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The goal is to be able to submit a table with metadata, or a list of accession numbers to a Galaxy instance. This can be accomplished by adding a button to send the current table or just the accession…
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Hello
Would it be possible that the downloading process generate fastq.gz files instead of fastq ?
I know that there is an option that can delete later those files but in the mean time it can take a…
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This is a far-in-the-future goal, and will probably use https://github.com/maxogden/dat and the [bionode](https://github.com/bionode/) toolkits:
- https://github.com/bionode/bionode-sra
- https://git…
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For #133 we use SRA as one of our sources. Optimizing our license for re-use would be greatly aided by having a summarized grade for NCBI's SRA.
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### Description of feature
Hi,
In SRA some of the run accessions have no associated files.
For example bioproject [`PRJEB18755`](https://www.ncbi.nlm.nih.gov/Traces/study/?query_key=1&WebEnv=MC…
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This looks like a more stable alternative https://github.com/saketkc/pysradb
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A script that downloads SRA entries so that a user can just specify taxa X, Y, and Z
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## Expected Behavior
Generating an SRA client from the SRA spec should produce a client that can properly validate its inputs.
## Current Behavior
Generating an SRA clie…
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We could benefit from downloading and formatting SRA accessions provided as input, to normalize also public available data. Exploring the SRA handling from htsjdk will help to improve it.
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### Download from SRA
Add a command-line option to pull FastQ files from SRA using `fastq-dump`.
It is worth stating that `fastq-dump` may be depreciated in the near future so it may be worth us…