ababaian/serratus issues and pull requests

#280 - rdrp5?

Issue - State: open - Opened by dhoconno 19 days ago - 1 comment

#100 - Incorporate CheckV for assessing binned viral genomes

Issue - State: closed - Opened by taltman over 4 years ago - 1 comment

#99 - Assembly QC by aligning reads to contigs

Issue - State: closed - Opened by rcedgar over 4 years ago - 2 comments

#98 - Update Summarizer in Production

Issue - State: closed - Opened by ababaian over 4 years ago - 2 comments

#97 - Digital kmer-based normalization

Issue - State: closed - Opened by taltman over 4 years ago - 16 comments

#96 - Sus scrofus samples with high or low virus abundance

Issue - State: closed - Opened by taltman over 4 years ago - 8 comments

#95 - Use human cell line samples with coronavirus DNA for developing benchmarking datasets

Issue - State: closed - Opened by taltman over 4 years ago - 2 comments

#94 - Reference-guided assembly pipeline

Issue - State: closed - Opened by taltman over 4 years ago - 4 comments

#93 - Incorporate auN metric from Heng Li

Issue - State: closed - Opened by taltman over 4 years ago - 3 comments

#92 - Make sure BCB2 team is on-boarded

Issue - State: closed - Opened by taltman over 4 years ago - 4 comments

#91 - Identify desired assembler output

Issue - State: closed - Opened by taltman over 4 years ago - 3 comments

#90 - Identify candidate read QC pipelines

Issue - State: closed - Opened by taltman over 4 years ago - 1 comment

#89 - Top candidates from first Zoonotic run for assembler testing

Issue - State: closed - Opened by rcedgar over 4 years ago - 27 comments

#88 - Disruption of write access to s3://serratus-public

Issue - State: closed - Opened by ababaian over 4 years ago
Labels: bug, AWS

#87 - Serratus mission statement

Issue - State: closed - Opened by rcedgar almost 5 years ago - 11 comments

#86 - State of Assembly

Issue - State: closed - Opened by ababaian almost 5 years ago - 13 comments
Labels: enhancement, Bioinformatics

#85 - Scheduler instance boot failure

Issue - State: closed - Opened by ababaian almost 5 years ago - 6 comments
Labels: bug, AWS

#84 - Datasets in 200505_zoonotic with human hosts?

Issue - State: closed - Opened by rcedgar almost 5 years ago - 3 comments

#83 - Run Meta-data and Organization

Issue - State: closed - Opened by rcedgar almost 5 years ago - 16 comments
Labels: AWS

#82 - Add indices to frequently queried columns in the scheduler.

Pull Request - State: closed - Opened by brietaylor almost 5 years ago

#81 - Increase the autoscaling desired size gradually, plus metrics improvements

Pull Request - State: closed - Opened by brietaylor almost 5 years ago

#80 - v0.1.4b hotfix

Pull Request - State: closed - Opened by ababaian almost 5 years ago

#79 - Regional blacklist

Issue - State: closed - Opened by rcedgar almost 5 years ago - 2 comments
Labels: enhancement, Bioinformatics

#78 - Tracking and processing of putative detections

Issue - State: closed - Opened by rcedgar almost 5 years ago - 1 comment
Labels: enhancement, Bioinformatics

#77 - Reference-based assembly

Issue - State: closed - Opened by rcedgar almost 5 years ago - 7 comments
Labels: Bioinformatics

#76 - cov3r pan-genome refinements

Issue - State: closed - Opened by ababaian almost 5 years ago - 7 comments

#75 - Serratus v0.1.4 Production

Pull Request - State: closed - Opened by ababaian almost 5 years ago

#74 - Scheduler autoscaling

Pull Request - State: closed - Opened by ababaian almost 5 years ago

#73 - Scheduler autoscaling --- big changes don't pull unless you're ready

Pull Request - State: closed - Opened by brietaylor almost 5 years ago - 1 comment

#72 - Assembler benchmarking

Issue - State: closed - Opened by rcedgar almost 5 years ago - 7 comments
Labels: enhancement, good first issue, Bioinformatics

#71 - List of assemblers -- please contribute!

Issue - State: closed - Opened by rcedgar almost 5 years ago - 42 comments
Labels: good first issue, Bioinformatics

#70 - Scale-in capability

Pull Request - State: closed - Opened by ababaian almost 5 years ago - 1 comment

#69 - Usability Improvements to Scheduler #1

Pull Request - State: closed - Opened by brietaylor almost 5 years ago

#68 - Infrastructure QoL Changes

Pull Request - State: closed - Opened by brietaylor almost 5 years ago

#67 - bwa integration into serratus

Pull Request - State: closed - Opened by ababaian almost 5 years ago

#66 - Add ECS Instance Role to monitor terraform

Pull Request - State: closed - Opened by ababaian almost 5 years ago - 2 comments

#65 - Assembly protocol of COV sequences

Issue - State: closed - Opened by JustinChu almost 5 years ago - 3 comments

#64 - Updates for cov3r pan-genome

Issue - State: closed - Opened by rcedgar almost 5 years ago - 20 comments
Labels: enhancement, Bioinformatics

#63 - Add download retry - `fastq-dump` timeout error 3

Issue - State: closed - Opened by ababaian almost 5 years ago - 1 comment
Labels: bug, BASH, Bioinformatics, Priority: High

#62 - Initial commit of bin/ and bin/bvfilter

Pull Request - State: closed - Opened by rcedgar almost 5 years ago

#61 - Genbank parser dev

Pull Request - State: closed - Opened by Bdegraaf1234 almost 5 years ago - 10 comments

#60 - Update documentation

Pull Request - State: closed - Opened by mathemage almost 5 years ago - 4 comments
Labels: bug, AWS, Docker, BASH

#59 - Initial commit of summarizer

Pull Request - State: closed - Opened by rcedgar almost 5 years ago - 15 comments

#58 - Repository Re-organization

Pull Request - State: closed - Opened by ababaian almost 5 years ago - 4 comments

#57 - Summarizer implementation

Issue - State: closed - Opened by rcedgar almost 5 years ago - 10 comments
Labels: enhancement, Bioinformatics

#56 - Update benchmarking script with new CLI

Pull Request - State: open - Opened by victorlin almost 5 years ago - 7 comments

#55 - Search the Zoonotic Reservoir for SARS-CoV-2

Issue - State: closed - Opened by ababaian almost 5 years ago - 2 comments
Labels: Priority: High, RUN

#54 - Testing bvfilter

Issue - State: closed - Opened by rcedgar almost 5 years ago - 2 comments
Labels: enhancement, Bioinformatics

#53 - Create S3 VPC endpoint

Issue - State: closed - Opened by Bluestreak2k5 almost 5 years ago - 5 comments
Labels: enhancement, AWS, Terraform

#52 - AWS architecture Diagrams

Issue - State: closed - Opened by Bluestreak2k5 almost 5 years ago - 1 comment

#51 - bvfilter bugs & fixes

Issue - State: closed - Opened by rcedgar almost 5 years ago - 3 comments
Labels: bug, Bioinformatics

#50 - To pair or not to pair

Issue - State: closed - Opened by rcedgar almost 5 years ago - 1 comment
Labels: Bioinformatics

#49 - Why just Cov?

Issue - State: closed - Opened by rcedgar almost 5 years ago - 3 comments
Labels: enhancement

#48 - Perform CoV Cross-validation (hold-out)

Issue - State: closed - Opened by rcedgar almost 5 years ago - 1 comment
Labels: Bioinformatics

#47 - Blacklist implementation

Issue - State: closed - Opened by rcedgar almost 5 years ago - 3 comments
Labels: enhancement, Bioinformatics

#46 - Preserving full headers in pan-genome

Issue - State: closed - Opened by rcedgar almost 5 years ago - 7 comments
Labels: enhancement, Bioinformatics

#45 - Taxonomy identifiers for Cov reference database

Issue - State: closed - Opened by rcedgar almost 5 years ago - 13 comments
Labels: enhancement, Bioinformatics

#44 - Max RAM in EC2 compute nodes

Issue - State: closed - Opened by rcedgar almost 5 years ago - 1 comment

#43 - Learning how to work with serratus repo

Issue - State: closed - Opened by rcedgar almost 5 years ago - 5 comments

#42 - What data should be collected from first pass (the "big compute")

Issue - State: closed - Opened by rcedgar almost 5 years ago - 5 comments

#41 - cov2 pan-genome refinements

Issue - State: closed - Opened by ababaian almost 5 years ago - 9 comments

#40 - Check updated Automation of project `TODO List`

Issue - State: closed - Opened by mathemage almost 5 years ago - 1 comment
Labels: enhancement, Github

#39 - Aggreggate Stats by ASG in Prometheus / Grafana

Issue - State: closed - Opened by brietaylor almost 5 years ago - 1 comment
Labels: enhancement

#38 - Implement a "Jump Server" for serratus

Issue - State: closed - Opened by brietaylor almost 5 years ago - 1 comment
Labels: enhancement, AWS

#37 - serratus-dl: Out of disk usage error

Issue - State: closed - Opened by ababaian almost 5 years ago
Labels: bug, AWS

#36 - cov1 Multiple Sequence Alignment

Issue - State: closed - Opened by ababaian almost 5 years ago - 9 comments
Labels: Bioinformatics

#35 - Hard Optimize `bowtie2` alignment parameters

Issue - State: closed - Opened by ababaian almost 5 years ago - 3 comments
Labels: optimization, Bioinformatics

#34 - include "WGS" in "Assay Type" field from SRA

Issue - State: closed - Opened by charlescongxu almost 5 years ago
Labels: enhancement, Bioinformatics

#33 - fatal error: unable to locate credentials

Issue - State: closed - Opened by brietaylor almost 5 years ago - 6 comments
Labels: bug, AWS, Priority: High

#32 - Error: No more processes: cannot run a single job.

Issue - State: closed - Opened by brietaylor almost 5 years ago - 4 comments
Labels: bug, Priority: High

#31 - Add ecsInstanceRole to terraform

Issue - State: closed - Opened by brietaylor almost 5 years ago - 1 comment
Labels: bug, Terraform

#30 - Allow adding public keys to terraform config

Issue - State: closed - Opened by brietaylor almost 5 years ago - 2 comments
Labels: enhancement, Terraform, Sunset

#29 - Refactor worker nodes into ECS

Issue - State: closed - Opened by brietaylor almost 5 years ago
Labels: enhancement, Terraform

#28 - Migrate `serratus-public` to US-East-1

Issue - State: closed - Opened by ababaian almost 5 years ago - 1 comment
Labels: bug, AWS

#27 - Benchmarking statistics for divergence simulation tests

Issue - State: closed - Opened by victorlin almost 5 years ago - 28 comments
Labels: BASH, Bioinformatics, Python

#26 - Unexpectedly high PUT/LIST usage on S3

Issue - State: closed - Opened by brietaylor almost 5 years ago - 2 comments
Labels: bug, AWS

#25 - Add `Homebrew` to base Serratus container

Issue - State: closed - Opened by ababaian almost 5 years ago
Labels: enhancement, good first issue, Docker

#24 - Explore Nextflow as an Alternative Architecture

Issue - State: closed - Opened by brietaylor almost 5 years ago - 4 comments
Labels: enhancement, AWS

#23 - Testing how divergence of CV genomes affects bloom filter homology detection

Issue - State: closed - Opened by emreerhan almost 5 years ago
Labels: documentation, Bioinformatics

#22 - `Serratus` CLI front-end wrapper script

Issue - State: open - Opened by ababaian almost 5 years ago
Labels: enhancement, BASH

#21 - Update readme

Pull Request - State: closed - Opened by victorlin almost 5 years ago
Labels: documentation

#20 - S3 Tier1 Requests are 5x higher than expected

Issue - State: closed - Opened by brietaylor almost 5 years ago - 3 comments
Labels: duplicate, AWS

#19 - Automatically spin down when finished

Issue - State: closed - Opened by brietaylor almost 5 years ago - 4 comments
Labels: enhancement, AWS, Python

#18 - Write a script to copy outputs

Issue - State: closed - Opened by brietaylor almost 5 years ago - 2 comments
Labels: enhancement, BASH, Terraform

#17 - Simulated test set using a baseline human transcriptome

Issue - State: closed - Opened by mathemage almost 5 years ago
Labels: Bioinformatics, Priority: High

#16 - Annotated list of SRA libraries with known Coronaviruses

Issue - State: closed - Opened by mathemage almost 5 years ago - 14 comments
Labels: documentation, question, Bioinformatics

#15 - Software implementations of `Bloom Filters`

Issue - State: closed - Opened by mathemage almost 5 years ago - 7 comments
Labels: documentation, optimization, Docker, Bioinformatics

#14 - `BLAST` containers

Issue - State: closed - Opened by mathemage almost 5 years ago - 2 comments
Labels: documentation, optimization, Docker, Priority: High

#13 - `serratus-align` into AWS Lambda

Issue - State: closed - Opened by mathemage almost 5 years ago - 3 comments
Labels: question, optimization, AWS, Bioinformatics, Priority:Low

#12 - `bam` and `fastq` files via `fusera`

Issue - State: closed - Opened by mathemage almost 5 years ago - 7 comments
Labels: enhancement, question, optimization

#11 - Improve monitoring with Grafana / Prometheus

Issue - State: closed - Opened by brietaylor almost 5 years ago - 1 comment
Labels: Terraform

#10 - Improve the HTML status page

Issue - State: closed - Opened by brietaylor almost 5 years ago - 4 comments
Labels: enhancement, good first issue, Python, HTML, R/Shiny, Sunset

#9 - Instance doesn't signal the scheduler when shutting down

Issue - State: closed - Opened by brietaylor almost 5 years ago - 12 comments
Labels: bug, AWS, Docker, BASH, Priority: High

#8 - Port/test `serratus-dl` and `serratus-align` containers to ARM (a1.instance)

Issue - State: closed - Opened by mathemage almost 5 years ago - 15 comments
Labels: optimization, Priority:Low, Sunset

#7 - Write a performance / cost simulation for autoscaling

Issue - State: closed - Opened by brietaylor almost 5 years ago - 5 comments
Labels: question, optimization, AWS, Python, Priority:Low

#6 - Do a price comparison for serratus-dl between using C5.large and i3.large instances

Issue - State: closed - Opened by brietaylor almost 5 years ago - 2 comments
Labels: Priority:Low

#5 - TODO List

Issue - State: closed - Opened by ababaian almost 5 years ago - 11 comments
Labels: good first issue

GitHub / ababaian/serratus issues and pull requests