• Home
  • Features
  • Pricing
  • Docs
  • Announcements
  • Sign In

broadinstitute / hellbender
79%
master: 81%

Build:
Build:
LAST BUILD BRANCH: dr_disentangle_spark_and_dataflow
DEFAULT BRANCH: master
Repo Added 06 Jan 2015 07:33PM UTC
Files 539
Badge
Embed ▾
README BADGES
x

If you need to use a raster PNG badge, change the '.svg' to '.png' in the link

Markdown

Textile

RDoc

HTML

Rst

LAST BUILD ON BRANCH lb_move_placement_of_travis_wait
branch: lb_move_placement_of_travis_wait
CHANGE BRANCH
x
Reset
  • lb_move_placement_of_travis_wait
  • AddLogStatements
  • BRUTest
  • CTBuilder
  • ak_AddOrReplaceReadGroups_test
  • ak_Annotator
  • ak_CalculateReadGroupChecksum_tests
  • ak_CigarUtils_tests
  • ak_CollectBaseDistributionByCycle_tests
  • ak_CollectQualityYieldMetrics_test
  • ak_CollectWgsMetrics_test
  • ak_LeftAlignIndels
  • ak_LiftOverIntervalList_test
  • ak_MeanQualityByCycle_spark2
  • ak_MisencodedBaseQualityReadTransformer
  • ak_QualityScoreDistribution_tests
  • ak_ReadLikelihoodCalculationEngine
  • ak_ReplaceSamHeader_test
  • ak_VariantAnnotatorEngine
  • ak_add_cloudera
  • ak_add_google
  • ak_analyzeCovariates
  • ak_apply_vqsr_onTranchesBranch
  • ak_bqsr_NPE
  • ak_bqsr_multiple_site_lists
  • ak_bqsr_part2
  • ak_bqsr_pipeline_test
  • ak_clipReads
  • ak_clone
  • ak_clp_test
  • ak_codecs
  • ak_copyright
  • ak_countBases_spark
  • ak_countReads_spark
  • ak_countReads_spark_moreTests
  • ak_coverage_spark
  • ak_dataflow_codereading
  • ak_dead_code_removal
  • ak_delete_BamToBfq
  • ak_delete_code_not_being_ported_from_picard
  • ak_diamonds
  • ak_diff_engine
  • ak_disable_broken_picard_tests
  • ak_enable_ReadCovariatesUnitTest
  • ak_exampleVariantWalker
  • ak_feature_input
  • ak_flagstat_spark
  • ak_gatreport
  • ak_genotyper
  • ak_good_read_filter
  • ak_hc_assemblygraph
  • ak_improve_testing_coverage
  • ak_left_tail_bqsr
  • ak_log4j2_xml
  • ak_logging_info_in_readme
  • ak_malformed_read_filter
  • ak_mark_duplicates
  • ak_meanqualitybycycle_tests
  • ak_pairhmm
  • ak_pileup_work
  • ak_printReadsOptionsAndTests
  • ak_printReads_spark
  • ak_readClipperUnitTests
  • ak_read_additional_filters
  • ak_readme_on_testing
  • ak_remove_multiThreading_from_ExtractIlluminaBarcodes
  • ak_remove_readFilterTest
  • ak_replaceCustomGamma_withApache
  • ak_simplify_covariates
  • ak_small_readme_edits
  • ak_snacks
  • ak_some_code_cleanup
  • ak_sparkToolName
  • ak_splitNCigarReads
  • ak_test_LeftAlignIndels
  • ak_validate_variants
  • ak_variant_filtration
  • ak_variant_recalibrator
  • ak_variant_walker
  • ak_vqsr_tranche_doc
  • ak_vqsr_tranches
  • ak_vqsr_variant_data_management
  • ak_warnings
  • ak_wellformed_filter_tests
  • akiezun-README-guidelines
  • akiezun-readme-style_tweaks
  • bh_prune_vcf
  • cn_filter_reads
  • cn_gatk_read
  • cn_haplotype_bamwriter
  • cn_log4j_picard
  • cn_read_filters
  • cn_select_variants
  • cn_set_log4j_level
  • cn_split_reads
  • cs_basicqcmetrics
  • da_auth
  • da_copy_deps
  • da_credential_factory
  • da_credentials
  • da_dataflow_version_bump
  • da_genomics_pipeline_deps
  • da_hook_up_mark_dupes
  • da_keyed_transforms
  • da_less_brittle_dataflow_tests
  • da_mark_dupes_fusion_fun
  • da_mark_dupes_refactor
  • da_playground2
  • da_read_pipeline
  • da_spark_integration
  • da_spark_integration_test
  • da_spark_local
  • da_spark_mark_dupes
  • da_spark_markdupes
  • da_spark_skeleton
  • da_spark_tuning
  • da_variant_start
  • db_covariance
  • db_genotyper_logarithms
  • db_kill_median
  • db_natural_log
  • db_target_collection
  • dek_CollectJumpingLibraryMetrics_IT
  • dek_CollectTargetedPcrMetrics_IT
  • dek_RenameSampleInVCF_test
  • dek_normalizeFasta_IT
  • dr_activate_cloud_tests_for_real
  • dr_add_dbsnp_vcf_for_chr1
  • dr_add_intellij_setup_to_readme
  • dr_add_large_test_files_with_git-lfs
  • dr_add_tests_to_ref_api_source
  • dr_add_yarn_executor_overhead
  • dr_artificialreadutils_specify_contig_in_artificial_uuid_methods
  • dr_authenticated_pipeline_options_test_helper
  • dr_change_logging_level
  • dr_clarify_testing_requirements_for_tools
  • dr_customize_reference_window_in_dataflow_sharding
  • dr_disable_parallel_tests
  • dr_disentangle_spark_and_dataflow
  • dr_dummy_feature
  • dr_dynamic_window_in_referencecontext
  • dr_expose_feature_headers
  • dr_extract_readssource_class
  • dr_feature_support
  • dr_feature_traversal_by_intervals
  • dr_featureinput_tostring
  • dr_features_as_intervals
  • dr_fix_featuredatasource_caching
  • dr_fix_gradle_fatjar
  • dr_fix_ioutils_createtempfile
  • dr_fix_sequence_dict_check_in_bqsr_dataflow
  • dr_gatkcoder_test
  • dr_gatksparktool
  • dr_handle_reads_that_consume_no_ref_bases_in_readwalkers
  • dr_initial_traversal_engine
  • dr_interval_walker
  • dr_lb_spark_bqsr
  • dr_lb_spark_bqsr_bak
  • dr_lb_spark_test
  • dr_make_context_objects_non_optional
  • dr_more_contigs_in_artificialreadutils
  • dr_move_simpleinterval_to_hellbender
  • dr_output_logging_messages_during_engine_initialization
  • dr_port_tools_to_readwalker_interface
  • dr_read_adapter_equals_tweak
  • dr_read_common_interfaces
  • dr_reenable_broken_bqsr_test
  • dr_refactor_exceptions
  • dr_relax_sequence_dictionary_checks
  • dr_remove_com_sun_import
  • dr_remove_protective_copies_from_spark_bqsr
  • dr_rename_sam_utils_package
  • dr_rev_htsjdk_to_1.132
  • dr_rev_htsjdk_to_1.139
  • dr_rev_htsjkd_to_1.138
  • dr_spark_pipeline_markdupes_sharding_fix
  • dr_stub_reads_pipelineTest
  • dr_test_cram_with_intervals
  • ek_comment_802
  • ek_countreads_590
  • ek_craminttests_675
  • ek_cramreference_606
  • ek_cramreference_677
  • ek_fixtests_659
  • ek_fixwarnings_359_377
  • ek_locatable_559
  • ek_npe_273
  • ek_refdict_802
  • ek_seqdict_101
  • ek_unmapped_766
  • ek_wordcount_537
  • expand_dataflow_test_contigs
  • firstCheckin
  • fix_gradle_one_more_time
  • gvda_authorlist_sorting
  • gvda_current_gatk_links
  • issue-948-option-duplicate-reads-exomereadcounts
  • jp_ApiMeansNoSecrets
  • jp_ApplyBQSR
  • jp_ApplyBQSRCloud2
  • jp_BaseRecalOutputs
  • jp_CEU_test_data
  • jp_CloudTests
  • jp_DFBR_cloud
  • jp_DF_BaseRecalibrator
  • jp_FewReadsWriter
  • jp_ReadSourceStringency
  • jp_RecalibrationTablesMerger
  • jp_adding_first_test
  • jp_apply_skel_rebased
  • jp_badtype_repro
  • jp_bigger_apiref
  • jp_binarysearch
  • jp_bqsr_newtest
  • jp_bqsr_skel_rerebased
  • jp_consistentWhitespace
  • jp_enable_working_tests
  • jp_fixFatJar
  • jp_fix_BaseRecal_test
  • jp_fix_refapisource
  • jp_fix_secrets
  • jp_intervalsskiplist
  • jp_perf_apply2
  • jp_perf_br
  • jp_perf_markdups
  • jp_readstest
  • jp_sam2gatk
  • jp_skel_01
  • jp_skel_03
  • jp_start_with_mandatory_tests
  • jp_start_with_mandatory_tests_rebased
  • jp_start_with_mandatory_tests_rebased2
  • jp_testReadWrite
  • jp_uprev_genomics-dataflow
  • jpm_bqsr
  • jt_typo
  • ks_print_reads_by_read_group
  • lb_add_key_for_travis
  • lb_add_packing_command
  • lb_add_rm_rf_shutdownhook_for_da
  • lb_bqsr_scaling_tweaks
  • lb_change_cran_mirror
  • lb_codeship
  • lb_coveralls
  • lb_dataflow
  • lb_dataflow_dependencies
  • lb_delete_commandlineparse_exception
  • lb_delete_compare_metrics
  • lb_delete_illumina_test_data
  • lb_delete_unused_classes_relating_to_MarkDuplicates
  • lb_dockerizing_for_execution_service
  • lb_enable_circle_ci
  • lb_error_message_when_R_doesnt_exist
  • lb_exception_hidden_by_onShutdown_exception
  • lb_expose_test_classes
  • lb_fix_137_truncate_names_with_whitespace
  • lb_fix_ambigous_parse_with_optional_args
  • lb_fix_bqsr_concurrency_issue
  • lb_fix_build_failure_from_no_git
  • lb_fix_default_collections
  • lb_fix_documentation_error
  • lb_fix_last_4_warnings
  • lb_fix_monstrous_error_message
  • lb_fix_required_collections
  • lb_fix_travis_button
  • lb_gatktool_argument_collection_enhancement
  • lb_hide_secret_key
  • lb_htsjdk_to_130
  • lb_improve_cli_output_for_collections
  • lb_improve_parsing_errors
  • lb_improved_R_installation
  • lb_insertSizeMetricDataflow
  • lb_java_logger_levels
  • lb_killing_warnings_again
  • lb_limit_circle_ci_gradle_memory
  • lb_lower_git_lfs_usage
  • lb_lsystem
  • lb_mail_test_result
  • lb_make_working_cloud_tests_mandatory
  • lb_mavenization
  • lb_minor_utils_cleanups
  • lb_misencoded_base_test_update
  • lb_move_testSortingFile_somewhere_sensible
  • lb_move_unreliable_test_to_dataflow_todo
  • lb_only_download_gsalib_when_needed
  • lb_optimize_GATKRead_getLength
  • lb_option_to_run_all_tests
  • lb_output_failed_tests
  • lb_parallel_tests
  • lb_port_gvcfwriter
  • lb_r_installation_refactoring
  • lb_r_output_improvement
  • lb_reduce_test_time_for_SplitNCigarReads
  • lb_reinstate_transformers_and_filters
  • lb_remove_deprecated
  • lb_remove_encrypted_key_for_now
  • lb_remove_min_max_elems_cli
  • lb_remove_sudo
  • lb_remove_the_vampire_that_haunts_valentine
  • lb_remove_unecessary_gradle_download
  • lb_remove_unused_genotypeutils
  • lb_rename_option
  • lb_rename_usage_short
  • lb_replace_TestPipeline_with_GatkTestPipeline
  • lb_replace_file_create_temp_file
  • lb_return_values
  • lb_scale_back_R
  • lb_scaling
  • lb_simple_interval_constructor
  • lb_sort_dependencies
  • lb_stop_creating_test_file_in_basedir
  • lb_suppress_warnings
  • lb_test_speedup
  • lb_transfer
  • lb_travis_container_build
  • lb_travis_lfs
  • lb_unix_style_options
  • lb_update_ReadSource_for_public_consumption
  • lb_update_dependencies
  • lb_update_gradle_to_2.7
  • lb_update_htsjdk
  • lb_update_license_to_bsd
  • lb_update_sam_header
  • lb_update_to_central_htsjdk
  • lb_update_to_snapshot_google_http
  • lb_updating_dataflow_sdk_and_others
  • lb_upload_test_reports
  • lb_version_number
  • lbergelson-readme-update
  • master
  • mds_cleanup_picard_package
  • mds_fix_compare_sams
  • mds_fix_picard_issues
  • mds_migrate_picard_sam
  • mds_picard_sam_2
  • mds_port_all_the_things
  • mds_resync_picard_sam
  • mds_update_integration_test
  • mds_vectorize_coveralls_badge
  • tn_mark_duplicates
  • tw_hadoop_bam_writer
  • tw_hadoop_references
  • tw_hadoop_unmapped_reads
  • tw_hadoop_use_seq_dict
  • tw_hadoop_variants
  • tw_local_base_recalibrator_test
  • tw_parallelism_comment
  • tw_r_groups
  • tw_shared_spark_context
  • tw_spark_fix_adam_deps
  • tw_spark_mark_dupes_sharded
  • tw_spark_markdupes
  • tw_spark_markdupes_optimization
  • tw_spark_sam_record_optimization
  • tw_spark_shadowjar_fix
  • tw_spark_sort_bam
  • tw_spark_test_group
  • tw_test
  • tw_ul_spark_bqsr
  • ul_parquet_io
  • ul_random_uuid_bdg
  • vrr_exome_depth
  • vrr_exons_from_file
  • vrr_feature_iterators
  • vrr_help_generation_on_enum_options_change_toSring_to_name
  • vrr_mark_duplicates_erc
  • vrr_pcov_erc
  • vrr_remove_genomeloc_from_erc
  • wb_copyright

pending completion
2043

push

travis-ci

lbergelson
fixing double running of gradle check

after the addition of travis_wait gradle check travis was executing gradle check twice
with ./gradlew and one with gradle.  This was happening because it was being run onces explicitly in the install phase and once implicitly in the script phase

this was causing some strange issues

instead of using travis_wait, I made the dataflow cloud tests output status information as they go
this similarly prevents travis from timing out due to lack of output, but doesn't need the travis_wait
if we add any really long running dataflow tests, or really highly spammy ones we'll have to revisit this

19398 of 24547 relevant lines covered (79.02%)

0.96 hits per line

Relevant lines Covered
Build:
Build:
24547 RELEVANT LINES 19398 COVERED LINES
0.96 HITS PER LINE
Source Files on lb_move_placement_of_travis_wait
  • List 0
  • Changed 2
  • Source Changed 0
  • Coverage Changed 2
Coverage ∆ File Lines Relevant Covered Missed Hits/Line

Recent builds

Builds Branch Commit Type Ran Committer Via Coverage
2043 lb_move_placement_of_travis_wait fixing double running of gradle check after the addition of travis_wait gradle check travis was executing gradle check twice with ./gradlew and one with gradle. This was happening because it was being run onces explicitly in the install phase an... push 21 Aug 2015 07:02PM UTC lbergelson travis-ci pending completion  
2037 lb_move_placement_of_travis_wait double fixup push 21 Aug 2015 05:10PM UTC lbergelson travis-ci pending completion  
2025 lb_move_placement_of_travis_wait fix to travis.yml to execute gradlew instead of gradle and move it to the script block push 21 Aug 2015 02:56PM UTC lbergelson travis-ci pending completion  
See All Builds (2517)
  • Repo on GitHub
STATUS · Troubleshooting · Open an Issue · Sales · Support · CAREERS · ENTERPRISE · START FREE · SCHEDULE DEMO
ANNOUNCEMENTS · TWITTER · TOS & SLA · Supported CI Services · What's a CI service? · Automated Testing

© 2025 Coveralls, Inc