Aggregation of feedback submitted since 2018-09 using the embed feedback form at the bottom of tutorials. Thank you everyone who submitted feedback!

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Assembly

125 responses
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9 responses
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Date What did you like? What could be improved?
Sep 4, 2024 short, comparison of two methods tool versions, answers to the questions, adding bandage to workflow, generated bandage pics look completely dfferent
Jun 24, 2024 Most of it! I'm mostly informing y'all at galaxy about a specific issue. The four images following this line "For a simple case, imagine a bacterial genome that contains a single repeated element in two separate places in the chromosome:" are unavailable for viewing.
Aug 11, 2023 Spades tutorial is correct Velvet tutorial is not working, I follow the instructions and didn't got a final image it went white all, so think is something up to the tutorial or the tool
Mar 25, 2019 Easy to follow
Sep 19, 2018 Everything works with provided data and the scale is good for use in class Could you provide the fragment size separating the paired ends? It would also be nice to have more info for instructors about the genome for doing additional exercises based on the assemblies.
32 responses
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Oct 8, 2024 Easy to understand for non experienced
Aug 24, 2024 tPlease, give more information, for exmaple to put a video or more information it was difficult to think at the end I needed to push run/play button. There is a need to indicate the files to use if there is one or multiple files.
May 30, 2024 that it explains why we are doing each step and how quality parameters should be, as well as telling you why our ensamble may be incorrect so you can correct your work perhaps, that it could include a little bit more of theory but it was fine as it´s just a tutorial (i used this for studying really, not for practicing an assembly)
Mar 22, 2024 the workshop with lots of details and solution for every question more detailed explanation about the Galaxy functions(how they work and the meaning of outputs)
Mar 1, 2024 it is friendly, and so useful
Dec 18, 2022 I could follow step by step the directions I was stacked in the velveth assembly cos I was in the wrong version of the program. Maybe is necessary to add this to the tutorial.
Nov 20, 2022 Everything, except the Velvet choice. Use another software besides Velvet, since it's deprecated and it's not working.
Jun 30, 2022 most of the functionsare different what is given here please insert screen shorts of the results, how the output look like
Apr 26, 2022 It is easy to follow up as you practice. More examples to practice with.
Mar 12, 2022 Simplicity. Considering this is an introduction to assembly, it would be helpful if the steps are complete as some steps may have been skipped. It would also be useful if pictures can be added for some steps. When ran, the results stated in this tutorial doesnt match with the output even if the instructions is strictly followed
Oct 26, 2021 Clarity, granularity, hands-on Could have a similar tutorial for long read assembly (Nanopore, PB) , and I suppose 'hybrid assembly' , but this one is probably adequate for all these purposes.
Feb 10, 2021 you may show the progression files in green to show us the file we have after each step i have problem with FASTQ interlacer i follow the tutorials and after this step i have two files one of them is empty and it's not working for the further stem with velveth so i'm stock at this step i don'understand why
Oct 9, 2020 Easy to follow The options that appear now, are not the same that this tutorial shows.
Jul 2, 2020 Simple enough. There isn't much information to give the learner the background to interpret their own data. There should be an introduction of what each of the parameters specified for the hands-on session means and why the learner should be setting them as instructed. That's the only way to know whether this tutorial is suitable for the learner's own dataset to follow.
Jun 9, 2020 The pace and the content covered are great!!!
Apr 18, 2020 the hands on exercises There was no Icarus viewer
Oct 21, 2019 Step by Step instructions Feeding in multiple samples at the same time for FastQC
Jun 3, 2019 the real data analysis provide links to the tool side by side
8 responses
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Jan 15, 2021 the explanations are well
Apr 16, 2019 easy to follow, step by step
1 responses
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Apr 1, 2020 I miss some screenshot of how my data should look. At one point, in one of the steps where I had to choose some columns from a matrix to work on, I kept getting a wrong result. And I think the reason was, that I had something different in some of the columns than what I should have (so if for example I was asked to choose column 1, the data I was trying to get was actually in column 2) - if there were some screenshots of what the data should look like, I might have been able to see if I had a column too much
7 responses
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Aug 13, 2021 The activity was very interactive with a good combination of theory and practical The last step on NCBI BLAST search was not clear enough to a biginner like me
May 18, 2021 The basics of each step explained very clearly. Maybe the names of the files which need to be put in the field for the tool. Took a bit of time to understand in few places.
Feb 19, 2021 How in depth and clear it was.
Feb 19, 2021 it was very helpful.
Jan 19, 2021 Très didactique Peut être ajouter des copies d'écrans de l'historique ? (repérer les numéro d'actions) Mais peut être "anxiogène" si on a refait certaines opérations et que l'on perd ce repère de numéro...Donc non en fait :)
Jul 28, 2020 It was very detailed and easy to follow
Apr 22, 2020 The format and outlining are fantastic Add a screen shot or graphic to illustrate the major steps in this workflow
29 responses
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Sep 12, 2024 I like the different tool options that the tutorial provided. I could not reproduce "View Reads" section with the direction given above.
May 22, 2023 Interesting genome for tutorial and explanation of how to do long read assembly with short read polishing.
Mar 31, 2022 pictures - screenshots can be added
Mar 22, 2022 I learnt new tools that i haven't used before
Mar 17, 2022 i liked on how to polish nano-pore reads
Mar 15, 2022 Very easy to use and effective
Mar 15, 2022 good intro course on assembly some more theory about polishing and why
Mar 15, 2022 All aspect Not much improvement
Dec 23, 2021 Circos plot of the data should also be included.
Nov 30, 2021 Very assertive and good guidance More intuitive guidance
Jul 10, 2021 The overall training session was really nice. However, some more information regarding the viewing in Jbrowse should be discussed like what to analyse in Jbrowse, how to spot irregularities and how to spot meaningful data? What kind of useful data can be visualized or can we get from the visualization in the Jbrowse.
Jun 30, 2021 The idea of comparing long and short reads and how to use short reads to polish the results It would be great if there was a little explanation of how the tools work
Feb 20, 2021 I´d like to know how I can get a unique assemble using more than one pair of Illumina reads for the same DNA, for example the same bacterial strain. It is possible?
Feb 16, 2021 Loved the self training with new data at the end. Helps user create a workflow to re run the steps rapidly and compare results. The tutorials were very clear and easy to understand
Feb 15, 2021 Clear and easy
Jan 2, 2021 Clear Explanations I noticed the "Note: this tool is heuristic; your results may differ slightly from the results here, and if repeated." But mine only showed one contig, with a length of 158kbp. I would consider this very different, not slightly different. Maybe add a few more examples of "slightly different" results I am running the tool again to see what I get. Additionally it took a long time to run this tool; almost an hour. So it would be nice to know approximately how long a tool is going to take, (given the fastq file & runtime parameters), or maybe show the log file while it is running (assuming the actual tool writes to the log file rather than just storing the info in memory and writing the log at the end...)
14 responses
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Oct 9, 2024 the messy assembly ;-)
Feb 15, 2024 Hi all -- the reads for this tutorial are incorrect at the zenodo site. Both are interleaved fastq, and the second (labeled as the "reverse" file) has a content problem. The tutorial workflow will happily process the data as-is, except for a fastqc failure on that second file (reported as truncated). > End-User Workaround: use only the first file, de-interlace as a new first step, rename the split files, get rid of the originals (to avoid mixing up data), then proceed with the remainder of the tutorial. Self-pinging so I can find this later @jennaj
Feb 12, 2024 Following the tutorial did not work in my hands. I loaded the data via Paste/Fetch, but already in the FastQC step I get an error for dataset 2: "An error occurred with this dataset: format txt database ?"
Jan 17, 2024 The explanations are very clear and the tutorial is very easy to follow The Table to GFF3 is no longer available, so I couldn't finish the tutorial. And I didn't find an alternative tool to Table to GFF3.
Jul 8, 2021 the lessons not sure
3 responses
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Dec 13, 2023 It is very well explained and it's in a easy way to understand all the commands and what they do.
Feb 21, 2022 A clean flowchart of methods with an explanation for the purpose of each step. As a case study, a bad genome assembly or an assembly with incorrect parameters in various steps could be shown
2 responses
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Sep 1, 2022 To test the tools of assembly in a control dataset I think it could be valable to understand the tools and the parameters of the tools while using them: to not do it without thinking it through. I think it is better to understand to remember.
Jun 8, 2022 straightforward would have liked to have some practice viewing the assembly graphs and with visual methods for comparing genomes (e.g. dot, synteny plots)
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Oct 25, 2022 Table to gff3 tool does not exist anymore. When I use the tutorial mode on galaxy and click on the table to gff3 hyperlink button, i get this message: Loading tool toolshed.g2.bx.psu.edu/repos/iuc/tbl2gff3/tbl2gff3/1.2 failed: Could not find tool with id 'toolshed.g2.bx.psu.edu/repos/iuc/tbl2gff3/tbl2gff3/1.2'. Do you have any advice on which other tool to use? Also, in a prior feedback I mentioned that I could not find select the lines, but it is actually there I found it in the end. sorry for the mistake.
Oct 25, 2022 It was easy to follow the steps and the functions ran in a good amount of time (relatively fast) - I got stuck in staramr. there was a recurrent error due to ERROR: 'Predicted Phenotype'. This error was reported. it appears to be due to a problem of compatibility with the pandas version (https://github.com/phac-nml/staramr/issues/115) - Genome annotation using Prokka, step 2 (Select lines that match an expression) has changed names to Search in Textfiles (grep) - Table to GFF3 function: I was unable to find this function under the Galaxy tools. downstream commands could not be ran.
5 responses
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Jul 6, 2024 the info structure
Jan 10, 2024 The 'easy-to-understand' way of explaining the whole process
1 responses
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Jun 26, 2023 Everything! It's awesome!
1 responses
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Jun 25, 2024 great! I liked that I was able to use multiple methods to check the quality of my genome assembly. The Chromeister tool is not available in the tools search menu as of today on Galaxy (the US instatnce). Also, I would have appreciated more orientation to the plots generated in " Hands-on: K-mer based evaluation with Merqury". I had a difficult answering the follow-up question because I was unsure what all of the axes and lables meant.
2 responses
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Aug 16, 2024 Very helpful to do the long pipeline with the Yeast then the short pipeline with your own data. In figure 7, you refer to Chub mackerel (Scomber japonicus), but then in the next sentence talk about zebra finch.
3 responses
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Oct 8, 2024 long reads, too short and very specific
5 responses
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Nov 11, 2024 gfastats was not working and I could not remove the sequences at the end of the tutorial
Nov 1, 2024 everything except the two points below in the "what could be improved" section In the Parse mitochondrial blast section, I got two output files. The tutorial doesn't mention that there are two, and it tells me to rename the output, but doesn't tell me which one. In the final step (gfastats), it's not clear what the input file should be. The tutorial just says, "output (Input dataset)"...which unless I missed something isn't helpful at all.
Oct 11, 2024 some details are lacking in instructions
Oct 8, 2024 blast took more than one hour, maybe the step can be omitted in the tutorial and the results file can be provided?
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Climate

8 responses
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3 responses
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Oct 14, 2021 Very nice intro. Learned about the difference between climate and weather!
Oct 8, 2021 Clear introduction in using galaxy to explore/map climate data. More detailed explanation of the inputs @map plot gridded (lat/lon) netCDF data. Did not understand the R as input “variable name as given in the netCDF file”. For other Essential Climate Variables I guess Ill have to change that input?
Jul 19, 2020 Exposure to climate concepts and tool choices.
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May 5, 2021 Sometimes it is hard to find a specific thing that we need to click on when we don't know where it is located on the screen.
2 responses
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1 responses
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Computational chemistry

40 responses
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5 responses
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Jan 19, 2024 step by step demos and the scientifc background behind each step
Jun 10, 2023 Everything If the NxN clustering dendrogram uses Tanimoto similarity, shouldn't it be the higher the the horizontal line, the more similar the data points are to each other?
Jul 31, 2021 AWWWWWWWWWWWWSOME
Sep 26, 2020 Its a neat tutorial. There is no source code for me to follow along. I pulled the autodock vina docker image down and am trying to learn how to use it and this did not give me any commands to execute in the docker container. Everything is coupled to this galaxy software and I just need source code.
Nov 11, 2019 The whole process of creating molecules A video or two illustrating the end goal
3 responses
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Feb 29, 2024 Everything is in steps and clearly explained. Very well done.
Nov 18, 2019 The feeling of creating something on my own Nothing
8 responses
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Aug 13, 2024 out of date , but corrected still
Oct 31, 2022 method present and images
Jun 8, 2022 The explanation of every step which provide understanding even to beginners. The different methods used in different steps of simulation should be explain in a such a way that the person can understand which method he should apply to his experiment.
Feb 26, 2022 Easy to follow and execute. The order of selecting parameters can be sequential as it appears on the galaxy platform
Dec 7, 2021 Easy to follow, good reasoning for each step, mostly successful results For some reason, I can't get this to work with NMR-derived pdb files
Jan 11, 2020 Interpretation of the results and being easy to follow Adding more explanation on how to visualize the trajectory, completing the analysis, also showing how to perform this run with a ligand also will be highly appreciated.
6 responses
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Oct 17, 2023 Extremely easy to follow and I was so impressed that it all works as described. Good maintenance :) I had the mental model of a Jupyter Notebook coming in, so I was trying to figure out how to open the tutorial in my usegalaxy.org account view.
Jan 12, 2023 The interpretation of RMSD, RMSF, and PCA plots.
Feb 26, 2022 The further analysis links seems to be broken/unavailable: https://github.com/galaxyproject/training-material/tree/main/topics/computational-chemistry/tutorials/analysis-md-simulations/workflows/advanced_workflow.ga
Oct 28, 2021 yes yes
May 21, 2020 Analysis of Rg, Hydrogen bonds can also be explained
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Mar 19, 2023 There are error when running it. Tools have different versions and some files create with one tool can not be read for another tool. This is the error in Gromacs log for the Production Simulation : "Attempting to read a checkpoint file of version 22 with code of version 20". And the same is happening in the other Galaxy history about Molecular Dynamics.
Mar 17, 2023 The tutorial try to explain what is doing when selecting params or values. Maybe, some animations about the simulation trajectory.
Aug 14, 2022 merge gromacs topologies doesn't exist in https://cheminformatics.usegalaxy.eu It was not possible to complete the tutorial without this tool
Mar 30, 2022 Great tutorial for intoducing the computational chemistry
Mar 29, 2022 optimization everything is perfect!
Mar 16, 2022 Very simple to understand easy to do Nothing, it is very complete
Jul 15, 2021 Easy to go through and explanations help to understand the results better. Too many abbreviations
Feb 28, 2021 Explanations and step by by procedure explained
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Sep 5, 2023 Very clear. Most of it worked. "Pose scoring with TransFS" crashed for me. Error message said "No score found for record xxxx" for every molecule

Contributing to the Galaxy Training Material

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Jun 28, 2024 Clear steps A warning that the 'listen' gem will guide you to the local instance via 'http://0.0.0.0:4000/training-material/' which gives an 'unable to connect' screen. Even changing to 'httpS://...' does not work. Because of that, I spent a bit too much time debugging that while the link provided in the tutorial (http://localhost:4000/training-material/) does work.
Oct 23, 2021 I have got the following error. The tutorial did not work for me. training-material$ make serve find: ‘_site/training-material’: No such file or directory find: ‘_site/training-material/*/*/slides/*’: No such file or directory find: ‘_site/training-material’: No such file or directory Tip: Want faster builds? Use 'serve-quick' in place of 'serve'. Tip: to serve in incremental mode (faster rebuilds), use the command: make serve FLAGS=--incremental mv: cannot stat 'Gemfile': No such file or directory mv: cannot stat 'Gemfile.lock': No such file or directory Configuration file: /home/alice/scchoi/downloads/training-material/_config.yml Dependency Error: Yikes! It looks like you don't have /home/alice/scchoi/downloads/training-material/_plugins/jekyll-environment_variables.rb or one of its dependencies installed. In order to use Jekyll as currently configured, you'll need to install this gem. If you've run Jekyll with `bundle exec`, ensure that you have included the /home/alice/scchoi/downloads/training-material/_plugins/jekyll-environment_variables.rb gem in your Gemfile as well. The full error message from Ruby is: 'cannot load such file -- bibtex' If you run into trouble, you can find helpful resources at https://jekyllrb.com/help/! ------------------------------------------------ Jekyll 4.2.1 Please append `--trace` to the `serve` command for any additional information or backtrace. ----------------------------
May 19, 2021 Everything :) "topics/introduction/tutorials/galaxy-intro-peaks2genes/tutorial.md" is no longer found, example can be changed to "topics/introduction/tutorials/r-basics/r_introduction.md" instead
Jun 19, 2019 Clearly explained. In the first step (install requirements) - does there need to be an extra step before step 5, that says "conda activate galaxy_training_material" ?
Feb 8, 2019 Clear wording. As a Windows user, I was not able to install requirements successfully.
Oct 22, 2018 Very very straightforward ! Nothing...
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Feb 16, 2019 the option to automatically extract all steps of my workflow instead of typing them all is sooooo increadibly helpful!!!
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May 28, 2024 I back 🇨🇦
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May 19, 2021 That it is a step by step <3 The master branch on my side is called main
Oct 21, 2020 Very clear directions - thank you! The key points at the end are a great concise summary.
Apr 20, 2020 Liked the clean explanation with visuals. Great Job. In clears the process flow for beginners. 1) In situations where I'm working on a feature "F1" in branch "B1", while I prepare to make a PR, do I need to keep my local up-to date with Upstream before PR? 2) After deciding my feature branch is good to go for PR, can I checkout to Master and pull my feature first? What's the process for updating my Master with my new feature I developed? Please answer this. I always have this confusion. Thanks.
Apr 19, 2020 The presentation was very clear
Aug 30, 2019 Every thing was great especially the graphics. Thanks for all the help!! Every thing is fine and up to date though I am not an expert!
Aug 26, 2019 It's easy to understand More diagrams
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Feb 11, 2020 the "Testing the workflow" part I had to deal with "fetch_url_whitelist" option, as my input file was located on my galaxy server.
Feb 11, 2020 the "Testing the workflow" part I had to deal with "fetch_url_whitelist" option, as my input file was located on my galaxy server.
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Aug 14, 2024 Everything is described very extensively and nicely and it's easy to follow Unfortunately, I wasn't able to get through the "Build and preview the GTN website" and "Editing Training Materials on GitPod", I can modify the md template, but it doesn't get reflected in the preview. Clicking on the server address also throws me an error :/
Mar 27, 2023 Good alternative to local running of GTN, thanks
Nov 29, 2022 step by step, screenshots, global structure of the training content, indications when things seem to get wrong when in fact it is not, good job! Difficult to know what to do when GitPod sends back an error after the "make serve-gitpod" command instead of serving a preview of GTN. I can guess it is a GitPod problem and not a GTN tutorial problem, still I feel helpless not knowing what to do to solve this problem.
Oct 12, 2021 Very detailed It would help if the sites name and the drop-down button at the top is static. So even when I scroll to to end of this page, I can easily click on the drop-down button and access other files without having to scroll all the way back up
Jul 8, 2021 Very complete, sufficiently detailed to allow non-computer-science people to go through this with all the questions we could have being answered. The video from GCC2021 training week corresponding to this topic is also very well. Maybe a link to this video for people who need to see things in movement to be reassured would be nice :)
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Mar 28, 2022 The directions on how to create a pull request i think a video could me made.
Oct 11, 2021 The tutorial is so detailed that even a preschooler would get it by simply following the steps! I found it so useful, I'm going to make my first contribution right away! I'd suggest each of the topics under the "objectives" in the overview box be made clickable, so each topic can be reached right from the top without having to scroll all the way down the page.

Development in Galaxy

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Jul 11, 2023 Comprehensive end data tag is missing in outputs section , xml will fail to lint
Mar 15, 2022 Explanations on how to create a galaxy tool Put planemo install first
Mar 15, 2022 clear for a beginner maybe planemo could be the first step, because needed in the wrapper section
Feb 21, 2022 As usal, the step by step procedures. It is not clear that we have to set up the test-data folder and collect the bam files by our own for passing the test in the planemo section.
Jul 1, 2021 Plenty of detail, teaching by example, and context provided > Written in markdown ### General - Should I be working in a clone of `galaxyproject/galaxy`? - Where are all the galaxy tools? They don't seem to be in the galaxy/tools/ dir? This is covered well in the "contributing" video at the end but could have mentioned briefly at the start. More generally, it would be good to explain that `galaxy-core` has built-in tools (with no `.shed.yml` file) and that all contributed tools (like we're building) are installed from an available toolshed. - I'm not sure if I should actually be following along with all of this... should I actually make a PR for a new Bioconda package in a tutorial? It would be great to clarify what the participant should be doing NOW versus what they would do in a genuine tool wrap. Also, presumably the package sometimes exists already in Bioconda? (I used an existing conda package in my 'practice' tool wrap). - At the end of the "Toolshed file" section: "In the case where the directory represents a group of tools or a ‘suite’, there are additional overarching sections into which the above tags fall" ... seems to imply that parent dirs can/should have a `.shed.yml` file too? Or is it only in `suite` and `suite/tool` dirs? Would be great to clarify or provide a link to a toolshed on GitHub as an example. - "Macros" section: should note that whitespace inside `<token>` tags matters, and it will not be trimmed by the XML parser! (Should be picked up by the `planemo lint`) ### Typos - `bellerophon.xml` typo under "discover datasets": `directory="outputs"/>>` - And "Outputs section" (should have closing `/>` on `<data>` according to planemo): `<data name="outfile" label="${tool.name} on ${on_string}" format="bam">` - "crate an ad-hoc Galaxy" ### Planemo - Didn't work when `pip` installed into `conda` env (dependancy errors). `pip` install into a `virtualenv` env worked. - `pip` installing `planemo` into virtualenv requires `apt install python3-venv` as a dependancy **Some small issues with Planemo** - `tool_test_output.html` output is a bit weird to navigate - buttons don't look like buttons (no hover effect) so most of the content is hidden until you realise there are clickable elements - `planemo serve` doesn't print the local address at the end of output (had to scroll up a few pages to find `http://127.0.0.1:9090`)
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Apr 18, 2023 - (Maybe just me) Too much content, too fast. - Account on a production Galaxy instance is required. I did not have one and it took me a while to get set up - Some familiarity with Jupyter Notebooks seems to be another prerequisite
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Dec 7, 2023 Good tutorial, but it is outdated. There is no training branch to be found on the galaxy Github (no old training, no new training2022 or the like). I managed to find the branch here: https://github.com/galaxyproject/galaxy/pull/14339 and cloned https://github.com/jdavcs/galaxy/tree/training2022 which made me able to do the training. But I believe that is the reason there were minor differences furtherdown the tutorial as it is a year old so I think this is the problem that would fix the rest. Updating to latest changes

Ecology

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Jan 20, 2021 Very clear Where to find the tools (not always easy in the toolbar)
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Apr 14, 2021 I liked that it is possible to use real data and explore multiple tools. It was relatively easy to follow all the way to the final step. I could also take the Structure output and run it through Structure in Galaxy or in my own PC to further demonstrate that the SNP data can be analysed with population genomic software. Some of the instructions need to be updated to the latest versions of the tools available in Galaxy. I could not tell which population (1 or 2) was the freshwater and which one was the oceanic, so I assumed 1=freshwater, 2=oceanic. It would also be good to see some of the "expected" results, just to verify that what has been done is working fine and that students are on the right track.
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Jul 27, 2023 Very helpful tutorial, thank you for posting it! You should state explicitly what the input file(s) should be at each step. Each function produces multiple outputs; It is not clear what I am supposed to run Stacks: populations ON, for instance.
Jul 12, 2023 I liked that there was an example dataset to follow along with, and questions to be answered as you went along. It really helped me understand what I was supposed to be looking for, whether something was actually working or not, and what real outputs would look like. Stacks (not sure about Stacks2) process_radtags doesn't work when the data are converted from fastqsanger.gz to fastqsanger. Data have to be left in the fastqsanger.gz format to properly demultiplex. I spent a lot of time trying to figure out why this step of the tutorial wasn't working. Also, I couldn't find the Charts function, so I ended up skipping this step of the tutorial.
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Nov 28, 2024 Hi, either I am doing something wrong, but recentrifuge returns an error, Unsupported file format, when submitted with Kraken2 Report file, as the tutorial suggests. It works with Kraken2 Classification file. Here is my history on Galaxy Europe: https://usegalaxy.eu/u/igor/h/recentrifuge
Mar 27, 2024 I found the tutorial very instructive, but special kudos to the contamination identification section with the Recentrifuge interactive plot. Many thanks! When clicking on the Recentrifuge reference pointing to the paper, I see the DOI appears incomplete: it should be 10.1371/journal.pcbi.1006967 (the last number is missing on the tutorial).
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Apr 23, 2024 Reusability and ease of execution, it's really neat! There seems to be more columns in OBIS data now, so it is maybe better to cut based on column names and not based on hard coded column number. May I also suggest to include the link to obisindicators in the text https://github.com/marinebon/obisindicators ? The text states "Obisindicators is an R library developed during the 2022 IOOS Code Sprint. The purpose was to create an ES50 diversity index within hexagonal grids following the diversity indicators notebook by Pieter Provoost linked above. " but I didn't manage to find the link. Thank you so much!!

Epigenetics

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Feb 3, 2024 Details For someone trying without support, there are some mandatory fields in hicbuildmatrix that are not explained: 1. Need to add the hicfindrestsite step to generate the compulsory contact bed file 2. Need to add a dangling sequence for the restriction enzyme for hicbuildmatrix
Jan 5, 2023 The tutorial was simple to follow and was a great balance between guidance and letting do things myself Some of the steps seem outdated with some parameter having changed names or being not available anymore. But it doesn't prevent the completion of the tutorial.
Jan 3, 2023 I like the detailed instructions of this tool. When I tred to follow the steps of hicBuildMatrix and ran it on usegalaxy. It showed that I need to provide BED file with all restriction cut places. Could you tell me how to choose to use the bin size or where I can find the BED file?
Feb 1, 2021 Covered all the steps Parameters could have been explained
Jul 19, 2020 step wise explanation was very clear comparison of two HiC datasets
Dec 9, 2019 Note from @jennaj: Noticed mismatched tools across tuto components. The "Reads mapping" step description states "We have used the HiCExplorer successfully with bwa, bowtie2 and hisat2. In this tutorial we will be using Map with BWA-MEM tool." *However* the "Hands-on: Mapping reads" box has the mapping tool specified as "Map with Bowtie". The tool name doesn't fully match a Galaxy wrapped tool but looks as if it was intended to match "Map with Bowtie for Illumina" tool from some earlier tutorial revision, but the tool options/settings are actually for "Bowtie2" (tweak SAM/BAM output). The tuto workflow uses "Map with BWA-MEM (Galaxy Version 0.8.0)" which isn't available at EU or ORG (or that version is hidden in the tool panel + tool versions menu). --------- Punchline ... three different tools are mixed up, at the first step of the tuto after loading the initial fastq inputs. Probably should adjust to make all for either Bowtie2 or BWA-MEM using a version available at EU (so it can be run there). Be nice to have this work at (at least) one of the usegalaxy.* servers :) ORG doesn't include HiC tools. Will ticket this and whatever else is found after reviewing the remainder of steps.
Feb 28, 2019 Nothing bad, just I do not have sufficient background knowledge to comprehend everything. Nevertheless, very well-structured for a beginner to learn.
Sep 18, 2018 perfect step by step !!!! maybe use human data ??
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Oct 24, 2024 option along with version numbres help
Oct 23, 2024 more example
Apr 7, 2024 Actually, I encountered an error while transforming the MethylDackel file to a bedgraph file. The error message was: "unrecognized line 1 of trackless: chr1 5190715 5190717 100 1 0". After that, I wasn’t able to replicate the subsequent steps. I suggest providing clearer instructions for each step. Additionally, I would like to know more about how to group the data for analysis. This part feels a bit too concise. Overall, this material has been helpful for me to apply it to my own data, although I may need to explore additional tools&Analysis on my own. Thank you! And I was wondering if it is possible to build a comprehensive analysis workflow for Methyl-BS-Seq data in Galaxy similar to the cross-package Bioconductor workflow for analyzing methylation array data (published in F1000Research). :)
Jun 9, 2022 nothing everything
Jan 13, 2022 Data set can not be found
Nov 17, 2021 The programs were not available at Galaxy
Sep 20, 2021 It would be great if this can be updated based on the newest version of the packages used in the tutorial. Some of the parameters cannot be set as shown in this tutorial or should be set in a different way.
Sep 8, 2021 Instructions about finding tutorial data in a Data Library need to be updated. In this tutorial and probably others. Tutorial data is now nested at usegalaxy.* servers -- and that change is confusing some learners. I've been telling people to search data libraries with the keyword "GTN" then to navigate down through the topic to the specific tutorial. Not all public servers will host the data in Data Libs, so even that advice needs a tune up to be consistent/accurate across tutorials. (@jennaj)
Mar 24, 2020 The degree of detail. I loved that even the parameters for the different tools were explained. I don't know if this is comparable to a real experiment analysis, but it surely felt as that. Congrats! The Genrich tool is only available at the GalaxyEurope server. It would be nice that a warning would be given at the beginning of the tutorial, so that the whole analysis could be done there and avoid migrating data between Galaxy servers.
Feb 4, 2020 The tutorial is self explanatory and very easy to follow for individual hands on
Sep 26, 2019 The good explanations during hands-on training Maybe too different analysis for one day (HiC and epigentics), maybe a longer session for each would help understanding
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Jun 13, 2022 it was clear maybe you could explain the file formats and what the tools do in a more clean way
Dec 16, 2021 Well detailed method of ChIPseq and associated explanations The title in itself doesn't really reflect the final results of the tutorial, with the data used one do not really identify TAD on the inactive X chromosome...
Jan 10, 2020 In step 6 it is explained to insert each of the datasets one after the other (with Concatenate datasets tail-to-head). However, one can insert more than one dataset at once with this tool, so why not do that? Also, it should read "Redo for the remaining four outputs of MACS2 callpeak" - it is six in total and in the first step you concatenate two and then add the remaining. Why are the bedgraph files created if they are not used for anything?
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Oct 25, 2024 easy to follow show how to use mulitiple replicates
Nov 30, 2022 For the areas where they mention that other analysis options or functions are available please link to other website containing information about those options
Mar 22, 2022 The fact that there are explanations for all steps. All were perfect!!!
Jun 18, 2021 Everything was explained in detail, easy to follow
May 10, 2021 The depth of the tutorial, the examples of bad quality data, the explanation why these tools are used and sometimes alternatives, and the overview figure in the conclusion.
Apr 21, 2021 Easy to follow
Oct 15, 2020 Everything it is good overall
May 29, 2020 Detailed explanation of each step Comparison of two ATAC-Seq datasets
May 28, 2020 Quite easy to follow Bit more interpretation of output
Apr 12, 2020 Entire organization, rationale for the steps taken link to smaple out put or all steps like EMBOSS tutorial does
Mar 24, 2020 The degree of detail. I loved that even the parameters for the different tools were explained. I don't know if this is comparable to a real experiment analysis, but it surely felt as that. Congrats! The Genrich tool is only available at the GalaxyEurope server. It would be nice that a warning would be given at the beginning of the tutorial, so that the whole analysis could be done there and avoid migrating data between Galaxy servers.
Mar 10, 2020 I have to say the full workflow is very useful for the people who did't know this for a long time, thank you so much. but the tool 'Genrich',I did't find it on the Galaxy... I can't find some tools in Galaxy,
Feb 26, 2020 so great!!! its so helpful!!!!! nothing.
Feb 25, 2020 The easiness and the clarity of the examples provided. A print version of the tutorial or pdf to save for offline use.
Dec 12, 2019 a good resource for a training session too many steps where you have to 'prepare' data, e.g. sorting the provided bed file
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Jul 1, 2021 update is required
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Aug 13, 2024 el tener una idea clara de como es el protocolo la última parte del análisis está pobre en imágenes de los resultados y es la parte más interesante del análisis del chip-seq.No pude hacer la parte de "Click “Visualize” on the page header and select “Create Visualization”" porque no aparecían esas opciones
Jul 11, 2023 It is a wonderful tutorial. I am extremely thankful for sharing such an informative and detailed tutorial. I wish that for all topics be the same.
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Nov 19, 2024 modification in MACS2 to detect peaks plotting heatmaps and explaining each part , more explanation in video format ,
Oct 17, 2024 customization for Cut and run using MACS2 and all the QC I would like ot understand more about each type of graphs how to understand for different Cut and run expt eg how input will differ from TF or the Histone mark antibodies, also would like a video of this sometimes there is better explanation than written.

Evolution

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Jun 29, 2024 Tools for identification of drug resistance and generating transmission cluster pattern
Oct 31, 2023 Very clear tutorial
Oct 8, 2023 It was great to see that I achieved results by following the tutorial. In Part-1 Rstudio step was difficult to understand for me.
Jan 7, 2023 All except the R studio that is not yet clear Rstudio
Jul 5, 2022 This hands on tutorial made me understands some of the concepts raised in the webnar A note on the estimated run time of the on the provided data, this will help to know if i have done something wrong.
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Jun 12, 2024 the ease of using RStudio to manipulate the phylogenetic tree It would have been an added bonus to show how to map multiple metadata (origin, time of sampling, DR-mutation, etc...at the same time) on the tree in R.
Oct 30, 2023 How to develop and analyse a phylogenetic tree
Oct 5, 2023 The pipelines Time to go through all tutorial.
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Jul 1, 2024 The materials presented and resources provided where put together well. I liked that questions could be asked throughout the presentation and that I could ask basic questions without feeling like they were too basic. I think the content was well pitched for someone like me who had phylogenetic training 20 years ago. I liked the breadth of the content covered but my knowledge is so poor that it did overwhelm me towards the end. That was expected though. Although I can see the workshop can't go any longer, as my brain couldn't cope, I did struggle towards the end to keep pace with everything. Having said that, it was good to get the breadth of content in and I will enjoy revisiting the resources provided to consolidate the knowledge. A follow up workshop is really needed as the distance matrices and the best models to choose seemed like they needed more time spent on them.
Jun 15, 2024 Please Provide the way to plot a mid point root tree.
May 28, 2024 It was clear and well handled from basics to hands on tutorial I would add an aminoacid sequence example

FAIR Data, Workflows, and Research

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Mar 11, 2024 It's a clear overview of all the functionality that's available in the ro-crate-py package - I feel like I have a good understanding of how to use it going forward - clearer distinction between commands that must be run in a terminal (e.g. mkdir) and commands that can be run in a notebook. Also the terminal commands are assuming JupyterLab is running on a Linux machine which may not be the case. - The example for the `rocrate add` command could be improved by creating a separate repo for the data rather than cloning the whole ro-crate-py repo. Having to deal with a long path of nested directories makes it harder to follow this section.
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Apr 2, 2024 I liked the topic itself, as well as the hands on guidelines with quiz The narrative is to long and to monotonous. It can be simplified.
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Oct 9, 2024 The rich documentation
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Foundations of Data Science

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Jun 10, 2024 Structured logically and well, Nice integration of Biological themes compared to other R tutorials. Received some outputs (using Posit Cloud) that were different than expected, causing some confusion: 'snp_positions[snp_positions > 100000000]' returned items LESS than that number, and '<' returned the item greater than that number.
May 24, 2024 The pace New tutorial working with sequencing data
May 25, 2023 Great explanations and pace
May 24, 2023 All the steps and the clarifications
Nov 9, 2022 Flow of information Add videos and demonstrations
Sep 9, 2021 none of the essentials is working gx_put(), gx_get(), and gx_save() none of the essentials is working gx_put(), gx_get(), and gx_save()
Mar 28, 2021 Simple languange, hands-on example and exercises with answers hidden. I know it is a lot to ask, but adding matrices would be helpful
Feb 17, 2021 I like the examples,being related to genomics . I am not sure if I would grasp it without previous knowledge.
Feb 15, 2021 Very helpful basics of R
Sep 19, 2020 The hands on explanations Couple of sections where the description is a little vague
Aug 2, 2020 Good with exercises > snp_chromosomes_2 <- as.numeric(snp_chromosomes_2) Warning message: NAs introduced by coercion In the above code, I think need to correct object name from snp_chromoosome_2 to chromosme_2 (we assigned this name)
Jun 30, 2020 Good guide, with usefull examples
Jun 7, 2020 Thank you so much for providing the related material for R
Apr 3, 2020 It was easy to follow
Feb 12, 2020 The instructions were clear and neat. Also, it covers important aspects of the language. There should be one task that push us to combine and use the learned knowledge.
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Dec 15, 2022 generally excellent the file used is different from the tutorial
Feb 15, 2021 Very interesting libraries (tidyr and dplyr) for data analysis More self training exercise
Dec 3, 2020 so easy and clear
Jul 3, 2020 Easy to follow and very usefull examples
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Nov 15, 2024 igv
Jul 10, 2023 The step-by-step explanation of the entire pipeline Some of the commands are incorrect, and some of the explanations are not clear enough
May 16, 2023 very intuitive and colors of the page helps alot, thank you
May 4, 2023 quite explanatory, understandable terms update it or make sure the platform possesses the features explained by the tutorial. "Less" command was not available. There is no command or instructions to generate dc folder
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Sep 1, 2023 It's so didactic, well thought over and it encompasses all the dark corners of jq usage. I had a hard finding the dataset used in this tutorial because the url are no longer available. Managed to find the .tsv files that I've converted back to json
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Jan 19, 2024 Its easy to understand Some videos would be more useful
Oct 19, 2023 I think it was very straightforward and easy to follow This part: Given the following variables: a = 2 b = 1 c = -1 I think the variables should be separated, I was really confused for a bit
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May 19, 2024 Explanatory steps to follow Points directs to the code rather than too many words to extract data
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Jun 19, 2024 Generally clear work flow examples Split file according to the values of a column does not appear as a too. I managed to use split by groups. The regular expressions section is totally unintelligible and needs a complete re-write for clarity
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Aug 19, 2024 When running the code to download the files, I was getting error messages and was unable to download them leaving me unable to get the full experience in the Jupyter notebook in the files and csv training in the introductory training.
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Sep 6, 2024 Well explained, lots of examples Was not able to download the dataset
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Sep 17, 2024 I liked the challenge it presented, especially as I got every single one wrong on the first try. I, good practice to make sure you get it right in the end. I am not sure that I would change anything, except, I am not sure if some of my answers were correct or not, which may or may not be done to using a mac.
Sep 16, 2024 The support in the troubleshooting room was great, they quickly helped clear up my initial confusion on what we were being asked to do. It wasn't clear in the guidance what we were being asked to do during the tutorial. It wasn't obvious to everyone that for the first section we weren't required to try out the code ourselves but instead had to just hit shift/enter to see the result of the examples given.
Sep 16, 2024 learning something new
Sep 16, 2024 I need a bit of guidance with this probably a one to one or a tutorial
Sep 16, 2024 That it showed you how the codes worked after running them and what they looked like before More of an explanation to help understand/remember the codes and why they work that way. It's a lot of information to take in for someone with no coding background.
Sep 16, 2024 Unfortunately nothing The instructions are not clear, this put me off python completely. I use excel so understand the text bit but accessing and interacting with the software did not work on my computor, the instructions are not direct, they say open a new terminal when "terminal" is not an option under file - new. Very frustrating experience, will not repeat.
Sep 16, 2024 Good to practice, explained pretty well, even to a novice!

Galaxy Server administration

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Mar 18, 2022 The straightforward pedagogical approach I think it is perfect as is
Mar 15, 2022 For me it is not clear wether the apikey example use of vaults is the best. Might it be better to set an example about ssh passwords to connect remote servers?
Nov 4, 2021 Really clearly written and well explained, including details that can go wrong or be confusing (the cowsay bit gave me a chuckle). Not overwhelming, unlike some other tutorials I tried.
Feb 1, 2021 It gave an excellent crash course in Ansible and how best to use it in Galaxy Possibly one or two links to other Ansible resources in the docco, but can't think of anything else.
Jan 25, 2021 The incremental approach to a rather complex system I was confused at first by the "service" service. More real, less abstract examples would be clearer, IMO
Jan 25, 2021 specifiying that all commands (including andible-galaxy) should be rin in the `intro` directory, I had to rsync my new `~/roles` folder to intro
Jan 25, 2021 It is easy to follow
Jan 25, 2021 Clear examples More information on using git repos with ansible would be helpful
Jul 17, 2020 This is something new. I enjoyed it.
Mar 2, 2020 All of it Looks very good, with basic sample tasks.
Feb 14, 2020 Step-by-Step guide, simple and well informative
Jul 1, 2019 Examples and documentation are easy to follow
Nov 15, 2018 TEST TEST
Nov 2, 2018 excellent intro, thanks!
Oct 30, 2018 It's easy to follow. For clean Ubuntu 18.04 Ansible couldn't find python (it was not installed, weird), so it crashed. There should be rule added to check and install python if it is not installed. Refer to this solution - https://gist.github.com/gwillem/4ba393dceb55e5ae276a87300f6b8e6f.
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Jun 19, 2023 very nice progression in the explanation! I like the practicality of the tasks the "openstack" provider has been demoted(?) so the source "terraform-provider-openstack/openstack" has to be added to the configuration to make this work now. it would be nice if the cluster example worked with a plain centos7 image. there does not seem to be a condor package in plain centos7, so I guess it would have to be replaced by some other cluster service, e.g., haproxy and nginx. still, it was nice to see the NFS setup - although the automounter did not work for me, that's not the point of the tutorial. thanks!
Jun 24, 2021 realistc examples More details regarding used scripts and templates
Jun 20, 2020 Basically I love all of them, It's simple, clear and easy to follow. Would be nice to have more complex examples to follow, if that possible
Dec 19, 2018 Really detailed, could use it for my project for creating my project maybe go deeper and show a template for a project
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Jul 31, 2024 The real life experience Error SSL uncert in my VM, as stated: https://github.com/galaxyproject/ansible-galaxy-tools/issues/52
Mar 17, 2022 I would be great if it could explain how to run ephemeris from a different machine (for example my local machine) but deploying galaxy on the vm
Mar 14, 2022 The slides gave a really useful overview of toolsheds and how to configure them. It would be useful if the links to ephemeris commands would open in a new tab (I would prefer this for links in general but especially in this case as you have to do it in the middle of a task and it's not just further reading)
Jun 29, 2021 The practical approach
Jan 27, 2021 easy to understand and follow
Jan 26, 2021 It shows me a really easy way of installing tools from tool shed avoiding the use of the graphical interface. That is perfect when you need to install many tools at once. It could be explained how to include this tasks in the ansible playbook (if possible) in the case of a full re-installation of Galaxy. Or maybe better separate the two steps...
Jan 26, 2021 all the examples worked The flow of the tutorial feels awkward in places - you extract the workflow but then install a tool singly before going back to the extracted .yml to do a batch. Not directly related to this tutorial but coming from the previous Galaxy setup tutorials, I'm left thinking - what happened to Ansible and the concept of reinstalling the entire Galaxy in one playbook?
Jan 26, 2021 very beneficial pace!
Jan 26, 2021 Everything, from top to bottom.
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Jul 26, 2024 Make me to the point Anyway, kinda stuck at some unexpected error en route (like my machine use python 3.12, hence lack 2to3 lib)
Mar 14, 2023 Everything <script>console.log("Helena Testing");</script>
Aug 30, 2022 The instructions were clear and helpful (especially with the video alongside) It would be super helpful if there were more subsection links! I set followed this tutorial to setup a server for my team, and when they had questions or wanted more info on why or how I did certain things it would have been nice to be able to link them more specifically to the step I wanted instead of the bigger section and then giving them key words to search for
Jul 28, 2022 relatively easy to follow, concept explanations are great
Jun 29, 2022 tree -l 2 was helpful as otherwise unclear which file goes where Current version of the tutorial is broken, consider rolling back to archive. Ansible errors very hard to troubleshoot - ideally add more tips where things can go wrong, for ex ansible vault seems to enter an unfixable state if you mess up the secret yml file and have to make it again
Mar 18, 2022 how seamless it was to deploy it
Mar 16, 2022 Clear and structured - everything ran without issues on my machines
Mar 16, 2022 the structure, it was very well organized
Feb 15, 2022 Pretty simple step-by-step; A couple of syntax errors are included to make things "interesting" when trying to deploy. Found another syntax error in the referenced tutorial: In the galaxy.j2 file, "location /_x_accel_redirect" should be "location /_x_accel_redirect/"
Jan 15, 2022 Code examples that you customize to your server set-up; hints and sidebars are very helpful; as is the in-depth explanation of what the code is doing. One solution to errors that arise would be to try newer playbook versions. Although the tutorial cautioned that newer versions could create problems - in my case it solved problems. I found that the version of galaxyproject.galaxy used in the tutorial-- version: 0.9.16 was incompatible with Ubuntu 20.04 LTS - resulting in a failure to install "futures". When I changed to the newest galaxyproject.galaxy version the problem was solved.
Sep 14, 2021 I think there is an error in the instructions around which galaxy release to use. https://training.galaxyproject.org/archive/2021-08-01/topics/admin/tutorials/ansible-galaxy/tutorial.html#galaxy step 9. Fails with a pip install error for attmap at galaxy dependency installation: FAILED! => {"changed": false, "cmd": ["/srv/galaxy/venv/bin/pip3", "install", "--index-url", "https://wheels.galaxyproject.org/simple/", "--extra-index-url", "https://pypi.python.org/simple", "-r", "/srv/galaxy/server/lib/galaxy/dependencies/pinned-requirements.txt"], "msg": "stdout: Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple\nIgnoring importlib-metadata: markers 'python_version < \"3.8\"' don't match your environment\nIgnoring importlib-resources: markers 'python_version < \"3.7\"' don't match your environment\nIgnoring pathlib2: markers 'python_version < \"3.6\"' don't match your environment\nIgnoring ruamel.yaml.clib: markers 'platform_python_implementation == \"CPython\" and python_version < \"3.8\"' don't match your environment\nIgnoring typing: markers 'python_version < \"3.5\"' don't match your environment\nIgnoring zipp: markers 'python_version < \"3.8\"' don't match your environment\nCollecting adal==1.2.4\n Using cached adal-1.2.4-py2.py3-none-any.whl (55 kB)\nCollecting amqp==2.6.0\n Using cached amqp-2.6.0-py2.py3-none-any.whl (47 kB)\nCollecting appdirs==1.4.4\n Using cached appdirs-1.4.4-py2.py3-none-any.whl (9.6 kB)\nCollecting attmap==0.12.11\n Using cached attmap-0.12.11.tar.gz (9.9 kB)\n\n:stderr: ERROR: Command errored out with exit status 1:\n command: /srv/galaxy/venv/bin/python -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '\"'\"'/tmp/pip-install-rswp62oy/attmap_d1e6f1f187954e539109df4d7760fde7/setup.py'\"'\"'; __file__='\"'\"'/tmp/pip-install-rswp62oy/attmap_d1e6f1f187954e539109df4d7760fde7/setup.py'\"'\"';f = getattr(tokenize, '\"'\"'open'\"'\"', open)(__file__) if os.path.exists(__file__) else io.StringIO('\"'\"'from setuptools import setup; setup()'\"'\"');code = f.read().replace('\"'\"'\\r\\n'\"'\"', '\"'\"'\\n'\"'\"');f.close();exec(compile(code, __file__, '\"'\"'exec'\"'\"'))' egg_info --egg-base /tmp/pip-pip-egg-info-2gc_ov_9\n cwd: /tmp/pip-install-rswp62oy/attmap_d1e6f1f187954e539109df4d7760fde7/\n Complete output (1 lines):\n error in attmap setup command: use_2to3 is invalid.\n ----------------------------------------\nWARNING: Discarding https://files.pythonhosted.org/packages/d0/d4/8b8fca155270a6675bac9a1e49b7c616ae763f66af7b836042ecfc805552/attmap-0.12.11.tar.gz#sha256=95b1f7dbcdad7278a3702fa921be6271046c96e1c9ed9feb10e0d4c13092b0a0 (from https://pypi.org/simple/attmap/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.\nERROR: Could not find a version that satisfies the requirement attmap==0.12.11 (from versions: 0.1, 0.1.1, 0.1.2, 0.1.4, 0.1.5, 0.1.6, 0.1.7, 0.1.8, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 0.10, 0.11, 0.12, 0.12.1, 0.12.2, 0.12.3, 0.12.4, 0.12.5, 0.12.6, 0.12.7, 0.12.8, 0.12.9, 0.12.10, 0.12.11, 0.13.0)\nERROR: No matching distribution found for attmap==0.12.11\n"} This occurs with galaxy_commit_id: release_20.09 (as per the instructions), but changing to release_21.05 makes the error go away.
Jul 1, 2021 Simple and short and easy THX
Jun 28, 2021 All points were very well explained
Feb 1, 2021 Some good things to note and keep track of regarding moving to production, especially updating the version.
Feb 1, 2021 Realy clear and solid explanations of how to use Ansible for Galaxy installation
Jan 27, 2021 The clear explanation of every part of the roles, modules etc. What they do why they're there. Even if I wasn't interested in everything it's good to know that if I ever need that information I can look back to this tutorial I don't know if it can be improved but the actual time of the tutorial is really long. After watching it, I totally understand why but if it could be something like 1 hour videos (or less) that would be less tiring. Of course I am fully aware that there is a broad range of topics that need to be covered.
Jan 27, 2021 the step by step exercises for me as a noob some diagrams or schemes would often be helpful to see how things relate to each others
Jan 25, 2021 very easy to follow; excellent documentation note about using non- let's encrypt certificate
Jan 25, 2021 very structured and understandable templates/nginx/galaxy.j2 -> "uwsgi_pass 127.0.0.1:8080" should not be configured statically and changed to a variable from the groups_vars if the port is changed there in the uwsgi variable settings
Aug 10, 2020 It is very practical tutorial I had to change those two variables to make it work on my ubuntu machine: "virtualenv_command: pyvenv" as it also recommends in README but not the default in the galaxy role "__galaxy_mutable_config_dir: "{{ galaxy_root }}/var/config" " my Ansible didn't understand the previous line defined variable, so I had to define "__galaxy_mutable_config_dir" base on "galaxy_root" variable
Jul 7, 2020 In the nginx-part, the template needs an update to reflect 20.05 changes. The folder /blue doesnt exist anymore, its just "alias {{ galaxy_server_dir }}/static/style" # The style directory is in a slightly different location location /static/style { alias {{ galaxy_server_dir }}/static/style/blue; expires 24h; }
Jul 6, 2020 In the section "Galaxy" we add uchida.miniconda which has to run as galaxy user and a few linse above is explained that a new user is created without sudo privileges for security reasons. The execution of uchida.miniconda with become: true and become_user: galaxy will fail, because this role requires sudo. I tried to install the dependencies tar and bzip2 in my playbook beforehand, but the role still requires sudo to check if the packages are installed. When i install the package with a root-user, it is possible to execute the /tmp/Miniconda...sh file with the galaxy user. Not sure if other stuff works in miniconda too. Why does this role need to be executed as galaxy user? This is somewhat unclear and leads to an installation-error.
May 8, 2020 The difference between galaxy_server_dir and galaxy_root is unclear. Should they be nested? Which of these is needed in a shared file-system? Maybe provide best-practice values for both, so it becomes more clear how they interact with each other.
May 5, 2020 Tutorial includes code steps very clearly. This is focused for paid distros. Centos 7/8 builds do not work due to package requirements and availability
Mar 2, 2020 Following the tutorial is pretty straightforward It would be interesting to have a big picture of the processes / config files. Literally a big picture about which parts are we configuring and what are the implications.
Mar 2, 2020 exhaustive it would be nice to go a bit slower during the Galaxy installation, it was quite quick !
Feb 14, 2020 Everthing
Jul 1, 2019 extremely well done - thank you training material authors and presenters 1) ssh connection timeout is too short, disconnects while running playbooks. (2) sometimes the insertion point for yaml section in the exercices could be more explicit
Jul 1, 2019 I already followed this tutorial by my own before GCC. I would add all the galaxy.yml and modify it instead of copy/paste some element in the playbook. For me, it's easier to get update shiped with each Galaxy update.
Jul 1, 2019 Very good step by step procedure. perhaps more emphasis on some steps (geerlingguy.pip during supervisord)
Jul 1, 2019 well explained :) sometimes it is not clear in the exercises which files have to be edited, or the code is not ready to copy-paste, which leads to misunderstandings. I would love to see the whole explanation of the variables of the config files you did (specially nginx) written down to check them when needed.
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Nov 4, 2024 clear and step by setp, but had to stop at Exploring the CVMFS Installation because it wasn't loading the cvmfs filesystem for data.galaxyproject.org. here is the output from autofs (cvmfs-config.cern.ch) (manager 'default') switching proxy from (none) to DIRECT. Reason: set random start proxy from the first proxy group Nov 04 15:01:29 csci-galactose cvmfs2[1305995]: (cvmfs-config.cern.ch) (manager 'default') geographic order of servers retrieved from cvmfs-stratum-one.cern.ch Nov 04 15:01:29 csci-galactose cvmfs2[1305995]: (cvmfs-config.cern.ch) (manager 'default') switching proxy from (none) to DIRECT. Reason: cloned Nov 04 15:01:30 csci-galactose cvmfs2[1305995]: (cvmfs-config.cern.ch) CernVM-FS: linking /cvmfs/cvmfs-config.cern.ch to repository cvmfs-config.cern.ch Nov 04 15:01:30 csci-galactose cvmfs2[1306050]: (data.galaxyproject.org) no public key loaded Nov 04 15:01:30 csci-galactose cvmfs2[1306050]: (data.galaxyproject.org) (manager 'default') switching proxy from (none) to DIRECT. Reason: set random start proxy from the first proxy group Nov 04 15:01:30 csci-galactose cvmfs2[1306050]: (data.galaxyproject.org) (manager 'default') switching proxy from (none) to DIRECT. Reason: cloned Nov 04 15:01:30 csci-galactose cvmfs2[1306050]: (data.galaxyproject.org) failed to download repository manifest (2 - malformed URL) Nov 04 15:01:30 csci-galactose cvmfs2[1306050]: (data.galaxyproject.org) Failed to initialize root file catalog (16 - file catalog failure)
Jul 27, 2024 The regular concise and easy to follow instruction CVMFS error describe in: https://help.galaxyproject.org/t/error-while-checking-cernvm-fs-for-setup/8877
Mar 18, 2022 Very clear! It's simple and very important to know
Mar 17, 2022 the pace, simon explains everything really well and understandable
Mar 15, 2022 Clear explanation of what CVMFS is for and how it works
Jun 29, 2021 Very clear explanation
Jan 28, 2021 CVMFS is a great addition both for Galaxy and in general. It was a great thing to know. In the tutorial nothing. It's perfect. I would like CVMFS to include reference genomes indexed for methylation analysis (e.g. with Bismark). I dropped a question about it in slack as well.
Jan 27, 2021 very easy to follow and understand.
Jan 27, 2021 This is really cool!!!! For the most used datasets (for ex. hg38) could we have a local copy, or would that be irrelevant? Could you explain how to calculate a good cache space? If I use a cluster, will I need to configure this FS in each node (given that the folder is at / directly)?
Jan 26, 2021 Clear, straightforward, brief and complete
Jan 26, 2021 You guys rock! this CVMFS thing is so coool!
Jul 4, 2019 the samples are great and its great to have the copy capacity, but some of those copies could mess people up (ones with ..., snippets of yaml that start with ---, etc)
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Jul 3, 2019 this was way super cool maybe specify that the parts in Setting admin... part 1 should go under the galaxy: heading for those not as familiar with galaxy configs? or can we assume they're all savvy? templates/deployment_web.yaml -> dash, not underscore
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Jul 1, 2021 Very clear, even though the material is complex
Jan 28, 2021 This is a very well written tutorial. I really appreciated how we were shown ways to thoroughly check that rabbitmq was working as expected before moving on to the next step.
Jan 28, 2021 Good detail The tutorial assumes a bit more knowledge than a lot of the others so it won't be as useful for someone who comes to it stand-alone as a pulsar via ansible setup guide
Jan 28, 2021 This is amazing!
Mar 4, 2020 Content Maybe still take it slow when editing the various files. It's sometimes hard to follow with the numerous kind of configuration files.
Mar 4, 2020 Very comprehensive tutorial. Helped me a lot
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Feb 5, 2021 The simplicity Add a short section on using nginx basic authentication to secure it from public eyes
Jan 29, 2021 quick and easy Link to guide on how to secure it
Mar 4, 2020 Thanks to ansible, easy to install :)
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Jul 1, 2021 The installation part was very clear and good to follow The Grafana part was difficult to follow because the version of the tutorial was different from the installed one
Jan 29, 2021 Ansible instructions worked I found the content on Grafana and monitoring/alerts really confusing, it felt almost like it is for an older version of Grafana.
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Jul 27, 2024 Easy to follow I meet the bug: https://github.com/apptainer/apptainer/issues/2027 Which fix by: `sudo apt install apptainer-suid fix the bug` Ref: https://www.reddit.com/r/HPC/comments/1cegt49/apptainer_without_fakeroot_or_setuid/ Please kindly update some kind of install apptainer-suid in the ansbile role
Mar 18, 2022 Very simple and clear
Jun 29, 2021 Very interesting, the step by step approach is very clear
Jan 27, 2021 all of it! maybe some notes about what may require proxies
Jan 26, 2021 Great clarity. Thorough tutorial, leaves no stones unturned "Modify the file" parts (e.g. points 1. and 5. of "Hands-on: Configure Galaxy to use Singularity") are clear and a useful exercise to better understand the ansible and galaxy hierarchy, but if for some reason you made a mistake in a previous step, it could be useful to also have a snippet of the whole modified code to fasten the correction process and avoid backtracking.
Jan 26, 2021 Nice, easy to follow I'm coming at this as a non-galaxy user so jumping straight into the interface was initially a bit confusing, a quick video tour of the Galaxy interface (~5 minutes) beforehand would have made this easier for me
Jan 26, 2021 Everything is great. sysadmin part could be little bit slower, its hard to catch on for us who are not from purely IT background.
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Jul 31, 2024 This feature is really covenient in my case I think what if you instruct us more about "non --legacy" case
Jul 12, 2021 very clear and straightforward.
Jun 29, 2021 Very clear step by step
Jan 29, 2021 There is a big chunk of the tutorial misssing from the video (the video is stuck in the setup stage).
Jan 27, 2021 very helpful some video issue around 8m
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Jun 30, 2021 Very clear explanations
Jan 28, 2021 Easy and useful Regarding 'expose_potentially_sensitive_job_metrics' , is there an option to expose different metrics for admins and general users? For example, creating different profiles in templates/galaxy/config/job_metrics_conf.xml.j2
Jan 27, 2021 I really need this knowledge. I have stuck in the part of editing templates/galaxy/config/job_conf.xml.j2 because some lines differ from the resulting file from previous session (namely singularity was set as default) and I had to compare the file showed in the video with the file I had. I took some time, but it worked at the end. It seems not so complicated now, but it will be when connecting to a living cluster. What happens when I have SLURM already configured at the server? And MUNGE (this guy made some nodes crash here because of very large log files), do I need to configure it in the cluster? It was not clear.
Jan 27, 2021 Easily digestible
Jan 27, 2021 fantastic, incredibly helpful. trainer is really great. Would like info on adding to existing clusters (ie., SGE, etc)
Jan 27, 2021 Just the right amount of content, Slurm is so large it would have been easy to get over complicated Minor: the references to pulsar in the examples could be confusing, might be worth adding a warning for anyone who is going through this tutorial before the pulsar tutorial
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Mar 17, 2022 The existence of the dynamic job destinations
Jul 22, 2021 Lots of detail and a selection of realistic examples The directories "./templates/galaxy/dynamic_job_rules/" and "./templates/galaxy/tools/" should actually be under another directory "./files/galaxy/ ... " for the latest Ansible roles to work!
Jun 30, 2021 Great introduction and very useful starting point for beginning to apply these features
Jan 28, 2021 This is a powerful way of controlling the resource usage according to tool requirements. This task includes many layers of complexity. It would be nice if, at the beginning or ending of each subtopic the needed changes were pointed in the file tree. For example, using the 'tree' command and then highlight all the files that have to be created / edited for this feature to work. It is just for better visualization of the modifications. I get something useful when calling git status.
Jan 27, 2021 I feel like I understand how to manage this quite well now The Python code and some of the xml seems to paste into the cli with loads of new tab characters, in vim I used ':set paste' to switch off auto indent. Doesn't happen with the yml though
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Jul 2, 2021 Clear explanation of the subject object_store_config_file: "{{ galaxy_config_dir }}/object_store_conf.xml.j2" should be object_store_config_file: "{{ galaxy_config_dir }}/object_store_conf.xml"
Jan 28, 2021 Easy to add local storage, the dropbox integration is good "Warning: switching object store types will cause issues" - suggest putting that at the top and emphasise that this is a tutorial that shouldn't be blindly followed on a proper install. The S3 section assumed quite a lot of knowledge - I didn't understand, but expect someone who manages data in an S3 bucket will!
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Mar 18, 2022 Is really cool to see lots of different admins pooling their knowledge and effort in this way From a voice control perspective, it would be useful if the hands-on gxadmin commands were in a copiable code block like they are in other tutorials – it really helps to be able to copy them with the single click. Also, the 'admin favourites' section could include the arguments for the functions listed, e.g. <job_id>, for a bit more clarity
Jul 1, 2021 Simple and clear The Hands-on: Adding a query did not work as the user ubuntu but had to be done as the user galaxy
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Jan 29, 2021 The whole concept of being able to separate training needs vs production needs is brilliant 3. We next need to configure this plugin in our job configuration (files/galaxy/config/job_conf.xml): Should be templates/galaxy/config/job_conf.xml.j2 to match rest of training?
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Jan 15, 2022 In-depth explanations and side bars of what the various commands are doing so you can easily troubleshoot and customize. There is an "error" in the example code for the Galaxy/FTP portion of galaxyservers.yml. if you intend to use separate upload directories (with email addresses as the folder name) for each user - as the tutorial indicates will happen - then the current code (below) will result in the uploads going into the parent directory "/uploads" instead of "uploads/user_email" . # FTP ftp_upload_dir: /data/uploads ftp_upload_site: "{{ inventory_hostname }}" Instead the code should be (add a "/"): # FTP ftp_upload_dir: /data/uploads/ ftp_upload_site: "{{ inventory_hostname }}" Took me a while to work out why it was going into the wrong directory. Also - it should be stated that there may be a newer version of the playbook that could solve errors/conflicts with newer operating system versions than those used in the tutorial. Also suggest highlighting parts in the code examples which should be customized to your server environment if you are using this as a guide to setup your own installation (primarily directories where stuff is located).
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Jun 8, 2022 The interactive tools perspective The requirement for wildcard SSL certificate and the poor support for fulfilling this requirement. This is a major issue for the deployment of Galaxy servers. From a historical perspective, before 2019, there were IEs. Not super easy to deploy, but doable with motivation and investment in Docker knowledge. After launching the new ITs, IEs became progressively useless and ITs stay either nice demos or running on very few big public servers. Even the latter is not so clear: for instance, usegalaxy.org.au is not really providing ITs, usegalaxy.org (!) seems providing it at first glance, but the Rstudio interface - for instance - remains full blank forever. Only usegalaxy.eu to my knowledge provides effectively running and usable generalist ITs (Rstudio, Jupyter,). Thus, on that matter, where is the initial slogan "data intensive analysis for everyone" ? Of course, I am not blaming the trainers and contributors to this tutorial in any way ! But I really think that the technical strategy relying on wildcard SSL certificate to get the ITs running should be discussed with the community as a serious limitation to their use and thereby their active development. As it stands since 3 years now, ITs are out of the possibilities of a majority of Galaxy server instances because too complicated to install.
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Jul 26, 2024 I like to custom my galaxy server, so I find this section really interesting When I choose new theme at the preferences, the server not automatically change unless I reload the page :(
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Jul 26, 2024 I like that it's worked :D I need a wiki page for all of this knowledge
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Dec 6, 2024 The section on using ephemeris to manage these mappings A warning that this will not work if you have the cvmfs from step 5 of the admin/ansible path still attached
Sep 16, 2024 Fetching new genomes with the instructions in this tutorial still doesn't work (at least for mm39).
Jul 31, 2024 This error still persist:https://help.galaxyproject.org/t/connection-timed-out-error-while-running-data-manager-fetch-genome-dbkeys-all-fasta/7241

Genome Annotation

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