk/portal/src/main/codeGeneration/FreemarkerTemplate/pise2property.ftl A /trunk/portal/src/main/codeGeneration/FreemarkerTemplate/pise2registry.ftl A /trunk/portal/src/main/codeGeneration/FreemarkerTemplate/pise2strutsXML.ftl A /trunk/portal/src/main/codeGeneration/FreemarkerTemplate/pise2validationJava.ftl A /trunk/portal/src/main/codeGeneration/FreemarkerTemplate/pise2validationXML_old.ftl A /trunk/portal/src/main/codeGeneration/FreemarkerTemplate/pise2valueDefaultTest.ftl A /trunk/portal/src/main/codeGeneration/FreemarkerTemplate/pise2valueDefaultTestInfile.ftl A /trunk/portal/src/main/codeGeneration/FreemarkerTemplate/pisePrecondExtract.ftl A /trunk/portal/src/main/codeGeneration/FreemarkerTemplate/tool_registry2list.ftl A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/CSR.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/PARSER A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/PARSER/README A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/PARSER/pise.dtd A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/PARSER/pise.xsd A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/Puzzle.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/RepeatMasker.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/XMLDIR A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/XMLDIR/blast_init.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/XMLDIR/emboss.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/XMLDIR/fastapath.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/XMLDIR/genewisepar_param.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/XMLDIR/glimmer_header.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/XMLDIR/hmmpar_param.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/XMLDIR/nucdbs.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/XMLDIR/phylip_header.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/XMLDIR/protdbs.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/aaindexextract.xml A 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/trunk/portal/src/main/codeGeneration/Pise_5.a_latest/preg.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/prettyalign.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/prettyplot.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/prettyseq.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/prima.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/primers.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/primersearch.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/primo.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/primo.xml.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/prodom.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/profit.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/prophecy.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/prophet.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/prose.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/prosearch.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/prot_nucml.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/protal2dna.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/protdbs.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/protdist.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/protnuc_ml.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/protpars.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/pscan.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/psiblast.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/psiblastpar.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/psort2.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/pyramids.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/pyreval.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/qatest.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/qstar.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/quicktree.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/readnexus.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/readseq.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/recoder.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/redata.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/remap.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/repeats.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/reputer.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/restover.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/restrict.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/revseq.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/rif.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/rnadistance.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/rnaeval.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/rnafold.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/rnaga.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/rnaheat.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/rnainverse.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/rnapdist.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/rnasubopt.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/sam2hmmer.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/sampleseqs.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/saps.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/satellites.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/scan_for_matches.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/scope.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/scopparse.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/screen2h.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/seqboot.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/seqclean.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/seqgen.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/seqinfo.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/seqmatchall.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/seqret.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/seqretall.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/seqretallfeat.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/seqretset.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/seqretsingle.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/seqsblast.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/seqstat.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/showalign.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/showdb.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/showfeat.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/showorf.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/showseq.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/shuffleseq.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/sig.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/sigcleave.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/siggen.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/sigplot.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/sigscan.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/silent.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/sirna.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/sixpack.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/skipseq.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/smile.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/smile2.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/sorttrans.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/spacne.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/splitter.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/sputnik.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/squizz.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/sreformat.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/ssearch.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/stamp.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/stamps.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/stretcher.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/stride.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/stssearch.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/supermatcher.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/swissparse.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/syco.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/t_coffee.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/tacg.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/tcode.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/tfscan.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/tipdate.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/titi.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/tmap.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/toppred.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/tranalign.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/transeq.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/transform.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/treealign.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/treetypedisplay.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/trimest.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/trimseq.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/trnascan.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/twofeat.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/union.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/unroot.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/vectorstrip.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/water.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/weighbor.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/whichdb.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/wise.xml A /trunk/portal/src/main/codeGeneration/Pise_5.a_latest/wise2.xml A 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/trunk/portal/src/main/codeGeneration/lib/jar/xml-apis.jar A /trunk/portal/src/main/codeGeneration/lib/jar/xmltask-v1.14.jar A /trunk/portal/src/main/codeGeneration/lib/struts-tools.xml A /trunk/portal/src/main/docs A /trunk/portal/src/main/docs/build-deploy.txt A /trunk/portal/src/main/java A /trunk/portal/src/main/java/org A /trunk/portal/src/main/java/org/ngbw A /trunk/portal/src/main/java/org/ngbw/web A /trunk/portal/src/main/java/org/ngbw/web/actions A /trunk/portal/src/main/java/org/ngbw/web/actions/ArchiveManager.java A /trunk/portal/src/main/java/org/ngbw/web/actions/CreateData.java A /trunk/portal/src/main/java/org/ngbw/web/actions/CreateTask.java A /trunk/portal/src/main/java/org/ngbw/web/actions/DataManager.java A /trunk/portal/src/main/java/org/ngbw/web/actions/DownloadAction.java A /trunk/portal/src/main/java/org/ngbw/web/actions/FolderManager.java A /trunk/portal/src/main/java/org/ngbw/web/actions/ManageTasks.java A 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/trunk/sdk/scripts/loadResults A /trunk/sdk/scripts/loadResultsD A /trunk/sdk/scripts/mailer.py A /trunk/sdk/scripts/perlEval A /trunk/sdk/scripts/piseEval A /trunk/sdk/scripts/recoverResults A /trunk/sdk/scripts/recoverResultsD A /trunk/sdk/scripts/remote_resource A /trunk/sdk/scripts/remote_resource/Readme.txt A /trunk/sdk/scripts/remote_resource/lib.py A /trunk/sdk/scripts/remote_resource/trestles A /trunk/sdk/scripts/remote_resource/trestles/RAxML-Light-1.0.9.sh A /trunk/sdk/scripts/remote_resource/trestles/beastonlywrapper A /trunk/sdk/scripts/remote_resource/trestles/beastwrapper A /trunk/sdk/scripts/remote_resource/trestles/checkjobs.py A /trunk/sdk/scripts/remote_resource/trestles/checkjobs_v2.py A /trunk/sdk/scripts/remote_resource/trestles/cipres-tgusage-new A /trunk/sdk/scripts/remote_resource/trestles/collectBootTrees.sh A /trunk/sdk/scripts/remote_resource/trestles/delete.py A /trunk/sdk/scripts/remote_resource/trestles/delete_v2.py A 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/trunk/sdk/scripts/userTgAllocation A /trunk/sdk/scripts/ws_cleanup.sh A /trunk/sdk/src A /trunk/sdk/src/main A /trunk/sdk/src/main/codeGeneration A /trunk/sdk/src/main/codeGeneration/FreemarkerTemplate A /trunk/sdk/src/main/codeGeneration/FreemarkerTemplate/pise2JSP.ftl A /trunk/sdk/src/main/codeGeneration/FreemarkerTemplate/pise2JSPAdvanced.ftl A /trunk/sdk/src/main/codeGeneration/FreemarkerTemplate/pise2JSPSimple.ftl A /trunk/sdk/src/main/codeGeneration/FreemarkerTemplate/pise2JavaScript.ftl A /trunk/sdk/src/main/codeGeneration/FreemarkerTemplate/pise2JavaScriptControl.ftl A /trunk/sdk/src/main/codeGeneration/FreemarkerTemplate/pise2JavaScriptWarning.ftl A /trunk/sdk/src/main/codeGeneration/FreemarkerTemplate/pise2Logic.ftl A /trunk/sdk/src/main/codeGeneration/FreemarkerTemplate/pise2action.ftl A /trunk/sdk/src/main/codeGeneration/FreemarkerTemplate/pise2action_defaultValues.ftl A /trunk/sdk/src/main/codeGeneration/FreemarkerTemplate/pise2action_old.ftl A 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/trunk/sdk/src/main/codeGeneration/lib A /trunk/sdk/src/main/codeGeneration/lib/jar A /trunk/sdk/src/main/codeGeneration/lib/jar/freemarker-2.3.8.jar A /trunk/sdk/src/main/codeGeneration/lib/jar/xmltask-v1.14.jar A /trunk/sdk/src/main/java A /trunk/sdk/src/main/java/org A /trunk/sdk/src/main/java/org/ngbw A /trunk/sdk/src/main/java/org/ngbw/examples A /trunk/sdk/src/main/java/org/ngbw/examples/BlastTaskSample.java.save A /trunk/sdk/src/main/java/org/ngbw/examples/BlastTransformation.java A /trunk/sdk/src/main/java/org/ngbw/examples/LoadTest1.java A /trunk/sdk/src/main/java/org/ngbw/examples/LocalProcessWorkerSample.java.save A /trunk/sdk/src/main/java/org/ngbw/examples/LuceneIndexerClient.java A /trunk/sdk/src/main/java/org/ngbw/examples/RaxmlTaskSample.java.save A /trunk/sdk/src/main/java/org/ngbw/examples/RayTraceDispatcher.java A /trunk/sdk/src/main/java/org/ngbw/examples/SimpleMetaQueryClient.java A /trunk/sdk/src/main/java/org/ngbw/examples/TestJob.java A 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/trunk/sdk/src/main/java/org/ngbw/pise/commandrenderer/pise/Category.java A /trunk/sdk/src/main/java/org/ngbw/pise/commandrenderer/pise/Code.java A /trunk/sdk/src/main/java/org/ngbw/pise/commandrenderer/pise/Command.java A /trunk/sdk/src/main/java/org/ngbw/pise/commandrenderer/pise/Comment.java A /trunk/sdk/src/main/java/org/ngbw/pise/commandrenderer/pise/Ctrl.java A /trunk/sdk/src/main/java/org/ngbw/pise/commandrenderer/pise/Ctrls.java A /trunk/sdk/src/main/java/org/ngbw/pise/commandrenderer/pise/Description.java A /trunk/sdk/src/main/java/org/ngbw/pise/commandrenderer/pise/Doclink.java A /trunk/sdk/src/main/java/org/ngbw/pise/commandrenderer/pise/Filenames.java A /trunk/sdk/src/main/java/org/ngbw/pise/commandrenderer/pise/Flist.java A /trunk/sdk/src/main/java/org/ngbw/pise/commandrenderer/pise/Format.java A /trunk/sdk/src/main/java/org/ngbw/pise/commandrenderer/pise/Group.java A /trunk/sdk/src/main/java/org/ngbw/pise/commandrenderer/pise/Head.java A 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/trunk/sdk/src/main/java/org/ngbw/pise/commandrenderer/pise/Vdef.java A /trunk/sdk/src/main/java/org/ngbw/pise/commandrenderer/pise/Vlist.java A /trunk/sdk/src/main/java/org/ngbw/pise/commandrenderer/pise/Withpipe.java A /trunk/sdk/src/main/java/org/ngbw/pise/commandrenderer/pise/package-info.java A /trunk/sdk/src/main/java/org/ngbw/sdk A /trunk/sdk/src/main/java/org/ngbw/sdk/BwbImporter.java A /trunk/sdk/src/main/java/org/ngbw/sdk/DataDetails.java A /trunk/sdk/src/main/java/org/ngbw/sdk/UserAuthenticationException.java A /trunk/sdk/src/main/java/org/ngbw/sdk/ValidationException.java A /trunk/sdk/src/main/java/org/ngbw/sdk/Workbench.java A /trunk/sdk/src/main/java/org/ngbw/sdk/WorkbenchException.java A /trunk/sdk/src/main/java/org/ngbw/sdk/WorkbenchSession.java A /trunk/sdk/src/main/java/org/ngbw/sdk/api A /trunk/sdk/src/main/java/org/ngbw/sdk/api/conversion A /trunk/sdk/src/main/java/org/ngbw/sdk/api/conversion/ConversionException.java A 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/trunk/sdk/src/main/java/org/ngbw/sdk/api/data/DataResourceQuery.java A /trunk/sdk/src/main/java/org/ngbw/sdk/api/data/DataResourceType.java A /trunk/sdk/src/main/java/org/ngbw/sdk/api/data/DatasetConfig.java A /trunk/sdk/src/main/java/org/ngbw/sdk/api/data/DatasetRegistry.java A /trunk/sdk/src/main/java/org/ngbw/sdk/api/data/DatasetRegistryBuilder.java A /trunk/sdk/src/main/java/org/ngbw/sdk/api/data/DatasetService.java A /trunk/sdk/src/main/java/org/ngbw/sdk/api/data/MetaQuery.java A /trunk/sdk/src/main/java/org/ngbw/sdk/api/data/QueryResult.java A /trunk/sdk/src/main/java/org/ngbw/sdk/api/data/ResultTuple.java A /trunk/sdk/src/main/java/org/ngbw/sdk/api/data/SearchHitCollection.java A /trunk/sdk/src/main/java/org/ngbw/sdk/api/data/SimpleQuery.java A /trunk/sdk/src/main/java/org/ngbw/sdk/api/data/SimpleSearchMetaQuery.java A /trunk/sdk/src/main/java/org/ngbw/sdk/api/data/package-info.java A /trunk/sdk/src/main/java/org/ngbw/sdk/api/tool A /trunk/sdk/src/main/java/org/ngbw/sdk/api/tool/AuthenticationType.java A /trunk/sdk/src/main/java/org/ngbw/sdk/api/tool/CommandRenderer.java A /trunk/sdk/src/main/java/org/ngbw/sdk/api/tool/FieldError.java A /trunk/sdk/src/main/java/org/ngbw/sdk/api/tool/FileHandler.java A /trunk/sdk/src/main/java/org/ngbw/sdk/api/tool/ParameterValidator.java A /trunk/sdk/src/main/java/org/ngbw/sdk/api/tool/ParameterValidator2.java A /trunk/sdk/src/main/java/org/ngbw/sdk/api/tool/ProcessResult.java A /trunk/sdk/src/main/java/org/ngbw/sdk/api/tool/ToolConfig.java A /trunk/sdk/src/main/java/org/ngbw/sdk/api/tool/ToolIOMode.java A /trunk/sdk/src/main/java/org/ngbw/sdk/api/tool/ToolRegistry.java A /trunk/sdk/src/main/java/org/ngbw/sdk/api/tool/ToolRegistryBuilder.java A /trunk/sdk/src/main/java/org/ngbw/sdk/api/tool/ToolResource.java A /trunk/sdk/src/main/java/org/ngbw/sdk/api/tool/ToolResourceType.java A /trunk/sdk/src/main/java/org/ngbw/sdk/api/tool/package-info.java A /trunk/sdk/src/main/java/org/ngbw/sdk/bioutils A /trunk/sdk/src/main/java/org/ngbw/sdk/bioutils/alignment A /trunk/sdk/src/main/java/org/ngbw/sdk/bioutils/alignment/Alignment.java A /trunk/sdk/src/main/java/org/ngbw/sdk/bioutils/alignment/AlignmentParser.java A /trunk/sdk/src/main/java/org/ngbw/sdk/bioutils/blast A /trunk/sdk/src/main/java/org/ngbw/sdk/bioutils/blast/blasttxt A /trunk/sdk/src/main/java/org/ngbw/sdk/bioutils/blast/blasttxt/BlastHit.java A /trunk/sdk/src/main/java/org/ngbw/sdk/bioutils/blast/blasttxt/BlastResult.java A /trunk/sdk/src/main/java/org/ngbw/sdk/bioutils/blast/blasttxt/BlastTEXTParser.java A /trunk/sdk/src/main/java/org/ngbw/sdk/bioutils/blast/blastxml A /trunk/sdk/src/main/java/org/ngbw/sdk/bioutils/blast/blastxml/BlastOutput.java A /trunk/sdk/src/main/java/org/ngbw/sdk/bioutils/blast/blastxml/BlastOutputDb.java A /trunk/sdk/src/main/java/org/ngbw/sdk/bioutils/blast/blastxml/BlastOutputIterations.java A /trunk/sdk/src/main/java/org/ngbw/sdk/bioutils/blast/blastxml/BlastOutputParam.java A /trunk/sdk/src/main/java/org/ngbw/sdk/bioutils/blast/blastxml/BlastOutputProgram.java A /trunk/sdk/src/main/java/org/ngbw/sdk/bioutils/blast/blastxml/BlastOutputQueryDef.java A /trunk/sdk/src/main/java/org/ngbw/sdk/bioutils/blast/blastxml/BlastOutputQueryID.java A /trunk/sdk/src/main/java/org/ngbw/sdk/bioutils/blast/blastxml/BlastOutputQueryLen.java A /trunk/sdk/src/main/java/org/ngbw/sdk/bioutils/blast/blastxml/BlastOutputReference.java A /trunk/sdk/src/main/java/org/ngbw/sdk/bioutils/blast/blastxml/BlastOutputVersion.java A /trunk/sdk/src/main/java/org/ngbw/sdk/bioutils/blast/blastxml/Hit.java A /trunk/sdk/src/main/java/org/ngbw/sdk/bioutils/blast/blastxml/HitAccession.java A /trunk/sdk/src/main/java/org/ngbw/sdk/bioutils/blast/blastxml/HitDef.java A /trunk/sdk/src/main/java/org/ngbw/sdk/bioutils/blast/blastxml/HitHsps.java A /trunk/sdk/src/main/java/org/ngbw/sdk/bioutils/blast/blastxml/HitId.java A /trunk/sdk/src/main/java/org/ngbw/sdk/bioutils/blast/blastxml/HitLen.java A /trunk/sdk/src/main/java/org/ngbw/sdk/bioutils/blast/blastxml/HitNum.java A /trunk/sdk/src/main/java/org/ngbw/sdk/bioutils/blast/blastxml/Hsp.java A /trunk/sdk/src/main/java/org/ngbw/sdk/bioutils/blast/blastxml/HspAlignLen.java A /trunk/sdk/src/main/java/org/ngbw/sdk/bioutils/blast/blastxml/HspBitScore.java A /trunk/sdk/src/main/java/org/ngbw/sdk/bioutils/blast/blastxml/HspEvalue.java A /trunk/sdk/src/main/java/org/ngbw/sdk/bioutils/blast/blastxml/HspHitFrame.java A /trunk/sdk/src/main/java/org/ngbw/sdk/bioutils/blast/blastxml/HspHitFrom.java A /trunk/sdk/src/main/java/org/ngbw/sdk/bioutils/blast/blastxml/HspHitTo.java A /trunk/sdk/src/main/java/org/ngbw/sdk/bioutils/blast/blastxml/HspHseq.java A /trunk/sdk/src/main/java/org/ngbw/sdk/bioutils/blast/blastxml/HspIdentity.java A /trunk/sdk/src/main/java/org/ngbw/sdk/bioutils/blast/blastxml/HspMidline.java A /trunk/sdk/src/main/java/org/ngbw/sdk/bioutils/blast/blastxml/HspNum.java A /trunk/sdk/src/main/java/org/ngbw/sdk/bioutils/blast/blastxml/HspPositive.java A /trunk/sdk/src/main/java/org/ngbw/sdk/bioutils/blast/blastxml/HspQseq.java A /trunk/sdk/src/main/java/org/ngbw/sdk/bioutils/blast/blastxml/HspQueryFrame.java A /trunk/sdk/src/main/java/org/ngbw/sdk/bioutils/blast/blastxml/HspQueryFrom.java A /trunk/sdk/src/main/java/org/ngbw/sdk/bioutils/blast/blastxml/HspQueryTo.java A /trunk/sdk/src/main/java/org/ngbw/sdk/bioutils/blast/blastxml/HspScore.java A /trunk/sdk/src/main/java/org/ngbw/sdk/bioutils/blast/blastxml/Iteration.java A /trunk/sdk/src/main/java/org/ngbw/sdk/bioutils/blast/blastxml/IterationHits.java A /trunk/sdk/src/main/java/org/ngbw/sdk/bioutils/blast/blastxml/IterationIterNum.java A /trunk/sdk/src/main/java/org/ngbw/sdk/bioutils/blast/blastxml/IterationStat.java A /trunk/sdk/src/main/java/org/ngbw/sdk/bioutils/blast/blastxml/ObjectFactory.java A /trunk/sdk/src/main/java/org/ngbw/sdk/bioutils/blast/blastxml/Parameters.java A /trunk/sdk/src/main/java/org/ngbw/sdk/bioutils/blast/blastxml/ParametersExpect.java A /trunk/sdk/src/main/java/org/ngbw/sdk/bioutils/blast/blastxml/ParametersFilter.java A /trunk/sdk/src/main/java/org/ngbw/sdk/bioutils/blast/blastxml/ParametersGapExtend.java A /trunk/sdk/src/main/java/org/ngbw/sdk/bioutils/blast/blastxml/ParametersGapOpen.java A /trunk/sdk/src/main/java/org/ngbw/sdk/bioutils/blast/blastxml/ParametersScMatch.java A /trunk/sdk/src/main/java/org/ngbw/sdk/bioutils/blast/blastxml/ParametersScMismatch.java A /trunk/sdk/src/main/java/org/ngbw/sdk/bioutils/blast/blastxml/Statistics.java A /trunk/sdk/src/main/java/org/ngbw/sdk/bioutils/blast/blastxml/StatisticsDbLen.java A /trunk/sdk/src/main/java/org/ngbw/sdk/bioutils/blast/blastxml/StatisticsDbNum.java A /trunk/sdk/src/main/java/org/ngbw/sdk/bioutils/blast/blastxml/StatisticsEffSpace.java A /trunk/sdk/src/main/java/org/ngbw/sdk/bioutils/blast/blastxml/StatisticsEntropy.java A /trunk/sdk/src/main/java/org/ngbw/sdk/bioutils/blast/blastxml/StatisticsHspLen.java A /trunk/sdk/src/main/java/org/ngbw/sdk/bioutils/blast/blastxml/StatisticsKappa.java A /trunk/sdk/src/main/java/org/ngbw/sdk/bioutils/blast/blastxml/StatisticsLambda.java A /trunk/sdk/src/main/java/org/ngbw/sdk/bioutils/blast/blastxml/package-info.java A /trunk/sdk/src/main/java/org/ngbw/sdk/bioutils/fastout A /trunk/sdk/src/main/java/org/ngbw/sdk/bioutils/fastout/FastaHit.java A /trunk/sdk/src/main/java/org/ngbw/sdk/bioutils/fastout/FastaOutParser.java A /trunk/sdk/src/main/java/org/ngbw/sdk/bioutils/fastout/FastaResult.java A /trunk/sdk/src/main/java/org/ngbw/sdk/bioutils/package-info.java A /trunk/sdk/src/main/java/org/ngbw/sdk/bioutils/pal A /trunk/sdk/src/main/java/org/ngbw/sdk/bioutils/sequence A /trunk/sdk/src/main/java/org/ngbw/sdk/bioutils/sequence/MolWeightCalculator.java A /trunk/sdk/src/main/java/org/ngbw/sdk/bioutils/sequence/PiCalculator.java A /trunk/sdk/src/main/java/org/ngbw/sdk/bioutils/sequence/SequenceUtils.java A /trunk/sdk/src/main/java/org/ngbw/sdk/bioutils/tree A /trunk/sdk/src/main/java/org/ngbw/sdk/clients A /trunk/sdk/src/main/java/org/ngbw/sdk/clients/Client.java A /trunk/sdk/src/main/java/org/ngbw/sdk/clients/ClientApplication.java A /trunk/sdk/src/main/java/org/ngbw/sdk/clients/UmbrellaUser.java A /trunk/sdk/src/main/java/org/ngbw/sdk/common A /trunk/sdk/src/main/java/org/ngbw/sdk/common/package-info.java A /trunk/sdk/src/main/java/org/ngbw/sdk/common/util A /trunk/sdk/src/main/java/org/ngbw/sdk/common/util/AsyncProcessRunner.java A /trunk/sdk/src/main/java/org/ngbw/sdk/common/util/BaseValidator.java A /trunk/sdk/src/main/java/org/ngbw/sdk/common/util/BeanUtils.java A /trunk/sdk/src/main/java/org/ngbw/sdk/common/util/ClassPath.java A /trunk/sdk/src/main/java/org/ngbw/sdk/common/util/ConvertEncoding.java A /trunk/sdk/src/main/java/org/ngbw/sdk/common/util/FTPUtils.java A /trunk/sdk/src/main/java/org/ngbw/sdk/common/util/FileUtils.java A /trunk/sdk/src/main/java/org/ngbw/sdk/common/util/GsiSSHProcessRunner.java A /trunk/sdk/src/main/java/org/ngbw/sdk/common/util/IOUtils.java A /trunk/sdk/src/main/java/org/ngbw/sdk/common/util/InputStreamCollector.java A /trunk/sdk/src/main/java/org/ngbw/sdk/common/util/InputStreamLogger.java A /trunk/sdk/src/main/java/org/ngbw/sdk/common/util/InvalidArgumentException.java A /trunk/sdk/src/main/java/org/ngbw/sdk/common/util/MapUtil.java A /trunk/sdk/src/main/java/org/ngbw/sdk/common/util/PServerClient.java A /trunk/sdk/src/main/java/org/ngbw/sdk/common/util/ProcessRunner.java A /trunk/sdk/src/main/java/org/ngbw/sdk/common/util/ProcessUtils.java A /trunk/sdk/src/main/java/org/ngbw/sdk/common/util/PropertyLoader.java A /trunk/sdk/src/main/java/org/ngbw/sdk/common/util/Resource.java A /trunk/sdk/src/main/java/org/ngbw/sdk/common/util/ResourceNotFoundException.java A /trunk/sdk/src/main/java/org/ngbw/sdk/common/util/SSHExecProcessRunner.java A /trunk/sdk/src/main/java/org/ngbw/sdk/common/util/SSHProcessRunner.java A /trunk/sdk/src/main/java/org/ngbw/sdk/common/util/SimpleFilenameFilter.java A /trunk/sdk/src/main/java/org/ngbw/sdk/common/util/SourceFileReader.java A /trunk/sdk/src/main/java/org/ngbw/sdk/common/util/StringType.java A /trunk/sdk/src/main/java/org/ngbw/sdk/common/util/StringUtils.java A /trunk/sdk/src/main/java/org/ngbw/sdk/common/util/SuperString.java A /trunk/sdk/src/main/java/org/ngbw/sdk/common/util/TimeUtils.java A /trunk/sdk/src/main/java/org/ngbw/sdk/common/util/UncompressInputStream.java A /trunk/sdk/src/main/java/org/ngbw/sdk/common/util/ValidationResult.java A /trunk/sdk/src/main/java/org/ngbw/sdk/common/util/WholeFileLock.java A /trunk/sdk/src/main/java/org/ngbw/sdk/common/util/XMLHelper.java A /trunk/sdk/src/main/java/org/ngbw/sdk/common/util/XMLValidation.java A /trunk/sdk/src/main/java/org/ngbw/sdk/common/util/package-info.java A /trunk/sdk/src/main/java/org/ngbw/sdk/conversion A /trunk/sdk/src/main/java/org/ngbw/sdk/conversion/BaseSourceDocumentConverter.java A /trunk/sdk/src/main/java/org/ngbw/sdk/conversion/BaseSourceDocumentReader.java A /trunk/sdk/src/main/java/org/ngbw/sdk/conversion/BlastTEXTReader.java A /trunk/sdk/src/main/java/org/ngbw/sdk/conversion/BlastTEXTRecordFilter.java A /trunk/sdk/src/main/java/org/ngbw/sdk/conversion/BlastXMLReader.java A /trunk/sdk/src/main/java/org/ngbw/sdk/conversion/DefaultConversionRegistry.java A /trunk/sdk/src/main/java/org/ngbw/sdk/conversion/DefaultConversionRegistryBuilder.java A /trunk/sdk/src/main/java/org/ngbw/sdk/conversion/DefaultConversionService.java A /trunk/sdk/src/main/java/org/ngbw/sdk/conversion/DefaultSequenceParser.java A /trunk/sdk/src/main/java/org/ngbw/sdk/conversion/FastaHeaderParser.java A /trunk/sdk/src/main/java/org/ngbw/sdk/conversion/FastaOutputReader.java A /trunk/sdk/src/main/java/org/ngbw/sdk/conversion/FastaOutputRecordFilter.java A /trunk/sdk/src/main/java/org/ngbw/sdk/conversion/FastaReader.java A /trunk/sdk/src/main/java/org/ngbw/sdk/conversion/FastaWriter.java A /trunk/sdk/src/main/java/org/ngbw/sdk/conversion/FlatfileParser.java A /trunk/sdk/src/main/java/org/ngbw/sdk/conversion/FlatfileReader.java A /trunk/sdk/src/main/java/org/ngbw/sdk/conversion/FlatfileRecordFilter.java A /trunk/sdk/src/main/java/org/ngbw/sdk/conversion/PdbFinderParser.java A /trunk/sdk/src/main/java/org/ngbw/sdk/conversion/SequenceAlignmentReader.java A /trunk/sdk/src/main/java/org/ngbw/sdk/conversion/SequenceFormatConverter.java A /trunk/sdk/src/main/java/org/ngbw/sdk/conversion/SequenceRecord.java A /trunk/sdk/src/main/java/org/ngbw/sdk/conversion/UnknownSourceDocumentReader.java A /trunk/sdk/src/main/java/org/ngbw/sdk/conversion/XMLFileRecordFilter.java A /trunk/sdk/src/main/java/org/ngbw/sdk/conversion/package-info.java A /trunk/sdk/src/main/java/org/ngbw/sdk/core A /trunk/sdk/src/main/java/org/ngbw/sdk/core/DefaultCoreRegistry.java A /trunk/sdk/src/main/java/org/ngbw/sdk/core/DefaultCoreRegistryBuilder.java A /trunk/sdk/src/main/java/org/ngbw/sdk/core/configuration A /trunk/sdk/src/main/java/org/ngbw/sdk/core/configuration/Configuration.java A /trunk/sdk/src/main/java/org/ngbw/sdk/core/configuration/ConfigurationBuilder.java A /trunk/sdk/src/main/java/org/ngbw/sdk/core/configuration/ServiceFactory.java A /trunk/sdk/src/main/java/org/ngbw/sdk/core/configuration/WorkbenchException.java A /trunk/sdk/src/main/java/org/ngbw/sdk/core/configuration/package-info.java A /trunk/sdk/src/main/java/org/ngbw/sdk/core/io A /trunk/sdk/src/main/java/org/ngbw/sdk/core/io/SSLConnectionManager.java A /trunk/sdk/src/main/java/org/ngbw/sdk/core/io/SSLConnectionPool.java A /trunk/sdk/src/main/java/org/ngbw/sdk/core/package-info.java A /trunk/sdk/src/main/java/org/ngbw/sdk/core/query A /trunk/sdk/src/main/java/org/ngbw/sdk/core/query/LogicalQueryOperator.java A /trunk/sdk/src/main/java/org/ngbw/sdk/core/query/MultiStringValueQueryOperator.java A /trunk/sdk/src/main/java/org/ngbw/sdk/core/query/MultiValueQueryOperator.java A /trunk/sdk/src/main/java/org/ngbw/sdk/core/query/NullValueQueryOperator.java A /trunk/sdk/src/main/java/org/ngbw/sdk/core/query/QueryOperator.java A /trunk/sdk/src/main/java/org/ngbw/sdk/core/query/SingleStringValueQueryOperator.java A /trunk/sdk/src/main/java/org/ngbw/sdk/core/query/SingleValueQueryOperator.java A /trunk/sdk/src/main/java/org/ngbw/sdk/core/query/TwoValueQueryOperator.java A /trunk/sdk/src/main/java/org/ngbw/sdk/core/query/package-info.java A /trunk/sdk/src/main/java/org/ngbw/sdk/core/shared A /trunk/sdk/src/main/java/org/ngbw/sdk/core/shared/DataRecordCollectionImpl.java A /trunk/sdk/src/main/java/org/ngbw/sdk/core/shared/DataRecordComparator.java A /trunk/sdk/src/main/java/org/ngbw/sdk/core/shared/DataRecordImpl.java A /trunk/sdk/src/main/java/org/ngbw/sdk/core/shared/DatasetId.java A /trunk/sdk/src/main/java/org/ngbw/sdk/core/shared/DatasetRecord.java A /trunk/sdk/src/main/java/org/ngbw/sdk/core/shared/GenericDataRecordCollectionImpl.java A /trunk/sdk/src/main/java/org/ngbw/sdk/core/shared/IndexedDataRecord.java A /trunk/sdk/src/main/java/org/ngbw/sdk/core/shared/IndexedDataRecordCollectionImpl.java A /trunk/sdk/src/main/java/org/ngbw/sdk/core/shared/IndexedDataRecordComparator.java A /trunk/sdk/src/main/java/org/ngbw/sdk/core/shared/SourceDocumentBean.java A /trunk/sdk/src/main/java/org/ngbw/sdk/core/shared/SourceDocumentType.java A /trunk/sdk/src/main/java/org/ngbw/sdk/core/shared/TaskRunStage.java A /trunk/sdk/src/main/java/org/ngbw/sdk/core/shared/UserRole.java A /trunk/sdk/src/main/java/org/ngbw/sdk/core/shared/package-info.java A /trunk/sdk/src/main/java/org/ngbw/sdk/core/transformation A /trunk/sdk/src/main/java/org/ngbw/sdk/core/transformation/BaseTransformer.java A /trunk/sdk/src/main/java/org/ngbw/sdk/core/transformation/BlastOutput2SequenceBlastHitTransformer.java A /trunk/sdk/src/main/java/org/ngbw/sdk/core/transformation/BlastOutput2StructureBlastHitTransformer.java A /trunk/sdk/src/main/java/org/ngbw/sdk/core/transformation/FastaOutput2SequenceFastaHitTransformer.java A /trunk/sdk/src/main/java/org/ngbw/sdk/core/transformation/FastaOutput2StructureFastaHitTransformer.java A /trunk/sdk/src/main/java/org/ngbw/sdk/core/transformation/ParseAndSearchTransformer.java A /trunk/sdk/src/main/java/org/ngbw/sdk/core/types A /trunk/sdk/src/main/java/org/ngbw/sdk/core/types/DataFormat.java A /trunk/sdk/src/main/java/org/ngbw/sdk/core/types/DataType.java A /trunk/sdk/src/main/java/org/ngbw/sdk/core/types/Dataset.java A /trunk/sdk/src/main/java/org/ngbw/sdk/core/types/EntityType.java A /trunk/sdk/src/main/java/org/ngbw/sdk/core/types/FieldDataType.java A /trunk/sdk/src/main/java/org/ngbw/sdk/core/types/RecordFieldType.java A /trunk/sdk/src/main/java/org/ngbw/sdk/core/types/RecordType.java A /trunk/sdk/src/main/java/org/ngbw/sdk/core/types/package-info.java A /trunk/sdk/src/main/java/org/ngbw/sdk/data A /trunk/sdk/src/main/java/org/ngbw/sdk/data/AdvancedSearchMetaQueryImpl.java A /trunk/sdk/src/main/java/org/ngbw/sdk/data/DatasetConfigBean.java A /trunk/sdk/src/main/java/org/ngbw/sdk/data/DefaultDatasetRegistry.java A /trunk/sdk/src/main/java/org/ngbw/sdk/data/DefaultDatasetRegistryBuilder.java A /trunk/sdk/src/main/java/org/ngbw/sdk/data/DefaultDatasetService.java A /trunk/sdk/src/main/java/org/ngbw/sdk/data/DefaultQueryResult.java A /trunk/sdk/src/main/java/org/ngbw/sdk/data/DefaultResultTuple.java A /trunk/sdk/src/main/java/org/ngbw/sdk/data/MetaQueryImpl.java A /trunk/sdk/src/main/java/org/ngbw/sdk/data/SearchHit.java A /trunk/sdk/src/main/java/org/ngbw/sdk/data/SearchHitCollectionImpl.java A /trunk/sdk/src/main/java/org/ngbw/sdk/data/SearchHitComparator.java A /trunk/sdk/src/main/java/org/ngbw/sdk/data/SimpleSearchMetaQueryImpl.java A /trunk/sdk/src/main/java/org/ngbw/sdk/data/package-info.java A /trunk/sdk/src/main/java/org/ngbw/sdk/database A /trunk/sdk/src/main/java/org/ngbw/sdk/database/Application.java A /trunk/sdk/src/main/java/org/ngbw/sdk/database/AutoGeneratedKey.java A /trunk/sdk/src/main/java/org/ngbw/sdk/database/BinaryColumn.java A /trunk/sdk/src/main/java/org/ngbw/sdk/database/BooleanColumn.java A /trunk/sdk/src/main/java/org/ngbw/sdk/database/C3P0ConnectionSource.java A /trunk/sdk/src/main/java/org/ngbw/sdk/database/CachedItem.java A /trunk/sdk/src/main/java/org/ngbw/sdk/database/Column.java A /trunk/sdk/src/main/java/org/ngbw/sdk/database/CompositeKey.java A /trunk/sdk/src/main/java/org/ngbw/sdk/database/ConnectionManager.java A /trunk/sdk/src/main/java/org/ngbw/sdk/database/ConnectionSource.java A /trunk/sdk/src/main/java/org/ngbw/sdk/database/Criterion.java A /trunk/sdk/src/main/java/org/ngbw/sdk/database/DataRecord.java A /trunk/sdk/src/main/java/org/ngbw/sdk/database/DateColumn.java A /trunk/sdk/src/main/java/org/ngbw/sdk/database/DbInputStream.java A /trunk/sdk/src/main/java/org/ngbw/sdk/database/DbReader.java A /trunk/sdk/src/main/java/org/ngbw/sdk/database/DriverConnectionSource.java A /trunk/sdk/src/main/java/org/ngbw/sdk/database/ExampleRow.java A /trunk/sdk/src/main/java/org/ngbw/sdk/database/FileColumn.java A /trunk/sdk/src/main/java/org/ngbw/sdk/database/Folder.java A /trunk/sdk/src/main/java/org/ngbw/sdk/database/FolderItem.java A /trunk/sdk/src/main/java/org/ngbw/sdk/database/Group.java A /trunk/sdk/src/main/java/org/ngbw/sdk/database/IntegerColumn.java A /trunk/sdk/src/main/java/org/ngbw/sdk/database/LongColumn.java A /trunk/sdk/src/main/java/org/ngbw/sdk/database/LongCriterion.java A /trunk/sdk/src/main/java/org/ngbw/sdk/database/MemoryValue.java A /trunk/sdk/src/main/java/org/ngbw/sdk/database/MonitoredList.java A /trunk/sdk/src/main/java/org/ngbw/sdk/database/MonitoredMap.java A /trunk/sdk/src/main/java/org/ngbw/sdk/database/MonitoredSet.java A /trunk/sdk/src/main/java/org/ngbw/sdk/database/NotExistException.java A /trunk/sdk/src/main/java/org/ngbw/sdk/database/RecordField.java A /trunk/sdk/src/main/java/org/ngbw/sdk/database/Row.java A /trunk/sdk/src/main/java/org/ngbw/sdk/database/RowOperation.java A /trunk/sdk/src/main/java/org/ngbw/sdk/database/RunningTask.java A /trunk/sdk/src/main/java/org/ngbw/sdk/database/SimpleKey.java A /trunk/sdk/src/main/java/org/ngbw/sdk/database/SourceDocument.java A /trunk/sdk/src/main/java/org/ngbw/sdk/database/SourceDocumentRow.java A /trunk/sdk/src/main/java/org/ngbw/sdk/database/Sso.java A /trunk/sdk/src/main/java/org/ngbw/sdk/database/StaleRowException.java A /trunk/sdk/src/main/java/org/ngbw/sdk/database/Statistics.java A /trunk/sdk/src/main/java/org/ngbw/sdk/database/StatisticsEvent.java A /trunk/sdk/src/main/java/org/ngbw/sdk/database/StreamColumn.java A /trunk/sdk/src/main/java/org/ngbw/sdk/database/StringColumn.java A /trunk/sdk/src/main/java/org/ngbw/sdk/database/StringCriterion.java A /trunk/sdk/src/main/java/org/ngbw/sdk/database/Task.java A /trunk/sdk/src/main/java/org/ngbw/sdk/database/TaskInputParameter.java A /trunk/sdk/src/main/java/org/ngbw/sdk/database/TaskInputSourceDocument.java A /trunk/sdk/src/main/java/org/ngbw/sdk/database/TaskLogMessage.java A /trunk/sdk/src/main/java/org/ngbw/sdk/database/TaskOutputParameter.java A /trunk/sdk/src/main/java/org/ngbw/sdk/database/TaskOutputSourceDocument.java A /trunk/sdk/src/main/java/org/ngbw/sdk/database/TextColumn.java A /trunk/sdk/src/main/java/org/ngbw/sdk/database/Tgusage.java A /trunk/sdk/src/main/java/org/ngbw/sdk/database/TomcatConnectionSource.java A /trunk/sdk/src/main/java/org/ngbw/sdk/database/User.java A /trunk/sdk/src/main/java/org/ngbw/sdk/database/UserDataItem.java A /trunk/sdk/src/main/java/org/ngbw/sdk/database/UserItemDataRecord.java A /trunk/sdk/src/main/java/org/ngbw/sdk/database/Value.java A /trunk/sdk/src/main/java/org/ngbw/sdk/database/VersionedRow.java A /trunk/sdk/src/main/java/org/ngbw/sdk/database/package-info.java A /trunk/sdk/src/main/java/org/ngbw/sdk/database/util A /trunk/sdk/src/main/java/org/ngbw/sdk/database/util/ComparatorUtils.java A /trunk/sdk/src/main/java/org/ngbw/sdk/database/util/FolderComparator.java A /trunk/sdk/src/main/java/org/ngbw/sdk/database/util/FolderItemComparator.java A /trunk/sdk/src/main/java/org/ngbw/sdk/database/util/FolderItemSortableField.java A /trunk/sdk/src/main/java/org/ngbw/sdk/database/util/FolderSortableField.java A /trunk/sdk/src/main/java/org/ngbw/sdk/database/util/TaskComparator.java A /trunk/sdk/src/main/java/org/ngbw/sdk/database/util/TaskSortableField.java A /trunk/sdk/src/main/java/org/ngbw/sdk/database/util/UserDataItemComparator.java A /trunk/sdk/src/main/java/org/ngbw/sdk/database/util/UserDataItemSortableField.java A /trunk/sdk/src/main/java/org/ngbw/sdk/database/util/package-info.java A /trunk/sdk/src/main/java/org/ngbw/sdk/dataresources A /trunk/sdk/src/main/java/org/ngbw/sdk/dataresources/lucene A /trunk/sdk/src/main/java/org/ngbw/sdk/dataresources/lucene/IndexFieldType.java A /trunk/sdk/src/main/java/org/ngbw/sdk/dataresources/lucene/LuceneDataResource.java A /trunk/sdk/src/main/java/org/ngbw/sdk/dataresources/lucene/LuceneDataResourceConfig.java A /trunk/sdk/src/main/java/org/ngbw/sdk/dataresources/lucene/LuceneDatasetIndexer.java A /trunk/sdk/src/main/java/org/ngbw/sdk/dataresources/lucene/LuceneSimpleQuery.java A /trunk/sdk/src/main/java/org/ngbw/sdk/dataresources/lucene/LuceneUtils.java A /trunk/sdk/src/main/java/org/ngbw/sdk/dataresources/lucene/RecordSourceFilter.java A /trunk/sdk/src/main/java/org/ngbw/sdk/dataresources/lucene/SFTPDirectory.java A /trunk/sdk/src/main/java/org/ngbw/sdk/dataresources/lucene/SFTPLockFactory.java A /trunk/sdk/src/main/java/org/ngbw/sdk/jobs A /trunk/sdk/src/main/java/org/ngbw/sdk/jobs/FileNotFoundException.java A /trunk/sdk/src/main/java/org/ngbw/sdk/jobs/Job.java A /trunk/sdk/src/main/java/org/ngbw/sdk/jobs/JobFile.java A /trunk/sdk/src/main/java/org/ngbw/sdk/jobs/JobMetadata.java A /trunk/sdk/src/main/java/org/ngbw/sdk/jobs/JobNotFoundException.java A /trunk/sdk/src/main/java/org/ngbw/sdk/jobs/JobOutput.java A /trunk/sdk/src/main/java/org/ngbw/sdk/jobs/JobStatus.java A /trunk/sdk/src/main/java/org/ngbw/sdk/jobs/JobWorkingDir.java A /trunk/sdk/src/main/java/org/ngbw/sdk/jobs/UserMismatchException.java A /trunk/sdk/src/main/java/org/ngbw/sdk/tool A /trunk/sdk/src/main/java/org/ngbw/sdk/tool/BaseProcessWorker.java A /trunk/sdk/src/main/java/org/ngbw/sdk/tool/DefaultToolRegistry.java A /trunk/sdk/src/main/java/org/ngbw/sdk/tool/DefaultToolRegistryBuilder.java A /trunk/sdk/src/main/java/org/ngbw/sdk/tool/DefaultToolResource.java A /trunk/sdk/src/main/java/org/ngbw/sdk/tool/DisabledResourceException.java A /trunk/sdk/src/main/java/org/ngbw/sdk/tool/FatalTaskException.java A /trunk/sdk/src/main/java/org/ngbw/sdk/tool/GlobusConfig.java A /trunk/sdk/src/main/java/org/ngbw/sdk/tool/GlobusCred.java A /trunk/sdk/src/main/java/org/ngbw/sdk/tool/GridFtpFileHandler.java A /trunk/sdk/src/main/java/org/ngbw/sdk/tool/GridFtpInputStream.java A /trunk/sdk/src/main/java/org/ngbw/sdk/tool/JobCompleteEvent.java A /trunk/sdk/src/main/java/org/ngbw/sdk/tool/LocalFileHandler.java A /trunk/sdk/src/main/java/org/ngbw/sdk/tool/OLD A /trunk/sdk/src/main/java/org/ngbw/sdk/tool/OLD/AbeRSL.java.save A /trunk/sdk/src/main/java/org/ngbw/sdk/tool/OLD/CipresRSL.java.save A /trunk/sdk/src/main/java/org/ngbw/sdk/tool/OLD/DrmaaProcessWorker.java.save A /trunk/sdk/src/main/java/org/ngbw/sdk/tool/OLD/GlobusProcessWorker.java.save A /trunk/sdk/src/main/java/org/ngbw/sdk/tool/OLD/LocalProcessWorker.java.save A /trunk/sdk/src/main/java/org/ngbw/sdk/tool/OLD/LonestarRSL.java.save A /trunk/sdk/src/main/java/org/ngbw/sdk/tool/OLD/QsubProcessWorker.java.save A /trunk/sdk/src/main/java/org/ngbw/sdk/tool/OLD/SSHLongProcessWorker.java.save A /trunk/sdk/src/main/java/org/ngbw/sdk/tool/OLD/SamlCred.java.save A /trunk/sdk/src/main/java/org/ngbw/sdk/tool/OutputDescription.java A /trunk/sdk/src/main/java/org/ngbw/sdk/tool/PropertyException.java A /trunk/sdk/src/main/java/org/ngbw/sdk/tool/RenderedCommand.java A /trunk/sdk/src/main/java/org/ngbw/sdk/tool/SFTPFileHandler.java A /trunk/sdk/src/main/java/org/ngbw/sdk/tool/SFTPInputStream.java A /trunk/sdk/src/main/java/org/ngbw/sdk/tool/SSHExecProcessWorker.java A /trunk/sdk/src/main/java/org/ngbw/sdk/tool/SSHProcessWorker.java A /trunk/sdk/src/main/java/org/ngbw/sdk/tool/SchedulerProperties.java A /trunk/sdk/src/main/java/org/ngbw/sdk/tool/SimpleCred.java A /trunk/sdk/src/main/java/org/ngbw/sdk/tool/TaskInitiate.java A /trunk/sdk/src/main/java/org/ngbw/sdk/tool/TaskMonitor.java A /trunk/sdk/src/main/java/org/ngbw/sdk/tool/TaskUpdater.java A /trunk/sdk/src/main/java/org/ngbw/sdk/tool/TaskValidator.java A /trunk/sdk/src/main/java/org/ngbw/sdk/tool/Tool.java A /trunk/sdk/src/main/java/org/ngbw/sdk/tool/ToolConfigBean.java A /trunk/sdk/src/main/java/org/ngbw/sdk/tool/WorkQueue.java A /trunk/sdk/src/main/java/org/ngbw/sdk/tool/WorkingDirectory.java A /trunk/sdk/src/main/java/org/ngbw/sdk/tool/package-info.java A /trunk/sdk/src/main/java/org/ngbw/utils A /trunk/sdk/src/main/java/org/ngbw/utils/AddExampleRow.java A /trunk/sdk/src/main/java/org/ngbw/utils/AddTestUser.java A /trunk/sdk/src/main/java/org/ngbw/utils/CancelUsersJobs.java A /trunk/sdk/src/main/java/org/ngbw/utils/CheckJobs.java A /trunk/sdk/src/main/java/org/ngbw/utils/DataInspector.java A /trunk/sdk/src/main/java/org/ngbw/utils/DebugImporter.java A /trunk/sdk/src/main/java/org/ngbw/utils/ImportTgusage.java A /trunk/sdk/src/main/java/org/ngbw/utils/LoadResults.java A /trunk/sdk/src/main/java/org/ngbw/utils/MigrateSourceDocTable.java A /trunk/sdk/src/main/java/org/ngbw/utils/RunTasks.java A /trunk/sdk/src/main/java/org/ngbw/utils/RunningTaskInspector.java A /trunk/sdk/src/main/java/org/ngbw/utils/ShowUserItems.java A /trunk/sdk/src/main/java/org/ngbw/utils/StageAndSubmitATask.java A /trunk/sdk/src/main/java/org/ngbw/utils/StoreRTaskOutput.java A /trunk/sdk/src/main/java/org/ngbw/utils/StoreTaskOutput.java A /trunk/sdk/src/main/java/org/ngbw/utils/SubmitJob.java A /trunk/sdk/src/main/java/org/ngbw/utils/TaskInspector.java A /trunk/sdk/src/main/java/org/ngbw/utils/TestSSHProcessRunner.java A /trunk/sdk/src/main/java/org/ngbw/utils/ThreadPoolTest.java A /trunk/sdk/src/main/java/org/ngbw/utils/ToolUsageReport.java A /trunk/sdk/src/main/java/org/ngbw/utils/UserCanSubmit.java A /trunk/sdk/src/main/java/org/ngbw/utils/UserDelete.java A /trunk/sdk/src/main/java/org/ngbw/utils/UserTgAllocation.java A /trunk/sdk/src/main/resources A /trunk/sdk/src/main/resources/checkJobs_log4j.xml A /trunk/sdk/src/main/resources/cog.properties A /trunk/sdk/src/main/resources/conversion A /trunk/sdk/src/main/resources/conversion/conversion-registry.cfg.xml A /trunk/sdk/src/main/resources/conversion/fasta-header-parser.cfg.xml A /trunk/sdk/src/main/resources/conversion/flatfile-parser.cfg.xml A /trunk/sdk/src/main/resources/conversion/flatfile-recordfilter.cfg.xml A /trunk/sdk/src/main/resources/conversion/sequence-parser.cfg.xml A /trunk/sdk/src/main/resources/conversion/xml-recordfilter.cfg.xml A /trunk/sdk/src/main/resources/core A /trunk/sdk/src/main/resources/core/core-registry.cfg.xml A /trunk/sdk/src/main/resources/core/ngbw.cfg.xml A /trunk/sdk/src/main/resources/data A /trunk/sdk/src/main/resources/data/dataset-registry.cfg.xml A /trunk/sdk/src/main/resources/database A /trunk/sdk/src/main/resources/database/database.properties A /trunk/sdk/src/main/resources/dataresources A /trunk/sdk/src/main/resources/dataresources/lucene.cfg.xml A /trunk/sdk/src/main/resources/globus.properties A /trunk/sdk/src/main/resources/loadResults_log4j.xml A /trunk/sdk/src/main/resources/log4j.properties A /trunk/sdk/src/main/resources/pisexml A /trunk/sdk/src/main/resources/pisexml/OBSOLETE A /trunk/sdk/src/main/resources/pisexml/OBSOLETE/garli.xml A /trunk/sdk/src/main/resources/pisexml/OBSOLETE/garli_abe.xml A /trunk/sdk/src/main/resources/pisexml/OBSOLETE/garli_lonestar.xml A /trunk/sdk/src/main/resources/pisexml/OBSOLETE/mafft.xml A /trunk/sdk/src/main/resources/pisexml/OBSOLETE/mafftnew.xml A /trunk/sdk/src/main/resources/pisexml/OBSOLETE/mrbayes.xml A /trunk/sdk/src/main/resources/pisexml/OBSOLETE/mrbayes_abe.xml A /trunk/sdk/src/main/resources/pisexml/OBSOLETE/mrbayes_lonestar.xml A /trunk/sdk/src/main/resources/pisexml/OBSOLETE/mrbayeshybrid_abe.xml A /trunk/sdk/src/main/resources/pisexml/OBSOLETE/raxml_light.xml A /trunk/sdk/src/main/resources/pisexml/OBSOLETE/raxmlhpc2.xml A /trunk/sdk/src/main/resources/pisexml/OBSOLETE/raxmlhpc2_abe727.xml A /trunk/sdk/src/main/resources/pisexml/OBSOLETE/raxmlhpc2_abe_727.xml A /trunk/sdk/src/main/resources/pisexml/OBSOLETE/raxmlhpc2_tg.xml A /trunk/sdk/src/main/resources/pisexml/OBSOLETE/raxmlhpc_abe.xml A /trunk/sdk/src/main/resources/pisexml/PARSER A /trunk/sdk/src/main/resources/pisexml/PARSER/README A /trunk/sdk/src/main/resources/pisexml/PARSER/pise.dtd A /trunk/sdk/src/main/resources/pisexml/PARSER/pise.xsd A /trunk/sdk/src/main/resources/pisexml/README.TXT A /trunk/sdk/src/main/resources/pisexml/XMLDIR A /trunk/sdk/src/main/resources/pisexml/XMLDIR/Path_Pfam_DB.xml A /trunk/sdk/src/main/resources/pisexml/XMLDIR/Path_Ppsearch_DB.xml A /trunk/sdk/src/main/resources/pisexml/XMLDIR/Path_Rpsblast_DB.xml A /trunk/sdk/src/main/resources/pisexml/XMLDIR/blastDBpath.xml A /trunk/sdk/src/main/resources/pisexml/XMLDIR/blocksDBpath.xml A /trunk/sdk/src/main/resources/pisexml/XMLDIR/fastaDBpath.xml A /trunk/sdk/src/main/resources/pisexml/XMLDIR/nucDBfasta.xml A /trunk/sdk/src/main/resources/pisexml/XMLDIR/nucdbs.xml A /trunk/sdk/src/main/resources/pisexml/XMLDIR/prositeDBpath.xml A /trunk/sdk/src/main/resources/pisexml/XMLDIR/protDBfasta.xml A /trunk/sdk/src/main/resources/pisexml/XMLDIR/protDBrpsblast.xml A /trunk/sdk/src/main/resources/pisexml/XMLDIR/protdbs.xml A /trunk/sdk/src/main/resources/pisexml/XMLDIR/triton_run_time.xml A /trunk/sdk/src/main/resources/pisexml/align.xml A /trunk/sdk/src/main/resources/pisexml/align2.xml.in A /trunk/sdk/src/main/resources/pisexml/beast_tg.xml A /trunk/sdk/src/main/resources/pisexml/beast_tg_test.xml A /trunk/sdk/src/main/resources/pisexml/bestscor.xml.in A /trunk/sdk/src/main/resources/pisexml/bl2seq.xml A /trunk/sdk/src/main/resources/pisexml/blast2.xml A /trunk/sdk/src/main/resources/pisexml/blastn.xml A /trunk/sdk/src/main/resources/pisexml/blastp.xml A /trunk/sdk/src/main/resources/pisexml/blastx.xml A /trunk/sdk/src/main/resources/pisexml/blimps.xml A /trunk/sdk/src/main/resources/pisexml/boxshade.xml A /trunk/sdk/src/main/resources/pisexml/bucky.xml A /trunk/sdk/src/main/resources/pisexml/clearcut.xml A /trunk/sdk/src/main/resources/pisexml/clique.xml A /trunk/sdk/src/main/resources/pisexml/clustalw.xml A /trunk/sdk/src/main/resources/pisexml/clustalw_dist.xml A /trunk/sdk/src/main/resources/pisexml/clustalw_n.xml A /trunk/sdk/src/main/resources/pisexml/clustalw_p.xml A /trunk/sdk/src/main/resources/pisexml/clustalw_profile.xml A /trunk/sdk/src/main/resources/pisexml/clustalw_tree.xml A /trunk/sdk/src/main/resources/pisexml/compass.xml A /trunk/sdk/src/main/resources/pisexml/consense.xml A /trunk/sdk/src/main/resources/pisexml/contralign.xml A /trunk/sdk/src/main/resources/pisexml/degapseq.xml A /trunk/sdk/src/main/resources/pisexml/dnadist.xml A /trunk/sdk/src/main/resources/pisexml/dnapars.xml A /trunk/sdk/src/main/resources/pisexml/dollop.xml A /trunk/sdk/src/main/resources/pisexml/dppdiv.xml A /trunk/sdk/src/main/resources/pisexml/drawgram.xml A /trunk/sdk/src/main/resources/pisexml/drawtree.xml A /trunk/sdk/src/main/resources/pisexml/dssp.xml A /trunk/sdk/src/main/resources/pisexml/epestfind.xml A /trunk/sdk/src/main/resources/pisexml/eprimer3.xml A /trunk/sdk/src/main/resources/pisexml/extractalign.xml A /trunk/sdk/src/main/resources/pisexml/extractseq.xml A /trunk/sdk/src/main/resources/pisexml/fasta_n.xml A /trunk/sdk/src/main/resources/pisexml/fasta_p.xml A /trunk/sdk/src/main/resources/pisexml/fastx.xml A /trunk/sdk/src/main/resources/pisexml/fasty.xml A /trunk/sdk/src/main/resources/pisexml/fingerprintscan.xml A /trunk/sdk/src/main/resources/pisexml/fitch.xml A /trunk/sdk/src/main/resources/pisexml/formatvalidator.xml A /trunk/sdk/src/main/resources/pisexml/fsa.xml A /trunk/sdk/src/main/resources/pisexml/garli.xml A /trunk/sdk/src/main/resources/pisexml/garli2_tgb.xml A /trunk/sdk/src/main/resources/pisexml/garli_abe.xml A /trunk/sdk/src/main/resources/pisexml/garli_conf_creator.xml A /trunk/sdk/src/main/resources/pisexml/garli_lonestar.xml A /trunk/sdk/src/main/resources/pisexml/garli_tg.xml A /trunk/sdk/src/main/resources/pisexml/helixturnhelix.xml A /trunk/sdk/src/main/resources/pisexml/hmmpfam.xml A /trunk/sdk/src/main/resources/pisexml/kitsch.xml A /trunk/sdk/src/main/resources/pisexml/lalign.xml A /trunk/sdk/src/main/resources/pisexml/lfasta.xml.in A /trunk/sdk/src/main/resources/pisexml/mafft.xml A /trunk/sdk/src/main/resources/pisexml/mafft_861.xml A /trunk/sdk/src/main/resources/pisexml/mafft_tg.xml A /trunk/sdk/src/main/resources/pisexml/mafftnew.xml A /trunk/sdk/src/main/resources/pisexml/mbsum.xml A /trunk/sdk/src/main/resources/pisexml/merger.xml A /trunk/sdk/src/main/resources/pisexml/mfold.xml A /trunk/sdk/src/main/resources/pisexml/mix.xml A /trunk/sdk/src/main/resources/pisexml/mrbayes.xml A /trunk/sdk/src/main/resources/pisexml/mrbayes321_restartbeta.xml A /trunk/sdk/src/main/resources/pisexml/mrbayes_321beta.xml A /trunk/sdk/src/main/resources/pisexml/mrbayes_321restartbeta.xml A /trunk/sdk/src/main/resources/pisexml/mrbayes_abe.xml A /trunk/sdk/src/main/resources/pisexml/mrbayes_lonestar.xml A /trunk/sdk/src/main/resources/pisexml/mrbayes_xsede.xml A /trunk/sdk/src/main/resources/pisexml/mrbayeshybrid312_tg.xml A /trunk/sdk/src/main/resources/pisexml/mrbayeshybrid_abe.xml A /trunk/sdk/src/main/resources/pisexml/mrbayeshybrid_gordon.xml A /trunk/sdk/src/main/resources/pisexml/mrbayeshybrid_tg.xml A /trunk/sdk/src/main/resources/pisexml/msa.xml A /trunk/sdk/src/main/resources/pisexml/muscle.xml A /trunk/sdk/src/main/resources/pisexml/mview_alig.xml A /trunk/sdk/src/main/resources/pisexml/mview_blast.xml A /trunk/sdk/src/main/resources/pisexml/nclconverter.xml A /trunk/sdk/src/main/resources/pisexml/neighbor.xml A /trunk/sdk/src/main/resources/pisexml/new_tool.xml A /trunk/sdk/src/main/resources/pisexml/oldmrbayeshybrid_tg.xml A /trunk/sdk/src/main/resources/pisexml/pars.xml A /trunk/sdk/src/main/resources/pisexml/paup.xml A /trunk/sdk/src/main/resources/pisexml/pauprat.xml A /trunk/sdk/src/main/resources/pisexml/pauprat_exp.xml A /trunk/sdk/src/main/resources/pisexml/pepinfo.xml A /trunk/sdk/src/main/resources/pisexml/pepstats.xml A /trunk/sdk/src/main/resources/pisexml/pepwindow.xml A /trunk/sdk/src/main/resources/pisexml/pfscan.xml A /trunk/sdk/src/main/resources/pisexml/pfsearch.xml A /trunk/sdk/src/main/resources/pisexml/pftools.xml.in A /trunk/sdk/src/main/resources/pisexml/phylobayes_xsede.xml A /trunk/sdk/src/main/resources/pisexml/phylobayes_xsede_restart.xml A /trunk/sdk/src/main/resources/pisexml/phyml.xml A /trunk/sdk/src/main/resources/pisexml/poy.xml A /trunk/sdk/src/main/resources/pisexml/poy2.xml A /trunk/sdk/src/main/resources/pisexml/ppsearch.xml A /trunk/sdk/src/main/resources/pisexml/primers.xml.in A /trunk/sdk/src/main/resources/pisexml/probalign.xml A /trunk/sdk/src/main/resources/pisexml/probcons.xml A /trunk/sdk/src/main/resources/pisexml/prosearch.xml A /trunk/sdk/src/main/resources/pisexml/protdist.xml A /trunk/sdk/src/main/resources/pisexml/proteus.xml A /trunk/sdk/src/main/resources/pisexml/proteus.xml.in A /trunk/sdk/src/main/resources/pisexml/protpars.xml A /trunk/sdk/src/main/resources/pisexml/prss.xml A /trunk/sdk/src/main/resources/pisexml/psiblast.xml A /trunk/sdk/src/main/resources/pisexml/psipred.xml A /trunk/sdk/src/main/resources/pisexml/randseq.xml.in A /trunk/sdk/src/main/resources/pisexml/raxml_light2.xml A /trunk/sdk/src/main/resources/pisexml/raxmlhpc.xml A /trunk/sdk/src/main/resources/pisexml/raxmlhpc2_abe.xml A /trunk/sdk/src/main/resources/pisexml/raxmlhpc2_tgb.xml A /trunk/sdk/src/main/resources/pisexml/raxmlhpc2_tgbi.xml A /trunk/sdk/src/main/resources/pisexml/raxmlhpc2bb.xml A /trunk/sdk/src/main/resources/pisexml/raxmlhpc2bb_abe.xml A /trunk/sdk/src/main/resources/pisexml/readseq.xml A /trunk/sdk/src/main/resources/pisexml/restrict.xml A /trunk/sdk/src/main/resources/pisexml/revseq.xml A /trunk/sdk/src/main/resources/pisexml/rid3paup.xml A /trunk/sdk/src/main/resources/pisexml/rid3raxml.xml A /trunk/sdk/src/main/resources/pisexml/rpsblast.xml A /trunk/sdk/src/main/resources/pisexml/saps.xml A /trunk/sdk/src/main/resources/pisexml/seqboot.xml A /trunk/sdk/src/main/resources/pisexml/seqretsplit.xml A /trunk/sdk/src/main/resources/pisexml/sixpack.xml A /trunk/sdk/src/main/resources/pisexml/sleep.xml A /trunk/sdk/src/main/resources/pisexml/spidey.xml A /trunk/sdk/src/main/resources/pisexml/ssearch_n.xml A /trunk/sdk/src/main/resources/pisexml/ssearch_p.xml A /trunk/sdk/src/main/resources/pisexml/tacg.xml A /trunk/sdk/src/main/resources/pisexml/tblastn.xml A /trunk/sdk/src/main/resources/pisexml/tblastx.xml A /trunk/sdk/src/main/resources/pisexml/tfasta.xml A /trunk/sdk/src/main/resources/pisexml/tfastx.xml A /trunk/sdk/src/main/resources/pisexml/tfasty.xml A /trunk/sdk/src/main/resources/pisexml/tmap.xml A /trunk/sdk/src/main/resources/pisexml/tmhmm.xml.in A /trunk/sdk/src/main/resources/pisexml/unroot.xml A /trunk/sdk/src/main/resources/recoverResults_log4j.xml A /trunk/sdk/src/main/resources/ssl.properties A /trunk/sdk/src/main/resources/submitJob_log4j.xml A /trunk/sdk/src/main/resources/tool A /trunk/sdk/src/main/resources/tool/job-html.ftl A /trunk/sdk/src/main/resources/tool/job-text.ftl A /trunk/sdk/src/main/resources/tool/spring-mail.xml A /trunk/sdk/src/main/resources/workbench.properties A /trunk/sdk/src/main/resources/xsd A /trunk/sdk/src/main/resources/xsd/ncbi-blast.xsd A /trunk/sdk/src/main/resources/xsd/pise.xsd A /trunk/sdk/src/main/resources/xsd/uniprot.ddl A /trunk/sdk/src/main/resources/xsd/uniprot.xsd A /trunk/sdk/src/test initial import ------------------------------------------------------------------------