ornl-oxford genben issues

ornl-oxford / genben

Benchmarking of software frameworks, and systems for storage and compute over large-scale genomic data.

MIT License

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issues

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PCA Benchmark: Dask Array Improvements & Allow All Variants to be Included

#50 eauel closed 5 years ago
0
Multiple Data Set Concatenation

#49 eauel closed 5 years ago
0
Add Configuration Options for Dask Scheduler Connection

#48 eauel closed 5 years ago
1
Add Configuration Options to PSV/CSV Output and Add InfluxDB Output Option

#47 eauel closed 5 years ago
0
Make LD Pruning Optional

#46 eauel closed 5 years ago
0
Ability to Limit Number of Variants and Samples for Allele Count and PCA Benchmarks

#45 eauel closed 5 years ago
0
Standardize Genotype Array Between Different Benchmarks

#44 eauel closed 5 years ago
0
Publish paper describing the benchmark and the results

#43 ebegoli opened 5 years ago
6
Data Service: Fix AttributeError when Performing VCF to Zarr Conversion

#42 eauel closed 5 years ago
1
[scikit-allel] Missing attributes DEFAULT_CHUNK_LENGTH and DEFAULT_CHUNK_WIDTH (scikit-allel 1.2.0)

#41 eauel closed 5 years ago
2
Catch Error When Running Unit Tests on new Travis CI Virtual Machines

#40 eauel closed 5 years ago
0
[PCA] Cannot Use LD Pruning with GenotypeDaskArray

#39 eauel opened 6 years ago
1
Implement Benchmark for PCA

#38 eauel closed 5 years ago
1
Change VCF dataset used in unit tests for data_service

#37 eauel closed 5 years ago
0
Implement Benchmark for Simple Aggregations

#36 eauel closed 5 years ago
0
Bugfix: Fix ValueError bug

#35 eauel closed 6 years ago
0
VCF to Zarr Conversion Fails When Attempting to Convert Certain VCF files

#34 eauel closed 6 years ago
5
Add Travis CI (Continuous Integration)

#33 eauel closed 5 years ago
1
[VCF to Zarr] Expose alt_number, chunk_length, and chunk_width as Configuration Options

#32 eauel closed 6 years ago
3
[VCF to Zarr] Expose alt_number, chunk_length, and chunk_width as Configuration Options

#31 eauel closed 6 years ago
0
Structure Project for setuptools and Expand Backwards Compatability

#30 eauel closed 5 years ago
4
Implement Benchmark Process

#29 eauel closed 5 years ago
4
Implement VCF to Zarr Conversion

#28 eauel closed 6 years ago
2
Implement FTP Downloading via Setup Command

#27 eauel closed 6 years ago
0
Config File Reading & Separation of CLI code from Config File Code

#26 eauel closed 6 years ago
1
Update project environment, default config file, and AUTHORS

#25 eauel closed 6 years ago
2
Added pull of small, dedicated VCF files into unit tests from the test FTP server.

#24 ebegoli opened 6 years ago
1
Implement a Zarr conversion

#23 ebegoli closed 6 years ago
0
Upgrade everything on the project for Python 3.5+

#22 ebegoli closed 5 years ago
0
Implemented a CLI, data service and unit test set.

#21 ebegoli closed 6 years ago
0
Implement a CLI option to generate a default benchmark configuration file.

#20 ebegoli closed 6 years ago
1
Fast forwarding the branch.

#19 ebegoli closed 6 years ago
0
Added CLI support in support of the issue #5.

#18 ebegoli closed 6 years ago
0
Implemented CLI argument parsing, and related unit tests.

#17 ebegoli closed 6 years ago
0
Establishment of the project structure, and general root level files for CI, unit testing, deployment.

#16 ebegoli closed 6 years ago
0
Simple aggregations example notebook

#15 alimanfoo closed 6 years ago
0
Setup project continuous integration with github webhooks.

#14 ebegoli closed 5 years ago
0
Setup project for automated and standardized testing via tox.

#13 ebegoli opened 6 years ago
0
Structure project for setuptools.

#12 ebegoli closed 5 years ago
0
Implement configuration options for Dask scheduler.

#11 ebegoli closed 5 years ago
0
Implement configuration options for how Zarr data is stored.

#10 ebegoli closed 6 years ago
0
Implement recording of the benchmark results.

#9 ebegoli closed 5 years ago
0
Implement the timer recording.

#8 ebegoli closed 5 years ago
0
Implement a configuration file reading, and use to control the execution.

#7 ebegoli closed 5 years ago
0
Implement a ftp pull for the benchmark data.

#6 ebegoli closed 6 years ago
1
Implement CLI interface and argument parser for the benchmark

#5 ebegoli closed 6 years ago
1
Added an outline.

#4 ebegoli closed 6 years ago
0
Develop a benchmark for Principal Components Analysis (PCA) -- master issue

#3 ebegoli closed 5 years ago
0
Develop a benchmark for simple aggregations over genotype data -- master issue

#2 ebegoli closed 5 years ago
1
VCF to Zarr example

#1 alimanfoo closed 6 years ago
2