diff --git a/.github/workflows/pythonpackage.yml b/.github/workflows/pythonpackage.yml
new file mode 100644
index 0000000..0137a09
--- /dev/null
+++ b/.github/workflows/pythonpackage.yml
@@ -0,0 +1,37 @@
+name: Python package
+
+on: [push]
+env:
+  POETRY_VERSION: 1.0
+
+jobs:
+  testing:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        PYTHON_VERSION: [3.8]
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python ${{matrix.PYTHON_VERSION}}
+      uses: actions/setup-python@v1
+      with:
+        python-version: ${{matrix.PYTHON_VERSION}}
+    - name: Install poetry
+      run: |
+        python -m pip install --upgrade pip
+        pip install poetry==${{env.POETRY_VERSION}}
+    - name: Install deps
+      run: |
+        poetry install
+    - name: Run pytest
+      run: |
+        poetry run python -m pytest --cov=pyfgaws --cov-branch
+    - name: Style checking
+      run: |
+        poetry run black --line-length 99 --check pyfgaws
+    - name: Run lint
+      run: |
+        poetry run flake8 --config=ci/flake8.cfg pyfgaws
+    - name: Run mypy
+      run: |
+        poetry run mypy -p pyfgaws --config=ci/mypy.ini
diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..fdfce86
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,16 @@
+# PyCharm
+.idea
+
+# Python compiled & optimized files
+*.pyc
+*.pyo
+
+# MyPy Cache directory
+.mypy_cache
+
+# for develop installs
+*.egg-info
+
+# venv set up
+.venv
+dist/
diff --git a/LICENSE b/LICENSE
new file mode 100644
index 0000000..197e38b
--- /dev/null
+++ b/LICENSE
@@ -0,0 +1,21 @@
+The MIT License
+
+Copyright (c) 2020 Fulcrum Genomics LLC
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.
diff --git a/ci/check.sh b/ci/check.sh
new file mode 100755
index 0000000..91e0ebf
--- /dev/null
+++ b/ci/check.sh
@@ -0,0 +1,51 @@
+#!/bin/bash
+
+function banner() {
+    echo
+    echo "================================================================================"
+    echo $*
+    echo "================================================================================"
+    echo
+}
+
+#####################################################################
+# Takes two parameters, a "name" and a "command".
+# Runs the command and prints out whether it succeeded or failed, and
+# also tracks a list of failed steps in $failures.
+#####################################################################
+function run() {
+    local name=$1
+    local cmd=$2
+
+    banner "Running $name [$cmd]"
+    set +e
+    $cmd
+    exit_code=$?
+    set -e
+
+    if [[ $exit_code == 0 ]]; then
+        echo Passed $name: "[$cmd]"
+    else
+        echo Failed $name: "[$cmd]"
+        if [ -z "$failures" ]; then
+            failures="$failures $name"
+        else
+            failures="$failures, $name"
+        fi
+    fi
+}
+
+parent=$(cd $(dirname $0) && pwd -P)
+
+banner "Executing in conda environment ${CONDA_DEFAULT_ENV} in directory ${root}"
+run "Unit Tests"     "python -m pytest -vv -r sx pyfgaws"
+run "Style Checking" "black --line-length 99 --check pyfgaws"
+run "Linting"        "flake8 --config=$parent/flake8.cfg pyfgaws"
+run "Type Checking"  "mypy -p pyfgaws --config $parent/mypy.ini"
+
+if [ -z "$failures" ]; then
+    banner "Checks Passed"
+else
+    banner "Checks Failed with failures in: $failures"
+    exit 1
+fi
diff --git a/ci/flake8.cfg b/ci/flake8.cfg
new file mode 100644
index 0000000..64f2e3f
--- /dev/null
+++ b/ci/flake8.cfg
@@ -0,0 +1,6 @@
+# flake8 config file
+
+[flake8]
+max_line_length = 100
+show-source = true
+ignore = E701 W504 W503
diff --git a/ci/mypy.ini b/ci/mypy.ini
new file mode 100644
index 0000000..6e117f5
--- /dev/null
+++ b/ci/mypy.ini
@@ -0,0 +1,6 @@
+[mypy]
+strict_optional = False
+ignore_missing_imports = True
+disallow_untyped_decorators = False
+follow_imports = "silent"
+disallow_untyped_defs = True
\ No newline at end of file
diff --git a/conda-requirements.txt b/conda-requirements.txt
new file mode 100644
index 0000000..acf9c18
--- /dev/null
+++ b/conda-requirements.txt
@@ -0,0 +1,3 @@
+# Setup python version and poetry
+python=3.8.2
+poetry=1.0.5
diff --git a/poetry.lock b/poetry.lock
new file mode 100644
index 0000000..6cb3ef1
--- /dev/null
+++ b/poetry.lock
@@ -0,0 +1,924 @@
+[[package]]
+category = "dev"
+description = "A small Python module for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
+name = "appdirs"
+optional = false
+python-versions = "*"
+version = "1.4.4"
+
+[[package]]
+category = "dev"
+description = "Atomic file writes."
+marker = "sys_platform == \"win32\""
+name = "atomicwrites"
+optional = false
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+version = "1.4.0"
+
+[[package]]
+category = "main"
+description = "Classes Without Boilerplate"
+name = "attrs"
+optional = false
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+version = "19.3.0"
+
+[package.extras]
+azure-pipelines = ["coverage", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "zope.interface", "pytest-azurepipelines"]
+dev = ["coverage", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "zope.interface", "sphinx", "pre-commit"]
+docs = ["sphinx", "zope.interface"]
+tests = ["coverage", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "zope.interface"]
+
+[[package]]
+category = "dev"
+description = "The uncompromising code formatter."
+name = "black"
+optional = false
+python-versions = ">=3.6"
+version = "19.10b0"
+
+[package.dependencies]
+appdirs = "*"
+attrs = ">=18.1.0"
+click = ">=6.5"
+pathspec = ">=0.6,<1"
+regex = "*"
+toml = ">=0.9.4"
+typed-ast = ">=1.4.0"
+
+[package.extras]
+d = ["aiohttp (>=3.3.2)", "aiohttp-cors"]
+
+[[package]]
+category = "main"
+description = "The AWS SDK for Python"
+name = "boto3"
+optional = false
+python-versions = "*"
+version = "1.13.20"
+
+[package.dependencies]
+botocore = ">=1.16.20,<1.17.0"
+jmespath = ">=0.7.1,<1.0.0"
+s3transfer = ">=0.3.0,<0.4.0"
+
+[[package]]
+category = "main"
+description = "Type annotations for boto3 1.13.20, generated by mypy-boto3-buider 1.0.9"
+name = "boto3-stubs"
+optional = false
+python-versions = ">=3.6"
+version = "1.13.20.0"
+
+[package.dependencies]
+mypy-boto3 = "1.13.20.0"
+
+[package.dependencies.mypy-boto3-batch]
+optional = true
+version = "1.13.20.0"
+
+[package.dependencies.mypy-boto3-logs]
+optional = true
+version = "1.13.20.0"
+
+[package.extras]
+accessanalyzer = ["mypy-boto3-accessanalyzer (1.13.20.0)"]
+acm = ["mypy-boto3-acm (1.13.20.0)"]
+acm-pca = ["mypy-boto3-acm-pca (1.13.20.0)"]
+alexaforbusiness = ["mypy-boto3-alexaforbusiness (1.13.20.0)"]
+amplify = ["mypy-boto3-amplify (1.13.20.0)"]
+apigateway = ["mypy-boto3-apigateway (1.13.20.0)"]
+apigatewaymanagementapi = ["mypy-boto3-apigatewaymanagementapi (1.13.20.0)"]
+apigatewayv2 = ["mypy-boto3-apigatewayv2 (1.13.20.0)"]
+appconfig = ["mypy-boto3-appconfig (1.13.20.0)"]
+application-autoscaling = ["mypy-boto3-application-autoscaling (1.13.20.0)"]
+application-insights = ["mypy-boto3-application-insights (1.13.20.0)"]
+appmesh = ["mypy-boto3-appmesh (1.13.20.0)"]
+appstream = ["mypy-boto3-appstream (1.13.20.0)"]
+appsync = ["mypy-boto3-appsync (1.13.20.0)"]
+athena = ["mypy-boto3-athena (1.13.20.0)"]
+autoscaling = ["mypy-boto3-autoscaling (1.13.20.0)"]
+autoscaling-plans = ["mypy-boto3-autoscaling-plans (1.13.20.0)"]
+backup = ["mypy-boto3-backup (1.13.20.0)"]
+batch = ["mypy-boto3-batch (1.13.20.0)"]
+budgets = ["mypy-boto3-budgets (1.13.20.0)"]
+ce = ["mypy-boto3-ce (1.13.20.0)"]
+chime = ["mypy-boto3-chime (1.13.20.0)"]
+cloud9 = ["mypy-boto3-cloud9 (1.13.20.0)"]
+clouddirectory = ["mypy-boto3-clouddirectory (1.13.20.0)"]
+cloudformation = ["mypy-boto3-cloudformation (1.13.20.0)"]
+cloudfront = ["mypy-boto3-cloudfront (1.13.20.0)"]
+cloudhsm = ["mypy-boto3-cloudhsm (1.13.20.0)"]
+cloudhsmv2 = ["mypy-boto3-cloudhsmv2 (1.13.20.0)"]
+cloudsearch = ["mypy-boto3-cloudsearch (1.13.20.0)"]
+cloudsearchdomain = ["mypy-boto3-cloudsearchdomain (1.13.20.0)"]
+cloudtrail = ["mypy-boto3-cloudtrail (1.13.20.0)"]
+cloudwatch = ["mypy-boto3-cloudwatch (1.13.20.0)"]
+codebuild = ["mypy-boto3-codebuild (1.13.20.0)"]
+codecommit = ["mypy-boto3-codecommit (1.13.20.0)"]
+codedeploy = ["mypy-boto3-codedeploy (1.13.20.0)"]
+codeguru-reviewer = ["mypy-boto3-codeguru-reviewer (1.13.20.0)"]
+codeguruprofiler = ["mypy-boto3-codeguruprofiler (1.13.20.0)"]
+codepipeline = ["mypy-boto3-codepipeline (1.13.20.0)"]
+codestar = ["mypy-boto3-codestar (1.13.20.0)"]
+codestar-connections = ["mypy-boto3-codestar-connections (1.13.20.0)"]
+codestar-notifications = ["mypy-boto3-codestar-notifications (1.13.20.0)"]
+cognito-identity = ["mypy-boto3-cognito-identity (1.13.20.0)"]
+cognito-idp = ["mypy-boto3-cognito-idp (1.13.20.0)"]
+cognito-sync = ["mypy-boto3-cognito-sync (1.13.20.0)"]
+comprehend = ["mypy-boto3-comprehend (1.13.20.0)"]
+comprehendmedical = ["mypy-boto3-comprehendmedical (1.13.20.0)"]
+compute-optimizer = ["mypy-boto3-compute-optimizer (1.13.20.0)"]
+config = ["mypy-boto3-config (1.13.20.0)"]
+connect = ["mypy-boto3-connect (1.13.20.0)"]
+connectparticipant = ["mypy-boto3-connectparticipant (1.13.20.0)"]
+cur = ["mypy-boto3-cur (1.13.20.0)"]
+dataexchange = ["mypy-boto3-dataexchange (1.13.20.0)"]
+datapipeline = ["mypy-boto3-datapipeline (1.13.20.0)"]
+datasync = ["mypy-boto3-datasync (1.13.20.0)"]
+dax = ["mypy-boto3-dax (1.13.20.0)"]
+detective = ["mypy-boto3-detective (1.13.20.0)"]
+devicefarm = ["mypy-boto3-devicefarm (1.13.20.0)"]
+directconnect = ["mypy-boto3-directconnect (1.13.20.0)"]
+discovery = ["mypy-boto3-discovery (1.13.20.0)"]
+dlm = ["mypy-boto3-dlm (1.13.20.0)"]
+dms = ["mypy-boto3-dms (1.13.20.0)"]
+docdb = ["mypy-boto3-docdb (1.13.20.0)"]
+ds = ["mypy-boto3-ds (1.13.20.0)"]
+dynamodb = ["mypy-boto3-dynamodb (1.13.20.0)"]
+dynamodbstreams = ["mypy-boto3-dynamodbstreams (1.13.20.0)"]
+ebs = ["mypy-boto3-ebs (1.13.20.0)"]
+ec2 = ["mypy-boto3-ec2 (1.13.20.0)"]
+ec2-instance-connect = ["mypy-boto3-ec2-instance-connect (1.13.20.0)"]
+ecr = ["mypy-boto3-ecr (1.13.20.0)"]
+ecs = ["mypy-boto3-ecs (1.13.20.0)"]
+efs = ["mypy-boto3-efs (1.13.20.0)"]
+eks = ["mypy-boto3-eks (1.13.20.0)"]
+elastic-inference = ["mypy-boto3-elastic-inference (1.13.20.0)"]
+elasticache = ["mypy-boto3-elasticache (1.13.20.0)"]
+elasticbeanstalk = ["mypy-boto3-elasticbeanstalk (1.13.20.0)"]
+elastictranscoder = ["mypy-boto3-elastictranscoder (1.13.20.0)"]
+elb = ["mypy-boto3-elb (1.13.20.0)"]
+elbv2 = ["mypy-boto3-elbv2 (1.13.20.0)"]
+emr = ["mypy-boto3-emr (1.13.20.0)"]
+es = ["mypy-boto3-es (1.13.20.0)"]
+essential = ["mypy-boto3-cloudformation (1.13.20.0)", "mypy-boto3-dynamodb (1.13.20.0)", "mypy-boto3-ec2 (1.13.20.0)", "mypy-boto3-lambda (1.13.20.0)", "mypy-boto3-rds (1.13.20.0)", "mypy-boto3-s3 (1.13.20.0)", "mypy-boto3-sqs (1.13.20.0)"]
+events = ["mypy-boto3-events (1.13.20.0)"]
+firehose = ["mypy-boto3-firehose (1.13.20.0)"]
+fms = ["mypy-boto3-fms (1.13.20.0)"]
+forecast = ["mypy-boto3-forecast (1.13.20.0)"]
+forecastquery = ["mypy-boto3-forecastquery (1.13.20.0)"]
+frauddetector = ["mypy-boto3-frauddetector (1.13.20.0)"]
+fsx = ["mypy-boto3-fsx (1.13.20.0)"]
+gamelift = ["mypy-boto3-gamelift (1.13.20.0)"]
+glacier = ["mypy-boto3-glacier (1.13.20.0)"]
+globalaccelerator = ["mypy-boto3-globalaccelerator (1.13.20.0)"]
+glue = ["mypy-boto3-glue (1.13.20.0)"]
+greengrass = ["mypy-boto3-greengrass (1.13.20.0)"]
+groundstation = ["mypy-boto3-groundstation (1.13.20.0)"]
+guardduty = ["mypy-boto3-guardduty (1.13.20.0)"]
+health = ["mypy-boto3-health (1.13.20.0)"]
+iam = ["mypy-boto3-iam (1.13.20.0)"]
+imagebuilder = ["mypy-boto3-imagebuilder (1.13.20.0)"]
+importexport = ["mypy-boto3-importexport (1.13.20.0)"]
+inspector = ["mypy-boto3-inspector (1.13.20.0)"]
+iot = ["mypy-boto3-iot (1.13.20.0)"]
+iot-data = ["mypy-boto3-iot-data (1.13.20.0)"]
+iot-jobs-data = ["mypy-boto3-iot-jobs-data (1.13.20.0)"]
+iot1click-devices = ["mypy-boto3-iot1click-devices (1.13.20.0)"]
+iot1click-projects = ["mypy-boto3-iot1click-projects (1.13.20.0)"]
+iotanalytics = ["mypy-boto3-iotanalytics (1.13.20.0)"]
+iotevents = ["mypy-boto3-iotevents (1.13.20.0)"]
+iotevents-data = ["mypy-boto3-iotevents-data (1.13.20.0)"]
+iotsecuretunneling = ["mypy-boto3-iotsecuretunneling (1.13.20.0)"]
+iotsitewise = ["mypy-boto3-iotsitewise (1.13.20.0)"]
+iotthingsgraph = ["mypy-boto3-iotthingsgraph (1.13.20.0)"]
+kafka = ["mypy-boto3-kafka (1.13.20.0)"]
+kendra = ["mypy-boto3-kendra (1.13.20.0)"]
+kinesis = ["mypy-boto3-kinesis (1.13.20.0)"]
+kinesis-video-archived-media = ["mypy-boto3-kinesis-video-archived-media (1.13.20.0)"]
+kinesis-video-media = ["mypy-boto3-kinesis-video-media (1.13.20.0)"]
+kinesis-video-signaling = ["mypy-boto3-kinesis-video-signaling (1.13.20.0)"]
+kinesisanalytics = ["mypy-boto3-kinesisanalytics (1.13.20.0)"]
+kinesisanalyticsv2 = ["mypy-boto3-kinesisanalyticsv2 (1.13.20.0)"]
+kinesisvideo = ["mypy-boto3-kinesisvideo (1.13.20.0)"]
+kms = ["mypy-boto3-kms (1.13.20.0)"]
+lakeformation = ["mypy-boto3-lakeformation (1.13.20.0)"]
+lambda = ["mypy-boto3-lambda (1.13.20.0)"]
+lex-models = ["mypy-boto3-lex-models (1.13.20.0)"]
+lex-runtime = ["mypy-boto3-lex-runtime (1.13.20.0)"]
+license-manager = ["mypy-boto3-license-manager (1.13.20.0)"]
+lightsail = ["mypy-boto3-lightsail (1.13.20.0)"]
+logs = ["mypy-boto3-logs (1.13.20.0)"]
+machinelearning = ["mypy-boto3-machinelearning (1.13.20.0)"]
+macie = ["mypy-boto3-macie (1.13.20.0)"]
+managedblockchain = ["mypy-boto3-managedblockchain (1.13.20.0)"]
+marketplace-catalog = ["mypy-boto3-marketplace-catalog (1.13.20.0)"]
+marketplace-entitlement = ["mypy-boto3-marketplace-entitlement (1.13.20.0)"]
+marketplacecommerceanalytics = ["mypy-boto3-marketplacecommerceanalytics (1.13.20.0)"]
+mediaconnect = ["mypy-boto3-mediaconnect (1.13.20.0)"]
+mediaconvert = ["mypy-boto3-mediaconvert (1.13.20.0)"]
+medialive = ["mypy-boto3-medialive (1.13.20.0)"]
+mediapackage = ["mypy-boto3-mediapackage (1.13.20.0)"]
+mediapackage-vod = ["mypy-boto3-mediapackage-vod (1.13.20.0)"]
+mediastore = ["mypy-boto3-mediastore (1.13.20.0)"]
+mediastore-data = ["mypy-boto3-mediastore-data (1.13.20.0)"]
+mediatailor = ["mypy-boto3-mediatailor (1.13.20.0)"]
+meteringmarketplace = ["mypy-boto3-meteringmarketplace (1.13.20.0)"]
+mgh = ["mypy-boto3-mgh (1.13.20.0)"]
+migrationhub-config = ["mypy-boto3-migrationhub-config (1.13.20.0)"]
+mobile = ["mypy-boto3-mobile (1.13.20.0)"]
+mq = ["mypy-boto3-mq (1.13.20.0)"]
+mturk = ["mypy-boto3-mturk (1.13.20.0)"]
+neptune = ["mypy-boto3-neptune (1.13.20.0)"]
+networkmanager = ["mypy-boto3-networkmanager (1.13.20.0)"]
+opsworks = ["mypy-boto3-opsworks (1.13.20.0)"]
+opsworkscm = ["mypy-boto3-opsworkscm (1.13.20.0)"]
+organizations = ["mypy-boto3-organizations (1.13.20.0)"]
+outposts = ["mypy-boto3-outposts (1.13.20.0)"]
+personalize = ["mypy-boto3-personalize (1.13.20.0)"]
+personalize-events = ["mypy-boto3-personalize-events (1.13.20.0)"]
+personalize-runtime = ["mypy-boto3-personalize-runtime (1.13.20.0)"]
+pi = ["mypy-boto3-pi (1.13.20.0)"]
+pinpoint = ["mypy-boto3-pinpoint (1.13.20.0)"]
+pinpoint-email = ["mypy-boto3-pinpoint-email (1.13.20.0)"]
+pinpoint-sms-voice = ["mypy-boto3-pinpoint-sms-voice (1.13.20.0)"]
+polly = ["mypy-boto3-polly (1.13.20.0)"]
+pricing = ["mypy-boto3-pricing (1.13.20.0)"]
+qldb = ["mypy-boto3-qldb (1.13.20.0)"]
+qldb-session = ["mypy-boto3-qldb-session (1.13.20.0)"]
+quicksight = ["mypy-boto3-quicksight (1.13.20.0)"]
+ram = ["mypy-boto3-ram (1.13.20.0)"]
+rds = ["mypy-boto3-rds (1.13.20.0)"]
+rds-data = ["mypy-boto3-rds-data (1.13.20.0)"]
+redshift = ["mypy-boto3-redshift (1.13.20.0)"]
+rekognition = ["mypy-boto3-rekognition (1.13.20.0)"]
+resource-groups = ["mypy-boto3-resource-groups (1.13.20.0)"]
+resourcegroupstaggingapi = ["mypy-boto3-resourcegroupstaggingapi (1.13.20.0)"]
+robomaker = ["mypy-boto3-robomaker (1.13.20.0)"]
+route53 = ["mypy-boto3-route53 (1.13.20.0)"]
+route53domains = ["mypy-boto3-route53domains (1.13.20.0)"]
+route53resolver = ["mypy-boto3-route53resolver (1.13.20.0)"]
+s3 = ["mypy-boto3-s3 (1.13.20.0)"]
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diff --git a/pyfgaws/__init__.py b/pyfgaws/__init__.py
new file mode 100644
index 0000000..5c84ed5
--- /dev/null
+++ b/pyfgaws/__init__.py
@@ -0,0 +1,3 @@
+from pyfgaws.core import logging
+
+logging.setup_logging()
diff --git a/pyfgaws/__main__.py b/pyfgaws/__main__.py
new file mode 100644
index 0000000..826094b
--- /dev/null
+++ b/pyfgaws/__main__.py
@@ -0,0 +1,56 @@
+"""Main entry point for all pyfgaws tools."""
+
+import logging
+import sys
+from typing import Any
+from typing import Callable
+from typing import Dict
+from typing import List
+
+import defopt
+import json
+
+from pyfgaws.batch.tools import run_job
+from pyfgaws.batch.tools import watch_job
+from pyfgaws.batch import Status
+from pyfgaws.logs.tools import watch_logs
+from mypy_boto3.batch.type_defs import KeyValuePairTypeDef as BatchKeyValuePairTypeDef  # noqa
+
+
+# The list of tools to expose on the command line
+TOOLS: List[Callable] = sorted([run_job, watch_job, watch_logs], key=lambda f: f.__name__)
+
+
+def _parse_key_value_pair_type(string: str) -> BatchKeyValuePairTypeDef:
+    """Parses a simple dictionary that must contain two key-value pairs."""
+    pair = json.loads(string)
+    assert isinstance(pair, dict), "argument is not a list"
+    assert "name" in pair, "name not found in key-value pair"
+    assert "value" in pair, "name not found in key-value pair"
+    assert len(pair.keys()) == 2, "Found extra keys in key-value pair: " + ", ".join(pair.keys())
+    return pair  # type: ignore
+
+
+def _parse_batch_status(string: str) -> Status:
+    raise Exception
+
+
+def _parsers() -> Dict[type, Callable[[str], Any]]:
+    """Returns the custom parsers for defopt"""
+    return {
+        Dict[str, Any]: lambda string: json.loads(string),
+        BatchKeyValuePairTypeDef: _parse_key_value_pair_type,
+        Status: _parse_batch_status,
+    }
+
+
+def main(argv: List[str] = sys.argv[1:]) -> None:
+    logger = logging.getLogger(__name__)
+    if len(argv) != 0 and all(arg not in argv for arg in ["-h", "--help"]):
+        logger.info("Running command: fgaws-tools " + " ".join(argv))
+    try:
+        defopt.run(funcs=TOOLS, argv=argv, parsers=_parsers())
+        logger.info("Completed successfully.")
+    except Exception as e:
+        logger.info("Failed on command: " + " ".join(argv))
+        raise e
diff --git a/pyfgaws/batch/__init__.py b/pyfgaws/batch/__init__.py
new file mode 100644
index 0000000..dce684a
--- /dev/null
+++ b/pyfgaws/batch/__init__.py
@@ -0,0 +1,3 @@
+from pyfgaws.batch.api import BatchJob, Status
+
+__all__ = ("BatchJob", "Status")
diff --git a/pyfgaws/batch/api.py b/pyfgaws/batch/api.py
new file mode 100644
index 0000000..cde8965
--- /dev/null
+++ b/pyfgaws/batch/api.py
@@ -0,0 +1,355 @@
+"""
+Utility methods for interacting with AWS Batch
+----------------------------------------------
+"""
+import copy
+import enum
+import logging
+import sys
+from typing import Any
+from typing import Dict
+from typing import List
+from typing import Optional
+
+import botocore
+import namegenerator
+from botocore.waiter import Waiter as BotoWaiter
+from mypy_boto3 import batch
+from mypy_boto3.batch.type_defs import ArrayPropertiesTypeDef  # noqa
+from mypy_boto3.batch.type_defs import ContainerDetailTypeDef  # noqa
+from mypy_boto3.batch.type_defs import ContainerOverridesTypeDef  # noqa
+from mypy_boto3.batch.type_defs import DescribeJobsResponseTypeDef  # noqa
+from mypy_boto3.batch.type_defs import JobDependencyTypeDef  # noqa
+from mypy_boto3.batch.type_defs import JobDetailTypeDef  # noqa
+from mypy_boto3.batch.type_defs import JobTimeoutTypeDef  # noqa
+from mypy_boto3.batch.type_defs import JobTimeoutTypeDef  # noqa
+from mypy_boto3.batch.type_defs import KeyValuePairTypeDef  # noqa
+from mypy_boto3.batch.type_defs import NodeOverridesTypeDef  # noqa
+from mypy_boto3.batch.type_defs import ResourceRequirementTypeDef  # noqa
+from mypy_boto3.batch.type_defs import RetryStrategyTypeDef  # noqa
+from mypy_boto3.batch.type_defs import SubmitJobResponseTypeDef  # noqa
+
+
+@enum.unique
+class Status(enum.Enum):
+    Submitted = "SUBMITTED"
+    Pending = "PENDING"
+    Runnable = "RUNNABLE"
+    Starting = "STARTING"
+    Running = "RUNNING"
+    Succeeded = "SUCCEEDED"
+    Failed = "FAILED"
+
+
+def get_latest_job_definition_arn(client: batch.Client, job_definition: str) -> str:
+    """Retrieves the latest job definition ARN.
+
+    Args:
+        client: the AWS batch client
+        job_definition: the AWS batch job definition name
+
+    Returns:
+        the latest job definition ARN.
+    """
+    response = client.describe_job_definitions(jobDefinitionName=job_definition)
+    latest = max(response["jobDefinitions"], key=lambda d: d["revision"])
+    return latest["jobDefinitionArn"]
+
+
+class BatchJob:
+    """Stores information about a batch job.
+
+    The following arguments override the provided container overrides: `cpus`, `mem_mb` (
+    overrides `memory`), `command`, `instance_type`, `environment`, and `resourceRequirements`.
+
+    Attributes:
+        client: the batch client to use
+        queue: the nae of the AWS batch queue
+        job_definition: the ARN for the AWS batch job definition, or the name of the job definition
+            to get the latest revision
+        name: the name of the job, otherwise one will be automatically generated
+        cpus: the number of CPUs to request
+        mem_mb: the amount of memory to request (in megabytes)
+        command: the command to use
+        instance_type: the instance type to use
+        environment: the environment variables to use
+        resource_requirements: a list of resource requirements for the job (type and amount)
+        array_properties: the array properties for this job
+        depends_on: the list of jobs to depend on
+        parameters: additional parameters passed to the job that replace parameter substitution
+            placeholders that are set in the job definition.
+        container_overrides: the container overrides that specify the name of a container in the
+            specified job definition and the overrides it should receive
+        node_overrides: list of node overrides that specify the node range to target and the
+            container overrides for that node range.
+        retry_strategy: the retry strategy to use for failed jobs from the `submit_job` operation.
+        timeout: the timeout configuration
+        logger: logger to write status messages
+    """
+
+    def __init__(
+        self,
+        client: batch.Client,
+        queue: str,
+        job_definition: str,
+        name: Optional[str] = None,
+        cpus: Optional[int] = None,
+        mem_mb: Optional[int] = None,
+        command: Optional[List[str]] = None,
+        instance_type: Optional[str] = None,
+        environment: Optional[List[KeyValuePairTypeDef]] = None,
+        resource_requirements: Optional[List[ResourceRequirementTypeDef]] = None,
+        array_properties: Optional[ArrayPropertiesTypeDef] = None,
+        depends_on: Optional[List[JobDependencyTypeDef]] = None,
+        parameters: Optional[Dict[str, str]] = None,
+        container_overrides: Optional[ContainerOverridesTypeDef] = None,
+        node_overrides: Optional[NodeOverridesTypeDef] = None,
+        retry_strategy: Optional[RetryStrategyTypeDef] = None,
+        timeout: Optional[JobTimeoutTypeDef] = None,
+        logger: Optional[logging.Logger] = None,
+    ) -> None:
+
+        self.client: batch.Client = client
+
+        # Get the latest job definition ARN if not given
+        if job_definition.startswith("arn:aws:batch:"):
+            if logger is not None:
+                logger.info(f"Using provided job definition '{job_definition}'")
+            self.job_definition_arn = job_definition
+        else:
+            if logger is not None:
+                logger.info(f"Retrieving the latest job definition for {job_definition}")
+            self.job_definition_arn = get_latest_job_definition_arn(
+                client=self.client, job_definition=job_definition
+            )
+            if logger is not None:
+                logger.info(f"Retrieved latest job definition '{job_definition}'")
+
+        # Main arguments
+        self.name: str = namegenerator.gen() if name is None else name
+        self.queue: str = queue
+        self.array_properties: ArrayPropertiesTypeDef = (
+            {} if array_properties is None else array_properties
+        )
+        self.depends_on: List[JobDependencyTypeDef] = (
+            [] if depends_on is None else copy.deepcopy(depends_on)
+        )
+        self.parameters = {} if parameters is None else copy.deepcopy(parameters)
+        self.container_overrides = (
+            {} if container_overrides is None else copy.deepcopy(container_overrides)
+        )
+        self.node_overrides: NodeOverridesTypeDef = {} if node_overrides is None else node_overrides
+        self.retry_strategy: RetryStrategyTypeDef = {} if retry_strategy is None else retry_strategy
+        self.timeout: JobTimeoutTypeDef = {} if timeout is None else timeout
+
+        # Add to container overrides
+        if cpus is not None:
+            self.container_overrides["vcpus"] = cpus
+        if mem_mb is not None:
+            self.container_overrides["memory"] = mem_mb
+        if command is not None:
+            self.container_overrides["command"] = copy.deepcopy(command)
+        if instance_type is not None:
+            self.container_overrides["instanceType"] = instance_type
+        if environment is not None:
+            self.container_overrides["environment"] = copy.deepcopy(environment)
+        if resource_requirements is not None:
+            self.container_overrides["resourceRequirements"] = copy.deepcopy(resource_requirements)
+
+        self.job_id: Optional[str] = None
+
+    @classmethod
+    def from_id(cls, client: batch.Client, job_id: str) -> "BatchJob":
+        """"Builds a batch job from the given ID.
+
+        Will lookup the job to retrieve job information.
+
+        Args:
+            client: the AWS batch client
+            job_id: the job identifier
+        """
+        jobs_response = client.describe_jobs(jobs=[job_id])
+        jobs = jobs_response["jobs"]
+        assert len(jobs) <= 1, "More than one job described"
+        assert len(jobs) > 0, "No jobs found"
+        job_info = jobs[0]
+
+        # Treat container overrides specially
+        container: ContainerDetailTypeDef = job_info.get("container", {})
+        container_overrides: ContainerOverridesTypeDef = {}
+        if "vpus" in container:
+            container_overrides["vcpus"] = container["vcpus"]
+        if "memory" in container:
+            container_overrides["memory"] = container["memory"]
+        if "command" in container:
+            container_overrides["command"] = container["command"]
+        if "instanceType" in container:
+            container_overrides["instanceType"] = container["instanceType"]
+        if "environment" in container:
+            container_overrides["environment"] = container["environment"]
+        if "resourceRequirements" in container:
+            container_overrides["resourceRequirements"] = container["resourceRequirements"]
+
+        job: BatchJob = BatchJob(
+            client=client,
+            name=job_info["jobName"],
+            queue=job_info["jobQueue"],
+            job_definition=job_info["jobDefinition"],
+            array_properties=job_info.get("arrayProperties", {}),
+            depends_on=job_info.get("dependsOn", []),
+            parameters=job_info.get("parameters", {}),
+            container_overrides=container_overrides,
+            retry_strategy=job_info.get("retryStrategy", {}),
+            timeout=job_info.get("timeout", {}),
+        )
+
+        job.job_id = job_id
+
+        return job
+
+    @property
+    def stream(self) -> Optional[str]:
+        """The log stream for the job, if available."""
+        return self.describe_job()["container"].get("logStreamName")
+
+    def submit(self) -> SubmitJobResponseTypeDef:
+        """Submits this job."""
+        return self.client.submit_job(
+            jobName=self.name,
+            jobQueue=self.queue,
+            arrayProperties=self.array_properties,
+            dependsOn=self.depends_on,
+            jobDefinition=self.job_definition_arn,
+            parameters=self.parameters,
+            containerOverrides=self.container_overrides,
+            nodeOverrides=self.node_overrides,
+            retryStrategy=self.retry_strategy,
+            timeout=self.timeout,
+        )
+
+    def _reason(self, reason: Optional[str] = None) -> str:
+        """The default reason for cancelling or terminating a job"""
+        return reason if reason is not None else "manually initiated"
+
+    def cancel_job(self, reason: Optional[str] = None) -> None:
+        """Cancels the given AWS Batch job. Does nothing if running or finished."""
+        assert self.job_id is not None, "Cannot cancel a job that has not been submitted"
+        self.client.cancel_job(jobId=self.job_id, reason=self._reason(reason=reason))
+
+    def terminate_job(self, reason: Optional[str] = None) -> None:
+        """Terminates this job."""
+        assert self.job_id is not None, "Cannot terminate a job that has not been submitted"
+        self.client.terminate_job(jobId=self.job_id, reason=self._reason(reason=reason))
+
+    def get_status(self) -> Optional[Status]:
+        """Gets the status of this job"""
+        if self.job_id is None:
+            return None
+        else:
+            return Status(self.describe_job()["status"])
+
+    def describe_job(self) -> JobDetailTypeDef:
+        """Gets detauled information about this job."""
+        jobs_response = self.client.describe_jobs(jobs=[self.job_id])
+        job_statuses = jobs_response["jobs"]
+        assert len(job_statuses) == 1
+        job = job_statuses[0]
+        assert (
+            job["jobName"] == self.name
+        ), f"""Job name mismatched: {self.name} != {job["jobName"]}"""
+        assert (
+            job["jobId"] == self.job_id
+        ), f"""Job id mismatched: {self.job_id} != {job["jobId"]}"""
+        assert (
+            job["jobQueue"] == self.queue
+        ), f"""Job queue mismatched: {self.queue} != {job["jobQueue"]}"""
+        return job_statuses[0]
+
+    def wait_on(
+        self,
+        status_to_state: Dict[Status, bool],
+        max_attempts: Optional[int] = None,
+        delay: Optional[int] = None,
+        after_success: bool = False,
+    ) -> batch.type_defs.JobDetailTypeDef:
+        """Waits for the given states with associated success or failure.
+
+        If some states are missing from the input mapping, then all statuses after the last
+        successful input status are treated as success or failure based on `after_success`
+
+        Args:
+            status_to_state: mapping of status to success (true) or failure (false) state
+            max_attempts: the maximum # of attempts until reaching the given state.
+            delay: the delay before waiting
+        """
+        assert len(status_to_state) > 0, "No statuses given"
+        assert any(value for value in status_to_state.values()), "No statuses with success set."
+
+        _status_to_state = copy.deepcopy(status_to_state)
+        # get the last status in the given mapping
+        last_success_status = None
+        for status in Status:
+            if _status_to_state.get(status, False):
+                last_success_status = status
+
+        # for all statuses after last_success_status, set to failure
+        set_to_failure = False
+        for status in Status:
+            if status == last_success_status:
+                set_to_failure = True
+            elif set_to_failure:
+                _status_to_state[status] = after_success
+
+        name = "Waiter for statues: [" + ",".join(s.value for s in _status_to_state) + "]"
+        config: Dict[str, Any] = {"version": 2}
+        waiter_body: Dict[str, Any] = {
+            "delay": 1 if delay is None else delay,
+            "operation": "DescribeJobs",
+            "maxAttempts": sys.maxsize if max_attempts is None else max_attempts,
+            "acceptors": [
+                {
+                    "argument": "jobs[].status",
+                    "expected": f"{status.value}",
+                    "matcher": "pathAll",
+                    "state": f"""{"success" if state else "failure"}""",
+                }
+                for status, state in _status_to_state.items()
+            ],
+        }
+        config["waiters"] = {name: waiter_body}
+        model: botocore.waiter.WaiterModel = botocore.waiter.WaiterModel(config)
+        waiter: BotoWaiter = botocore.waiter.create_waiter_with_client(name, model, self.client)
+        waiter.wait(jobs=[self.job_id])
+        return self.describe_job()
+
+    def wait_on_running(
+        self, max_attempts: Optional[int] = None, delay: Optional[int] = None
+    ) -> batch.type_defs.JobDetailTypeDef:
+        """Waits for the given states with associated success or failure.
+
+        Args:
+            max_attempts: the maximum # of attempts until reaching the given state.
+            delay: the delay before waiting
+        """
+        return self.wait_on(
+            status_to_state={Status.Running: True},
+            max_attempts=max_attempts,
+            delay=delay,
+            after_success=True,
+        )
+
+    def wait_on_complete(
+        self, max_attempts: Optional[int] = None, delay: Optional[int] = None
+    ) -> batch.type_defs.JobDetailTypeDef:
+        """Waits for the given states with associated success or failure.
+
+        Args:
+            max_attempts: the maximum # of attempts until reaching the given state.
+            delay: the delay before waiting
+        """
+        return self.wait_on(
+            status_to_state={Status.Succeeded: True, Status.Failed: True},
+            max_attempts=max_attempts,
+            delay=delay,
+            after_success=False,
+        )
diff --git a/pyfgaws/batch/tests/__init__.py b/pyfgaws/batch/tests/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/pyfgaws/batch/tests/test_api.py b/pyfgaws/batch/tests/test_api.py
new file mode 100644
index 0000000..7849416
--- /dev/null
+++ b/pyfgaws/batch/tests/test_api.py
@@ -0,0 +1,162 @@
+"""Tests for :module:`~pyfgaws.batch.api`"""
+
+from typing import List
+from typing import Optional
+
+import botocore.session
+import pytest
+from botocore.stub import Stubber
+from mypy_boto3.batch import Client
+from mypy_boto3.batch.type_defs import DescribeJobDefinitionsResponseTypeDef  # noqa
+from mypy_boto3.batch.type_defs import DescribeJobsResponseTypeDef  # noqa
+from mypy_boto3.batch.type_defs import SubmitJobResponseTypeDef  # noqa
+from py._path.local import LocalPath as TmpDir
+
+from pyfgaws.batch import BatchJob
+from pyfgaws.batch import Status
+from pyfgaws.tests import stubbed_client
+
+
+def stubbed_client_submit_job(
+    submit_job_response: SubmitJobResponseTypeDef,
+    describe_job_definitions_response: Optional[DescribeJobDefinitionsResponseTypeDef] = None,
+) -> Client:
+    client = botocore.session.get_session().create_client("batch", region_name="us-east-1")
+    stubber = Stubber(client)
+
+    if describe_job_definitions_response is not None:
+        stubber.add_response(
+            method="describe_job_definitions", service_response=describe_job_definitions_response
+        )
+
+    stubber.add_response(method="submit_job", service_response=submit_job_response)
+
+    stubber.activate()
+    return client
+
+
+def stubbed_client_describe_jobs(service_responses: List[DescribeJobsResponseTypeDef]) -> Client:
+    return stubbed_client(
+        service_name="batch", method="describe_jobs", service_responses=service_responses
+    )
+
+
+def valid_describe_job_definitions_response() -> DescribeJobDefinitionsResponseTypeDef:
+    return {
+        "jobDefinitions": [
+            {
+                "type": "container",
+                "jobDefinitionName": "job-definition-name",
+                "jobDefinitionArn": "arn:aws:batch:some-arn-1",
+                "revision": 1,
+            },
+            {
+                "type": "container",
+                "jobDefinitionName": "job-definition-name",
+                "jobDefinitionArn": "arn:aws:batch:some-arn-2",
+                "revision": 2,
+            },
+            {
+                "type": "container",
+                "jobDefinitionName": "job-definition-name",
+                "jobDefinitionArn": "arn:aws:batch:some-arn-3",
+                "revision": 3,
+            },
+        ],
+        "nextToken": "next-token",
+    }
+
+
+def valid_submit_job_response() -> SubmitJobResponseTypeDef:
+    return {"jobName": "job-name", "jobId": "job-id"}
+
+
+def test_submit_job(tmpdir: TmpDir) -> None:
+    for job_definition in ["job-definition-name", "arn:aws:batch:some-arn"]:
+        client: Client
+        submit_job_response: SubmitJobResponseTypeDef = valid_submit_job_response()
+        describe_job_definitions_response: Optional[DescribeJobDefinitionsResponseTypeDef] = None
+
+        if not job_definition.startswith("arn:aws:batch:"):
+            describe_job_definitions_response = valid_describe_job_definitions_response()
+
+        client = stubbed_client_submit_job(
+            submit_job_response=submit_job_response,
+            describe_job_definitions_response=describe_job_definitions_response,
+        )
+
+        job = BatchJob(
+            client=client, name="job-name", queue="job-queue", job_definition=job_definition
+        )
+
+        response = job.submit()
+
+        assert response == submit_job_response
+
+
+def build_describe_jobs_response(status: Status) -> DescribeJobsResponseTypeDef:
+    return {
+        "jobs": [
+            {
+                "jobName": "job-name",
+                "jobId": "job-id",
+                "jobQueue": "job-queue",
+                "jobDefinition": "arn:aws:batch:some-arn",
+                "startedAt": 1,
+                "status": status.value,
+            }
+        ]
+    }
+
+
+def build_describe_jobs_responses(*status: Status) -> List[DescribeJobsResponseTypeDef]:
+    assert all(s in Status for s in status)
+    return [build_describe_jobs_response(status=s) for s in status]
+
+
+@pytest.mark.parametrize(
+    "statuses",
+    [
+        [Status.Succeeded],
+        # [Status.Failed],
+        # [
+        #     Status.Submitted,
+        #     Status.Pending,
+        #     Status.Runnable,
+        #     Status.Runnable,
+        #     Status.Running,
+        #     Status.Succeeded,
+        # ],
+        # [
+        #     Status.Submitted,
+        #     Status.Pending,
+        #     Status.Runnable,
+        #     Status.Runnable,
+        #     Status.Running,
+        #     Status.Failed,
+        # ],
+    ],
+)
+def test_wait_for_job(statuses: List[Status]) -> None:
+    service_responses: List[DescribeJobsResponseTypeDef] = []
+    # add a response for the `describe_jobs` in `BatchJob.from_id`
+    service_responses.append(build_describe_jobs_response(status=Status.Submitted))
+
+    # add the expected responses
+    service_responses.extend(build_describe_jobs_responses(*statuses))
+
+    # add a three more terminal responses, since we have a waiter that's job-exists and then
+    # job-running, before job-complete, with a final `describe_jobs` after it completes
+    last_response = service_responses[-1]
+    service_responses.append(last_response)
+    service_responses.append(last_response)
+    service_responses.append(last_response)
+
+    assert len(service_responses) > 1
+    client: Client = stubbed_client_describe_jobs(service_responses=service_responses)
+
+    job: BatchJob = BatchJob.from_id(client=client, job_id="job-id")
+    assert job.job_id is not None, str(job)
+    response = job.wait_on_complete(delay=0)
+
+    assert response == service_responses[-1]["jobs"][0], str(response)
diff --git a/pyfgaws/batch/tools.py b/pyfgaws/batch/tools.py
new file mode 100644
index 0000000..e143755
--- /dev/null
+++ b/pyfgaws/batch/tools.py
@@ -0,0 +1,174 @@
+"""
+Command-line tools for interacting with AWS Batch
+-------------------------------------------------
+"""
+
+import logging
+import threading
+import time
+from typing import Any
+from typing import Dict
+from typing import List
+from typing import Optional
+
+import boto3
+from mypy_boto3 import batch
+from mypy_boto3 import logs
+from mypy_boto3.batch.type_defs import DescribeJobsResponseTypeDef  # noqa
+from mypy_boto3.batch.type_defs import KeyValuePairTypeDef  # noqa
+from mypy_boto3.batch.type_defs import SubmitJobResponseTypeDef  # noqa
+
+from pyfgaws.batch import BatchJob
+from pyfgaws.batch import Status
+from pyfgaws.logs import DEFAULT_POLLING_INTERVAL as DEFAULT_LOGS_POLLING_INTERVAL
+from pyfgaws.logs import Log
+
+
+def _log_it(region_name: str, job: BatchJob, logger: logging.Logger) -> None:
+    """Creates a background thread to print out CloudWatch logs.
+
+    Args:
+        region_name: the AWS region
+        job: the AWS batch job
+        logger: the logger to which logs should be printed
+    """
+    # Create a background thread
+    logs_thread = threading.Thread(
+        target=_watch_logs, args=(region_name, job, logger), daemon=True
+    )
+    logs_thread.start()
+
+
+def watch_job(*, job_id: str, region_name: Optional[str] = None, print_logs: bool = True,) -> None:
+    """Watches an AWS batch job.
+
+    Args:
+        job_id: the AWS batch job identifier
+        region_name: the AWS region
+        print_logs: true to print CloudWatch logs, false otherwise
+    """
+    logger = logging.getLogger(__name__)
+
+    client: batch.Client = boto3.client(
+        service_name="batch", region_name=region_name  # type: ignore
+    )
+
+    # Create the job
+    job: BatchJob = BatchJob.from_id(client=client, job_id=job_id)
+
+    logger.info(f"Watching job with name '{job.name}' and id '{job.job_id}'")
+    if print_logs:
+        _log_it(region_name=region_name, job=job, logger=logger)
+
+    job.wait_on_complete()
+    logger.info(
+        f"Job completed with name '{job.name}', id '{job.job_id}', and status '{job.get_status()}'"
+    )
+
+
+def run_job(
+    *,
+    job_definition: str,
+    name: Optional[str] = None,
+    region_name: Optional[str] = None,
+    print_logs: bool = True,
+    queue: Optional[str] = None,
+    cpus: Optional[int] = None,
+    mem_mb: Optional[int] = None,
+    command: List[str] = [],
+    parameters: Optional[Dict[str, Any]] = None,
+    environment: Optional[KeyValuePairTypeDef] = None,
+    watch_until: List[Status] = [],
+    after_success: bool = False,
+) -> None:
+    """Submits a batch job and optionally waits for it to reach one of the given states.
+
+    Args:
+        job_definition: the ARN for the AWS batch job definition, or the name of the job definition
+            to get the latest revision
+        name: the name of the job, otherwise one will be automatically generated
+        region_name: the AWS region
+        print_logs: true to print CloudWatch logs, false otherwise
+        queue: the name of the AWS batch queue
+        cpus: the number of CPUs to request
+        mem_mb: the amount of memory to request (in megabytes)
+        command: the command(s) to use
+        parameters: the (JSON) dictionary of parameters to use
+        environment: the (JSON) dictionary of environment variables to use
+        watch_until: watch until any of the given statuses are reached.  If the job reaches a
+            status past all statuses, then an exception is thrown.  For example, `Running` will
+            fail if `Succeeded` is reached, while `Succeeded` will fail if `Failed` is reached.  To
+            wait for the job to complete regardless of status, use both `Succeeded` and `Failed`.
+            See the `--after-success` option to control this behavior.
+        after_success: true to treat states after the `watch_until` states as success, otherwise
+            failure.
+    """
+    logger = logging.getLogger(__name__)
+
+    batch_client: batch.Client = boto3.client(
+        service_name="batch", region_name=region_name  # type: ignore
+    )
+
+    job = BatchJob(
+        client=batch_client,
+        queue=queue,
+        job_definition=job_definition,
+        name=name,
+        cpus=cpus,
+        mem_mb=mem_mb,
+        command=command,
+        environment=None if environment is None else [environment],
+        parameters=parameters,
+        logger=logger,
+    )
+
+    # Submit the job
+    logger.info("Submitting job...")
+    job.submit()
+    logger.info(f"Job submitted with name '{job.name}' and id '{job.job_id}'")
+
+    # Optionally wait on it to complete
+    # Note: watch_until should be type Optional[List[Status]], but see:
+    # - https://github.com/anntzer/defopt/issues/83
+    if len(watch_until) > 0:
+        if print_logs:
+            _log_it(region_name=region_name, job=job, logger=logger)
+
+        # Wait for the job to reach on of the statuses
+        job.wait_on(
+            status_to_state=dict((status, True) for status in watch_until),
+            after_success=after_success,
+        )
+        logger.info(
+            f"Job name '{job.name}' and id '{job.job_id}' reached status '{job.get_status()}'"
+        )
+
+
+def _watch_logs(
+    region_name: str,
+    job: BatchJob,
+    logger: logging.Logger,
+    polling_interval: int = DEFAULT_LOGS_POLLING_INTERVAL,
+) -> None:
+    """A method to watch logs indefinitely.
+
+    Args:
+        region_name: the AWS region
+        job: the AWS batch job
+        logger: the logger to which logs should be printed
+        polling_interval: the default time to wait for new CloudWatch logs after no more logs are
+            returned
+    """
+    # wait until it's running to get the CloudWatch logs
+    job.wait_on_running()
+
+    client: Optional[logs.Client] = boto3.client(
+        service_name="logs", region_name=region_name  # type: ignore
+    )
+    log: Log = Log(client=client, group="/aws/batch/job", stream=job.stream)
+
+    while True:
+        for line in log:
+            logger.info(line)
+        time.sleep(polling_interval)
+        log.reset()
diff --git a/pyfgaws/core/__init__.py b/pyfgaws/core/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/pyfgaws/core/logging.py b/pyfgaws/core/logging.py
new file mode 100644
index 0000000..5a9e7d5
--- /dev/null
+++ b/pyfgaws/core/logging.py
@@ -0,0 +1,42 @@
+"""
+Methods for setting up logging for tools.
+-----------------------------------------
+"""
+
+import logging
+import socket
+from threading import RLock
+
+
+# Global that is set to True once logging initialization is run to prevent running > once.
+__PYFGAWS_LOGGING_SETUP: bool = False
+
+# A lock used to make sure initialization is performed only once
+__LOCK = RLock()
+
+
+def setup_logging(level: str = "INFO") -> None:
+    """Globally configure logging for all modules under pyfgaws.
+
+    Configures logging to run at a specific level and output messages to stderr with
+    useful information preceding the actual log message.
+    """
+    global __PYFGAWS_LOGGING_SETUP
+
+    with __LOCK:
+        if not __PYFGAWS_LOGGING_SETUP:
+            format = (
+                f"%(asctime)s {socket.gethostname()} %(name)s:%(funcName)s:%(lineno)s "
+                + "[%(levelname)s]: %(message)s"
+            )
+            handler = logging.StreamHandler()
+            handler.setLevel(level)
+            handler.setFormatter(logging.Formatter(format))
+
+            logger = logging.getLogger("pyfgaws")
+            logger.setLevel(level)
+            logger.addHandler(handler)
+        else:
+            logging.getLogger(__name__).warn("Logging already initialized.")
+
+        __PYFGAWS_LOGGING_SETUP = True
diff --git a/pyfgaws/logs/__init__.py b/pyfgaws/logs/__init__.py
new file mode 100644
index 0000000..e029158
--- /dev/null
+++ b/pyfgaws/logs/__init__.py
@@ -0,0 +1,3 @@
+from pyfgaws.logs.api import DEFAULT_POLLING_INTERVAL, Log
+
+__all__ = ("DEFAULT_POLLING_INTERVAL", "Log")
diff --git a/pyfgaws/logs/api.py b/pyfgaws/logs/api.py
new file mode 100644
index 0000000..2814537
--- /dev/null
+++ b/pyfgaws/logs/api.py
@@ -0,0 +1,71 @@
+"""
+Utility methods for interacting with AWS CloudWatch Logs
+--------------------------------------------------------
+"""
+
+import queue
+from typing import Iterator
+from typing import Optional
+
+from mypy_boto3 import logs
+
+# The number of seconds to wait to poll for a job's status
+DEFAULT_POLLING_INTERVAL: int = 5
+
+
+class Log(Iterator[str]):
+    """Log to iterate through CloudWatch logs.
+
+    Iterating over this class returns all available events.
+
+    The `reset()` method allows iterating across any newly available events since the last
+    iteration.
+
+    Attributes:
+        client: the logs client
+        group: the log group name
+        stream: the log stream name
+        next_token: the token for the next set of items to return, or None if the oldest events.
+    """
+
+    def __init__(
+        self, client: logs.Client, group: str, stream: str, next_token: Optional[str] = None
+    ) -> None:
+        self.client: logs.Client = client
+        self.group: str = group
+        self.stream: str = stream
+        self.next_token: Optional[str] = next_token
+        self._events: queue.Queue = queue.Queue()
+        self._is_done: bool = False
+
+    def __next__(self) -> str:
+        if not self._events.empty():
+            return self._events.get()
+        elif self._is_done:
+            raise StopIteration
+
+        # add more events
+        if self.next_token is None:
+            response = self.client.get_log_events(
+                logGroupName=self.group, logStreamName=self.stream, startFromHead=True,
+            )
+        else:
+            response = self.client.get_log_events(
+                logGroupName=self.group,
+                logStreamName=self.stream,
+                nextToken=self.next_token,
+                startFromHead=True,
+            )
+        for event in response["events"]:
+            string: str = f"""{event["timestamp"]} {event["message"]}"""
+            self._events.put(item=string)
+        old_next_token = self.next_token
+        self.next_token = response["nextForwardToken"]
+        self._is_done = self.next_token == old_next_token
+
+        return self.__next__()
+
+    def reset(self) -> "Log":
+        """Reset the iterator such that new events may be returned."""
+        self._is_done = False
+        return self
diff --git a/pyfgaws/logs/tests/__init__.py b/pyfgaws/logs/tests/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/pyfgaws/logs/tests/test_api.py b/pyfgaws/logs/tests/test_api.py
new file mode 100644
index 0000000..67592ba
--- /dev/null
+++ b/pyfgaws/logs/tests/test_api.py
@@ -0,0 +1,81 @@
+"""Tests for :module:`~pyfgaws.logs.api`"""
+
+from typing import List
+
+import pytest
+from mypy_boto3.logs import Client
+from mypy_boto3.logs.type_defs import GetLogEventsResponseTypeDef  # noqa
+
+from pyfgaws.logs import Log
+from pyfgaws.tests import stubbed_client
+
+
+def stubbed_client_get_log_events(service_responses: List[GetLogEventsResponseTypeDef]) -> Client:
+    return stubbed_client(
+        service_name="logs", method="get_log_events", service_responses=service_responses
+    )
+
+
+def valid_empty_service_response() -> GetLogEventsResponseTypeDef:
+    return {"events": [], "nextForwardToken": "token-2", "nextBackwardToken": "token-2"}
+
+
+def valid_single_event_service_response() -> GetLogEventsResponseTypeDef:
+    return {
+        "events": [{"timestamp": 123, "message": "message", "ingestionTime": 123}],
+        "nextForwardToken": "token-2",
+        "nextBackwardToken": "token-1",
+    }
+
+
+def valid_multiple_event_service_response() -> GetLogEventsResponseTypeDef:
+    return {
+        "events": [
+            {"timestamp": 1, "message": "message-1", "ingestionTime": 11},
+            {"timestamp": 2, "message": "message-2", "ingestionTime": 12},
+        ],
+        "nextForwardToken": "token-2",
+        "nextBackwardToken": "token-1",
+    }
+
+
+def valid_multiple_service_responses() -> List[GetLogEventsResponseTypeDef]:
+    return [
+        {
+            "events": [{"timestamp": 123, "message": "message", "ingestionTime": 123}],
+            "nextForwardToken": "token-2",
+            "nextBackwardToken": "token-1",
+        },
+        {
+            "events": [
+                {"timestamp": 1, "message": "message-1", "ingestionTime": 11},
+                {"timestamp": 2, "message": "message-2", "ingestionTime": 12},
+            ],
+            "nextForwardToken": "token-3",
+            "nextBackwardToken": "token-2",
+        },
+        {"events": [], "nextForwardToken": "token-3", "nextBackwardToken": "token-3"},
+    ]
+
+
+@pytest.mark.parametrize(
+    "service_responses",
+    [
+        [valid_empty_service_response(), valid_empty_service_response()],
+        [valid_single_event_service_response(), valid_empty_service_response()],
+        [valid_multiple_event_service_response(), valid_empty_service_response()],
+        valid_multiple_service_responses(),
+    ],
+)
+def test_get_log_events(service_responses: List[GetLogEventsResponseTypeDef]) -> None:
+    client = stubbed_client_get_log_events(service_responses=service_responses)
+
+    events = list(Log(client=client, group="name", stream="name"))
+
+    expected = [
+        f"""{item["timestamp"]} {item["message"]}"""
+        for service_response in service_responses
+        for item in service_response["events"]
+    ]
+
+    assert events == expected
diff --git a/pyfgaws/logs/tools.py b/pyfgaws/logs/tools.py
new file mode 100644
index 0000000..57886f9
--- /dev/null
+++ b/pyfgaws/logs/tools.py
@@ -0,0 +1,51 @@
+"""
+Command-line tools for interacting with AWS CloudWatch Logs
+-----------------------------------------------------------
+"""
+
+import logging
+import time
+from typing import Optional
+
+import boto3
+
+from pyfgaws.logs import DEFAULT_POLLING_INTERVAL
+from pyfgaws.logs import Log
+
+
+def watch_logs(
+    *,
+    group: str,
+    stream: str,
+    region_name: Optional[str] = None,
+    polling_interval: int = DEFAULT_POLLING_INTERVAL,
+    raw_output: bool = False,
+) -> None:
+    """Watches a cloud watch log stream
+
+    Args:
+        group: the name of the log group
+        stream: the name of the log stream
+        region_name: the AWS region
+        polling_interval: the time to wait before polling for new logs
+        raw_output: output the logs directly to standard output, otherwise uses the internal
+            logger.
+    """
+    logger = logging.getLogger(__name__)
+
+    client = boto3.client(
+        service_name="logs", region_name=region_name  # type: ignore
+    )
+
+    logger.info(f"Polling log group '{group}' and stream '{stream}'")
+
+    log: Log = Log(client=client, group=group, stream=stream)
+
+    while True:
+        for line in log:
+            if raw_output:
+                print(line)
+            else:
+                logger.info(line)
+        time.sleep(polling_interval)
+        log.reset()
diff --git a/pyfgaws/tests/__init__.py b/pyfgaws/tests/__init__.py
new file mode 100644
index 0000000..e3e8cd8
--- /dev/null
+++ b/pyfgaws/tests/__init__.py
@@ -0,0 +1,43 @@
+"""Testing utilities for :module:`~pyfgaws`"""
+
+from typing import Any
+from typing import List
+
+import botocore.session
+import pytest
+from botocore.stub import Stubber
+
+
+def _to_name(tool) -> str:  # type: ignore
+    """Gives the tool name for a function by taking the function name and replacing
+    underscores with hyphens."""
+    return tool.__name__.replace("_", "-")
+
+
+def test_tool_funcs(tool, main) -> None:  # type: ignore
+    name = _to_name(tool)
+    argv = [name, "-h"]
+    with pytest.raises(SystemExit) as e:
+        main(argv=argv)
+    assert e.type == SystemExit
+    assert e.value.code == 0  # code should be 0 for help
+
+
+def stubbed_client(service_name: str, method: str, service_responses: List[Any]) -> Any:
+    """Creates a stubbed client.
+
+    Args:
+        service_name: the name of the AWS service (ex. logs, batch) to stub
+        method: The name of the client method to stub
+        service_responses: one or more service responses to add
+
+    Returns:
+        an activated stubbed client with the given responses added
+    """
+
+    client = botocore.session.get_session().create_client(service_name, region_name="us-east-1")
+    stubber = Stubber(client)
+    for service_response in service_responses:
+        stubber.add_response(method=method, service_response=service_response)
+    stubber.activate()
+    return client
diff --git a/pyfgaws/tests/test_main.py b/pyfgaws/tests/test_main.py
new file mode 100644
index 0000000..4209fc7
--- /dev/null
+++ b/pyfgaws/tests/test_main.py
@@ -0,0 +1,73 @@
+"""Tests for :module:`~pyfgws.tools.__main__`
+
+Motivation
+~~~~~~~~~~
+
+The idea is to run help on the main tools method (`-h`) as well as on
+each tool (ex. `tool-name -h`).  This should force :module:`~defopt`
+to parse the docstring for the method.  Since :module:`~defopt` uses
+:module:`~argparse` underneath, `SystemExit`s are raised, which are
+different than regular `Exceptions`.  The exit code returned by help
+(the usage) is 0.  A improperly formatted docstring throws a
+:class:`NotImplementedException`.  We add a few test below to show
+this.
+"""
+
+import defopt
+import pytest
+
+from pyfgaws.__main__ import TOOLS
+from pyfgaws.__main__ import main
+from pyfgaws.tests import test_tool_funcs as _test_tool_funcs
+
+
+def invalid_docs_func(*, a: str) -> None:
+    """This is a dummy method with incorrectly formatted docs
+
+        * this is bad
+
+    Args:
+        a: some string
+    """
+    print(a)
+
+
+def valid_docs_func(*, a: int) -> None:
+    """Some func
+
+    * this is good
+
+    Args:
+        a: some int
+    """
+    print(a)
+
+
+def test_incorrect_docs() -> None:
+    """A little test to demonstrate that when the error when a tools docs are
+    incorrectly formatted, a TypeError is thrown"""
+    with pytest.raises(TypeError):
+        defopt.run(invalid_docs_func, argv=["-a", "str"])
+
+
+def test_incorrect_param_type() -> None:
+    """A little test to demonstrate that when the input arg has the wrong type,
+    a SystemExit is thrown with exit code 2"""
+    with pytest.raises(SystemExit) as e:
+        defopt.run(valid_docs_func, argv=["-a", "str"])
+    assert e.type == SystemExit
+    assert e.value.code == 2  # code should be 2 for parse error
+
+
+def test_tools_help() -> None:
+    """ Tests that running dts.tools with -h exits OK"""
+    argv = ["-h"]
+    with pytest.raises(SystemExit) as e:
+        main(argv=argv)
+    assert e.type == SystemExit
+    assert e.value.code == 0  # code should be 0 for help
+
+
+@pytest.mark.parametrize("tool", TOOLS)
+def test_tool_funcs(tool) -> None:  # type: ignore
+    _test_tool_funcs(tool, main)
diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 0000000..f9f2ca2
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,49 @@
+[tool.poetry]
+name = "pyfgaws"
+version = "0.0.1"
+description = "Tools and python libraries for working with AWS."
+authors = ["Nils Homer", "Tim Fennell"]
+license = "MIT"
+readme = "README.md"
+homepage = "https://github.com/fulcrumgenomics/pyfgaws"
+repository = "https://github.com/fulcrumgenomics/pyfgaws"
+keywords = ["aws", "bioinformatics"]
+classifiers = [
+	"Development Status :: 3 - Alpha",
+    "Environment :: Console",
+	"Intended Audience :: Developers",
+	"Intended Audience :: Science/Research",
+	"License :: OSI Approved :: MIT License",
+    "Operating System :: OS Independent",
+	"Programming Language :: Python :: 3",
+	"Topic :: Scientific/Engineering :: Bio-Informatics",
+    "Topic :: Software Development :: Documentation",
+    "Topic :: Software Development :: Libraries :: Python Modules",
+]
+include = [
+    "LICENSE",
+]
+
+
+[tool.poetry.dependencies]
+python = "^3.8"
+attrs = "^19.3.0"
+defopt = "^6.0"
+boto3 = "^1.13.18"
+botocore = "^1.13.18"
+boto3-stubs = {extras = ["batch", "logs"], version = "^1.13.19"}
+namegenerator = "^1.0.6"
+
+[tool.poetry.dev-dependencies]
+pytest = "^5.4.2"
+mypy = "^0.770"
+flake8 = "^3.8.1"
+black = "^19.10b0"
+pytest-cov = ">=2.8.1"
+
+[tool.poetry.scripts]
+fgaws-tools = "pyfgaws.__main__:main"
+
+[build-system]
+requires = ["poetry>=0.12"]
+build-backend = "poetry.masonry.api"