Move FAQs to the GTN

[beatrizserrano]

This issue keeps track of the FAQs in the Community Hub moved to the GTN FAQs. Please indicate with a comment below which ones you plan to work on.

💡 TIP: To get faster reviews (and merges), you can create the PRs in the GTN for each FAQ separately and add a meaningful title (something like "Moving FAQ Download datasets").

Please use icons in FAQs to help users. Here is a list of all available icons in the GTN and instructions on how to use them. If you want to use an icon you see in Galaxy that is not in the list, please let us know and we will add it!

Using Galaxy FAQs

Basics

Accounts

• [x] Registering for a Galaxy account (PR by @bernandez and @mesode)
• [x] Updating account preferences (PR @bernandez)

Loading data

• [x] Get Data: Upload (PR by @bernandez)
• [x] Get Data: EBI-SRA (PR @bernandez)
• [x] Get Data: Upload tool used with FTP (PR by @bernandez)

Downloading data

• [x] Download datasets (PR by @Melkeb)
• [x] Download entire histories (PR by @Melkeb)
• [x] Transfer/Upload entire histories (PR by @AnomalyCodes)
• [x] Dataset downloading incompletely? (@Melkeb)
• [x] Dataset(s) not downloading at all? ( PR by @Melkeb)

Finding tools

• [x] Finding tools (PR by @garimavs)

Tool help

• [x] Where is the tool help? (PR by @otatadeabigail, taken over by @Beachyesh in this PR)

Job details

• [x] Job details: bug, info, and other useful dataset icons (PR by @garimavs)

Managing Datasets

• [ ] Managing Datasets (@Beachyesh and @garimavs)

Datasets and how jobs execute

• [x] Datasets and how jobs execute (PR by @garimavs)
• [x] More about moving Datasets and Histories (external GVL blog) (PR by @Melkeb)

Data Options

Sharing and Publishing your work

• [x] Sharing with individual users (@NdzeRegina, PR by @anayo-hub)
• [x] Sharing via Web Link and Publishing an Item (@NdzeRegina)

Data Privacy Features

• [ ] Data Privacy Features (@Melkeb PR by @desmond-jasper)

Troubleshooting

Account

• [x] My history is missing! Good news, it probably isn't. (PR by @Melkeb)
• [x] My dataset is missing (PR by @Melkeb)
• [x] A history was shared with me, where can I find it? (PR by @garimavs)

The account usage quota seems incorrect

• [x] Does your account usage quota seem incorrect? (@AfiMaameDufie, PR by @Nurzhamalyrys)
• [x] How to log in or out of Galaxy? (@adi-1999 PR by @Samanthaanjei)
• [x] I need more space for my work (@adi-1999, PR by @andreasSune)
• [x] Find all Histories and purge (aka permanently delete) (@adi-1999 PR by @Samanthaanjei)
• [x] Find all Datasets or just review those in the active history and purge (aka permenently delete) those not needed (@adi-1999, PR by @Nurzhamalyrys)
• [x] Find Histories that have been shared with you, and unshare those not needed (PR by @garimavs)
• [x] Reduce quota usage while still retaining prior work (data, tools, methods) (PR by @bernandez)

Reset password or Change email, username, password

• [x] Update email, username, or password (PR @Melkeb)
• [x] Forgotten password reset (PR by @Melkeb)

Unexpected results

My job ended with an error. What can I do?

• [x] Determining the job failure type (several PRs by @garimavs)
  • [x] Reporting Usage Issues or Software bugs (PR by @garimavs)

Getting inputs right

• [x] How to format fastq data for tools that require .fastqsanger format? (@otatadeabigail, PR by @Melkeb)
• [x] Understanding compressed fastq data (fastq.gz) (@otatadeabigail, PR by @Melkeb)
• [x] Reformatting fastq data loaded with NCBI SRA (@otatadeabigail, PR by @Melkeb)
• [x] Format help for Tabular/BED/Interval Datasets (PR by @Beachyesh)
• [ ] Common datatypes explained (@otatadeabigail)
• [x] The tool I'm using does not recognize any input datasets. Why? (PR by @Melkeb)
• [x] How do I find, adjust, and/or correct metadata? (PR by @Beachyesh)
• [x] Tool error? Try Sorting Your Inputs (@otatadeabigail PR by @garimavs)
• [x] Preparing and using a Custom Reference Genome or Build (@otatadeabigail, PR by @Nurzhamalyrys)
• [x] Mismatched Chromosome identifiers (and how to avoid them) (@otatadeabigail, several PRs by @Melkeb)
• [x] Extended Help for Differential Expression Analysis Tools (@otatadeabigail)

[garimavs]

Hello @beatrizserrano, I would like to work on the remaining part of Dataset and how jobs execute and A history was shared with me, where can I find it?. Kindly add my name, if possible!

I also think that we can cover Checking for active vs deleted vs permanently deleted (purged) datasets and histories under Managing Datasets as it is its sub-part.

[beatrizserrano]

Hello @beatrizserrano, I would like to work on the remaining part of Dataset and how jobs execute and A history was shared with me, where can I find it?. Kindly add my name, if possible!

Done, thanks!

I also think that we can cover Checking for active vs deleted vs permanently deleted (purged) datasets and histories under Managing Datasets as it is its sub-part.

Good catch, I've moved it 😺

[bernandez]

Hello @beatrizserrano i would like to work on Getting an account at Galaxy Main (https://usegalaxy.org) and Loading Data.

[otatadeabigail]

Hi @beatrizserrano i would like to work on How to format fastq data for tools that require .fastqsanger format? and "Where is the tool help?"

[beatrizserrano]

Updated! Thank you very much @bernandez and @otatadeabigail :)

[ManaliPawar]

hello @beatrizserrano , i would like to work on managing datasets (https://galaxyproject.org/learn/managing-datasets/)

[garimavs]

Hey @beatrizserrano, I would like to merge all Known Issues links under one FAQ in GTN to access all known issues easily. I would love to know your opinion!

[Melkeb]

Hey I'm only working on my history is missing and my dataset is missing anything after sharing history I didn't include.

[garimavs]

Hey I'm only working on my history is missing and my dataset is missing anything after sharing history I didn't include.

Oh, thanks for clarifying, will edit my previous text!

[Beachyesh]

Hey @beatrizserrano I would like to pick the following FAQs: Format help for Tabular/BED/Interval Datasets How do I find, adjust, and/or correct metadata?

[beatrizserrano]

Hey @beatrizserrano, I would like to merge all Known Issues links under one FAQ in GTN to access all known issues easily. I would love to know your opinion!

Merging them sounds good to me. However, I'm wondering whether this FAQ would be really useful to have in the GTN. Any thoughts on this? @jennaj @shiltemann @hexylena

[shiltemann]

Hey @beatrizserrano, I would like to merge all Known Issues links under one FAQ in GTN to access all known issues easily. I would love to know your opinion!

Merging them sounds good to me. However, I'm wondering whether this FAQ would be really useful to have in the GTN. Any thoughts on this? @jennaj @shiltemann @hexylena

I agree, the average Galaxy/GTN user won't know what to do with the GitHub issues, but that said maybe the list of known issues could be added to the end of the bug reporting FAQ?

[garimavs]

Hey @beatrizserrano, I would like to merge all Known Issues links under one FAQ in GTN to access all known issues easily. I would love to know your opinion!

Merging them sounds good to me. However, I'm wondering whether this FAQ would be really useful to have in the GTN. Any thoughts on this? @jennaj @shiltemann @hexylena

I agree, the average Galaxy/GTN user won't know what to do with the GitHub issues, but that said maybe the list of known issues could be added to the end of the bug reporting FAQ?

I see that in Reporting Usage Issues or Software bugs, the link is provided to these known issues, should I include them while writing about usage problem reporting?

[otatadeabigail]

@beatrizserrano please i'd like to work on these:

[Understanding compressed fastq data (fastq.gz) [Reformatting fastq data loaded with NCBI SRA] [Common datatypes explained] [Tool error? Try Sorting Your Inputs] [Preparing and using a Custom Reference Genome or Build] [Mismatched Chromosome identifiers (and how to avoid them)] [Extended Help for Differential Expression Analysis Tools]

However, kindly help me review the pull request of one of the FAQ's I moved, so i'd be sure I did the right thing before moving on to others. Thanks

[beatrizserrano]

Hey @beatrizserrano, I would like to merge all Known Issues links under one FAQ in GTN to access all known issues easily. I would love to know your opinion!

Merging them sounds good to me. However, I'm wondering whether this FAQ would be really useful to have in the GTN. Any thoughts on this? @jennaj @shiltemann @hexylena

I agree, the average Galaxy/GTN user won't know what to do with the GitHub issues, but that said maybe the list of known issues could be added to the end of the bug reporting FAQ?

I see that in Reporting Usage Issues or Software bugs, the link is provided to these known issues, should I include them while writing about usage problem reporting?

I am not sure to be honest. I think that this can be hard for users to browse, but @jennaj may have a different view.

[AfiMaameDufie]

Hi @beatrizserrano, I would like to work on :

The account usage quota seems incorrect under accounts

and [Known Issues - Galaxy] [Known Issues - Main https] [Known Issues - Tools-devteam] [Known Issues - Tools-iuc]

under Known issues

Can I go ahead?

[FrozenGirl-spd]

Hey @beatrizserrano, May I work on: Known Issues - Main https://usegalaxy.org Known Issues - Tools-devteam

[Watiriroyalty]

Hello @beatrizserrano I would like to work on Understanding the Analysis History

[Watiriroyalty]

@beatrizserrano : I would like to work on Help Guides Why develop tools for Galaxy? Galaxy Tricks Commercial Galaxy Support

[adi-1999]

@beatrizserrano please I would like to work on these: Known Issues - Galaxy Known Issues - Main https://usegalaxy.org Known Issues - Tools-devteam Known Issues - Tools-iuc Reset password or Change email, username, password Why develop tools for Galaxy? Galaxy Tricks Commercial Galaxy Support Understanding the Analysis History Moving data between Galaxy servers (any!)

[bernandez]

Hello @beatrizserrano i would also like to work on

• The account usage quota seems incorrect

[beatrizserrano]

Hi @beatrizserrano, I would like to work on :

The account usage quota seems incorrect under accounts

Added, thanks! I've divided that one into several, so let me know if you want to work on all the ones under the same page.

and [Known Issues - Galaxy] [Known Issues - Main https] [Known Issues - Tools-devteam] [Known Issues - Tools-iuc]

We have been discussing leaving those out as they are too technical for users

[beatrizserrano]

Hey @beatrizserrano, May I work on: Known Issues - Main https://usegalaxy.org Known Issues - Tools-devteam

Hi @FrozenGirl-spd! We have decided to skip those FAQs, could you select another one? Thanks!

[beatrizserrano]

Hello @beatrizserrano I would like to work on Understanding the Analysis History

Hi @Watiriroyalty. This one was marked as done because it's already a tutorial, so no need to create a FAQ. Could you pick another one? Thanks :)

[beatrizserrano]

@beatrizserrano : I would like to work on Help Guides Why develop tools for Galaxy? Galaxy Tricks Commercial Galaxy Support

these are also marked as done, sorry :(

[beatrizserrano]

@beatrizserrano please I would like to work on these: Known Issues - Galaxy Known Issues - Main https://usegalaxy.org Known Issues - Tools-devteam Known Issues - Tools-iuc Reset password or Change email, username, password Why develop tools for Galaxy? Galaxy Tricks Commercial Galaxy Support Understanding the Analysis History Moving data between Galaxy servers (any!)

Hi @adi-1999. All those FAQs are either marked as done or selected by another person. Could you select some free ones? Thanks!

[garimavs]

Hey @beatrizserrano, Can I work on Updating account preferences

[beatrizserrano]

Hey @beatrizserrano, Can I work on Updating account preferences

Sure, assigned! Thanks

[bernandez]

Hi @beatrizserrano I had worked on updating account preference. You had assigned this to me. A pull request has been opened for this FAQ.

[beatrizserrano]

Hi @beatrizserrano I had worked on updating account preference. You had assigned this to me. A pull request has been opened for this FAQ.

True! Sorry @bernandez and @garimavs. I'm afraid that there might be more mistakes, it's a bit confusing...

[adi-1999]

Hi @beatrizserrano , can I please work on :- Understanding the Analysis History How to log in or out of Galaxy? My job ended with an error. What can I do? I need more space for my work Find all Histories and purge (aka permanently delete) Find all Datasets or just review those in the active history and purge (aka permenently delete) those not needed Find Histories that have been shared with you, and unshare those not needed Understanding the Analysis History

[beatrizserrano]

Hi @beatrizserrano , can I please work on :- Understanding the Analysis History How to log in or out of Galaxy? My job ended with an error. What can I do? I need more space for my work Find all Histories and purge (aka permanently delete) Find all Datasets or just review those in the active history and purge (aka permenently delete) those not needed Find Histories that have been shared with you, and unshare those not needed Understanding the Analysis History

Updated, thanks! But please note that some of them are already done

[garimavs]

Hi @beatrizserrano I had worked on updating account preference. You had assigned this to me. A pull request has been opened for this FAQ.

True! Sorry @bernandez and @garimavs. I'm afraid that there might be more mistakes, it's a bit confusing...

Oh no worries!

[AnomalyCodes]

Hi @beatrizserrano. I would like to work on Transfer/Upload entire histories Please assign it to me as I can see that it's available. Thank you.

[bernandez]

Hi @beatrizserrano I would also like to work on [Reduce quota usage while still retaining prior work (data, tools, methods)]. Thank you.

[garimavs]

Hey @otatadeabigail, I would like to work with you on Understanding compressed fastq data (fastq.gz) and Tool error? Try Sorting Your Inputs, unless you have already submitted a pr for the mentioned.

[Samanthaanjei]

hello @beatrizserrano right now I m working on DEVELOPING A CULTURE OF WELLBEING FOR OPEN-SOURCE PROJECTS – THE GALAXY COMMUNITY AS A USE CASE. PROJECT 1.docx

for now I have been to answer the first part of the questions but in order to proceed answering the rest i will need to ask you a few questions concerning the Galaxy Community. thank you

[bernandez]

Hello @Samanthaanjei welcome. I would love to help you out on this.

[Samanthaanjei]

Thank you very much @bernandez. Please inorder to proceed I will like to find out about the culture of wellbeing of the galaxy community as a whole that is its systems as well as members

[annefou]

hello @beatrizserrano right now I m working on DEVELOPING A CULTURE OF WELLBEING FOR OPEN-SOURCE PROJECTS – THE GALAXY COMMUNITY AS A USE CASE. PROJECT 1.docx

for now I have been to answer the first part of the questions but in order to proceed answering the rest i will need to ask you a few questions concerning the Galaxy Community. thank you

Awseome! for such discussions, this issue may not be the best place. Shall we discuss in our outreachy chat instead?

[Samanthaanjei]

Alright @annefou I will 🙏🏿

[anayo-hub]

hi @beatrizserrano I would love to work on https://galaxyproject.org/learn/share/#sharing-via-web-link-and-publishing-an-item

[desmond-jasper]

@beatrizserrano Sharing via Web Link and Publishing an Item

[annefou]

hi @beatrizserrano I would love to work on https://galaxyproject.org/learn/share/#sharing-via-web-link-and-publishing-an-item

@anayo-hub I think you can check it and work with @NdzeRegina. @desmond-jasper is also interested.

@beatrizserrano Sharing via Web Link and Publishing an Item

@desmond-jasper ok. Make sure you discuss together and agree on who is doing what and how. Thanks.

[anayo-hub]

@desmond-jasper and @NdzeRegina, can we talk through the channel

[desmond-jasper]

@anayo-hub @NdzeRegina sure

[Abraham-Deng]

Hello colleagues, am seeing the same issues almost being shared by all contributors. but am interested in the following issues;

1. Why develop tools for Galaxy?
   2. Galaxy Tricks
   3. Commercial Galaxy Support @beatrizserrano Please let me know if there are more different issues not being done by other contributors, so I can choose them instead of those ones. OR you may add me more.

[beatrizserrano]

Thanks @Abraham-Deng, we will be happy to discuss this in our chat channel and/or our call next week :)

[mesode]

Hello @beatrizserrano I would like to begin working on Understanding the Analysis History

[beatrizserrano]

Hello @beatrizserrano I would like to begin working on Understanding the Analysis History

Thanks @mesode. That FAQ is already checked because it's a tutorial, I'll remove it to avoid confusion. Could you pick another one that is not check and coordinate with the person that is taking care?