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Tp bgen reader #48

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cseed opened this issue Oct 29, 2015 · 0 comments
Closed

Tp bgen reader #48

cseed opened this issue Oct 29, 2015 · 0 comments

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@cseed
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cseed commented Oct 29, 2015

From @tpoterba on October 1, 2015 18:27

Read my code and weep at its bloat

Copied from original issue: cseed/hail/pull/70
@cseed cseed closed this as completed Oct 29, 2015
cseed added a commit to cseed/hail that referenced this issue Sep 22, 2018
@cseed @danking
authenticate docker to push to gcr.io (hail-is#48)
547b05c 
* authenticate docker to push to gcr.io

* add gcloud quiet (-q)

* remove errant tab

* logging to match ci

* do callback asynchronously

* do callback asynchronously
danking pushed a commit that referenced this issue Sep 25, 2018
@cseed @danking
Merge batch (#4414)
945d68d 
* initial revision

* wip

* added deployment

updated logging

* added service

* wip

* wip

* cancellation, primitive client library

(unused) bidict
jupyter deployment

* batches, higher level api

* fixed readme

* minor

* added tests, reorg

* tests run in itself

* wip

added attributes
removed job names
create batch objects
added callback (untested)

* added callbacks, callback test

* makefile changes

* wip

try to get callback test working on k8s cluster

* tweaks

* callback test works on k8s

* starting to play with containerized spark

some cleanup

* Create setup.py

* move setup.py to correct location

* ignore compiled pyc files

* describe how to use minikube with local docker images

* add special note about `imagePullPolicy`

* add an environment yaml

* add a getting started section

* add a dockerignore file

* do not fail if callback fails

* expose pod/container volumes

* fix volumeMounts field name

* add resources

* add tolerations

* add jobs listing

* add jobs test

* fix the environment

* update Batch.create_job for all the new parameters

* fix missing id

* avoid crashing on bad event types

* update dockerignore

* retry event loops

* Update server.py

* fix dockerignore

* fix dockerignore

* stash the attributes sent by api

* cache the status

* fixed tests (#28)

* Pr builder image (#27)

* added pr-builder image logic

* added missing files

* address comments

* add hail-ci-build.sh (#30)

* add hail-ci-build.sh wip

* wip

* make hail-ci script work

added shutdown endpoint

* fix

* don't log the (pod) log (#29)

* added bash to pr-builder image (#32)

* Add git (#35)

* test

* added git to pr-builder image

* add python alias in pr-builder image

* added curl to pr-builder image

* Job delete (#36)

* wip: added job/delete

need to test

* added delete, various

* tag executable images (#38)

* update deployment (#39)

* make batch single threaded (#40)

* make batch single threaded

polling and k8s watch thread request into main thread
in addition to k8s notifications, periodically poll k8s state

* address comments

* label batch job pods (#41)

* add hail-ci-deploy.sh (#42)

* added hail-ci-deploy.sh

add docker to pr-builder image

* added missing deployment.yaml.in

removed deployment.yaml

* consistency

* addessed comments

* install kubectl in image (#44)

`gcloud components install kubectl` is failing with a non-obvious error message so I installed it directly

* make batch subproject (#46)

* make batch subproject

fixed more deployment bugs

* updated build image

* fix test race condition

job can complete before it is cancelled

* authenticate docker to push to gcr.io (#48)

* authenticate docker to push to gcr.io

* add gcloud quiet (-q)

* remove errant tab

* logging to match ci

* do callback asynchronously

* do callback asynchronously

* expose pod name as well (#49)

* restart ci on deploy (#50)

* Fix SHA check (#51)

* Update hail-ci-deploy.sh

* Update deployment.yaml.in

* Update hail-ci-deploy.sh

* Update hail-ci-deploy.sh

* add /jobs/<id>/log endpoint (#52)

* add /jobs/<id>/log endpoint

added to api, client
return completed job logs (including deleted ones)
return in-progress logs (if there are any)
return 404 (not empty) if there no logs to be found

status['log'] returns the same log

* fixed bug

* fixed typo

* prep to merge into monorepo

clean up unused files, experiments (jupyter, spark, etc.)

* updated build image

* fixes

hail-ci-build.sh handles all known projects
fix batch to deploy only when changed

* fixed typo

* fixed README.md conflict.

* activate environment

* add cloudtools to list of project-changed.py projects
tpoterba pushed a commit to tpoterba/hail that referenced this issue Feb 12, 2019
@jbloom22 @tpoterba
Update README.md (hail-is#48)
bd556cc
danking pushed a commit that referenced this issue May 8, 2019
@cseed @danking
Add cloudtools (#6010)
6c231c0 
* update

* update

* update

* updatE

* Create README.md

* Update README.md

* Update README.md

* Update README.md

* Update README.md

* Update README.md

* Update README.md

* Update README.md

* Update README.md

* Update README.md

* Update README.md

* Update README.md

* Update README.md

* Update README.md

* Update README.md

* update

* Update README.md

* Update README.md

* Update README.md

* Update README.md

* update

* Update README.md

* Update README.md

* Update README.md

* Update README.md

* Update README.md

* Update README.md

* Update README.md

* added default Spark configs to init_notebook.py

* updatE

* update

* update

* add time delay to allow Jupyter to start

* add time delay to allow Jupyter to start

* revert log change

* update

* updatE

* updated README

* set maxResultSize property to unlimited

* changed default worker to n1-standard-8

* merged init_default.py functionality into init_notebook.py

* merged init_default.py functionality into init_notebook.py

* updated README

* updated README

* updated README

* updated README

* updated README

* updated README

* updated README

* updated README

* updated README

* updated README

* updated README

* fixed order of code in init script

* fixed ports argument in start-up script

* moved waiting for Jupyter code to init script

* updated alias code block

* fixed init script filename

* Google Chrome check needs to be fixed

* added gitignore

* highmem worker by default with --vep.

* added --hash option to start_cluster.py to reference older Hail builds

* Merge pull request #5 from Nealelab/dev

added --hash option to start_cluster.py to reference older Hail builds

* decoupled default conf in Jupyter notebook Spark from /etc/spark/conf/spark-defaults.conf

* typo in submit_cluster

* modified init_notebook script

* Update stop_cluster.py

* Now passes extra properties to gcloud

* added ability to specifiy custom Hail jar and zip for Jupyter notebook on startup

* Some tightening of options

* Moving into main

* Removed duplicate keyword argument

* remove duplicate argument

* Added diagnose_cluster.py

Compiles log files for a cluster to a local directory or a google bucket

```
python diagnose_cluster.py -n my-cluster -d my-cluster-diagnose/
python diagnose_cluster.py -n my-cluster -d gs://my-bucket/my-cluster-diagnose/
```

```
usage: diagnose_cluster.py [-h] --name NAME --dest DEST [--hail-log HAIL_LOG]
                           [--overwrite] [--no-diagnose] [--compress]
                           [--workers [WORKERS [WORKERS ...]]] [--take TAKE]

optional arguments:
  -h, --help            show this help message and exit
  --name NAME, -n NAME  Cluster name
  --dest DEST, -d DEST  Directory for diagnose output -- must be local
  --hail-log HAIL_LOG, -l HAIL_LOG
                        Path for hail.log file
  --overwrite           Delete dest directory before adding new files
  --no-diagnose         Do not run gcloud dataproc clusters diagnose
  --compress, -z        GZIP all files
  --workers [WORKERS [WORKERS ...]]
                        Specific workers to get log files from
  --take TAKE           Only download logs from the first N workers
```

- Runs `gcloud dataproc clusters diagnose`
- Grabs following log files from master node

```
/var/log/hive/hive-*
/var/log/google-dataproc-agent.0.log
/var/log/dataproc-initialization-script-0.log
/var/log/hadoop-mapreduce/mapred-mapred-historyserver*
/var/log/hadoop-hdfs/*-m.*
/var/log/hadoop-yarn/yarn-yarn-resourcemanager-*-m.*
/home/hail/hail.log # can be modified with command line argument
```

- Grabs following log files from workers

```
/var/log/hadoop-hdfs/hadoop-hdfs-datanode-*.*
/var/log/dataproc-startup-script.log
/var/log/hadoop-yarn/yarn-yarn-nodemanager-*.*
/var/log/hadoop-yarn/userlogs/*
```

Output directory has following structure:

```
diagnostic.tar
master/my-cluster-m/...
workers/my-cluster-w-*/...
hadoop-yarn/userlogs/application*/container*
```

* sec worker fix

* Break apart ssh options.

Saw failures with some version of gcloud/ssh.

* Exposed --metadata and fixed problem with creating directory

* Recapitulating subprocess fixes of PR #11

* Fix typo in README

* Added executable

* Updates to support multiple Hail versions and new deployment locations.

 - init_notebook is now versioned for compatibility. This commit uses
   version 2, which I've uploaded to gs://hail-common/init_notebook-2.py.
 - Hail now deploys both 0.1 and devel versions, so I added an argument to
   allow either to be used. The stable version should of course be used by
   default.
 - The init arg is now empty by default, because the init_notebook script
   should always be run (and requires the compatibility version to decide
   the correct path). It is still possible to use additional init actions.

* small fix in init_notebook; updated submit script to reflect new Hail deployment

* packaged commands under umbrella 'cluster' module

* updated diagnose

* updated readme; added --quiet flag to stop command

* updated readme with optional arguments

* Update LICENSE.txt

* make notebook default for cluster connect

* Overhaul CLI using argparse subparsers; interface change

 - More informative help messages
 - Added default args to --help output
 - Interface change: module comes before name

* Fixed HAIL_VERSION metadata variable.

* updated setup.py to reflect v1.1

* changed some instances of check_call to call to avoid redundant errors

* Remove zsh artifacts from README

* added --args option to submit script to allow passing arguments to submitted Hail scripts

* incremented to v1.1.2

* Update README.md

* Remove sleep

* removed Anaconda from notebook init; added --pkgs option to cluster start

* Fix deployment issues by bumping compatibility version

* fixed jar distribution issues

* forgot something

* Updating spark version to dataproc 1.2

* a few fixes for 2.2.0

* COMPAT version changes

* Made the os.mkdir statements safer and free from race conditions

* Fix cloudtools to work with Hail devel / 0.2 (#47)

* Update README.md (#48)

* Unify hail 0.1 and 0.2 again, fix submit (#49)

* Unify hail 0.1 and 0.2 again, fix submit

* Fixed submit help message

* Bump version

* Update init_notebook.py (#51)

* Add parsimonious (#52)

* Parameterize master memory fraction (#53)

* Parameterize master memory fraction

* Parameterize master memory fraction

* Parameterize master memory fraction

* add bokeh to imports (#54)

* Use specific version of decorator (#56)

* Update README.md (#57)

* add modify jar and zip (#59)

* * Fixed zip copying (#60)

* Added gs:// support

* rolling back google-cloud version (#62)

* moved up package installation in init script (#63)

* use beta for max-idle option (#61)

* use beta for max-idle option

* bug fix

* added Intel MKL to init script (#64)

* added Intel MKL to init script

* fix

* another fix

* Update default version to devel / spark 2.2.0; update README (#65)

* Update default version to devel / spark 2.2.0; update README

* fix

* Added initialization time-out option. (#71)

* add async option to stop (#73)

* check for errors in start, stop, submit, and list (#74)

* update version to 1.14 (#75)

* Syntax error (#76)

* fix syntax error

* bump versino

* add a bucket parameter (#78)

* add a bucket parameter

* also document deployment

* use config files to set some default properties (#77)

* do... something

* set image based on spark version

* tweak to run using paths that deploy will spit out

* fix

* fix rebase

* Set up Continuous Integration (#80)

* wip hail ci

* fix formatting

* ignore emacs temp files

* add cluster sanity checks

* Update setup.py

* Update cluster-sanity-check-0.2.py

* Fix CI Build (#81)

* Update hail-ci-build.sh

* Update hail-ci-build.sh

* add more necessary things

* fix build image and update file

* fix build image maybe

* use python2

* fix image

* Update hail-ci-build.sh

* Update hail-ci-build.sh

* Continuous Deployment (#82)

* add deploy script

* document deployment secret creation

* fix readme

* fix if check

* ensure twine is in build image

* kick ci

* set required property? apparently?

* bump to 0.2 (#79)

* add make to image (#85)

* fix deploy (#86)

* copy some lessons from hail (#84)

copying some ideas from the discussion at #4241

* Update hail-ci-deploy.sh (#87)

* fix (#88)

* fix cloudtools published check (#89)

* add warning, versioned hash lookup (#90)

* fix deploy script version checking (#92)

* Test python 3.6 and fix python 3.7 incompatibility (#91)

* test python3

* also fix async is reserved word

* checked in bad build file

* unneeded var

* shush pip

* kick ci

* update build hash

* Ignore INT and TERM in shutdown_cluster

* parse init script list (#94)

* parse init script list

* Update __init__.py

* switched devel vep to use docker init (#96)

* bump version for vep init (#98)

* deploy python2 and python3 to pypi (#93)

* Update start.py (#99)

* Update start.py

* Update start.py

* Update __init__.py (#100)

* fix python3 deploy (#101)

* Fix pkgs logic (#102)

* Adding more options to modify (#67)

* Added options to modify clusters

* Update modify.py

* Add a max-idle 40m to test clusters (#103)

* Add a max-idle 40m to test clusters

* need gcloud beta components

* Pin dependency versions (#105)

* pin dependency versions

* update the version of cloudtools

* install all packages together to ensure dependencies are calculated together

* fail when subprocess fails

* fix conda invocation

* compatibility with python2

* Revert "fail when subprocess fails"

This reverts commit 25e7c0a524823d91894b538427f179611e79f271.

* blah

* wtf

* if was backwards

* restart tests

* Improve Error Messages when Subprocesses Fail (#111)

* add and use safe_call

* fail when subprocess fails

* use safe_call

* use safe_call extensively

* simplify and make correct safe_call

* fix splat

* fix

* foo

* update verison (#113)

* Added describe to get Hail file info/schema (#112)

* Added describe to get Hail file info/schema

* f -> format

* Update setup.py

* Update __init__.py (#115)

* Fix cloudtools (#116)

* fix

* bump version

* fix (#117)

* bump ver (#118)

* fixed describe ordering for python2 (#119)

* devel => 0.2 (#121)

* add latest (#120)

* added --max-age option. (#123)

* added --max-age option.

* bump version

* update to 3.0.0 (#122)

* update to 3.0.0

* bump

* bump

* s/devel/0.2

* Fix packages again (#124)

* Fix packages again

* fix

* Add 'modify' and 'list' command docs (#125)

* Update connect.py (#126)

* Rollout fix for chrome 72 (#130)

* Add python files or folders from environment variable; zip files together (#127)

* Add python files or folders from environment variable; zip files together

* bumping version

* files -> pyfiles

* missed one

* overloaded variable

* updating VEP init script (#129)

* updating VEP init script

* Update __init__.py

* files -> pyfiles once more (#131)

* fix for jupyter/tornado incompatibility (#133)

* Adding project flag (#134)

* Adding project flag

* Adding configuration option as well

* Adding support for GRCh38 VEP (#135)

* Adding support for GRCh38 VEP

* version bump

* Fixing VEP version for 38 (#136)

* Adding support for GRCh38 VEP

* version bump

* fix for 38 VEP version

* Update __init__.py

* Disable stackdriver on cloudtools clusters (#138)

* Update default spark version (#139)

* Update default spark version

* Clean up imports

* allowing pass-through args for submit (#140)

* allowing pass-through args for submit

* bump version

* moar version

* moved cloudtools to subdirectory project for inclusion in monorepo

* moved .gitignore

* bump

* bump
daniel-goldstein referenced this issue in daniel-goldstein/hail Feb 3, 2022
@lgruen
Merge pull request #48 from populationgenomics/upstream
9d69512 
Upstream
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@cseed