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Prepare Metavisitor Galaxy instance for analyses

Once you know how to access to your Metavisitor Galaxy instance with a web browser and are able to perform basic start/stop/restart operations, there is still some work needed to import and configure reference data (reference genomes and databases) so that they are directly available to all Galaxy users for running tools and workflows.

Here we provide the step-by-step description of what we did to prepare our Metavisitor instance before performing the analyses described here.

1. Connect to your Metavisitor Galaxy admin account with your web browser

2. Import reference data in an history "References"

At first, you need to import and prepare the reference datasets you will need for most of the Metavisitor analyses. As a Galaxy admin you will make latter some of these references directly accessible to the Galaxy tools, and/or accessible to any other users by putting them in a Galaxy public library.

a. Preliminary actions

  • Click on the Analyze Data menu
  • rename the Unnamed history to References

b. Upload nucleotide vir2 fasta file

  • Click on the upload_button button on top of the tool bar (left handside of the Galaxy interface)
  • In the open window, click on the Rule-based tab rule-based
  • Make sure "Upload data as:" is set to datasets and "Load tabular data from:" is set to Pasted Table
  • Copy - paste the following table (not including the header)
Name URL
nucleotide vir2 https://ndownloader.figshare.com/files/11005121
protein vir2 https://ndownloader.figshare.com/files/11005124
dm6 ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r6.10_FB2016_02/fasta/dmel-all-chromosome-r6.10.fasta.gz
AgamP4 https://www.vectorbase.org/sites/default/files/ftp/downloads/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4.fa.gz
P. berghei ftp://ftp.ensemblgenomes.org/pub/release-28/protists/fasta/plasmodium_berghei/dna/Plasmodium_berghei.May_2010.28.dna_sm.genome.fa.gz
hg38 ftp://ftp.ensembl.org/pub/release-84/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz
  • Click on the Build button on the bottom right
  • Click on the + Rules button on the bottom left rules
  • Select Add / Modify Column Definitions from the list
  • Click the + Add Definition button, then select Name from the list and set column "A" as Name column
  • Click the + Add Definition button, select URL and set the "B" column as URL column
  • Click the Apply button. Finally click the Upload button in the bottom right

The reference genomes should be uploaded shortly to Galaxy.

3. Prepare Blast databases

  • Use the tool NCBI BLAST+ makeblastdb
What to set in each form field for nucleotide vir2 protein vir2
Molecule type of input nucleotide protein
Input FASTA files(s) dataset 1 (nucleotide vir2) dataset 2 (protein vir2)
Title for BLAST database nucleotide vir2 blastdb protein vir2 blastdb
  • Leave the rest of the form unchanged and click the Execute button
  • Rename the generated datasets "nucleotide vir2 blast database" and "protein vir2 blast database" for clarity

4. Creating Galaxy dbkey and fasta references accessible to tools for every user

Be sure that the References history is selected in the background, otherwise the uploaded genomes will not be available.

  • Go to the admin panel
  • Click Local data in the left menu
  • Select the Create DBKey and Reference Genome in the "Data Managers" table
What to set in each form field for nucleotide vir2 dm6 AgamP4 hg38
Use existing dbkey or create a new one New New New New
dbkey vir2 dm6 AgamP4 hg38
Choose the source for the reference genome History History History History
FASTA file nucleotide vir2 dm6 AgamP4 hg38
  • Leave the rest of the fields empty and click the Execute button

Tip: Once you have run the first job. You can expand the new dataset that appeared in your history and click on the redo button, instead of going back to the admin panel.

5. Creating Galaxy bowtie indexes accessible to tools for every user

Now we are going to generate the bowtie indexes using another data manager tool.

  • Go to the admin panel
  • Click Local data in the left menu
  • Select the Bowtie index builder in the "Data Managers" table
  • Select "vir2" in the "Source FASTA Sequence"
  • Leave the other options empty and click the Execute button
  • Expand the "bowtie index" dataset that appeared in your history and click the redo button
  • Repeat the previous 3 steps for "dm6", "AgamP4" and "hg38"

Note that the preparation of bowtie indexes can be long (several hours for the vir2 bowtie index for instance)

6. Creating Galaxy bowtie2 indexes accessible to tools for every user

Finally, we are going to generate the bowtie2 indexes using another data manager tool.

  • Go to the admin panel
  • Click Local data in the left menu
  • Select the Bowtie2 index builder in the "Data Managers" table
  • Select "vir2" in the "Source FASTA Sequence"
  • Leave the other options empty and click the Execute button
  • Expand the "bowtie index" dataset that appeared in your history and click the redo button
  • Repeat the previous 3 steps for "AgamP4" and "hg38"

Note that the preparation of bowtie2 indexes can be long too (several hours for the vir2 bowtie2 index for instance)