bigdatagenomics/eggo

Issues

• Upgrade Spark from 1.3 to 1.5 to make use of project Tungsten performance improvements.

  #142 opened 9 years ago by NeillGibson
  6

• results of "genotype count" are different - depending on used programs

  #140 opened 9 years ago by jerryivanhoe
  2

• sql query on Adam's flattened file -> Non-local session path expected to be non-null;

  #141 opened 9 years ago by jerryivanhoe
  4

• Verify that requested AMIs are consistent with the requested region/AZ

  #134 opened 9 years ago by laserson
  1

• how to set the instance type for master, manager and workers separately ?

  #138 opened 9 years ago by jerryivanhoe
  1

• No handlers could be found for logger "cm_api.resource"

  #139 opened 9 years ago by jerryivanhoe
  2

• Default parallelism set to 2 on cluster with 4 executor nodes?

  #133 opened 9 years ago by NeillGibson
  2

• eggo-cluster provision - fails with return code 12 while executing

  #136 opened 9 years ago by jerryivanhoe
  1

• Remove minCount line from aws.conf

  #137 opened 9 years ago by laserson
  0

• tried to substitute ami-00a11e68 w/o success

  #132 opened 9 years ago by jerryivanhoe
  9

• us-east-1b is hardcoded into cloudformation.template

  #135 opened 9 years ago by laserson
  2

• AMI in eu-west-1 ?

  #131 opened 9 years ago by jerryivanhoe
  6

• asking for password

  #130 opened 9 years ago by jerryivanhoe
  4

• dnload_raw operation requires the ability to `sudo -u hdfs`

  #127 opened 9 years ago by laserson
  2

• Extract Hive queries into separate reusable files

  #129 opened 9 years ago by laserson
  0

• `dnload_raw` shouldn't hardcode `ec2-user` when it `chown`s data

  #128 opened 9 years ago by laserson
  0

• 1000 Genomes Phase 3 VCF data set to be hosted in S3 in parquet format

  #121 opened 9 years ago by laserson
  4

• Platinum Genomes data set

  #124 opened 9 years ago by laserson
  0

• Reduce number of CM/CDH restarts during cluster config

  #123 opened 9 years ago by laserson
  0

• ENCODE data set to be hosted in S3 in parquet format

  #122 opened 9 years ago by laserson
  0

• Create doc with list of assumptions about cluster

  #119 opened 9 years ago by laserson
  1

• Investigate provisioning on Google's cloud

  #118 opened 9 years ago by laserson
  0

• dbSNP VCF data set to be hosted in S3 in parquet format

  #120 opened 9 years ago by laserson
  0

• ExAC data set to be hosted in S3

  #117 opened 9 years ago by laserson
  0

• Consider Director Server to speed up cluster bootstrap

  #116 opened 9 years ago by laserson
  0

• eggo teardown errors out when trying to terminate the launcher instance

  #115 opened 9 years ago by laserson
  1

• If possible, make "cluster name" the core arg required by eggo

  #114 opened 9 years ago by laserson
  2

• Current cloudformation template opens up entire cluster to the wild

  #113 opened 9 years ago by laserson
  1

• Add support for specifying "default" options through ini file

  #112 opened 9 years ago by laserson
  0

• Ensure that CLI code calls fabric's disconnect_all

  #110 opened 9 years ago by laserson
  0

• Add bona fide RTD-style docs

  #111 opened 9 years ago by laserson
  0

• Refactor: stop using Luigi

  #109 opened 9 years ago by laserson
  4

• Ensure that director-provisioned EC2 instances are tagged

  #81 opened 9 years ago by laserson
  1

• Refactor: deprecate spark-ec2 and local mode; focus on director

  #108 opened 9 years ago by laserson
  0

• Resulting parquet files from Jenkins test are no longer deterministic

  #107 opened 9 years ago by laserson
  4

• Jenkins job should modify their corresponding eggo config files with runtime info

  #104 opened 9 years ago by laserson
  1

• fabric_cli imports director, which tries to access eggo_config aws options that may not exist

  #91 opened 9 years ago by laserson
  2

• Add virtualenv info to [local] section of config

  #101 opened 9 years ago by laserson
  1

• Add a method to verify the worker environments

  #102 opened 9 years ago by laserson
  1

• Fabric CLI tools should install Spark for local mode

  #99 opened 9 years ago by laserson
  1

• Fabric CLI tools should install Hadoop for local mode

  #100 opened 9 years ago by laserson
  1

• Add jenkins job to test Director

  #92 opened 9 years ago by laserson
  1

• Add test Feature data type

  #90 opened 9 years ago by laserson
  1

• Replace fabric sudo and run with alternatives that delegate depending on exec ctx

  #95 opened 10 years ago by laserson
  0

• Luigi tasks are not failing when their underlying hadoop/spark jobs fail

  #93 opened 10 years ago by laserson
  0

• Support Luigi 1.2.1

  #96 opened 10 years ago by tomwhite
  1

• Support local execution

  #87 opened 10 years ago by laserson
  0

• EGGO_HOME not being set on master worker for toast command

  #88 opened 10 years ago by laserson
  0

• AWS eggo config values are unset if ENV vars are not set

  #84 opened 10 years ago by laserson
  0

• Create separate S3 bucket specific to eggo testing

  #80 opened 10 years ago by laserson
  0