aws-sdk
htslib
aws-sdk | htslib | |
---|---|---|
10 | 7 | |
64 | 775 | |
- | 1.5% | |
3.9 | 8.9 | |
3 months ago | 3 days ago | |
C | ||
GNU General Public License v3.0 or later | GNU General Public License v3.0 or later |
Stars - the number of stars that a project has on GitHub. Growth - month over month growth in stars.
Activity is a relative number indicating how actively a project is being developed. Recent commits have higher weight than older ones.
For example, an activity of 9.0 indicates that a project is amongst the top 10% of the most actively developed projects that we are tracking.
aws-sdk
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AWS SDK v3 + DAX
From this GitHub issue and this one from 2021 it seems like AWS just doesn't care about this - so, asking here if anyone knows of a workaround (other than "just keep using v2"... that's not a long-term solution), or if any AWS devs can shed some light on the situation.
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The Truth About CloudWatch Pricing
AWS SDKs
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Amazon ECS Exec to access your Windows containers on Amazon EC2 and AWS Fargate
Please note that ECS Exec is supported via AWS SDKs, AWS CLI, as well as AWS Copilot. In the future, we will enable this capability in the AWS Console. Also, this feature only supports Linux containers (Windows containers support for ECS Exec is not part of this announcement).
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Using AWS for Text Classification Part-1
Set up the AWS CLI and AWS SDKs.
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Tips for scalable workflows on AWS
One common pattern to integrate with AWS from a workflow job is to call additional services using the AWS CLI. Overall, this works well, but there are a few considerations one should note when doing so. First and foremost, a workflow job needs to know where the AWS CLI installed and how to use it. You can do this by either installing the AWS CLI on the host compute and bind mounting it into the container job, or including the AWS CLI as part of the container image. That said, see my notes above on keeping container images small for associated caveats. Second, while the AWS CLI is great for scripting, for more complex operations direct integration via the AWS SDK is a better fit.
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Waiting for things to happen and paginating responses with boto3
I like how you can imagine what the Python implementation that uses this looks like from this structure. If there are no waiters for what you need, you can create an Issue in the AWS SDK repository because the service teams provide those. I tried that for DynamoDB Streams, and I'm curious to see how long it will take them to add that.
- Will AWS SDKs make Terraform useless in the future?
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Sending Emails with SES, Terraform and TypeScript
Amazon Simple Email Service (SES) is a serverless service for sending emails from your applications. Like other AWS services, you can send emails with SES using the AWS REST API or the AWS SDKs. In this article, I want to look at how to send emails using SES with TypeScript specifically.
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The Evolution of AWS from a Cloud-Native Development Perspective: Serverless, Event-Driven, Developer-Friendly, Sustainable
In 2002, Jeff Bezos's so-called API Mandate forced all Amazon teams to expose their data and functionality through service interfaces. Amazon has built AWS around the same principles: every service is programmatically controllable, from starting a virtual machine to accessing a satellite. While this is an essential property of an effective cloud platform, it is not necessarily developer-friendly. By now, AWS has incrementally and significantly improved in this space. Besides using their APIs, we can control services and infrastructure with a unified Command Line Interface (CLI), Software Development Kits (SDK), CloudFormation, and, since July 2019, the AWS Cloud Development Kit (CDK). The CDK had a massive impact on developer productivity and satisfaction. While teams could already access and control services and infrastructure using the AWS SDK and their favorite programming language, infrastructure was primarily defined using incredible amounts of mostly punctuation marks and whitespace, also known as YAML or JSON. CDK — initially only flavored TypeScript and Python — finally gave developers an AWS-native means to define Infrastructure as actual Code. Since its introduction, AWS has added support for more languages, like Java, C#, and Go.
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AWS SSO integration with G suite
Yes, no AWS api to create users/groups: https://github.com/aws/aws-sdk/issues/25
htslib
- Gentoo -Os vs -O3 application startup time?
- Does anyone know of a repository for actual genetic data?
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Pigz: A parallel implementation of gzip for multi-core machines
There is another nice multi-core gzip based library called BGZF[1]. It is commonly used in bioinformatics. BGZF has the added advantage that it is block compressed with built in indexing method to permit seeking in compressed files.
[1] https://github.com/samtools/htslib
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Tips for scalable workflows on AWS
In contrast, processing can start immediately and only transfer what is necessary if tooling can read bytes of data directly from Amazon S3. Tools based on htslib can do this, so you can run something like:
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Software Development Project
Another idea is add in reading cloud data natively e.g. htslib which samtools relies on can read s3 directly. https://github.com/samtools/htslib
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Interested in Bioinformatics / C pair-programming opportunity / learning / portfolio project.
Greetings! I'm a bioinformatics software dev in San Francisco and I'm looking for others interested in working on a high-performance genetic data analysis project. The project is in C, using https://github.com/samtools/htslib.
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ffi-bitfield
I'm working on a bioinformatics-related binding called ruby-htslib. htslib makes heavy use of bit fields throughout the library, so supporting bit fields is inevitable.
What are some alternatives?
botocore - The low-level, core functionality of boto3 and the AWS CLI.
genozip - A modern compressor for genomic files (FASTQ, SAM/BAM/CRAM, VCF, FASTA, GFF/GTF/GVF, 23andMe...), up to 5x better than gzip and faster too
amazonka - A comprehensive Amazon Web Services SDK for Haskell.
seqtk - Toolkit for processing sequences in FASTA/Q formats
amazon-sagemaker-examples - Example 📓 Jupyter notebooks that demonstrate how to build, train, and deploy machine learning models using 🧠 Amazon SageMaker.
bwa-mem2 - The next version of bwa-mem
serverless-haskell - Deploying Haskell applications to AWS Lambda with Serverless
cyvcf2 - cython + htslib == fast VCF and BCF processing
aws-route53 - A Haskell AWS Route53 client library
aws-genomics-workflows - Genomics Workflows on AWS
libdna - ♥ Essential Functions for DNA Manipulation