Installing tools and creating indexes with data managers

#1

I uploaded a fasta sequence of a genome to my history.
I installed data manager bwa mem index builder.
I can see the tool under Admin–> manage tools however in the Analyze Data tab, when I search bwa I do not see my tool, did I not install it properly?

I notice that the Analyze Data tool is missing many of the tools from the usegalaxy.org, I would eventually like to install the tools I need so that I have access to them in the Analyze Data and Workflows.

I see I can still have access to the tool through Admin --> local data however it does not seem to recognize the fasta sequence in my history as the field “source fasta sequence” says no options available?

Thank you

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#2

You are on the right path. The data managers are admin only tools so they will never show in the tool panel under ‘analyze data’ - you access them through the admin panel, as you found out.

it does not seem to recognize the fasta sequence

make sure your dataset format is fasta, maybe it was wrongly set or detected, you can always change the datatype by clicking on the pencil icon of dataset and directly entering the datatype you know

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#3

FAQ: https://galaxyproject.org/support/#getting-inputs-right

#4

Hello,

Thank you, I see other tools I installed are available in the Analyze Data tab.

I did ensure it was fasta format, I checked the dataset type, it still does not recognize? I have bwa installed, as this is a requirement. I have tried re-starting since installing the tools.

#5

Other tools in the Analyze Data tab can recognize the file, so I am assuming it is a problem with Data Managers not recognizing the dataset

#6

I used the Data Manager “Create DBKey and Reference Genome Fetching” to upload fasta file directly from NCBI, and now the BWA Index will recognize that fasta file.

Parameters for fetching: I used existing DB key (species name), input NCBI accession number and sort chromosomes “As is”

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#7

Using an existing dbkey can create mismatch problems. Species is not a close enough match, the genome build/version should also be a match.

This prior Q&A explains the problem/solution for another user that ended up with a mismatched dbkey: BamLeftAlign error unable to find fasta index -- use "fasta" version of genome or natively indexed genome