Update "Download and Extract Reads in X format from NCBI SRA" tools

[jennaj]

MTS Repo (updated 2019-09-10): https://toolshed.g2.bx.psu.edu/view/iuc/sra_tools/f5ea3ce9b9b0

Tools at usegalaxy.org to update to version 2.10.4

• Download and Extract Reads in BAM format from NCBI SRA (Galaxy Version 2.9.1.4)
• Download and Extract Reads in FASTA/Q format from NCBI SRA (Galaxy Version 2.9.1.3)

Questions @mvdbeek @nekrut @natefoo

1. Do not install the Download and Generate Pileup Format if these are still true? #181 && galaxyproject/tools-iuc#2171

2. Not sure if the new Faster Download and Extract Reads in FASTQ tool is appropriate or not for usegalaxy.org. Appears to require additional dependencies/configuration that are not installed as part of the repo. May also be confusing for end-users to have two options for FastQ data download.

[jennaj]

Tools suite updated (four tools).

Included "Faster Download" (new, extremely interesting output structure) and "Pileup" (previously removed from ORG, on purpose)

Testing at ORG

• History: https://usegalaxy.org/u/jen/h/test-history-ncbi-tools---sra
• Fails, looks like during prefetch step: Download and Extract Reads in FASTA/Q format from NCBI SRA (Galaxy Version 2.10.4)
• All other tools worked

Testing at EU, for comparison

• History: https://usegalaxy.eu/u/jenj/h/test-history-ncbi-tools---sra---2104-version-update-in-1909-pre-release
• All tools worked

[jennaj]

Re-test for Download and Extract Reads in FASTA/Q format from NCBI SRA (Galaxy Version 2.10.4) was successful and Jenkins tests passed.

Closing & thanks to whoever helped fixed the problem.

[jennaj]

Note to end-users:

Included in this update was the tool "Download and Generate Pileup Format". It is known to be unreliable and may be removed.

A better path is to download the fastq, map the data yourself, and call variants. 

Or, if the BAM exists, you could download that but you won't really know how the mapping was done, or it may just contain sequences. Most Galaxy tools will need a fastq (specifically, "fastqsanger") formatted dataset as an input. This means downloading the BAM only to then need to extract the fastq sequence, which will use up more of your quota space.

Pileup results are even one more step removed, do not exist for all accessions, and you won't know how the data was mapped or how pileup was run.

Galaxy Tutorials, see the "Variant Analysis" tool group. https://training.galaxyproject.org/

Galaxy FAQs, start here: https://galaxyproject.org/support/#troubleshooting