epam / epam/cloud-pipeline

SRA integration for data transfer automation

Open
#299 0 comments 0 reactions 1 assignee Claimed by @rodichenko View on GitHub
kind/enhancement priority/low sys/core sys/gui
Dominant language
Java
Stars
163
Forks
65
Avg merge
11h 46m
Merged PRs (30d)
29

Description

**GUI**
1. Add a new parameter type "SRA Run Accesion ID"
2. Such parameter shall shown as a `string` param but validated using `SRR` accession naming scheme
3. When a run is launched - it shall be set as an `input` parameter

**SRA Toolkit**
1. Add the [ncbi/sra-tools](https://github.com/ncbi/sra-tools) binaries to the distribution bucket at `cloud-pipeline-oss`
2. Add installation/configuration steps to the `launch.sh` dependencies installation

**Data localization**
1. Tune the localization logic to parse `SRR` accession naming scheme
2. If `SRR` ID is matched - fetch and unpack data using [ncbi/sra-tools](https://github.com/ncbi/sra-tools)
3. Resulting FASTQ/Contents directories locations shall be exported to the environment variables. Original parameter name/value shall be persisted

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