Jb filtlang4 #113
Merged
Jb filtlang4 #113
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| @@ -44,7 +44,7 @@ object ExportSamples extends Command { | |||
| reflective compilation has failed: | |||
|
|
|||
| ';' expected but '.' found. */ | |||
| fatal("parse error in condition: " + e.message.split("\n").last) | |||
| fatal("parse error in condition: " + e.message)//.split("\n").last) | |||
There was a problem hiding this comment.
We should strip off the leading "reflective compilation has failed:" and then print the remainder. Splitting on newlines failed because of multi-line error messages.
|
Back to you. FYI, you have conflicts. |
# Conflicts: # src/test/scala/org/broadinstitute/hail/methods/ExportSuite.scala
tpoterba
pushed a commit
to tpoterba/hail
that referenced
this pull request
Feb 12, 2019
danking
pushed a commit
that referenced
this pull request
May 8, 2019
* 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 pull request
in daniel-goldstein/hail
Feb 3, 2022
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Still need to complete genotype filtering based on option types, but all indication are that it'll work based on included FilterGenotype tests.