####################################################################################################### I have decided to record every change, whether or not it impacts the REST API. This will help me remember. It will be obvious from the description if the change is consequential for REST API. -mark ####################################################################################################### For each change you commit, this info is needed: =================================================================================================================================== Pise Filename: Committer name: Branch/Rev #/Date Committed: Branch/Rev #/Date Committed: ... one for each branch/trunk you commit to Purpose of Change: Fogbugz url: (if we're still using fogbugz) Parameters Changed/Description: ==================================================================================================================================== A totally fictional, nonsense example entry: raxmlhpc2bb.xml Committed by: TS Committed To: - trunk: 8309: 6/21/2014 11:00 am - portal-R30: 8349: 6/21/2014 11:10 am Purpose: Correct 2 invalid preconditions. Users were unable to supply a constraint tree when running bootstraps. Fogbugz: Parameters Changed: - bootstop - changed precond from: '!$use_bootstopping' to '$use_bootstopping' - constraint - changed precond from: '!defined binary_backbone' to '!defined binary_backbone && $use_bootstopping' =================================================================================================================================== Pise Filename:raxmlhpc2_tgb.xml Committed by: MAM Branch/Rev #/Date Committed: - trunk: 8343: 6/22/2014 9:39 am - sdk-R30: 8349: 6/23/2014 7:15 am Purpose of Change: Correct incorrect ctrl. A ctrl was activated when it shouldn't have been, giving users a non-sensical error message, and preventing submission of a legitimate job. Fogbugz url: http://phylo-bugz.sdsc.edu/fogbugz/default.asp?353839#803682 Parameters Changed/Description: The element thorough_opt had a ctrl activated by !defined $treetop. This was incorrect because it made submission impossible for situations where when -x was de-selected. To correct the error, we activate the ctrl only when both $thorough_opt && !defined $treetop are true. In other words, the requirement for the tree is only present when thorough optimization is requested. =================================================================================================================================== Pise Filename:beast_tg.xml Committed by: MAM Branch/Rev #/Date Committed: - trunk: 8343: 6/24/2014 2:37 pm - sdk-R30: 8349: 6/24/2014 2:35 pm Purpose of Change: Made all jobs submitted with -threads 8. Also moved the location of the No BEAGLE option. Fogbugz url: None Parameters Changed/Description: These are text changes and are inconsequential =================================================================================================================================== Pise Filename:raxmlhpc2_tgb.xml Committed by: MAM Branch/Rev #/Date Committed: - trunk: 8343: 7/22/2014 9:39 am - sdk-R31: 8349: 7/22/2014 11:10 am Purpose of Change: Add some new model options for protein data sets. Fogbugz url: This was a user request from Sonia Andrade via email. Parameters Changed/Description: The element prot_matrix_spec was missing some model values now available. These were added. DUMMY DUMMY2 AUTO LG4M LG4X PROT_FILE GTR_UNLINKED =================================================================================================================================== Pise Filename:raxmlhpc2bb.xml Committed by: MAM Branch/Rev #/Date Committed: - trunk: 8343: 7/3/2014 3:04 pm - sdk-R31: 8498: 8.4.2014 3:57 PM Purpose of Change: Remove -T 6 from the command line. Fogbugz url: None. Parameters Changed/Description: The element raxmlhpc_hybridlogic3 had the value -T 6 removed, because it is redundant with Bryan's wrapper. =================================================================================================================================== Pise Filename:raxmlhpc2bb.xml Committed by: MAM Branch/Rev #/Date Committed: - trunk: 8343: 7/3/2014 3:04 pm - sdk-R31: 8498: 8/4/2014 3:57 PM Purpose of Change: Remove -T 6 from the command line. Fogbugz url: None. Parameters Changed/Description: The element raxmlhpc_hybridlogic3 had the value -T 6 removed, because it is redundant with Bryan's wrapper. =================================================================================================================================== Pise Filename:pauprat.xml Committed by: MAM Branch/Rev #/Date Committed: (this is an aggregate of several commits over several days) - trunk: 8520: 8/8/2014 7:51 am - sdk-R31: 8521: 8/8/2014 8:36 am Purpose of Change: Several changes required in preparation for release in MorphoBank. Fogbugz url: None. Via correspondence with Seth Kaufmann and Terri and Mark. Parameters Changed/Description: 1. specify_nchar now has the ismandatory="1" flag 2. the element setup_hidden1 was changed, The string nrep = 1 replaced a variable set by the user. This should always have been nrep = 1. 3. the element intiation_string was changed. the flag -n was added so PAUP would work non-interactively. This eliminates a problematic error message. 4. for PAUPrat, the set_multrees option should always be "no", though it was exposed as an option. We eliminated this option and set it as a string always "no". the parameter is now hard coded. =================================================================================================================================== Pise Filename:mafft_tg.xml Committed by: MAM Branch/Rev #/Date Committed: (this is an aggregate of several commits over several days) - trunk: 8421: 7/10/2014 12:08 PM - sdk-R31: 8420: 7/10/2014 12:07 PM Purpose of Change: Several changes required in text strings, but these are not consequential preparation for release in MorphoBank. Fogbugz url: None. Parameters Changed/Description: MAFFT was running on 32 threads, and this was changed to make it run on 8. The changes are all textual and occur in several places. =================================================================================================================================== Pise Filename:beast2_xsede.xml Committed by: MAM Branch/Rev #/Date Committed: Several changes over a few days. - trunk: 8488: 8/1/2014 12:21 PM - sdk-R31: 8500: 8/4/2014 4:27 PM Purpose of Change: A users file required us to implement the -overwrite flag Fogbugz url: None. Parameters Changed/Description: 1. The element overwrite_logs was added to allow users to run certain files that will otherwise fail. It is a switch, 0 is the default, 1 allows log overwriting. 2. Re-write submission rules, eliminating elements that created a dependence on partition numbers. Comment out these elements: nu_partitions,is_partitioned,partitions_4, partitions_2; set "-threads 8" explicitly in partitions_1; correct text in runtime element. 3. correct spelling error in element beast_nobeagle_trestles command line string =================================================================================================================================== Pise Filename:raxmlhpc2_tgb.xml Committed by: MAM Branch/Rev #/Date Committed: - trunk: 8 - sdk-R31: Purpose of Change: The RAXML interface had to be modified to add parameters required by raxmlGUI Fogbugz url: None: This was anticipation of the raxmlGUI requirements. No FB report. Parameters Changed/Description: Several elements were added: 1. outsuffix: this is a string that specifies the extension name for all output files. by default it is set to result. The flag is -n $outsuffix 2. disable_ratehet: this is a switch that adds the -V flag to the command line. It is 0 by default. It is only valid when CAT models are used. Other use causes a failure. 3. number_cats: a precond was repaired on this, it should have no consequence in the interface for rest users 4. MLsearch_CAT: this is a switch that adds the -F flag to the command line. by default it is set to 0. =================================================================================================================================== Pise Filename:raxmlhpc2_tgb.xml Committed by: MAM Branch/Rev #/Date Committed: - trunk: 8/21/2014 - sdk-R31: Purpose of Change: The RAXML interface had to be modified to add parameters requested by a user. Fogbugz url: http://phylo-bugz.sdsc.edu/fogbugz/default.asp?354465 Parameters Changed/Description: Several elements were added: 1. added the -f u option. element = morpho_weight_calibration 2. added the -f v option. element = classify_into_reftree 3. added the -a option. element = set_weights 4. to use the -f u option, we had to make it ok to provide a parsimony seed with the -f u option. Changed precond on provide_parsimony_seed 5. to use the -f u option, we had to make it ok to use the -N (specify_runs) option with -f u: specify_runs 6. added a control so the parameter outsuffix is required. 7. preconds were added to a number of elements to suppress their availability in the presence of the new options -f u and -f v =================================================================================================================================== Pise Filename:raxmlhpc2_tgb.xml Committed by: MAM Branch/Rev #/Date Committed: - trunk: 8/22/2014 - sdk-R31: 9/9/2014 2:04 PM Purpose of Change: The RAXML interface had to be modified to correct the implementation of -J as requested by a user. Fogbugz url: http://phylo-bugz.sdsc.edu/fogbugz/default.asp?354616 Parameters Changed/Description: 1. The -J option is unique for RaxML in requiring the -z flag instead of the -s flag for the input file. As a result, we had to modify the -s infile element. We split the infile element from the code that specifies -s infile on the command line, then we put a precond on the element that specifies -s infile (whenever -J is not called), and added a second element that specifies -z infile when -J is called. 2. The -J option has some other flags, and these were implemented. These are new options on the -J flag: STRICT, MR_DROP, STRICT_DROP 3. Repaired some precons involving gtrgamma 4. Changed the precond on the -z option so it cant be run with -J. Because -z is the invocation line. =================================================================================================================================== Pise Filename:raxmlhpc2_tgb.xml Committed by: MAM Branch/Rev #/Date Committed: - trunk: 9/18/2014 - sdk-R31: 9/18/2014 9:11 AM Purpose of Change: The RAXML interface had to be modified to correct the default max bootstraps allowed. Fogbugz url: http://phylo-bugz.sdsc.edu/fogbugz/default.asp?354752 Parameters Changed/Description: 1. The max value for bootstraps is 1,000, but the interface allowed 5,000. Fixed this 2. Changed precond on element mrbootstopping_type to depend only on $mr_bootstopping =================================================================================================================================== Pise Filename:raxmlhpc2_tgb.xml Committed by: MAM Branch/Rev #/Date Committed: - trunk: 9/22/2014 7:08 AM - sdk-R31: 9/22/2014 8:03 AM Purpose of Change: The RAXML interface had to be modified to incorporate the request for -j and -D options. Fogbugz url: http://phylo-bugz.sdsc.edu/fogbugz/default.asp?354779 and 354752 Parameters Changed/Description: 1. The max value for bootstraps is 1,000, but the interface allowed 5,000. Fixed this 2. Changed precond on element mrbootstopping_type to depend only on $mr_bootstopping =================================================================================================================================== Pise Filename:clearcut.xml; clustalw.xml; consense.xml, contralign.xml; muscle.xml; nclconverter.xml; pauprat_exp.xml; pauprat.xml; poy.xml; probalign.xml; probcons.xml; readseq.xml, seqboot.xml Committed by: MAM Branch/Rev #/Date Committed: - trunk: 10/20/2014 4-4:12 PM - sdk-R31: Purpose of Change: Get rid of the &runtime parameter. =================================================================================================================================== Pise Filename:clearcut.xml; clustalw.xml; consense.xml, contralign.xml; muscle.xml; nclconverter.xml; pauprat_exp.xml; pauprat.xml; poy.xml; probalign.xml; probcons.xml; readseq.xml, seqboot.xml Committed by: MAM Branch/Rev #/Date Committed: - trunk: 10/22-23/2014 various PM - sdk-R31: Purpose of Change: Get make sure the start.txt, term.txt, and done.txt files are returned. consense, muscle, poy, probcons, readseq, seqboot. "Result" Elements were added to return eahc of the noted files. =================================================================================================================================== Pise Filename:dppdiv.xml Committed by: MAM Branch/Rev #/Date Committed: - trunk: 12/2 - sdk-R32:12/2 -REST3:12/2 Purpose of Change:Fix the dphp element so it accepts a numerical value. This was missing before. =================================================================================================================================== Pise Filename:raxmlhpc2_tgb.xml Committed by: MAM Branch/Rev #/Date Committed: - trunk: 12/4 - sdk-R32:12/4 -REST3:12/4 Purpose of Change:Fix a precond on the -f x option, so a -t tree is possible but not required. =================================================================================================================================== Pise Filename:raxmlhpc2_tgb.xml Committed by: MAM Branch/Rev #/Date Committed: - trunk: 12/11 - sdk-R32:12/11 -REST3:12/11 Purpose of Change:Add the element ascertainment_corr, which allows the user (the user must choose) an ascertainment correction type if they choose ascertainment correction.