 
= Building =

	You can build the project by running using the following different methods:
	
	1. COMMAND LINE:	mvn clean package
	
	2. M2ECLIPSE:		Right-click and select Run As --> Maven Build...
						Under Goals enter "clean package"
						Click Run
	
	The maven build produces the build artifacts under the ${project}/target folder.

	
= Setup =
	
	Prior to running any project executables, the following must be setup:
	
	1. Setup your UNIX environment:

		1.1		open terminal
		1.2		cd ${project}
		1.3		mvn clean package	# runs the build to create the distribution
		1.4		source setupEnv.sh	# inspects the target folder to setup env vars	

		
= Running =
	
	Execute any of the CLI scripts from your shell.  Since all scripts are prefixed
	with "bior" by convention, TAB'ing after typing "bior" will show you all of 
	the CLI commands.

	
= Functional Tests =

	These are implemented as JUnit test cases executed by the maven-failsafe-plugin
	http://maven.apache.org/surefire/maven-failsafe-plugin that is designed to run
	functional/integration tests.  The plugin finds the correct JUnit test cases via
	the classname suffix "ITCase".
	
	To execute the functional tests, you need to run the maven build w/ the "verify" phase:
	
	1. COMMAND LINE:	mvn clean verify
	
	2. M2ECLIPSE:		Right-click and select Run As --> Maven Build...
						Under Goals enter "clean verify"
						Click Run
						
	You will need access to the BioR catalogs on RCF.  To connect via CIFS to /data5 on RCF using a Mac:
	1. Open a "Finder" window
	2. Click "Go" menu, "Connect to Server", enter "cifs://rcfcluster-cifs/data5" and click "Connect"
	3. Enter your username (mxxxxxx) and password



	
	
	
=============================================================================================
This repo was moved
Date: 2018-07-12
From: https://tfs.mayo.edu/tfs/MayoClinic/IMA/BioR/_git/bior-toolkit
To:   https://tfs.mayo.edu/tfs/MayoClinic/LPEA/_git/LPEA_GSU_bior_toolkit

Details:
# -------------
# Move to new Repo:
R5036906:NewGitRepos m054457$ git clone --mirror https://tfs.mayo.edu/tfs/MayoClinic/IMA/BioR/_git/bior-toolkit
R5036906:NewGitRepos m054457$ cd bior-toolkit.git/
R5036906:bior-toolkit.git m054457$ git push --mirror https://tfs.mayo.edu/tfs/MayoClinic/LPEA/_git/LPEA_GSU_bior_toolkit
Counting objects: 23076, done.
Delta compression using up to 8 threads.
Compressing objects: 100% (8927/8927), done.
Writing objects: 100% (23076/23076), 32.77 MiB | 7.86 MiB/s, done.
Total 23076 (delta 10258), reused 23076 (delta 10258)
remote: Analyzing objects... (23076/23076) (6170 ms)
remote: Storing packfile... done (2587 ms)
remote: Storing index... done (123 ms)
To https://tfs.mayo.edu/tfs/MayoClinic/LPEA/_git/LPEA_GSU_bior_toolkit
 * [new branch]        bior-toolkit-4.3.1 -> bior-toolkit-4.3.1
 * [new branch]        bior_pipeline_4.1.1_2016-09-22 -> bior_pipeline_4.1.1_2016-09-22
 * [new branch]        dev -> dev
 * [new branch]        master -> master
 * [new branch]        mmeiners_20180712_updateGlobalPropertiesToUseNewSageFormat -> mmeiners_20180712_updateGlobalPropertiesToUseNewSageFormat
 * [new branch]        origin/BIOR2.1.1 -> origin/BIOR2.1.1
 * [new branch]        origin/HEAD -> origin/HEAD
 * [new branch]        origin/bior_pipeline_2.4.1 -> origin/bior_pipeline_2.4.1
 * [new branch]        origin/master -> origin/master
 * [new tag]           4.1.1 -> 4.1.1
 * [new tag]           bior-toolkit-2.4.2--2016-10-05 -> bior-toolkit-2.4.2--2016-10-05
 * [new tag]           bior-toolkit-4.1.2--2016-10-05 -> bior-toolkit-4.1.2--2016-10-05
 * [new tag]           bior-toolkit-4.2.0--2016-11-22 -> bior-toolkit-4.2.0--2016-11-22
 * [new tag]           bior-toolkit-4.3.0--2017-04-18 -> bior-toolkit-4.3.0--2017-04-18
 * [new tag]           bior-toolkit-4.3.0-snapshot--2017-03-27a -> bior-toolkit-4.3.0-snapshot--2017-03-27a
 * [new tag]           bior-toolkit-4.3.0RC2--2017-04-12 -> bior-toolkit-4.3.0RC2--2017-04-12
 * [new tag]           bior-toolkit-4.3.1--2017-09-29 -> bior-toolkit-4.3.1--2017-09-29
 * [new tag]           bior-toolkit-4.4.0-snapshot--2017-06-25a -> bior-toolkit-4.4.0-snapshot--2017-06-25a
 * [new tag]           bior-toolkit-4.4.0-snapshot--2017-07-10a -> bior-toolkit-4.4.0-snapshot--2017-07-10a
 * [new tag]           bior_pipeline_2.1.0_2013-09-11 -> bior_pipeline_2.1.0_2013-09-11
 * [new tag]           bior_pipeline_2.2.0_2013-11-27 -> bior_pipeline_2.2.0_2013-11-27
 * [new tag]           bior_pipeline_2.2.1_2014-02-13 -> bior_pipeline_2.2.1_2014-02-13
 * [new tag]           bior_pipeline_2.3.0_2014-04-22 -> bior_pipeline_2.3.0_2014-04-22
 * [new tag]           bior_pipeline_2.4.1_2015-04-12 -> bior_pipeline_2.4.1_2015-04-12
 
# -------------
# Ran unit tests on fresh repo, "dev" branch:
R5036906:bior-toolkit.git m054457$ cd ..
R5036906:NewGitRepos m054457$ git clone https://tfs.mayo.edu/tfs/MayoClinic/LPEA/_git/LPEA_GSU_bior_toolkit
R5036906:NewGitRepos m054457$ cd LPEA_GSU_bior_toolkit/
R5036906:LPEA_GSU_bior_toolkit m054457$ git checkout dev
Branch 'dev' set up to track remote branch 'dev' from 'origin'.
Switched to a new branch 'dev'
R5036906:LPEA_GSU_bior_toolkit m054457$ # NOTE: Connect to cifs shared folder for BioR catalogs by opening Finder, click "Go" - "Connect to Server...", enter "cifs://rcfcluster-cifs.mayo.edu/data5", then click "Connect"
R5036906:LPEA_GSU_bior_toolkit m054457$ # NOTE: Not all tests are passing at this time.  These need to be resolved.
R5036906:LPEA_GSU_bior_toolkit m054457$ mvn clean verify
....

Results :

Failed tests:   testStartAndStopSteps(edu.mayo.bior.buildcatalog.BuildCatalogStepTest): (..)
  testStartAndStopSteps_withCmd(edu.mayo.bior.buildcatalog.BuildCatalogStepTest): (..)
  testBasic(edu.mayo.bior.catalog.CatalogTabixEntryTest): expected: java.lang.Integer<2> but was: java.lang.Long<2>
  testSampleSize(edu.mayo.bior.catalog.verification.CatalogVerifierTest)
  testRefAssembly_BadRefs_ShouldThrowErrors(edu.mayo.bior.catalog.verification.CatalogVerifierTest): (..)
  testBuildCatalogCommand_makeJsonThruPropsSteps(edu.mayo.bior.cli.cmd.BuildCatalogCommandTest)
  testBuildCatalogCommand_verifyStepOnly(edu.mayo.bior.cli.cmd.BuildCatalogCommandTest): expected:<[Chromosome 5: _refAllele values that DO NOT match the reference sequence is [1].]> but was:<[]>
  createCatalogUsingGzipTempFiles(edu.mayo.bior.pipeline.createcatalog.TjsonToCatalogTest): expected:<3> but was:<5>
  lineToVcf_optionalFields(edu.mayo.bior.pipeline.TjsonToVcfPipeTest): Exception thrown when trying to assert JSON equality.(..)
  handleSpacesAndOtherOddCharsGoingIntoInfoCol(edu.mayo.bior.pipeline.TjsonToVcfPipeTest): Exception thrown when trying to assert JSON equality.(..)
  pipeJustJson(edu.mayo.bior.pipeline.TjsonToVcfPipeTest): Exception thrown when trying to assert JSON equality.(..)
  collapseBiorColsBackIntoExistingInfoCol(edu.mayo.bior.pipeline.TjsonToVcfPipeTest): Exception thrown when trying to assert JSON equality.(..)

Tests in error: 
  testGetVEPCommand(edu.mayo.bior.pipeline.VEP.VEPEXETest): /var/folders/gl/wdqzn5ws0jz5qtzy41x7h0d9ygjpzy/T/junit4629850685488057640/junit5011932476487238257/junit8262489876339842448/bior.properties (No such file or directory)
  testWithUserInputs(edu.mayo.bior.pipeline.VEP.VEPEXETest): /var/folders/gl/wdqzn5ws0jz5qtzy41x7h0d9ygjpzy/T/junit4629850685488057640/junit5011932476487238257/junit8262489876339842448/bior.properties (No such file or directory)

Tests run: 572, Failures: 12, Errors: 2, Skipped: 9

[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 01:27 min
[INFO] Finished at: 2018-07-12T14:41:07-05:00
[INFO] Final Memory: 24M/276M
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.apache.maven.plugins:maven-surefire-plugin:2.12.4:test (default-test) on project bior-toolkit: There are test failures.
[ERROR] 
[ERROR] Please refer to /Users/m054457/TEMP/NewGitRepos/LPEA_GSU_bior_toolkit/target/surefire-reports for the individual test results.
[ERROR] -> [Help 1]
[ERROR] 
[ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.
[ERROR] Re-run Maven using the -X switch to enable full debug logging.
[ERROR] 
[ERROR] For more information about the errors and possible solutions, please read the following articles:
[ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/MojoFailureException




=============================================================================================
These commands, properties files, and tests were removed in v5.0.0  (2018-07-24)
Related to:
	- bior_annotate (and bior_annotate_blaster)
	- bior_vep
	- bior_snpeff
In the next release we should remove all code related to these tests and commands
NOTE: There is a class (Bior.java) that is used by R to get annotation, similar to what the old bior_annotate did.
      Be careful that we don't accidentally remove the classes needed by this command.
=============================================================================================
	deleted:    src/main/resources/cli/AnnotateCommand.properties
	deleted:    src/main/resources/cli/SNPEffCommand.properties
	deleted:    src/main/resources/cli/VEPCommand.properties
	deleted:    src/main/scripts/_bior_annotate_blaster_chunker
	deleted:    src/main/scripts/_bior_annotate_blaster_concat
	deleted:    src/main/scripts/bior_annotate_blaster
	deleted:    src/test/java/edu/mayo/bior/cli/func/remoteexec/Bior2VCFITCase.java
	deleted:    src/test/java/edu/mayo/bior/cli/func/remoteexec/ManyCmdsITCase.java
	deleted:    src/test/java/edu/mayo/bior/cli/func/remoteexec/SNPEFFEXEITCase.java
	deleted:    src/test/java/edu/mayo/bior/cli/func/remoteexec/SNPEFFPipelineITCase.java
	deleted:    src/test/java/edu/mayo/bior/cli/func/remoteexec/SNPEffCommandITCase.java
	deleted:    src/test/java/edu/mayo/bior/cli/func/remoteexec/TreatExitCodesITCase.java
	deleted:    src/test/java/edu/mayo/bior/cli/func/remoteexec/TreatMultiCmdITCase.java
	deleted:    src/test/java/edu/mayo/bior/cli/func/remoteexec/TreatSingleThreadITCase.java
	deleted:    src/test/java/edu/mayo/bior/cli/func/remoteexec/VEPCommandITCase.java
	deleted:    src/test/java/edu/mayo/bior/cli/func/remoteexec/VEPEXEITCase.java
	deleted:    src/test/java/edu/mayo/bior/cli/func/remoteexec/VEPPipelineITCase.java
	deleted:    src/test/java/edu/mayo/bior/pipeline/SNPEff/SNPEFFEXETest.java
	deleted:    src/test/java/edu/mayo/bior/pipeline/SNPEff/SNPEFFMergeTest.java
	deleted:    src/test/java/edu/mayo/bior/pipeline/SNPEff/SNPEffOutputTest.java
	deleted:    src/test/java/edu/mayo/bior/pipeline/SNPEff/SNPEffectColInfo.java
	deleted:    src/test/java/edu/mayo/bior/pipeline/SNPEff/VCFProgram2HistoryPipeTest.java
	deleted:    src/test/java/edu/mayo/bior/pipeline/Treat/format/BaseFormatterTest.java
	deleted:    src/test/java/edu/mayo/bior/pipeline/Treat/format/BgiFormatterTest.java
	deleted:    src/test/java/edu/mayo/bior/pipeline/Treat/format/CosmicFormatterTest.java
	deleted:    src/test/java/edu/mayo/bior/pipeline/Treat/format/DbsnpClinvarFormatterTest.java
	deleted:    src/test/java/edu/mayo/bior/pipeline/Treat/format/DbsnpFormatterTest.java
	deleted:    src/test/java/edu/mayo/bior/pipeline/Treat/format/EspFormatterTest.java
	deleted:    src/test/java/edu/mayo/bior/pipeline/Treat/format/HapmapFormatterTest.java
	deleted:    src/test/java/edu/mayo/bior/pipeline/Treat/format/HgncFormatterTest.java
	deleted:    src/test/java/edu/mayo/bior/pipeline/Treat/format/MirBaseFormatterTest.java
	deleted:    src/test/java/edu/mayo/bior/pipeline/Treat/format/NCBIGeneFormatterTest.java
	deleted:    src/test/java/edu/mayo/bior/pipeline/Treat/format/OmimFormatterTest.java
	deleted:    src/test/java/edu/mayo/bior/pipeline/Treat/format/SNPEffFormatterTest.java
	deleted:    src/test/java/edu/mayo/bior/pipeline/Treat/format/ThousandGenomesFormatterTest.java
	deleted:    src/test/java/edu/mayo/bior/pipeline/Treat/format/UcscBlacklistedFormatterTest.java
	deleted:    src/test/java/edu/mayo/bior/pipeline/Treat/format/UcscConservationFormatterTest.java
	deleted:    src/test/java/edu/mayo/bior/pipeline/Treat/format/UcscEnhancerFormatterTest.java
	deleted:    src/test/java/edu/mayo/bior/pipeline/Treat/format/UcscRegulationFormatterTest.java
	deleted:    src/test/java/edu/mayo/bior/pipeline/Treat/format/UcscRepeatFormatterTest.java
	deleted:    src/test/java/edu/mayo/bior/pipeline/Treat/format/UcscTfbsFormatterTest.java
	deleted:    src/test/java/edu/mayo/bior/pipeline/Treat/format/UcscTssFormatterTest.java
	deleted:    src/test/java/edu/mayo/bior/pipeline/Treat/format/UcscUniqueFormatterTest.java
	deleted:    src/test/java/edu/mayo/bior/pipeline/Treat/format/VEPFormatterTest.java
	deleted:    src/test/java/edu/mayo/bior/pipeline/VEP/VEPEXETest.java
	deleted:    src/test/java/edu/mayo/bior/pipeline/VEP/VepCsqSeqOntComparatorTest.java
	deleted:    src/test/java/edu/mayo/bior/pipeline/VEP/VepCsqSiftPolyphenComparatorTest.java
	deleted:    src/test/java/edu/mayo/bior/pipeline/VEP/VepFunctionsTest.java