Merge pull request #3205 from shiltemann/morefaqs

_config.yml

@@ -164,6 +164,7 @@ icon-tag:
   text-document: fas fa-file-alt
   tip: far fa-lightbulb
   tool: fas fa-wrench
+  tool-versions: fas fa-cubes
   topic: far fa-folder
   trophy: fas fa-trophy
   tutorial: fas fa-laptop

_layouts/faq-page.html

@@ -56,3 +56,11 @@ <h2 id="bibliography">{{locale['references']| default: "References" }}</h2>
 {% bibliography --cited %}
 {% endif %}
 
+
+<br><br><hr>
+<h5>Still have questions?</h5>
+
+{% include _includes/button.html link="https://gitter.im/Galaxy-Training-Network/Lobby" label="Gitter Chat Support" colour="yellow" buttonsize="medium" %}
+
+{% include _includes/button.html link="https://help.galaxyproject.org" label="Galaxy Help Forum" colour="purple" buttonsize="medium" %}
+

faqs/galaxy/analysis_jobs_not_running.md

@@ -13,7 +13,7 @@ contributors: [shiltemann]
 
 3. **Be patient**. Galaxy is a free service, when a lot of people are using it, you may have to wait longer than usual (especially for 'big' jobs, e.g. alignments).
 
-4. **Contact Support**. If you really think something is wrong with the server. [You can ask for support]({{site.baseurl}}/faqs/galaxy/support.html)
+4. **Contact Support**. If you really think something is wrong with the server, you can [ask for support]({{site.baseurl}}/faqs/galaxy/support.html)
 
 
 

faqs/galaxy/tools_change_version.md

@@ -0,0 +1,14 @@
+---
+title: changing the tool version
+area: tools
+box_type: tip
+layout: faq
+contributors: [shiltemann]
+---
+
+Tools are frequently updated to new versions. Your Galaxy may have multiple versions of the same tool available. By default, you will be shown the latest version of the tool.
+
+**Switching to a different version** of a tool:
+  - Open the tool
+  - Click on the {% icon tool-versions %} versions logo at the **top right**
+  - Select the desired version from the dropdown list

topics/dev/tutorials/debugging/faqs/no_tests_no_yarn.md

@@ -0,0 +1,10 @@
+---
+title: I cannot run client tests because yarn is not installed.
+box_type: question
+layout: faq
+contributors: [shiltemann]
+---
+
+Make sure you have executed `scripts/common_startup.sh` and have activated the virtual environment (`. .venv/vin/activate`) in your *current terminal session*.
+
+

topics/dev/tutorials/debugging/faqs/selenium_error.md

@@ -0,0 +1,28 @@
+---
+title: When I try to run a Selenium test, I get an error
+box_type: question
+layout: faq
+contributors: [assuntad23]
+---
+
+If you get the following error:
+
+```bash
+selenium.common.exceptions.SessionNotCreatedException (...This version of ChromeDriver only supports Chrome version...)
+```
+
+Make sure that (a) the version of your ChromeDriver is the same as the version of Chrome:
+
+```bash
+$ chromedriver --version
+$ chrome --version
+```
+
+If they are not the same:
+- download the appropriate version of [ChromeDriver](https://chromedriver.chromium.org/downloads).
+- unzip the file
+- move the chromedriver file into the appropriate location.
+  - On Linux, that could be `/usr/bin`, `$HOME/.local/bin`, etc.
+  - Use the `which` command to check the location: `$ which chromedriver`
+- Make sure the permissions are correct (755).
+

topics/dev/tutorials/tool-from-scratch/faqs/bioconda_files_exist.md

@@ -0,0 +1,11 @@
+---
+title: The folder `recipes/belerophon/` and the file `meta.yaml` already exist in bioconda?
+box_type: question
+layout: faq
+contributors: [astrovsky01,davebx,bernt-matthias]
+---
+
+The recipe has already been added previously. If you want to create the recipe from scratch you may just do this in another directory below `recipes/`.
+
+
+

topics/dev/tutorials/tool-from-scratch/faqs/get_planemo.md

@@ -0,0 +1,15 @@
+---
+title:  Where can I get planemo?
+box_type: question
+layout: faq
+contributors: [astrovsky01,davebx,bernt-matthias]
+---
+
+Plese see [the installation section](https://training.galaxyproject.org/training-material/topics/dev/tutorials/tool-from-scratch/tutorial.html#installing-planemo). Essentially you can `pip install planemo`. If you don’t have pip, you need to install this first.
+
+On windows you’ll need `WSL2` and then you can `apt-get install python3-pip`, same for ubuntu. For OSX users it is probably present.
+
+
+
+
+

topics/dev/tutorials/tool-generators/faqs/collections_test.md

@@ -0,0 +1,14 @@
+---
+title: I want to use a collection for outputs but it always passes the test even when the script fails. Why?
+box_type: question
+layout: faq
+contributors: [fubar2]
+---
+
+- Collections are tricky for generating tests.
+  - The contents appear only after the tool has been run and even then may vary with settings.
+- A manual test override is currently the only way to test collections properly.
+- Automation is hard. If you can help, pull requests are welcomed.
+- Until it's automated, please take a look at the plotter sample.
+- It is recommended that you modify the test over-ride that appears in that sample form. Substitute one or more of the file names you expect to see after the collection is filled by your new tool for the `<element.../>` used in the plotter sample's tool test.
+

topics/dev/tutorials/tool-generators/faqs/error_closure_args.md

@@ -0,0 +1,10 @@
+---
+title: My Rscript tool generates a strange R error on STDOUT about an invalid operation on a closure called 'args' ?
+box_type: question
+layout: faq
+contributors: [fubar2]
+---
+
+Did your code declare the `args vector` with something like `args = commandArgs(trailingOnly=TRUE)` before it tried to access args[1] ?
+See the plotter tool for a sample
+

topics/dev/tutorials/tool-generators/faqs/error_compose.md

@@ -0,0 +1,18 @@
+---
+title: "`docker-compose up` fails with error `/usr/bin/start.sh: line 133: /galaxy/.venv/bin/uwsgi: No such file or directory`"
+box_type: question
+layout: faq
+contributors: [fubar2]
+---
+
+
+- This is why it's useful to watch the boot process without detaching
+- This can happen if a container has become corrupt on disk after being interrupted
+  - cured by a complete cleanup.
+- Make sure no docker galaxy-server related processes are running - use docker ps to check and stop them manually
+- delete the `..compose/export directory` with `sudo rm -rf export/*` to clean out any corrupted files
+- run `docker system prune` to clear out any old corrupted containers, images or networks. Then run `docker volume prune` in the same way to remove the shared volumes.
+- run `docker-compose pull` again to ensure the images are correct
+- run `docker-compose up` to completely rebuild the appliance from scratch. **Please be patient**.
+
+

topics/dev/tutorials/tool-generators/faqs/formats.md

@@ -0,0 +1,11 @@
+---
+title: What file/data formats are defined for I/O in Galaxy?
+box_type: question
+layout: faq
+contributors: [fubar2]
+---
+
+- [Galaxy Datatypes](https://galaxyproject.org/learn/datatypes)
+- `[galaxy-root]/config/datatypes_conf.xml` is read at startup so new datatypes can be defined.
+
+

topics/dev/tutorials/tool-generators/faqs/job_grey.md

@@ -0,0 +1,16 @@
+---
+title: First job I submitted remains grey or running for a long time - is it broken?
+box_type: question
+layout: faq
+contributors: [fubar2]
+---
+
+- Check with `top` or your system monitor - if Conda is running, things are working but it's slow the first time a dependency is installed.
+- The first run generally takes a while to install all the needed dependencies.
+- Subsequent runs should start immediately with all dependencies already in place.
+- Installing new Conda dependencies just takes time so tools that have new Conda packages will take longer to run the first time if they must be installed.
+- In general, a `planemo_test` job usually takes around a minute - planemo has to build and tear down a new Galaxy for generating test results and then again for testing properly. Longer if the tool has Conda dependencies.
+- The very first test in a fresh appliance may take 6 minutes so be patient.
+
+
+

topics/dev/tutorials/tool-generators/faqs/local_install.md

@@ -0,0 +1,11 @@
+---
+title: Why do I need that big (~5GB!) complicated Docker thing - can I just install the ToolFactory into our local galaxy server from the toolshed?
+box_type: question
+layout: faq
+contributors: [fubar2]
+---
+
+You can but it can’t really be very useful. The ToolFactory is a Galaxy tool, but it installs newly generated tools automatically into the local Galaxy server. This is not normally possible because a tool cannot escape Galaxy's job execution environment isolation. The ToolFactory needs to write to the normally forbidden server's configuration so the new tool appears in the tool menu and is installed in the TFtools directory which is a subdirectory of the Galaxy tools directory.
+The Appliance is configured so the ToolFactory and the Planemo test tool use remote procedure calls (RPC using rpyc) to do what tools cannot normally do. The rpyc server runs in a separate container. Without it, tool installation and testing are difficult to do inside Galaxy tools.
+Known good tools can be uploaded to a local toolshed from your private appliance for installation to that server of yours. Debugging tools on a production server is not secure SOP. You just never know what might break. *That’s why a desktop disposable appliance is a better choice.*
+

topics/dev/tutorials/tool-generators/faqs/planemo_multiple.md

@@ -0,0 +1,12 @@
+---
+title: Only one Planemo test runs at a time. Why doesn't the server allow more than one at once?
+box_type: question
+layout: faq
+contributors: [fubar2]
+---
+
+- When a new dependency is being installed in the Planemo Conda repository, there is no locking to prevent a second process from overwriting or otherwise interfering with it's own independent repository update.
+- The result is not pretty.
+- Allowing two tests to run at once has proven to be unstable so the Appliance is currently limited to one.
+
+

topics/dev/tutorials/tool-generators/faqs/replace_manual_install.md

@@ -0,0 +1,11 @@
+---
+title: Is the ToolFactory a complete replacement for manual tool building?
+box_type: question
+layout: faq
+contributors: [fubar2]
+---
+
+- No, except where all the requirements for the package or script can be satisfied by the limited automated functions of the code generator, or where there is a script with all the complex logic that might otherwise go into XML
+- Many advanced XML features are not available such as output filters.
+- Adding DIY output filters, XML macros and some other advanced features is possible if anyone is sufficiently enthusiastic - some features in the galaxyxml package would be relatively straightforward to add.
+

topics/metagenomics/tutorials/metatranscriptomics/faqs/fastq_interlacer_vs_joiner.md

@@ -0,0 +1,10 @@
+---
+title: Why do we use FASTQ interlacer and not the FASTQ joiner?
+box_type: question
+layout: faq
+contributors: [subinamehta]
+---
+
+The reason ASaiM-MT uses FASTQ-interlacer than FASTQ-joiner for combining forward and reverse reads is because the joiner tool combines the forward and reverse read sequence together while the interlacer puts the forward and reverse read sequences in the same file while retaining the entity of each read along with an additional file with unpaired sequences and it maintains the integrity of the reads while helping us distinguish between the forward and reverse reads.
+
+

topics/metagenomics/tutorials/metatranscriptomics/faqs/multiple_inputs.md

@@ -0,0 +1,10 @@
+---
+title: Can we use the ASaiM-MT workflow on multiple input files at the same time?
+box_type: question
+layout: faq
+contributors: [subinamehta]
+---
+
+Currently, that is one of its limitations. However, Galaxy offers a workflow within workflow feature which can help process multiple files at the same time and this output can be combined into one using the `MT2MQ` tool.
+
+

topics/metagenomics/tutorials/metatranscriptomics/faqs/single_end.md

@@ -0,0 +1,9 @@
+---
+title: Can this ASaiM workflow be used for single-end data?
+box_type: question
+layout: faq
+contributors: [subinamehta]
+---
+
+Yes, the inputs have to be changed to a single-end file rather than a paired-end.
+

topics/metagenomics/tutorials/metatranscriptomics/faqs/vsearch.md

@@ -0,0 +1,9 @@
+---
+title: Why don't we perform the V-Search dereplication step of ASaiM for metatrascriptomic data?
+box_type: question
+layout: faq
+contributors: [subinamehta]
+---
+
+In the metatranscriptomics data, duplicated reads are expected. And to keep the integrity of the sample, we would like to retain the reverse reads.
+

topics/proteomics/tutorials/encyclopedia/faqs/advantages.md

@@ -0,0 +1,10 @@
+---
+title: What advantages does a Chromatogram Library have over a DDA-generated library or predicted spectral library?
+box_type: question
+layout: faq
+contributors: [emmaleith]
+---
+
+While generating a Chromatogram Library is the most time consuming step of the EncyclopeDIA workflow, it is beneficial to DIA data analysis. DIA is a novel technique and methods for DIA data analysis are still being developed. One method commonly used includes searching DIA data against DDA-generated libraries. However, there are limitations in this method. Firstly, DDA-generated libraries are not always an accurate representation of DIA data: differences in the methods of data collection play an important role in the efficacy of the library. Secondly, DDA-generated libraries often require labs to run completely separate DDA experiments to simply generate a library with which to analyze their DIA data.
+Chromatogram Libraries mitigate some of the previous shortcomings mentioned. DIA data is incorporated into the generation of the Chromatogram Library and therefore provides context to the DIA data being analyzed. Secondly, the ELIB format of the Chromatogram Library allows for extra data to be included in the analysis of the DIA data, including intensity, m/z ratio, and retention time compared to the use of a DDA-generated DLIB library. Lastly, a Chromatogram Library can be generated without the use of a spectral library (as mentioned in the last question). Therefore, it is possible to forgo DDA data collection as the DLIB DDA-generated library is not strictly needed for Chromatogram Library generation and to run the EncyclopeDIA workflow (saving time and resources).
+

topics/proteomics/tutorials/encyclopedia/faqs/without_spectral_library.md

@@ -0,0 +1,12 @@
+---
+title: Can EncyclopeDIA be run on a DIA-MS dataset without a spectral library?
+box_type: question
+layout: faq
+contributors: [emmaleith]
+---
+
+Yes. In this GTN, the workflow presented is the Standard EncyclopeDIA workflow; however, there is a variation upon the Standard EncyclopeDIA workflow, named the WALNUT EncyclopeDIA workflow in which a spectral library is not required. Simply, the WALNUT variation of the workflow omits the DLIB spectral/PROSIT library input, hence requiring just the GPF DIA dataset collection, Experimental DIA dataset collection, and the FASTA Protein Database file. Therefore, the Chromatogram Library is generated using the GPF DIA dataset collection and the FASTA Protein Database alone. This method does generate fewer searches than if a spectral library is used. The Galaxy-P team tested the efficacy of the WALNUT workflow compared to the Standard EncyclopeDIA workflow, and more information on that comparison and those results can be found at this [link](http://galaxyp.org/wp-content/uploads/2020/10/BCC_2020-Pratik.pdf).
+
+
+
+

topics/transcriptomics/tutorials/de-novo/faqs/different_results.md

@@ -0,0 +1,13 @@
+---
+title: I get a different number of transcripts with a significant change in gene expression between the G1E and megakaryocyte cellular states. Why?
+area: support
+box_type: question
+layout: faq
+contributors: [malloryfreeberg]
+---
+
+This is okay! Many aspects of the tutorial can potentially affect the exact results you obtain. For example, the reference genome version used and versions of tools. It’s less important to get the exact results shown in the tutorial, and more important to understand the concepts so you can apply them to your own data.
+
+
+
+

topics/transcriptomics/tutorials/droplet-quantification-preprocessing/faqs/alevin_version.md

@@ -0,0 +1,11 @@
+---
+title: Why is Alevin is not working?
+box_type: question
+layout: faq
+contributors: [nomadscientist, mtekman]
+---
+
+Check your tool version, you need to use `1.3.0+galaxy2`
+
+Follow [these instructions]({% link faqs/galaxy/tools_change_version.md %}) to switch between tool versions.
+

topics/transcriptomics/tutorials/scrna-seq-basic-pipeline/faqs/findmarkers_empty.md

@@ -0,0 +1,8 @@
+---
+title: My Scanpy FindMarkers step is giving me an empty table
+box_type: question
+layout: faq
+contributors: [nomadscientist, mtekman]
+---
+
+Try selecting: “Use programme defaults: Yes” and see if that fixes it.

topics/transcriptomics/tutorials/scrna-seq-basic-pipeline/faqs/plotembed_fails.md

@@ -0,0 +1,8 @@
+---
+title:  On Scanpy PlotEmbed, the tool is failing
+box_type: question
+layout: faq
+contributors: [nomadscientist, mtekman]
+---
+
+Try selecting “Use raw attributes if present: NO”

topics/transcriptomics/tutorials/scrna-seq-basic-pipeline/faqs/plotembed_results_missing.md

@@ -0,0 +1,12 @@
+---
+title: On the Scanpy PlotEmbed step, my object doesn’t have Il2ra or Cd8b1 or Cd8a etc.
+box_type: question
+layout: faq
+contributors: [nomadscientist, mtekman]
+---
+
+Check your `Anndata` object - it should be `7874 x 14832`, i.e. 7874 cells x 14832 genes. Is it actually 2000 genes only (i.e. and therefore missing the above markers)? You may have selected to remove genes at the Scanpy FindVariableGenes step (last toggle, ‘Remove genes not marked as highly variable’ < Select NO.) (Most likely you did this correctly the first time, but later in investigating how many got marked as highly variable, may have run this tool again and removed the nonvariable ones. We’ve updated the text to more clearly prevent this, but you may have gotten caught out!)
+
+
+
+