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 (genomes) so that they are directly available to all instance users for running tools and workflows

Here we provide the step-by-step description of what we actually did ourselves 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 vir1 fasta file

Click on the small arrow icon at the top of the tool bar (left handside of the Galaxy interface)
In the open window, click on the Paste/Fetch data button
Paste the URL https://ndownloader.figshare.com/files/4949173
Click the start button.

A first dataset will show up in your history, first in grey (the job is starting), then yellow (the job - upload - is running), and eventually green (job is successfully done).

When finished, rename the dataset 1 https://ndownloader.figshare.com/files/4949173 to nucleotide vir1 for clarity (using the small pencil icon).

c. Upload protein vir1 fasta file

Repeat the same operation as in b. using the url https://ndownloader.figshare.com/files/4949170. When finished, rename the dataset 2 https://ndownloader.figshare.com/files/4949170 to protein vir1 for clarity.

d. Upload the Drosophila melanogaster release 6 genome

Repeat the same operation as in b. using the url ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r6.10_FB2016_02/fasta/dmel-all-chromosome-r6.10.fasta.gz. When finished, rename the dataset 3 ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r6.10_FB2016_02/fasta/dmel-all-chromosome-r6.10.fasta.gz to dm6 for clarity.

e. Upload the Anopheles gambiae release P4

Repeat the same operation as in b. using the url https://www.vectorbase.org/sites/default/files/ftp/downloads/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4.fa.gz. When finished, rename the dataset 4 https://www.vectorbase.org/sites/default/files/ftp/downloads/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4.fa.gz to AgamP4 for clarity.

f. Upload the Plasmodium berghei genome

Repeat the same operation as in b. using the url ftp://ftp.ensemblgenomes.org/pub/release-28/protists/fasta/plasmodium_berghei/dna/Plasmodium_berghei.May_2010.28.dna_sm.genome.fa.gz. When finished, rename the dataset 5 ftp://ftp.ensemblgenomes.org/pub/release-28/protists/fasta/plasmodium_berghei/dna/Plasmodium_berghei.May_2010.28.dna_sm.genome.fa.gz to P. berghei for clarity.

g. Upload the Homo sapiens release GRCh38/hg19

Repeat the same operation as in b. using the url ftp://ftp.ensembl.org/pub/release-84/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz. When finished, rename the dataset 6 ftp://ftp.ensembl.org/pub/release-84/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz to hg19 for clarity.

3. Prepare Blast databases

a. Nucleotide vir1 blast database

Use the tool NCBI BLAST+ makeblastdb, check the radio button "nucleotide", select the dataset 1 (nucleotide vir1), give "nucleotide vir1 blastdb" as a "Title for BLAST database", leave the rest of the tool form unchanged and click "Execute" button.

Rename the generated dataset 7 "nucleotide BLAST database from data 1" to "nucleotide vir1 blast database" for clarity

b. Protein vir1 blast database

Use the tool NCBI BLAST+ makeblastdb, check the radio button "protein", select the dataset 2 (protein vir1), give "protein vir1 blastdb" as a "Title for BLAST database", leave the rest of the tool form unchanged and click "Execute" button.

Rename the generated dataset 8 "protein BLAST database from data 2" to "protein vir1 blast database" for clarity

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

Here we are going in the admin panel, click Local data in the left menu and select the Create DBKey and Reference Genome in the "Run Data Manager Tools" (last line of the top section).

a. nucleotide vir1

in the newly open browser window (from the last click on Create DBKey and Reference Genome) - select "New" for Use existing dbkey or create a new one - enter "vir1" in the dbkeyfield - leave "Display name for dbkey", Name of sequence and ID for sequence empty ! - select history in the Choose the source for the reference genome menu - select "nucleotide vir1" in the FASTA File menu - let Sort by chromosome name selected on As is - press the executebutton !

b. dm6

Repeat the operation described in a., but this time

  • put "dm6" for the dbkey field
  • select "3: dm6" in the FASTA File menu

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

c. AgamP4

Repeat the operation described in a., but this time

  • put "AgamP4" for the dbkey field
  • select "4: AgamP4" in the FASTA File menu

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

d. hg19

Repeat the operation described in a., but this time

  • put "hg19" for the dbkey field
  • select "6: hg19" in the FASTA File menu

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

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. But before doing this, we have to perform a low level Galaxy admin task: restart the Galaxy server instance so that the dbkey and the fasta genomes that we've just created for the server are registered and seen by the tools.

Depending on your skill level, you have the simple, dirty way:

  • reboot the machine where the galaxy server is running !

or the clean, freaking (for non-Geek normal biologists) way:

  • Connect to the server where the Galaxy instance has been installed either through an ssh connection or using your local terminal. and type

sudo supervisorctl restart galaxy:

If everything went fine you should see in your terminal

# supervisorctl restart galaxy:
galaxy_web: stopped
handler0: stopped
handler1: stopped
handler0: started
handler1: started
galaxy_web: started

freaking insn't it ?

a. vir 1 bowtie index

Now, Go back to your web browser and the admin panel, click again Local data in the left menu and select this time the Bowtie index - builder in the "Run Data Manager Tools" (top section).

select "vir1" in the Source FASTA Sequence menu of the Bowtie index builder tool form, leave the other options empty, and click execute.

b. dm6 bowtie index

Go back to your web browser and the admin panel, click again Local data in the left menu and select this time the Bowtie index - builder in the "Run Data Manager Tools" (top section).

select "dm6" in the Source FASTA Sequence menu of the Bowtie index builder tool form, leave the other options empty, and click execute.

c. AgamP4 bowtie index

Go back to your web browser and the admin panel, click again Local data in the left menu and select this time the Bowtie index - builder in the "Run Data Manager Tools" (top section).

select "AgamP4" in the Source FASTA Sequence menu of the Bowtie index builder tool form, leave the other options empty, and click execute.

d. hg19 bowtie index

Go back to your web browser and the admin panel, click again Local data in the left menu and select this time the Bowtie index - builder in the "Run Data Manager Tools" (top section).

select "hg19" in the Source FASTA Sequence menu of the Bowtie index builder tool form, leave the other options empty, and click execute.

Note that the preparation of bowtie indexes can be long ! (several hours for the vir1 bowtie index for instance)

When bowtie indexes are ready (green in the Data Manager History (automatically created)) restart the Galaxy server instance as explained above, so that the bowtie indexes that we've just created for the server are registered and seen by the tools.

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. If not done before, restart the Galaxy instance as explained above.

a. vir 1 bowtie2 index

Now, Go back to your web browser and the admin panel, click again Local data in the left menu and select this time the Bowtie2 index - builder in the "Run Data Manager Tools" (top section).

select "vir1" in the Source FASTA Sequence menu of the Bowtie index builder tool form, leave the other options empty, and click execute.

b. AgamP4 bowtie2 index

Go back to your web browser and the admin panel, click again Local data in the left menu and select this time the Bowtie2 index - builder in the "Run Data Manager Tools" (top section).

select "AgamP4" in the Source FASTA Sequence menu of the Bowtie index builder tool form, leave the other options empty, and click execute.

c. hg19 bowtie2 index

Go back to your web browser and the admin panel, click again Local data in the left menu and select this time the Bowtie2 index - builder in the "Run Data Manager Tools" (top section).

select "hg19" in the Source FASTA Sequence menu of the Bowtie index builder tool form, leave the other options empty, and click execute.

Note that the preparation of bowtie2 indexes can be long too ! (several hours for the vir1 bowtie2 index for instance)

When bowtie2 indexes are ready (green in the Data Manager History (automatically created)) restart the Galaxy server instance as explained above, so that the bowtie indexes that we've just created for the server are registered and seen by the tools.