[Google Form] New FAQ!

faqs/galaxy/importing-data-from-sierra-lims.md

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+---
+title: Importing data from Sierra LIMS
+layout: faq
+area: data upload
+box_type: tip
+google_form_id: 1730224450
+contributors:
+- hexhowells
+---
+This section will guide you through generating external links to your data stored in the Sierra LIMS system to be downloaded directly into Galaxy.
+
+1. Go to the [Sierra portal](https://www.bioinformatics.babraham.ac.uk/sierra/sierra.pl) and login to your account. 2. Click on the **Sample ID** of the sample you want to download data from. 3. Click on the **Edit Sample Details** button. 4. At the bottom of the page there will be an input box for creating a link, enter a description for the link in the **Reason for link** section, and click **Create link**. This will reload the page and add a new link to the sample under **Authorised links to this sample**. 6. Go back to the sample page or click on the hyperlink called **link** to take you back. 7. In the **Results** section select the lane you want to access your data from. 8. The bottom of the page, under the **Links** section, will now contain a list of `wget` commands with links for accessing all the files within that sample/lane.
+
+9. Since this list is for `wget` commands, you need to extract out the links from the command. You can copy the link in the first set of double quotes for each line and paste them directly into Galaxy to download the files.

faqs/galaxy/request-galaxy-tools-on-a-specific-server.md

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+---
+title: Request Galaxy tools on a specific server
+layout: faq
+area: tools
+box_type: tip
+google_form_id: 1728577286
+contributors:
+- nomadscientist
+---
+To request tools that already exist in the [Galaxy toolshed](https://toolshed.g2.bx.psu.edu), but not in your server, please raise an issue at:
+
+- *Europe - usegalaxy.eu* | https://github.com/usegalaxy-eu/usegalaxy-eu-tools
+
+- *USA - usegalaxy.org* | https://github.com/galaxyproject/usegalaxy-tools
+
+- *Australia - usegaalxy.org.au* | https://github.com/usegalaxy-au/usegalaxy-au-tools/tree/master/usegalaxy.org.au

faqs/galaxy/why-isnt-my-history-updating.md

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+---
+title: Why isn't my history updating?
+layout: faq
+area: "(Other --  Write in comments field)"
+box_type: tip
+google_form_id: 1729851011
+contributors:
+- hexylena
+---
+Have you ever experienced that you would submit a job but your history wouldn't update? Maybe it doesn't scroll or the datasets stay permanently grey even when you know they should be complete, *until you refresh the webpage*?
+
+One possible cause of this can be a difference in the clocks of your browser and the server. Check that your clocks match, and if not, reconfigure them! If you are following the Galaxy Admin Training, you will have setup `chrony`. Check that your `chrony` configuration is valid and requesting time from a local pool.
+
+``` # chronyc -n sources 210 Number of sources = 1 MS Name/IP address
+
+
+
+
+
+
+
+ Stratum Poll Reach LastRx Last sample
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+=============================================================================== ^? 169.254.169.123
+
+
+
+
+
+
+
+
+
+
+
+
+
+ 0
+
+ 7
+
+
+
+ 0
+
+
+
+ -
+
+
+
+ +0ns[
+
+ +0ns] +/-
+
+
+
+0ns
+
+```
+
+This command should return some valid sources. THe above shows an example of a time source that isn't working, 0ns is not a realistic office and LastRx is empty. Instead it should look more like::
+
+``` # chronyc -n sources 210 Number of sources = 5 MS Name/IP address
+
+
+
+
+
+
+
+ Stratum Poll Reach LastRx Last sample
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+=============================================================================== ^? 169.254.169.123
+
+
+
+
+
+
+
+
+
+
+
+
+
+ 0
+
+ 6
+
+
+
+ 0
+
+
+
+ -
+
+
+
+ +0ns[
+
+ +0ns] +/-
+
+
+
+0ns ^? 178.239.19.58
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ 0
+
+ 6
+
+
+
+ 0
+
+
+
+ -
+
+
+
+ +0ns[
+
+ +0ns] +/-
+
+
+
+0ns ^? 194.104.0.153
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ 2
+
+ 6
+
+
+
+ 1
+
+
+
+ 0
+
+ +138us[ +138us] +/-
+
+ 30ms ^? 45.138.55.61
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+1
+
+ 6
+
+
+
+ 1
+
+
+
+ 1
+
+ -103us[ -103us] +/- 3158us ^? 178.239.19.57
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ 2
+
+ 6
+
+
+
+ 1
+
+
+
+ 1
+
+ -301us[ -301us] +/- 3240us ```
+
+Here we see a number of sources, with more plausible offsets and non-empty LastRx.
+
+If your time was misconfigured, you might now see something like:
+
+``` # chronyc -n tracking Reference ID
+
+
+
+: B950F724 (185.80.247.36) Stratum
+
+
+
+
+
+
+
+ : 2 Ref time (UTC)
+
+: Tue Oct 22 09:44:29 2024 System time
+
+
+
+ : 929.234680176 seconds slow of NTP time ```
+
+as chrony slowly adjusts the system clock to match NTP time.
+<!-- This must go in the admin topic  -->

faqs/gtn/using-answer-key-histories.md

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+---
+title: Using answer key histories
+layout: faq
+area: learners
+box_type: tip
+google_form_id: 1728648609
+contributors:
+- nomadscientist
+---
+If you are struggling with a tutorial and you can't figure out why, you can use the answer history (if it's available) which is linked at the top of the tutorial.
+
+1. Select the *Answer history* and choose the appropriate link from the resulting drop-down menu.
+
+2. Import the history (If you aren't sure how, [go to the Import History FAQ]({% link faqs/galaxy/histories_import.md %})) 3. Select *View Here* or otherwise navigate to the imported history. 4. Find the dataset that was not outputting for you. You might be able to sport errors from looking at this dataset - such as, you may see that a different tool version was used, or different parameters were run, or different inputs were used. You may find that the input dataset itself is different, and perhaps something has gone wrong earlier in the tutorial for you.
+
+ If you can't find what has gone wrong, you can then: 5. [Ask for help] ({% link faqs/gtn/instructors_getting_help.md %}).
+
+6. [Copy the necessary datasets over from the answer history into your history]({% link faqs/galaxy/histories_copy_dataset.md %}) so that you can continue your analysis from wherever you got stuck!
+<!-- It would be awesome if this was automatically added to any tutorial that has answer key histories -->