I've forwarded your request to the galaxy-dev mail list as this is where issues
like this are discussed.
I want to make sure I'm clear on this issue. Can you provide some
On Apr 11, 2012, at 5:05 AM, Leandro Hermida wrote:
> Based on our initial use of the sample tracking system I haven't found
> any additional bugs, but we did realize one big functionality that is
> missing which makes the system somewhat hard to use.
> The current mechanism to link datasets to their corresponding samples
> is very cumbersome and takes a long time as it has to be done one
> sample at a time with a lot of UI clicking and there is a big
> potential for human error. I would say without an easier way to do
> this it would detract people from using the sample tracking system. Do
> you have any ideas to change/enhance the way this is done?
The current UI is something that we have plans to improve - the underlying
framework is flexible and allows for improvement in several areas. We will
certainly consider any recommendations from the community, including yours
> My initial
> suggestion would be that when you upload the samples using a CSV file
> that you can have a field like "DatasetsName" after FolderName where
> you can have a colon (:) separated list of file paths from the
> configured external service? That would solve it I think and make
> things much easier.
I've pasted an example screenshot below for reference. At the point that you
are importing samples from a CSV file, the sequence run is not yet started
(generally speaking), so there are no sequence run datasets (file names) yet
produced. So in order to create the csv file with the correct sequence run
file names, the user will have to know beforehand the resulting files produced
by the sequencer. Will this always be possible with your "Illumina external
service"? If so, what are the names of the files, and how are they
distinguished between runs? Do they just go in different directories in the
sequencer that are also know beforehand?
On the other hand, are you saying that your lab will perform the sequence run
and wait until the run is complete and the datasets are produced and then
create the csv file, entering the known dataset file names to produce the
sample line items for the sequencing request? The weakness of this process is
that your lab's customers will not be able to use Galaxy sample tracking to
view the status of their requests throughout their lifecycle since the
request's sample line items will not be created until the run is finished.
I'll work on implementing this enhancement, but I want to understand how you're
lab will use it. Any additional information you can provide will be helpful.
Add samples to sequencing request "one"
Name State Data Library Folder History Workflow
For each sample, select the data library and folder in which you would like the
run datasets deposited. To automatically run a workflow on run datastets,
select a history first and then the desired workflow.
Sample form layout 1
Copy samples from sample
Select the sample from which the new sample should be copied or leave selection
as None to add a new "generic" sample.
Click the Add sample button for each new sample and click the Save button when
you have finished adding samples.
Import samples from csv file
The csv file must be in the following format.
The [:FieldValue] is optional, the named form field will contain the value
after the ':' if included.
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