The next sections explain how to qualify and calibrate the nitrate sensor mounted on the argo float 4903881 tool by tool or running a pre-design galaxy workflow. This requires 2 premliminary steps to prepare the environment. The explanations of the procedure are therefore organized as follows:
For your information, execution time for running tools depends on the number of files, their size and/or the number of people working on Galaxy.
Prerequisites¶
Galaxy¶
Galaxy tips and tricks
Once you are login, Galaxy is divided into 4 vertical panels whose (Figure 1):
the far left : Galaxy action list with “interactive Tools”, “Upload”, “Tools” …
the far right : History section.
Figure 1:Galaxy organisation
All symbols have a name that appears when you point your mouse on the symbol. Their name will be indicated with {} in the following tutorial.
The history section stores all your job results with the following color code :
grey : canceled
orange : running
green : finished with success
red : failed
It is possible to organise your history with sub-directory :
Creation of new history
Click on the symbol + on the top-right in the history section
Click on the pencil aligned to Unnamed history
Give an explicit name, annotation (optional), tag (optional)
Save
Switching from one history to another one
Click on the symbole ⇄ on the top-right in the history section
Select the history in the pop-up
Copy/paste dataset from one history to another one
Click on {Operations} (Figure 2)
Select Copier des jeux de données in the pop-up
In the central panel left to history section, select the file(s) you want to copy from the source history (left) to the destination history (right)
Figure 2:Galaxy operation symbol
Galaxy execution constraints
a quota per user account. Please check it and open the storage space used by your account by clicking in the history panel, on the database icon (see
ain the Figure 3). On the center panel, the storage manager page will open. It is noteworthy that when you delete a file in the history panel (right panel), it has not freed your storage space. To delete permanently files, click on “Review and clear xx GB” (seebin the Figure 3).
Figure 3:Galaxy quota information
a time execution limitation for interactive tools (such as ODV). This limit is 24h. When the limit is reached, the tool automatically closes.
It is not advised to launch workflows over the week-end. The week-end is the moment when Galaxy upgrades are performed. These upgrades will for sure close open interactive tools and may have impact on other tools (depending on the upgrade content of course).
it is not possible to launch more than 2 interactives tools in the same time
Nitrate Calibration¶
Manage your data¶
Step1 : Get your data¶
For uploading the argo data files (meta, core and BGC) of the float 4903881 from the S3 service:
Click on Upload (see
ain the Figure 4) on the Galaxy action list vertical panel on the left. A pop-up window will open.Click on Choose from repository (see
bin the Figure 4) at the bottom of the pop-up. A new pop-up window will open.Search argo in the top search bar. Argo marine floats data and metadata from Global Data Assembly Centre (Argo GDAC) appears in the label column just below
Select it, then pub/dac/coriolis/4903881 and tick 4903881_meta.nc & profiles/
Click on Select on the bottom right of the pop-up. The list of the files to download is displayed (see
cin the Figure 4)Remove the Synthetic files SR4903881_.nc* (not useful for qualification & calibration actions) by clicking on the corresponding trash icon on the right
Click on Start on the bottom of the pop-up. Once the download is completed (green color), close the window;
Wait until all files are stored in your history on the right (green color).
Figure 4:Get your data from S3 server
for uploading the argo data files (meta, core and BGC) of the float 4903881 or Word Ocean Atlas climatology from your computer:
Click on Upload (see
ain the Figure 5) on the Galaxy action list vertical panel on the left. A pop-up window will open.Click on Choose local file (see
bin the Figure 5) at the bottom of the popup. Your directory window will open.Select file(s) to be added and Click on Open at the bottom of the popup. The list of the files to download is displayed (see
cin the Figure 5)Click on Start on the bottom of the pop-up. Once the download is complete (green color), close the window.
Wait until all files are stored in your history on the right (green color).
Figure 5:Get your data from your computer
Step2 : Organize your data¶
Creation of a dataset list/collection¶
For creating a dataset list/collection, useful for platforms with many NetCDF original files as the Argo float 4903881.
Not useful for WOA
Choose below the case corresponding to your history section before dowloading 4903881 files
Click on {Select item} (see
ain the Figure 6)Click on Select all that has just appeared on the right (see
bin the Figure 6)Click on All ## selected that just replaced Select all. A window will pop up just below
Select Auto build list. A pop-up window will open in the central panel
Enter the name of the data collection : 4903881 (see
cin the Figure 7)Turn off Remove the file extension (see
din the Figure 7)Click on Build on the bottom right of the pop-up (see
ein the Figure 7)
Once the collection is ready, everything is green in the history panel. It is possible to limit the history to useful files or collections by clicking on the eyes above the files list in the history.
Figure 6:Select data from empty history
Figure 7:Dataset creation list
Click on {Select item} (see
ain the Figure 8)Tick all interesting files
Click on ## of ## selected (see
bin the Figure 8). A window will pop up just belowSelect Auto build list. A pop-up window will open in the central panel
Enter the name of the data collection : 4903881 (see
cin the Figure 9)Turn off Remove the file extension (see
din the Figure 9)Click on Build on the bottom right of the pop-up (see
ein the Figure 9)
Once the collection is ready, everything is green in the history panel. It is possible to limit the history to useful files or collections by clicking on the eyes above the files list in the history.
Figure 8:Select data from not empty history
Figure 9:Dataset creation list
File change extension¶
Because galaxy does not manage h5 extension very well, please change it for WOA(if needed). In the history section,
Select woa###_.nc file
Click on the pencil on the right. A new window opens in the central panel (see
ain the Figure 10)Select Datatype (see
bin the Figure 10)Inform the New Type with NetCDF (see
cin the Figure 10)Save (see
din the Figure 10)
Figure 10:Change of file extension
Q.C.V Nitrate workfow¶
The procedure can be performed: