RAxML HPC Workflow REST

RAxML Workflow interface: raxmlhpc2_workflow.xml

This is one of several RAxML interfaces that can be used from the REST API. Others include raxmlhpc2_tgb.xml, raxmlhpc2bb.xml, raxmlhpc2_tgb_rest.xml, and raxmlhpc8_rest_xsede.xml. This interface was created to support the multiple command workflows offered by raxmlGUI. The preferred interface for non-workflow jobs is the raxmlhpc8_rest_xsede.xml interface.

The Tool ID for this interface is RAXMLHPC2_WORKFLOW. It is selected with toolId=RAXMLHPC2_WORKFLOW

The goal of the raxmlhpc2_workflow.xml interface is to support all four of the multiple command workflow options that raxmlGUI currently supports. Since CIPRES generates all files for a given job run in a single working directory, all files produced by each step of the workflow are available for the subsequent steps. Analyses that are supported by raxmlGUI, but that use a single command line are best accomplished using the raxmlhpc8_rest_xsede.xml. Separate documentation for that interface is available.

Instructions for this interface:

To use the raxmlhpc2_workflow.xml interface, choose the workflow type, using

vparam.specify_workflow_=, where = FTS, BOOTCON, MLS, and MLTB, default = FTS

The choices correspond to the four possible multiple command options supported by raxmlGUI. Fast Tree Search (FTS), Bootstrap/Consensus Tree (BOOTCON); Max Likelihood Search (MLS); and Maximum Likelihood /Thorough Bootstrap (MLTB). default is FTS.

Once a workflow selection is made, other options (setting the model, adding constraints, etc) can be chosen. In addition to most of the general RAxML configuration options, several options must be selected that are specific to each workflow type. The workflow-specific options are described below, while the general options are described in detail elsewhere. This interface currently only supports what raxmlGUI supports, and it does not support changing RAxML’s -f options, as these are specified by the individual workflow types.

Supported workflow parameters:
vparam.runtime_   - Float - required parameter, default= 0.25
vparam.nchar_ - Integer - Number of patterns in the data set. Default=1000.
vparam.specify_workflow_ - Excl - required parameter.  FTS, MLTB, MLS, BOOTCON default=FTS
vparam.altrun_number_ - Integer - Specify the number alternative runs on distinct starting trees (-#/-N), for MLTB and MLS workflows only. Values between 2 and 1000 are allowed. default=10.
vparam.choose_bootstop - Excl -Specify bootstrap protocol: a specific number of bootstraps, or auto bootstopping. Only available when vparam.specify_workflow_ is set to MLTB or BOOTCON. Allowed values are specify and bootstop. default=specify.
vparam.bootstrap_value_ - Integer -  Number of Bootstrap iterations (-N). Only if vparam.choosebootstop=specify. default=100
vparam.bootstopping_type_ - Excl - only when vparam.choose_bootstop_=bootstop. Select Bootstopping Criterion: (-N) autoFC, autoMR,autoMRE, autoMRE_IGN, default=autoMRE
vparam.no_bfgs_ - Switch - not available for FastTree Search. Turns of the bfgs algorithm. default=0

Additionally, any input files required for a given job run must be provided.At minimum, input.infile_=infile.txt is required. Other input files, such as constraint, starting trees, etc, must also be provided using the input._=

Please see raxmlhpc8_rest_xsede.xml documentation for more information about options that require file uploads.

Specific workflow options:
vparam.specify_workflow_=FTS; FTS=Fast Tree search:

Example command line generated:
raxmlHPC-PTHREADS     -T 8 -f E -p 12345 -m GTRGAMMA -n infile.tre    -s infile.txt -O
&& raxmlHPC-PTHREADS     -T 8 -f e -t RAxML_fastTree.infile.tre -n brL.infile.tre -s infile.txt -m GTRGAMMA  -O
&& raxmlHPC-PTHREADS     -T 8 -f J -t RAxML_result.brL.infile.tre -n sh.infile.tre -s infile.txt -m GTRGAMMA  -O

parameters for the FTS workflow, values are only allowed if specify_workflow=FTS
vparam.outsuffix_FTS_ - String -  required. Set a name for output files in the FTS workflow. –n .tre default=infile.
vparam.fasttreesearch_workflow2_ - Switch (0/1) -  Optimize model parameters and branch lengths (-f e). default=0. This parameter turns on the second step of the workflow, the optimization. This stpe is not required.
vparam.fasttreesearch_workflow3 - Switch (0/1) - This switch turns on the third step., find SH-like values (-f J). default=0 The third step is also not required. And the second and third steps are independent of each other.
vparam.parsimony_seed_val2_ - Integer -  Enter a random seed value for parsimony inferences for the SH- like value step. default = 12345

vparam.specify_workflow_=MLTB;  MLTB=Maximum Likelihood /Thorough Bootstrapping
Example command line for this option:
raxmlHPC-PTHREADS.exe -T 2   -b 762 -m PROTGAMMABLOSUM62  -p 801 -N 100 -o 1_Euglena_gracilis -s infile2.txt -n testR -O
&&raxmlHPC-PTHREADS.exe -T 2 -f d -m PROTGAMMABLOSUM62  -o 1_Euglena_gracilis -s infile2.txt -N 10 -n testB -p 603 -O
&&raxmlHPC-PTHREADS.exe -T 2 -f b -t RAxML_bestTree.testB  -z RAxML_bootstrap.testR -m PROTGAMMABLOSUM62  -s infile2.txt -n test.tre -O

parameters for the MLTB workflow, values are only allowed if specify_workflow=MLTB
vparam.mulparambootstrap_seed_val_ - Integer - Enter a random seed value for multi-parametric bootstrapping. This appears in the command line as –b . default=12345
vparam.outsuffix_MLTB1_ - String -  Name for output files from the bootstrapping step, step 1. (delivered on the first command line as –n $value). default-testR. Also used to name the –z file, in step 3
vparam.parsimony_seed_val_MLTB2_ - Integer -Enter a random seed value for MLTB sampling step (Step 2). default value=12345.
vparam.outsuffix_MLTB2_ - String - Name for the output files in step 2 of the ML + thorough bootstrap workflow. Delivered as –n $value to the second command line. Also used to name the –t file, in step 3. default=testB.
vparam.outsuffix_MLTB3_ - String -  Set a name for output files in step 3 of the ML thorough bootstrapping analysis. Delivered as –n $value to the third command line. default=MLTB_output

vparam.specify_workflow_=MLS;  MLS=Maximum Likelihood Search
Example command line:
raxmlHPC-PTHREADS.exe -T 2 -f d -m PROTGAMMABLOSUM62F -N 1 -p 130 -o 1_Euglena_gracilis -s infile2.txt -n infile2.tre -O
&&raxmlHPC-PTHREADS.exe -T 2 -f J -m PROTGAMMABLOSUM62F -t RAxML_bestTree.infile2.tre"  -n sh.infile2.tre -s infile2.txt -O
 && cat RAxML_result.infile2.tre* > combined_results.infile2.tre

parameters for the MLS workflow, values are only allowed if specify_workflow=MLS
vparam.outsuffix_MLS_ - String - Set a name for output files in the MLS workflow. Delivered as –n $value to first command lines. Also used to name subsequent output files. default=infile                                          
vparam.mlsearch_shlike_ - Switch (0/1) - Add the second step in this workflow, find SH-like values (-f J). default=0. This step is not required.
vparam.mlsearch_combine_ - Switch (0/1) - Cat the results in to a single big tree file. default=0. This activates the third step in the workflow. This step can be run without the second step.

vparam.specify_workflow_=BOOTCON; BOOTCON=Bootstrap/Consensus Search
Example command line:
Bootstrap + Consensus: Two Steps
raxmlHPC-PTHREADS.exe -T 2 -m GTRGAMMA -n infile.tre -s  infile.txt -O -x 4 -N 100 -p 368
&& raxmlHPC-PTHREADS.exe -T 2 -m GTRGAMMA -n con.infile.tre -J MR -z infile.tre    
Both steps are required.

parameters for the BOOTCON workflow, values are only allowed if specify_workflow=BOOTCON
vparam.outsuffix_BOOTCON_ - String -  Set a name for output files from the Rapid Bootstrap Step. Delivered as –n $value on the first line of the workflow. default=boot
vparam.rapidbootstrap_seed_val_ - Integer -  Enter a random seed value for multi-parametric bootstrapping. default=12345
vparam.outsuffix_BOOTCON2_ - String - Name for output files from the Consensus Tree Step. Delivered on the second line as –n $value. default = con.tre.

Please do report any issues noted.

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