elastic-blast - 1.4.0

Improvements:

• Upgrade to GCP Artifact Registry

Bug fixes:

• Better handling of job completion status in kubernetes version 1.30+

- Python
Published by christiam 11 months ago

elastic-blast - 1.3.1

Bug fixes:

• Fix for checking kubectl version

- Python
Published by christiam over 1 year ago

elastic-blast - 1.3.0

Improvements:

• Upgrade to BLAST+ 2.16.0, including runtime improvements to blastp, blastx, and psiblast

Bug fixes:

• Better tracking of cloud resource IDs to facilitate resource clean up in case of errors
• Use specified AWS region when getting available instance types

- Python
Published by christiam over 1 year ago

elastic-blast -

Improvements:

• Upgrade to BLAST+ 2.15.0, including improved performance for taxonomy limited searches and automatic selection of threading model
• Automatically select client vs. cloud query splitting based on query file size
• Support for kubernetes versions 1.26 and greater
• New ElasticBLAST batch lengths for threading by query

Bug fixes:

• Fixed bug that led to timeouts in GCP waiting for the persistent volume claim (PVC) to bind
• Improve error message if -entrez_query option is given

- Python
Published by christiam about 2 years ago

elastic-blast -

Improvements:

• Default batch sizes for blastn and dc-megablast lead to improved runtimes
• Improve AWS quota check based on the number of vCPUs per instance
• Improved logging of dependent tools

Bug fixes:

• Fixed AWS API calls to select instances on all AWS regions

- Python
Published by christiam almost 3 years ago

elastic-blast - 1.0.0

Note to ElasticBLAST users on GCP

ElasticBLAST versions prior to 1.0.0 will stop working after January 31, 2023 because they rely on version 1.21 of kubernetes, which will reach its end of life on the Google Kubernetes Engine on that date. Please upgrade your installation of ElasticBLAST to its latest version.

Improvements:

• ElasticBLAST on AWS now defaults to the faster and cheaper EBS gp3 disk type
• ElasticBLAST on GCP now supports all of the versions of kubernetes offered by Google Kubernetes Engine
• ElasticBLAST on GCP defaults to the stable version of kubernetes offered by Google Kubernetes Engine

Bug fixes:

• ElasticBLAST uses GCP's recommended way of dealing with read/write persistent disk
• Long user names no longer cause errors in AWS
• Fixed error caused by APIs not being enabled in GCP

- Python
Published by boratyng about 3 years ago

elastic-blast -

Improvements:

• Query splitting module supports streaming data from cloud buckets
• Improved AWS region validation

Bug fixes:

• Fixed problem when AWSDEFAULTREGION is not set
• Bug fixes for --dry-run mode
• --batch-len command line option is recognized

- Python
Published by christiam over 3 years ago

elastic-blast - 0.2.6

New features:

• A new config parameter cloud-providers/gke-version to select Google Kubernetes Engine version, defaults to 1.21

Improvements:

• GCP project config parameter is now optional. If missing elastic-blast will use CLOUDSDK_CORE_PROJECT environment variable or the default GCP project set in gcloud config.
• GCP zone config parameter now defaults to us-east4-b
• Improved error message when persistent disk size exceeds user’s quota

Bug fixes:

• Fixed a persistent disk problem in GCP
• Invalid janitor schedule string does not cause resource leak and is properly reported

- Python
Published by boratyng over 3 years ago

elastic-blast - 0.2.5

Improvements:

• elastic-blast status always reports BLAST errors
• BLAST+ updated to version 2.13.0

- Python
Published by boratyng almost 4 years ago

elastic-blast -

Improvements:

• elastic-blast status updated to report when ElasticBLAST is submitting jobs to the cloud

- Python
Published by christiam almost 4 years ago

elastic-blast -

Bug fixes:

• Fix bug that leads to invalid GKE cluster names

- Python
Published by christiam about 4 years ago

elastic-blast -

Bug fixes:

• Fix bug that causes ElasticBLAST on AWS to fail to read from S3

- Python
Published by christiam about 4 years ago

elastic-blast -

Improvements:

• Improve support for multiple local SSDs on AWS
• Consistent tagging of AWS EC2 Launch Template
• Machine selection in AWS is now stable

Bug fixes:

• User names with certain characters do not result in cloud provider errors any more

- Python
Published by christiam about 4 years ago

elastic-blast - 0.2.0 beta release

New features:

• Provide support for BLASTDB metadata files version 1.2
• Add support for --exit-code option in elastic-blast status
• Check for resource files in PEX
• Provide scripts to check for undeleted ElasticBLAST searches

Improvements:

• elastic-blast status --verbose prints BLAST+ error message, if a search failed due to BLAST errors
• Additional checks for num-cpus parameter that prevent unschedulable search jobs
• Improved error message for BLAST database initialization with local SSD in GCP
• Cluster name can be set via cluster.name configuration parameter
• Incorporate mt_mode choice when selecting machine-type
• created tag is recorded in UTC time

Bug fixes:

• User names with certain characters do not result in cloud provider errors any more
• Limit the number of concurrent aws s3 invocations when downloading BLASTDB to prevent OOM
• Initialize local SSD before tagging to ensure they are ready to use in spite of tagging errors

- Python
Published by christiam about 4 years ago

elastic-blast -

New features

• Provide scripts to create ElasticBLAST janitor role in AWS
• Search for canonical ElasticBLAST janitor role in AWS to enable its functionality
• Validate CSP region

Improvements

• Improve error message when ElasticBLAST Janitor in GCP cannot run due to missing permissions
• Provide error messages when invalid BLAST+ options are specified
• Disable auto-upgrade in GKE clusters
• Improved batch-len defaults
• Restore janitor in AWS

Bug fixes

• Additional fix for GCP disk leak: wait for PV to unmount when jobs are still running

- Python
Published by christiam about 4 years ago

elastic-blast -

New features

• Job submission on the cloud for GCP
• Auto-shutdown for AWS
• Add programmatic SSD quota check

Improvements

• elastic-blast automatically sets memory-limit(s) by default
• Make cleanup-stale-gcp-resources.py public
• Change batch-length on the fly if number of query batches is less than number possible BLAST parallel jobs
• Run summary retrieves paginated results, tracks all runtimes, speed collection improved (letters/sec/CPU)

Bug fixes

• Autoscaling while job submission is taking place may lead to kubectl disconnects

- Python
Published by christiam about 4 years ago

elastic-blast -

New features

• Job submission on the cloud for AWS

Improvements

• Elastic-blast disallows use of ARM instances
• Program = megablast is no longer allowed

- Python
Published by christiam about 4 years ago

elastic-blast -

New features

• Automatic shutdown for GCP
• Cloud query splitting for GCP implemented
• Cloud query splitting for GCP and AWS enabled by default

Improvements

• Blast tuner - memory split based on number of jobs per node (defined by CPU allocation)
• Code refactoring to provide homogeneous handling of GCP and AWS execution
• Simplified run summary user interface
• More solid run summary data handling

Bug fixes

• Fixed negative values in run summary
• Fixed run summary exceptions
• Fixed apparent disk leaks for GCP

- Python
Published by christiam about 4 years ago

elastic-blast -

Improvements

• Documentation includes installation from PyPI and BioConda
• blast-tuner incorporates new mt_mode=1 guidance
• blast-tuner recommends only a subset of all available AWS instance types

- Python
Published by christiam about 4 years ago

elastic-blast -

Improvements

• ncbi/elb docker image is now pulled from GCR and ECR repositories
• ElasticBLAST reports misspelled and misplaced config parameters
• Default number of CPUs is now 16 or the number of available CPUs
• Custom search tags are added to default ones
• Default disk size for AWS is now 1T

Bug fixes

• blast-tuner.py no longer reports aws-region for a GCP search
• blast-tuner.py recommends AWS instance types from M5, C5, and R5 families only

- Python
Published by christiam about 4 years ago

elastic-blast -

New features

• Upgrade to BLAST+ 2.12.0
• Experimental 2-stage cloud query split
• Record configuration in results bucket metadata
• Stress test added
• ElasticBLAST is available from PyPI and BioConda now

Improvements

• blast-tuner uses mem-limit and machine-type suggestions based on BLASTDB metadata
• OutOfMemoryError bug handled systematically

- Python
Published by christiam about 4 years ago

elastic-blast -

New features

• Implement tool to create BLASTDB metadata
• Distribute ElasticBLAST on PyPI.org: https://pypi.org/project/elastic-blast/0.1.4/

Improvements

• Add negative_taxidlist support to ElasticBLAST
• Use autoscaling by default for ElasticBLAST on GCP

Bug fixes

• Detect unbalanced quotation marks in BLAST options and report error

- Python
Published by christiam about 4 years ago

elastic-blast -

Improvements

• Added verbose option for elastic-blast status
• Selection of MT mode, number of CPUs and batch length in blast-tuner
• Elastic-blast can use instances with local SSD in AWS
• Elastic-blast works with "optimal" instance type in AWS
• Creation of PEX files on github
• Resubmission of an elastic-blast search elicits an error message

Bug fixes

• Cleaning of query batches on local machine's /tmp directory

- Python
Published by christiam about 4 years ago

elastic-blast -

Improvements

• Output file names unified over GCP and AWS versions

Bug fixes

• Retry logic implemented to handle database download errors and job structural timeouts

- Python
Published by christiam about 4 years ago