DateFiles / Description
2017/05/31 A number of fixes/improvements for SRS Prisma: Improved stability when using batch queues, Fixed a reporting issus for the check phase, where remote site check problems weher not reported in the Prisma Reports, Fixed a number of problems which where Prisma would show error messages, where actually nothing was wrong
icarus/lion/prisma/reformatPhase.i
icarus/lion/prisma/pretransPhase.i
icarus/lion/prisma/remoteConnection.i
icarus/lion/prisma/movePrismaData.i
icarus/workflows/coreCheckClasses.i
icarus/workflows/buildPhase.i
icarus/lion/prisma/prismaCheckMain.i
icarus/lion/prisma/dbSync.i
icarus/lion/prisma/generateCalendar.i
icarus/lion/prisma/checkRemoteFiles.i
icarus/lion/prisma/configUpdate/srssection_off
icarus/lion/prisma/setReportPhase.i
icarus/workflows/linkPhase.i
icarus/lion/prisma/prismatime.is
icarus/workflows/getSystemLibs.i
icarus/lion/prisma/moveLibs.i
icarus/lion/prisma/prismaCheckClasses.i
2016/04/14 Improved date checking when comparing file date stamps with those on a remote location in cases where datafiles are not unpacked
icarus/lion/prisma/dbSync.i
2015/12/23 Fixed some issues with chunk and chunksize parallelization
icarus/workflows/buildPhase.i
icarus/workflows/linkPhase.i
2015/10/27 Improved stability of the code for drawing the Prisma CPU slot usage image
icarus/lion/prisma/cpuslots.il
2015/08/13 fix for a problem with creating blast indices from file which is already in fasta format
icarus/lion/prisma/reformatPhase.i
2015/03/25 Fix for errors thrown during the removal of partial link indices
icarus/workflows/linkPhase.i
2015/01/23 Fix for a problem induced by the new virtual library defintions for the 2015 release of Medline
icarus/workflows/buildPhase.i
icarus/lion/prisma/prismaCheckClasses.i
icarus/workflows/getSystemLibs.i
icarus/lion/prisma/analyseLibs.i
icarus/workflows/linkPhase.i
icarus/workflows/coreCheckClasses.i
2014/12/08 Update for SRS Prisma and srscheck which includes
  • A new -p option which allows you to include parent/dependent libraries on the command line without having to specify all of them, like "runPrisma -l embl" to update all libraries involved in the EMBL virtual library
  • A significant speedup during the check phase for very large libraries, like the WGS sections of EMBL/GenBank/DDBJ
  • Improved statbility in cases where the exit status of Sun Grid Engine qrsh does not reliably reflect a failure
  • Fix for an issue with the removal of partial .mergeinf files during the merge phase
  • A few other minor bug fixes
icarus/workflows/getSystemLibs.i
icarus/lion/prisma/prismaCheckMain.i
icarus/lion/prisma/prismaCheckClasses.i
icarus/workflows/srsCheckClasses.i
icarus/workflows/linkPhase.i
icarus/lion/prisma/analyseLibs.i
icarus/workflows/buildPhase.i
icarus/workflows/srsCheckMain.i
etc/runPrisma
2014/08/04 Update for SRS Prisma to handle https connections correctly. Note that differing versions of the shared ssl libaries may mean that you will have to compile the wgetPrisma binaries yourself (the source code is provided in SRSROOT/gnu_src)
icarus/lion/prisma/remoteConnection.i
2014/07/10 Improved stability of data processing by SRS Prisma by catching situations where a batch queue returns a exit status of 0 despite failing to execute a command. This has been seen with SGE
icarus/workflows/linkPhase.i
icarus/lion/prisma/pretransPhase.i
icarus/workflows/buildPhase.i
icarus/lion/prisma/reformatPhase.i
icarus/lion/prisma/downloadPhase.i
2014/04/14 Fix for a problem with the localcopy command for processing of non-SRS data by SRS Prisma
icarus/workflows/buildPhase.i
2014/03/20 Fix for a problem in srscheck with database dependencies if only link indices are build
icarus/workflows/moveIndicesPhase.i
2014/03/18 Change so srscheck and SRS Prisma will be able to recognize link indices which have become unreadable after an index structure change and then remove and rebuild them.
icarus/workflows/linkPhase.i
2014/03/17 Fix for a problem caused by an = sign in the datafiles for the intact databases. The = sign has a special meaning the the makefiles SRS Prisma generates, and its presence in a file name would break the processing of the makfile, resulting in complete failures of SRS Prisma runs
icarus/lion/prisma/downloadPhase.i
2014/01/28 Change so the -t (touch) option for srscheck will also touch link indices and cache and sortset files
icarus/workflows/buildPhase.i
2014/01/28 Change soe SRS Prisma can determine time stamps from file listings which contain a space in the group name, and a fix for a problem with recursive updates using the file (copy) protocol
icarus/lion/prisma/remoteConnection.i
2014/01/28 Change the way the number of download/index chains is calculated, which should allow for a more efficient usage of download and index cpu slots during updates
icarus/lion/prisma/downloadPhase.i
2014/01/28 Fix for a file installation problem if a file is both an indexed SRS database and a FASTA searchable database
icarus/lion/prisma/reformatPhase.i
2014/01/28 Fix for a potential problems with the setting for the maximum number of simultaneous downloads allowed by SRS Prisma
icarus/lion/prisma/dbSync.i
2014/01/13 Fix for a problems with the Prisma test databases if blast is not enabled
icarus/lion/prisma/PrismaToolsTestDb/testdb.i
2014/01/08 Change so restartPrisma cannot be used if the Prisma job has entered the move phase (at which point it is too late for a restart), and a change so restartPrisma will pick up the original runPrisma command line parameters
etc/runPrisma
etc/restartPrisma
2014/01/08 Improved output for resource and tool tests
icarus/lion/prisma/PrismaToolsTestDb/prismaToolTest1.i
icarus/lion/prisma/qualityReport/resourceObjectCheck.i
icarus/lion/prisma/getappls.i
icarus/lion/prisma/PrismaToolsTestDb/testdb.i
icarus/lion/prisma/qualityReport/toolTests.i
icarus/lion/prisma/toolsTestSets.i
icarus/lion/prisma/PrismaToolsTestDb/prismaToolTest
2013/12/06 Added a new errorLimit option to our fasta sequence conversion tool, which allows you to set a maximum number of errors allowed before exiting with a fail
icarus/lion/prisma/getFastaSequence.i
2013/11/29 Change so getFastaSequence.i will print out the entry name in the error output if it cannot retrieve a sequence
icarus/lion/prisma/getFastaSequence.i
2013/10/24 Fix for a problem with Prisma reports for file downloads if files are in subdirectories on the remote site
icarus/lion/prisma/setReportPhase.i
icarus/lion/prisma/prismaCheckClasses.i
icarus/lion/prisma/prismaCheckClasses.i
icarus/lion/prisma/printDownloadPages.i
2013/09/05 Fix for a problem where prisma would hang on building the prismatimelinks database on some platforms, and removed an unnecessary error message generated by archive checking
icarus/lion/prisma/prismatime.is
icarus/lion/prisma/prismaArchive.i
2013/08/13 Fixed a problem with database dependencies, which was giving problems for several Kegg databases
icarus/lion/prisma/localcopyPhase.i
2013/08/05 Fix for problems caused by different levels of escaping needed by batchqueues and plain shelld when backticks are used in unPackCommands
icarus/lion/prisma/pretransPhase.i
2013/07/24 Improved the touch option of srscheck (invoked by "srscheck -t") so it will now also touch link indices and the various caches and sortset files which srs uses
icarus/workflows/linkPhase.i
icarus/workflows/moveIndicesPhase.i
2013/05/17 Added a --cache=off option to prisma download commands to prevent problems caused by proxies persisiting in caching old versions of a file
icarus/lion/prisma/remoteConnection.i
2013/03/01 Fix a problem in prisma remote connection testing
icarus/lion/prisma/testRemoteConnection.i
2013/02/27 Fix for a problem where filenames used for downloads could get corrupted during retries, and improvevents to the lock file mechanism which is used to limit the number of simutaneous downloads, with better lock file names and more debug info
icarus/lion/prisma/remoteConnection.i
icarus/lion/prisma/checkRemoteFiles.i
icarus/lion/prisma/dbSync.i
2013/02/20 Change so remaining download lock files are removed between update retries
etc/runPrisma
2013/02/18 Change to improve robustness to errors during the unpack/pretranslation phase
icarus/lion/prisma/pretransPhase.i
2013/02/18 Fixed a problem with the reporting in Prisma on the moving of indices and data online
icarus/lion/prisma/movePrismaData.i
icarus/lion/prisma/setReportPhase.i
icarus/workflows/moveIndicesPhase.i
2013/01/21 Fix for a problem with cached file listings if prismacheck is used as a standalone program
icarus/workflows/coreCheckClasses.i
2013/01/09 Fix for a crash in usage reporting if no files are downloaded during a prisma run
icarus/lion/prisma/printUsageReport.i
2013/01/07 Fix for a problem in the Prisma reports calender if the current month does not have any reports
icarus/lion/prisma/generateCalendar.i
2013/01/04 Fixes for some prisma tool tests
icarus/lion/prisma/PrismaToolsTestDb/prismaToolTest1.i
icarus/lion/prisma/PrismaToolsTestDb/prismaToolTest2.i
2013/01/04 New hmm data so the prisma test suite works for hmmscan
icarus/lion/prisma/PrismaToolsTestDb/testdb/hmm.testdata
icarus/lion/prisma/PrismaToolsTestDb/testdb/hmm.testdata.h3p
icarus/lion/prisma/PrismaToolsTestDb/testdb/hmm.testdata.h3m
icarus/lion/prisma/PrismaToolsTestDb/testdb/hmm.testdata.h3f
icarus/lion/prisma/PrismaToolsTestDb/testdb/hmm.testdata.h3i
2012/12/17 Fix for a problem where the prisma installer would hang
icarus/lion/prisma/generateCalendar.i
2012/12/17 Fix for crashes in srscheck caused by recent code changes for SRS Prisma
icarus/workflows/coreCheckClasses.i
2012/12/17 Implementented a more accurate estimate for actual download times in the usage report - taking parallel downloads in account
icarus/lion/prisma/printUsageReport.i
2012/12/10 A large number of improvements and some fixes for SRS Prisma. See README.PRISMA.201212 for full details. Please use the prisma.latest_update.tar.gz archive to install the updates
icarus/lion/prisma/decisionReport.i
icarus/lion/prisma/pretransPhase.i
icarus/lion/prisma/dumpTarget.i
icarus/lion/prisma/prismaCheckClasses.i
etc/prismaDownloadProgressCheck
etc/runPrisma
icarus/lion/prisma/reformatPhase.i
icarus/lion/prisma/prismaCheckMain.i
icarus/lion/prisma/downloadPhase.i
icarus/workflows/coreCheckClasses.i
icarus/lion/prisma/printUsageReport.i
icarus/lion/prisma/remoteConnection.i
icarus/lion/prisma/moveLibs.i
icarus/lion/prisma/localcopyPhase.i
icarus/lion/prisma/cpuslots.il
icarus/workflows/moveIndicesPhase.i
icarus/workflows/moveData.i
icarus/lion/prisma/configurePrisma.i
icarus/lion/prisma/printMainPage.i
icarus/lion/prisma/prismadata.i
icarus/lion/prisma/generateCalendar.i
icarus/lion/prisma/movePrismaData.i
icarus/lion/prisma/checkRemoteFiles.i
icarus/lion/prisma/prismaArchive.i
icarus/util/classAttic/Class_PrismaLibResourceUsage_577213218.i
2012/05/16 Change to prevent prisma from hanging on gibberish in the command timing records
icarus/lion/prisma/prismatime.i
2012/04/30 Fixed some usage/options display issues for the -help option
etc/runPrisma
2012/02/29 Change so SRS Prisma will not descend into all subdirectories during recursive downloads if it is clear from the wanted filename patterns that a path can never match those patterns. When applying this update also update the dbsnp.it and dbsnplocation.it files, otherwise prisma will not be able to download dbsnp data
icarus/lion/prisma/remoteConnection.i
2012/02/29 Fix for a problem where Prisma would try to re-index dependent databases without first having linked the online data to the offline directories
icarus/workflows/buildPhase.i
icarus/lion/prisma/pretransPhase.i
icarus/lion/prisma/localcopyPhase.i
2012/02/29 Fix for a problem where prisma would not index data files in the correct order if only a few fields need re-indexing
icarus/workflows/checkLocalFiles.i
icarus/workflows/coreCheckClasses.i
2012/02/29 Fixes for various problems where SRS would build unneccesary virtual link sets, or would not move them online
icarus/workflows/getSystemLibs.i
icarus/workflows/linkPhase.i
2011/12/16 Fix for a problem where partial link databases for uniprot_trembl where not removed during indexing due too a removal command which was too long for the shell (resulting in an "Argument list too long" error
icarus/workflows/linkPhase.i
2011/11/03 Added a new option (-novirtual), which will exclude virtual libraries from checking. This is useful in combination with the -nolinks option during first time updates
icarus/workflows/srsCheckMain.i
icarus/workflows/srsCheckClasses.i
icarus/lion/prisma/prismaCheckClasses.i
icarus/lion/prisma/prismaCheckMain.i
icarus/workflows/getSystemLibs.i
etc/runPrisma
2011/11/03 Change to ensure that (memory intensive) sort operations are done sequentially and not simultaneously
icarus/workflows/buildPhase.i
2011/11/03 Change which should result in better parallization if there are multiple unpack commands
icarus/lion/prisma/pretransPhase.i
icarus/lion/prisma/pretransPhase.i
2011/11/03 Fix for a problem in srscheck which occurs if the -L option is used in combination with -nolinks
icarus/workflows/moveData.i
2011/11/03 Fix for a problem with makefile target names when using srscheck with libraries which have dependencies
icarus/workflows/srsCheckMain.i
2011/11/03 Fix to ensure that all links for relational databases with a staticlinks setting are build
icarus/workflows/getSystemLibs.i
icarus/workflows/linkPhase.i
2011/10/07 Fix for a problem where srscheck correctly detects offline data files which need indexing, but then fails to use the offline settings in the resulting indexing and data move commands
icarus/workflows/moveData.i
icarus/workflows/srsCheckMain.i
2011/08/15 Fix for a problems where prisma would time-out on or misinterpret symbolic links on remote download sites
icarus/lion/prisma/remoteConnection.i
2011/08/15 Made some changes to the building of links for virtual databases, so a few unnecessay files are no longer build
icarus/workflows/linkPhase.i
2011/08/12 Some changes so srscheck knows abou database depedencies. This means that databases which share data files (like emblnewfiles/emblnew, refseqfiles/refseqnew or uniseq/uniest) can be indexed in the same srsheck/srsdo run
icarus/workflows/srsCheckMain.i
icarus/workflows/moveData.i
icarus/workflows/moveIndicesPhase.i
2011/08/11 Fixes for some problems in prisma, where it would loose track of index files created, or datafiles to be installed, occuring within database dependencies when prisma is used to re-index databases locally. Also a few other minor corrections
icarus/lion/prisma/prismaCheckClasses.i
icarus/lion/prisma/pretransPhase.i
icarus/lion/prisma/movePrismaData.i
icarus/lion/prisma/localcopyPhase.i
icarus/lion/prisma/checkDependentDbs.i
icarus/lion/prisma/remoteConnection.i
icarus/lion/prisma/reformatPhase.i
2011/08/08 Fixes for several issues with srscheck (and also prisma), which in some circomstances could result in srscheck not detecting valid on-line data files, warnings for duplicate targets when running srsdo or prisma, and some wrong link dependencies when multiple links exist between libraries
icarus/workflows/buildPhase.i
icarus/workflows/linkPhase.i
icarus/workflows/coreCheckClasses.i
2011/08/03 Fix for a problem where srscheck might not find valid online files
icarus/workflows/coreCheckClasses.i
2011/06/07 Conversion information needed for old usage objects after extending usage recording in prisma
icarus/util/classAttic/Class_PrismaResourceUsage_1123318200.i
icarus/util/classAttic/Class_PrismaLibResourceUsage_2429876272.i
2011/05/19 Change so the main dates on the prisma reports refer to the date a prisma run was started, and no longer to the date the report was generated (but we still mention the generation date)
icarus/lion/prisma/printPretransPages.i
icarus/lion/prisma/printMovePages.i
icarus/lion/prisma/decisionReport.i
icarus/lion/prisma/printMainPage.i
icarus/lion/prisma/printLinkPages.i
icarus/lion/prisma/printDownloadPages.i
icarus/lion/prisma/printBuildPages.i
icarus/lion/prisma/generateLinkReports.i
icarus/lion/prisma/dumpTarget.i
icarus/lion/prisma/printReformatPages.i
2011/05/19 Change to include the display of cpu/walltime and dowload size and time in the prisma usage reports
icarus/lion/prisma/setReportPhase.i
icarus/lion/prisma/prismatime.i
icarus/lion/prisma/cpuslots.il
icarus/lion/prisma/prismaCheckClasses.i
icarus/lion/prisma/printUsageReport.i
2011/05/19 Change to reduce the amount of STDOUT when downloading large files, and a change to allow for a odd behaviour of the ls command on SELinux systems
icarus/lion/prisma/remoteConnection.i
2011/05/19 Fix for a problem with sending reports by Email in some configurations
icarus/lion/prisma/printMainPage.i
icarus/lion/prisma/prismaRunWatcher.i
etc/runPrisma
2011/04/20 Fix for a problem where srscheck or prisma might not detect valid online datafiles
icarus/workflows/coreCheckClasses.i
2011/04/08 Fix for a problem where srscheck and prisma might not find the current datafiles if the indices are missing
icarus/workflows/coreCheckClasses.i
icarus/workflows/checkLocalFiles.i
icarus/workflows/coreCheckClasses.i
2011/04/08 Fix for an email problem if reporting is invoked using the reportPrisma command
icarus/lion/prisma/printMainPage.i
2011/03/29 Fix for a problem where fasta/blast file generation result in duplicates if a fasta file generated by a previous Prisma run is still present in an offline location when a new Prisma run is started
icarus/lion/prisma/reformatPhase.i
2011/03/28 Fix for a problem where fasta data generated during the Prisma Reformat phase could end up in the STDOUT of a command instead of in a datafile
icarus/lion/prisma/reformatPhase.i
2011/03/23 Change so srscheck and Prisma will keep the file order for multiple files of the original indexing job in cases where only a few fields are (re-)indexed.
icarus/workflows/buildPhase.i
icarus/workflows/coreCheckClasses.i
2011/03/21 Removed a debug print statement
icarus/lion/prisma/prismastatus.is
2011/03/01 Change needed to be able to traverse the website from which drugbank can be downloaded. Note that this also requires the latest version of the wgetPrisma binaries
icarus/lion/prisma/remoteConnection.i
2011/03/01 Change so one cannot activate on obsolete feature image generation feature which we had in provious version of SRS/Prisma
icarus/lion/prisma/configurePrisma.i
2011/03/01 Fix for a potential crash during the generation of the usage report image if all commands timed during a prisma run have take very little time to complete
icarus/lion/prisma/cpuslots.il
2011/03/01 Fix for a problem with sending Emails during reporting and monitoring of a prisma run
icarus/lion/prisma/printMainPage.i
icarus/lion/prisma/prismaRunWatcher.i
2011/03/01 We added the collection of timing information to the various checking steps in prisma, so the usage report can show how much time is spend in these stages. Added more timestamps in the debug output, which should help troubleshooting. Removed some duplication of tasks which was occuring between update rounds in prisma.
icarus/lion/prisma/inspectClasses.i
icarus/lion/prisma/prismaCheckMain.i
icarus/workflows/coreCheckClasses.i
etc/runPrisma
icarus/lion/prisma/reformatPhase.i
icarus/lion/prisma/dumpTarget.i
icarus/lion/prisma/prismadata.i
2011/03/01 We implemented a new mechanism for staging the index merge steps for large databases, which should greatly reduce the number of partial index files which accumulates in the offline index directory. This can be controlled via a new -mergeThreads command line option available to both srscheck and runPrisma. For a full explanation see README.mergethreads
icarus/workflows/buildPhase.i
icarus/workflows/srsCheckMain.i
icarus/workflows/srsCheckClasses.i
icarus/lion/prisma/checkRemoteFiles.i
2011/03/01 We made some changes to the prisma status database to prevent duplicate ID errors occuring during a prisma run
icarus/lion/prisma/prismaCheckClasses.i
icarus/lion/prisma/prismastatus.i
icarus/lion/prisma/prismaInvalidate.i
icarus/lion/prisma/prismaview.i
icarus/lion/prisma/prismastatus.is
2011/01/28 Improve error handling for contigs/joins when extracting sequences
icarus/lion/prisma/getFastaSequence.i
2010/11/01 Extend the method for estimating the uncompressed file size for remote data by using existing local data as a guide to zip archives
icarus/lion/prisma/checkRemoteFiles.i
2010/11/01 Fix so the inspection part of prisma will not crash if a tool is not part of a group
icarus/lion/prisma/inspectReport.i
icarus/lion/prisma/inspectReport.i
2010/10/26 Fix for a problem with dependent databases which are updated by mirroring, where SRS/Prisma might try to index the data before the downloading of the data has finished.
icarus/lion/prisma/pretransPhase.i
2010/10/18 Fix for a crash during the generation of tool quality reports in prisma, caused by the fact that the new chemicalsearch tool is not part of a group
icarus/lion/prisma/inspectReport.i
2010/09/22 Change so prisma will print out a warning during the checking phase if a subdirectory cannot be accessed while traversing a directory tree
icarus/lion/prisma/remoteConnection.i
2010/09/21 Change to allow for somewhat more flexibility in specifying non-standard fasta and blast converters
icarus/lion/prisma/reformatPhase.i
2010/09/20 Change which allows the use of database dependencies for libraries which are updateded by mirroring, so they can be scheduled later in the update cycle
icarus/lion/prisma/prismaCheckClasses.i
icarus/lion/prisma/localcopyPhase.i
icarus/lion/prisma/checkDependentDbs.i
2010/07/21 Change to allow for a %d placeholder in an updateCheckCommand
icarus/lion/prisma/checkRemoteFiles.i
2010/07/21 Fix so prisma will not stop an update if a subdirectory is inaccessible during a recursive download
icarus/lion/prisma/remoteConnection.i
2010/03/29 Fix for a daylight saving time problem (Dates would be one day out of sync with their day names) with the calendar in the prisma report.
icarus/lion/prisma/generateCalendar.i
2010/02/17 Fixes for several problems with non-standard link names
icarus/workflows/moveIndicesPhase.i
icarus/workflows/linkPhase.i
2009/12/10 Fix for a problem where SRS or prisma has problems linking/removing/installing datafiles where the file names contain non standard characters. Note that this not cover cases where the filename contains a ?, *, [, ] or single quote
icarus/lion/prisma/localcopyPhase.i
icarus/workflows/coreCheckClasses.i
icarus/workflows/srsCheckMain.i
icarus/workflows/moveData.i
icarus/lion/prisma/movePrismaData.i
2009/12/07 Added an extra safety in our new method of estimating uncompressed file sizes to prevent problems when files grow a lot between releases
icarus/lion/prisma/checkRemoteFiles.i
2009/12/07 Fix for an access problem for the geneseq download site
icarus/lion/prisma/remoteConnection.i
icarus/lion/prisma/remoteConnection.i
2009/12/04 Fixed a problem with building links for databases with mixed case database names
icarus/lion/prisma/setReportPhase.i
icarus/workflows/linkPhase.i
icarus/lion/prisma/moveLibs.i
2009/12/04 Some improvements to the usage report: we make clearer on which nodes failures occur (these node names are now in red), and we now display all failures (previously we only displayed them if they had a runtime of more than one minute). Note that short processes which failed may still be invisible as they can be hidden by subsequent successfull processes in the graph
icarus/lion/prisma/cpuslots.il
2009/12/03 Fix for a LONG to INT overflow which could cause wrong sizes/times to be reported in the usage reports
icarus/lion/prisma/prismaCheckClasses.i
icarus/lion/prisma/printUsageReport.i
2009/11/03 Fixed an issue with some proxies, and an error reporting issue which could cause a crash
icarus/lion/prisma/remoteConnection.i
2009/10/21 Implemented a better way of estimating the size of uncompressed datafiles, using older versions of those files (if available) as a template. This should ensure more evenly distributed part sizes when indexing large databases in parts
icarus/lion/prisma/checkRemoteFiles.i
2009/10/21 Small change to correct a proxy setting for wgetPrisma
icarus/lion/prisma/remoteConnection.i
2009/08/24 Implemented a new way of removing partial index files after index merging, in order to prevent performence problems due to NFS congestion
icarus/lion/prisma/prismaCheckMain.i
icarus/workflows/buildPhase.i
icarus/workflows/srsCheckMain.i
icarus/workflows/linkPhase.i
2009/07/24 Changed the getFastaSequence.i script so it will also construct contig sequences. This script is used by the built in fastaconverters in prisma
icarus/lion/prisma/getFastaSequence.i
2009/06/05 Change to fix a problem with calculating partsizes if the partsize is set to very hight values (there was an error in th earlier fix)
icarus/workflows/linkPhase.i
2009/05/21 Chanage to fix a problem with calculating partsizes if the partsize is set to very hight values
icarus/workflows/buildPhase.i
icarus/workflows/linkPhase.i
2009/05/21 Improved the removal of symlinked index (and other srs files) from the off-line index directory. They could be left in the off-line index directory after a crash, and a subsequent srscheck or prisma run could try to install them in the online index directory, resulting in self-referential links. The removal of these links at the start of a run (during the check phase for a library) should prevent this.
icarus/workflows/getSystemLibs.i
icarus/workflows/coreCheckClasses.i
icarus/workflows/srsCheckMain.i
2009/05/11 Fix for a problem when detecting a time window for installing new data
icarus/lion/prisma/checkTimeWindow.i
2009/04/23 Change so we will not use a username and password for anonymous http access, as this can cause problems with some proxy servers
icarus/lion/prisma/remoteConnection.i
2009/04/23 Fix for a problem where prisma would not run reformat commands with the -forceReformat option if there is nothing else to update
icarus/lion/prisma/prismaCheckMain.i
2009/02/24 Two major changes in prisma reporting. We now also report the results of the remote checking in the main prisma report page (previously this was in other files, making it difficult to see if there was a problem with access to remote sites), and we now sort the entries in the report so that failures and errors are at the top of the various lists, so you no longer have to scroll through the entire report to find problems
icarus/lion/prisma/printPretransPages.i
icarus/lion/prisma/report_resources/images/local_copy2_completed.gif
icarus/lion/prisma/printMovePages.i
icarus/lion/prisma/report_resources/images/local_copy2_compErrors.gif
icarus/lion/prisma/printMainPage.i
icarus/lion/prisma/setReportPhase.i
icarus/lion/prisma/printLinkPages.i
icarus/lion/prisma/report_resources/images/local_copy2_white.gif
icarus/lion/prisma/printDownloadPages.i
icarus/lion/prisma/report_resources/images/local_copy2_skipped.gif
icarus/lion/prisma/report_resources/images/check_white.gif
icarus/lion/prisma/printBuildPages.i
icarus/lion/prisma/report_resources/images/check_failed.gif
icarus/lion/prisma/prismaCheckClasses.i
icarus/lion/prisma/report_resources/images/check_completed.gif
icarus/lion/prisma/report_resources/images/check_compErrors.gif
icarus/lion/prisma/PrismaToolsTestDb/prismaToolTest
icarus/lion/prisma/report_resources/images/local_copy2_failed.gif
icarus/lion/prisma/report_resources/images/local_copy2_waiting.gif
icarus/lion/prisma/checkRemoteFiles.i
icarus/lion/prisma/qualityReport/indicesTest.i
icarus/lion/prisma/prismastatus.is
icarus/lion/prisma/qualityReport/checkindexsize.i
icarus/lion/prisma/prismadata.i
icarus/lion/prisma/dbSync.i
icarus/lion/prisma/qualityReport/checkidsize.i
icarus/lion/prisma/report_resources/images/local_copy2_running.gif
icarus/lion/prisma/printReformatPages.i
2009/02/11 Fix for a problem where the usage history in the prisma reports would not display statistics (CPU etc) of previous prisma runs. Note that prisma will start to build up a usage history after applying this fix
icarus/lion/prisma/printUsageReport.i
2009/02/11 fix for a spurious error thrown by rm during the archiving of prisma reports
icarus/lion/prisma/prismaArchive.i
2008/12/09 Fix for an issue where prisma sometimes would build link-indices on-line
icarus/workflows/linkPhase.i
2008/11/20 Fix for a problem where in some cases a missing offline data directory could cause prisma to crash
icarus/lion/prisma/movePrismaData.i
2008/11/13 Changes to make maintenance easier by reducing the number of changes made to these files when ensembl, prisma or emboss are installed. In order to reduce the risk of system confusion about what changes have been made by these packages, we would recommend to first uninstall these packages by running "srspackage -remove srsprisma/emboss/EnsemblRD" (whatever is appropriate in your situation), update srsgen.i and srsdb.i (in you SRSSITE directory), and then reinstalling the packages. For prisma this is done by running "srspackage -install $SRSLION/packages/srsprisma.ip" (make sure you get the latest version of this file). For ensembl this is done by running "srspackage -install $SRSLION/packages/ensembl.ip". For emboss this is done by running "srssetup -emboss" - but see also the notes on upgrading to EMBOSS 6. After applying this update all these packages do is setting the enabled:y flag for the relevant libraries in srsdb.i file, and no changes are made to srsgen.i.
icarus/lion/packages/srsprisma.ip
2008/11/11 Added a new feature in prisma reports: the usage report will now contain a graph showing the usage of each cpu slot during a prisma run. This can be useful in locating bottlenecks during data processing
icarus/lion/prisma/prismaGui.i
icarus/lion/prisma/printUsageReport.i
icarus/lion/prisma/cpuslots.il
icarus/lion/prisma/report_resources/wz_tooltip.js
2008/11/11 Added an option to runPrisma to ignore data move scheduling conditions (-ignoreMoveDataConditions), and improved verbosity indicating why prisma is waiting with moving data online
icarus/lion/prisma/checkTimeWindow.i
etc/runPrisma
2008/11/11 Change so srscheck and prisma will remove symbolic links in the offline index directory when checking on a library. This will prevent the srsbuild process from writing to these links, and will also prevent these links being moved online, which could result in these files ending up being self-referential links
icarus/workflows/coreCheckClasses.i
2008/11/11 fixes for some minor tool testing issues in prisma reports
icarus/lion/prisma/PrismaToolsTestDb/testdb.i
icarus/lion/prisma/PrismaToolsTestDb/testdata.is
icarus/lion/prisma/srsinspect.i
icarus/lion/prisma/qualityReport/toolTests.i
icarus/lion/prisma/inspectReport.i
icarus/lion/prisma/inspectClasses.i
icarus/lion/prisma/generateCalendar.i
icarus/lion/prisma/PrismaToolsTestDb/testdb/hmm.testdata
icarus/lion/prisma/toolsTestSets.i
icarus/lion/prisma/PrismaToolsTestDb/testdb/distmat.testdata
2008/11/03 Fix so prisma will correctly handle failures occurring during the merging of read-link indices
icarus/workflows/linkPhase.i
2008/10/02 change so the prisma test databases no longer show up in the web interface
icarus/lion/prisma/PrismaToolsTestDb/testdb.i
2008/09/04 Fix for a problem where prisma would not honour all timewindows for data installation
icarus/lion/prisma/checkTimeWindow.i
2008/08/08 Changes needed for correctly moving link indices online if there are multiple links between two databases
icarus/lion/prisma/moveLibs.i
2008/08/08 Fix for a problem where prisma would not pick up an update scheduled to run on Sundays
icarus/lion/prisma/prismaCheckClasses.i
2008/08/08 Some fixes for importing settings from older srs installations when installing Prisma
icarus/lion/prisma/importPrismaProperties.i
2008/06/09 Fixed various minor issues with prisma reporting, and fixed links to the prisma documentation (the prisma 4.3 documention is included in the SRS8.3.0.1 patch release)
icarus/lion/prisma/printPretransPages.i
icarus/lion/prisma/printMovePages.i
icarus/lion/prisma/decisionReport.i
icarus/lion/prisma/printMainPage.i
icarus/lion/prisma/printLinkPages.i
icarus/lion/prisma/printDownloadPages.i
icarus/lion/prisma/printBuildPages.i
icarus/lion/prisma/prismatime.is
icarus/lion/prisma/inspectReport.i
icarus/lion/prisma/generateLinkReports.i
icarus/lion/prisma/tracePhase.i
icarus/lion/prisma/generateKey.i
icarus/lion/prisma/prismaGuiCal.i
icarus/lion/prisma/prismaGui.i
icarus/lion/prisma/prismaPage.i
icarus/lion/prisma/prismaArchive.i
icarus/lion/prisma/dumpTarget.i
icarus/lion/prisma/printUsageReport.i
icarus/lion/prisma/printReformatPages.i
2008/05/22 Changes needed to handle cases where there are multiple links defined between two libraries
icarus/workflows/linkPhase.i
2008/04/18 Change so prisma will honour a defaultBatchCommand if no specific batch command is defined for a task
icarus/lion/prisma/prismaCheckClasses.i
2008/04/17 Fix for a problem where prisma would not execute a reformat command for a dependend library when the -forceReformat option is specified
icarus/lion/prisma/checkDependentDbs.i
2008/04/09 Change so the fileCountTolerance used by srscheck and prisma is also applied if the nunber of files decreases
icarus/workflows/checkLocalFiles.i
2008/04/01 Change so the prisma installation procedure will no longer hardcode the full path to the icarus include files for the prisma test databases in srsdb.i
icarus/lion/packages/srsprisma.ip
2008/03/27 Fix for a problem with recursive traversion of directories on a remote ftp site
icarus/lion/prisma/remoteConnection.i
2008/03/27 Fix to ensure we remove old content from the current report directory, and an extra check so prisma will not accidentally wipe out all prisma directories
icarus/lion/prisma/prismaCheckMain.i
icarus/lion/prisma/prismaArchive.i
2008/03/26 Fix to ensure we remove old content from the prisma reports
icarus/lion/prisma/prismaCheckMain.i
2008/03/10 Change needed so prisma tools testing will not fail on the userprotein/dna tools
icarus/lion/prisma/toolsTestSets.i
2008/03/10 Workaround for a case where the calender generation mechians gets confused by daylight savings time
icarus/lion/prisma/generateCalendar.i
2008/03/05 Various fixes for prisma quality reporting: Fix for a possible crash during tool testing, fixed various hypertext links in prisma reports, and removed an obsolete test for relational databases
icarus/lion/prisma/inspectReport.i
icarus/lion/prisma/getappls.i
icarus/lion/prisma/qualityReport/rdbTests.i
2008/02/28 Fixes for various minor inconsistencies with images in prisma reports
icarus/lion/prisma/printPretransPages.i
icarus/lion/prisma/decisionReport.i
icarus/lion/prisma/printMainPage.i
icarus/lion/prisma/report_resources/images/loadersTest_up.png
icarus/lion/prisma/printLinkPages.i
icarus/lion/prisma/report_resources/images/suggested_action.gif
icarus/lion/prisma/printDownloadPages.i
icarus/lion/prisma/printBuildPages.i
icarus/lion/prisma/report_resources/images/bwfavicon.ico
icarus/lion/prisma/report_resources/images/bw_logo.gif
icarus/lion/prisma/report_resources/images/backMainPage_up.png
icarus/lion/prisma/report_resources/images/backMainPage_down.png
icarus/lion/prisma/report_resources/images/UsageReport_up.png
icarus/lion/prisma/report_resources/images/QuickReference.gif
icarus/lion/prisma/report_resources/images/QualityReport_up.png
icarus/lion/prisma/report_resources/images/PrismaReport_up.png
icarus/lion/prisma/inspectReport.i
icarus/lion/prisma/report_resources/images/DecisionReport_up.png
icarus/lion/prisma/generateCalendar.i
icarus/lion/prisma/generateCalendar.i
icarus/lion/prisma/prismaTreeImage.i
icarus/lion/prisma/prismaGuiCal.i
icarus/lion/prisma/prismaGuiCal.i
icarus/lion/prisma/prismaGui.i
icarus/lion/prisma/prismaGui.i
icarus/lion/prisma/dumpTarget.i
icarus/lion/prisma/printUsageReport.i
icarus/lion/prisma/report_resources/images/viewReport_up.png
icarus/lion/prisma/report_resources/images/toolsTest_up.png
icarus/lion/prisma/printReformatPages.i
2008/02/18 Fix to prevent crashes during tool tests
icarus/lion/prisma/getappls.i
2008/01/29 Fix for a problem with dependent databases when a local re-indexing is done
icarus/lion/prisma/localcopyPhase.i
2008/01/21 Removed icaIsDebug parameter as it is obsolete
icarus/lion/prisma/prismaCheckMain.i
2008/01/15 Changes needed to handle the fact the general.it is now residing in SRSSITE
icarus/lion/prisma/configUpdate/srssection_off
icarus/lion/prisma/configUpdate/srssection_off.i
2007/12/20 Added SRSFLAGS setting preservation for use with integrated config file updates
etc/runPrisma
etc/runPrisma