Questions tagged [aws]
Acronym for Amazon Webservices
6
questions
2
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1
answer
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Error Registering Job Definition AWS
I am in the process of creating a bioinformatics pipeline and I am currently trying to setup the AWS infrastructure for which it will run.
The script I am running to setup the AWS batch job looks like ...
- 101
0
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0
answers
108
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Why is bcl2fastq2 taking so long to calculate stats?
Our lab has been using bcl2fastq v2.20.0.422 to demultiplex RNA-seq data sequenced on an Illumina Novaseq machine on a beefy EC2 instance and we've run into the strange problem: namely that while ...
- 101
2
votes
1
answer
146
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How does cromwell and AWS batch decide which compute environment (on-demand or spot) to use?
For processing genomics workflows I make use of widdle and cromwell with an AWS back-end. I have followed all examples on the AWS cromwell tutorial. In my AWS batch console I can see there are 2 job ...
- 21
0
votes
1
answer
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Pointing Cromwell to local EBS mounted storage on AWS Batch
I'm trying to run the WDL tasks from the GTEx RNA-Seq pipeline with Cromwell using AWS Batch as a backend.
I store the STAR alignment index on an Elastic Block Store since my Cromwell server instance ...
- 105
3
votes
1
answer
2k
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Downloading SRA Files from AWS
I want to download the original BAM files that the authors had uploaded to SRA. Normally, I would just use sam-dump, but the files are having issues that seem ...
- 621
2
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3
answers
525
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Accessing .bam/.cram files from AWS S3?
What's the best/easiest way for accessing .bam/.cram files from S3?
I have .bam/.bai .cram/.crai and .bed + .gff files that I want to make available easily to others so they can browse in IGV and ...
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