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galaxyproject / training-material

A collection of Galaxy-related training material
https://training.galaxyproject.org
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GCC2019 CoFest Generic Introduction to Galaxy #1473

Closed nagoue closed 4 years ago

nagoue commented 4 years ago

Introduction -slides modification Galaxy 101 for every one (new tutorial based on "Journals for pubs" list)

chrisbarnettster commented 4 years ago

From Issue #1465

annefou commented 4 years ago

The slides "Introduction to Galaxy" are ready for review.

yvanlebras commented 4 years ago

I think the answer is no, but is there a way to see the "compiled" version somewhere ?

yvanlebras commented 4 years ago

Great job! Seems ok for me (noly based on the content, not the rendering ;) )

yvanlebras commented 4 years ago

+1000

yvanlebras commented 4 years ago

Thank you for initiating the Galaxy 101 for everyone. Will have a look ASAP. A question coming to my mind is that tools using regular expressions or things similar (like the awk tool ) are very powerful and maybe the more "it" oriented thing we can ask a generic user to understand and use. For sure we have to create a dedicated training but maybe it is relevant to introduce these powerful things here.... or on a advanced 101 for everyone ?

annefou commented 4 years ago

@yvanlebras Great idea! We just did not know this tool was available in Galaxy!!! We could for instance select rows where Val1 > sepal length > Val2 What do you think?

yvanlebras commented 4 years ago

Why not ;) One problem can be that the awk usegalaxy.eu tool is not working properly for now... Maybe an occasion to look at this ?

nagoue commented 4 years ago

What does it mean : doesn't work properly ? Is there an issue somewhere ?

yvanlebras commented 4 years ago

I don't know, we just saw that this week with @sbenateau for our tuto. The tool don't submit a job, but this is maybe "just" a transient .eu instance issue? Maybe exchange with @erasche directly to look at this

bgruening commented 4 years ago

It has some security issues that we need to address ...

yvanlebras commented 4 years ago

Thank you! So maybe we can, at least for now, taking another tool like filter data on any column or slect line that match an expression, something like that ? What do you think @annefou ?

annefou commented 4 years ago

Sure. I suggest we first finalize a very simple workflow and then work on improving it.

martenson commented 4 years ago

the website after this PR is deployed here: https://training-material-prev-pr-1473.herokuapp.com/

annefou commented 4 years ago

the website after this PR is deployed here: https://training-material-prev-pr-1473.herokuapp.com/

@martenson Is it always true or do we need to do something on our side to deploy at https://training-material-prev-pr-1473.herokuapp.com/

We are getting ready with our tutorial and it would be nice to review from https://training-material-prev-pr-1473.herokuapp.com/

Thanks.

bebatut commented 4 years ago

Let me know when you need it. I can trigger the deployment again but then it will last only few hours (we will need to see how to make it longer on the long run) So better to tell me when you need it

annefou commented 4 years ago

Ok! It makes sense. No urgency. Le's look at it next week (if you have time). This afternoon, I am taking part of "Fridays for Future global climate strike". #ClimateStrike Thanks.

nagoue commented 4 years ago

@erasche @martenson @nsoranzo '101 for everyone' is ready ! Thank you for reviewing !!

yvanlebras commented 4 years ago

What a wonderful job! Thank you!!!! I just look at it and see a very little typo. Another comment is related to the "Changing the datatype" section -> it appears to me potentially of interest to add a warning as using the "pencil" space is a manual operation and here the user can force associating a bad datatype so this is better to use convertion tool if existing to be sure.

jennaj commented 4 years ago

Another comment is related to the "Changing the datatype" section -> it appears to me potentially of interest to add a warning as using the "pencil" space is a manual operation and here the user can force associating a bad datatype so this is better to use convertion tool if existing to be sure.

Another (the maybe better) choice is to use the pencil icon > Edit Attributes > Datatype > "Detect Datatype" function. Format validations are applied, the same as the Upload tool's "autodetect datatype" function. This was a new feature added in release 19.05. Extremely useful to include in an intro tuto, IMO.

annefou commented 4 years ago

Another comment is related to the "Changing the datatype" section -> it appears to me potentially of interest to add a warning as using the "pencil" space is a manual operation and here the user can force associating a bad datatype so this is better to use convertion tool if existing to be sure.

Another (the maybe better) choice is to use the pencil icon > Edit Attributes > Datatype > "Detect Datatype" function. Format validations are applied, the same as the Upload tool's "autodetect datatype" function. This was a new feature added in release 19.05. Extremely useful to include in an intro tuto, IMO.

I am not sure to fully understand the requested changes; in the tutorial, we used the pencil to convert from CSV to tabular: is it what one should do? For adding a note/warning: Would it be OK to add a note (after the conversion from CSV to tabular) on how to use the pencil icon to detect/validate the data format?

yvanlebras commented 4 years ago

Another comment is related to the "Changing the datatype" section -> it appears to me potentially of interest to add a warning as using the "pencil" space is a manual operation and here the user can force associating a bad datatype so this is better to use convertion tool if existing to be sure.

Another (the maybe better) choice is to use the pencil icon > Edit Attributes > Datatype > "Detect Datatype" function. Format validations are applied, the same as the Upload tool's "autodetect datatype" function. This was a new feature added in release 19.05. Extremely useful to include in an intro tuto, IMO.

I am not sure to fully understand the requested changes; in the tutorial, we used the pencil to convert from CSV to tabular: is it what one should do? For adding a note/warning: Would it be OK to add a note (after the conversion from CSV to tabular) on how to use the pencil icon to detect/validate the data format?

Converting is ok for me. Just If I'm not wrong there was a section where "manual" modification of datatype is proposed. ''' Check the datatype. The datatype of the iris dataset is csv. Change datatype if it is different then csv. ''' But answer proposed by @jennaj is really perfect! Cool to have this ""new"" feature!

annefou commented 4 years ago

Converting is ok for me. Just If I'm not wrong there was a section where "manual" modification of datatype is proposed. ''' Check the datatype. The datatype of the iris dataset is csv. Change datatype if it is different then csv. ''' But answer proposed by @jennaj is really perfect! Cool to have this ""new"" feature!

Yes! I got it now! I will change the section where we check the datatype (and use this new feature instead of "Change datatype" button.)

nagoue commented 4 years ago

@abretaud Would you have time for reviewing ?

shiltemann commented 4 years ago

Thanks a lot @nagoue! I pushed some tweaks to the first half of the tutorial (let me know if it looks ok to you) will get to the second half soon :)

I was thinking, we could create a workflow as a final step and maybe rerun on the cars dataset from R? instead of species we'd have country of origin. Could really reemphasize the utility of Galaxy also outside of biology, what do you think?

nagoue commented 4 years ago

@shiltemann @abretaud thanks a lot for your feedback !!

shiltemann commented 4 years ago

Thanks everyone for this awesome contribution! :tada::tada: