GTN Feedback

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

Overall

1828 responses
Rating Distribution

By topic

Assembly galaxy_instance

63 responses
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4 responses
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Detailed feedback
Date What did you like? What could be improved?
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.
18 responses
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Detailed feedback
Date What did you like? What could be improved?
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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Date What did you like? What could be improved?
Jan 15, 2021 the explanations are well
Apr 16, 2019 easy to follow, step by step
1 responses
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Date What did you like? What could be improved?
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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Detailed feedback
Date What did you like? What could be improved?
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
21 responses
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Detailed feedback
Date What did you like? What could be improved?
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...)
3 responses
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Date What did you like? What could be improved?
Jul 8, 2021 the lessons not sure
1 responses
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Date What did you like? What could be improved?
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

Climate galaxy_instance

6 responses
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3 responses
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Date What did you like? What could be improved?
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.
1 responses
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Date What did you like? What could be improved?
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.
1 responses
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Date What did you like? What could be improved?
1 responses
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Date What did you like? What could be improved?

Computational chemistry galaxy_instance

19 responses
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3 responses
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Date What did you like? What could be improved?
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
2 responses
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Date What did you like? What could be improved?
Nov 18, 2019 The feeling of creating something on my own Nothing
3 responses
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Date What did you like? What could be improved?
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.
3 responses
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Date What did you like? What could be improved?
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
7 responses
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Detailed feedback
Date What did you like? What could be improved?
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
1 responses
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Date What did you like? What could be improved?

Contributing to the Galaxy Training Material galaxy_instance

21 responses
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5 responses
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Date What did you like? What could be improved?
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...
1 responses
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Date What did you like? What could be improved?
Feb 16, 2019 the option to automatically extract all steps of my workflow instead of typing them all is sooooo increadibly helpful!!!
1 responses
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Date What did you like? What could be improved?
6 responses
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Date What did you like? What could be improved?
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
3 responses
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Date What did you like? What could be improved?
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.
3 responses
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Detailed feedback
Date What did you like? What could be improved?
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 :)
2 responses
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Date What did you like? What could be improved?
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 galaxy_instance

4 responses
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4 responses
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Detailed feedback
Date What did you like? What could be improved?
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 `` 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 `` according to planemo): `` - "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`)

Ecology galaxy_instance

6 responses
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2 responses
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Date What did you like? What could be improved?
1 responses
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Date What did you like? What could be improved?
2 responses
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Date What did you like? What could be improved?
Jan 20, 2021 Very clear Where to find the tools (not always easy in the toolbar)
1 responses
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Date What did you like? What could be improved?
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.

Epigenetics galaxy_instance

43 responses
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1 responses
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Date What did you like? What could be improved?
6 responses
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Date What did you like? What could be improved?
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 ??
8 responses
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Detailed feedback
Date What did you like? What could be improved?
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
6 responses
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Date What did you like? What could be improved?
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?
20 responses
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Date What did you like? What could be improved?
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
2 responses
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Date What did you like? What could be improved?
Jul 1, 2021 update is required

Foundations of Data Science galaxy_instance

22 responses
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14 responses
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Date What did you like? What could be improved?
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.
6 responses
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Date What did you like? What could be improved?
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
1 responses
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1 responses
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Date What did you like? What could be improved?

Galaxy Server administration galaxy_instance

152 responses
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18 responses
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Date What did you like? What could be improved?
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.
8 responses
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Date What did you like? What could be improved?
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
13 responses
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Date What did you like? What could be improved?
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.
29 responses
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Detailed feedback
Date What did you like? What could be improved?
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.
16 responses
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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)
1 responses
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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
1 responses
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7 responses
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Date What did you like? What could be improved?
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
3 responses
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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 :)
1 responses
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4 responses
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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.
14 responses
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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.
9 responses
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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
10 responses
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Jun 30, 2021 Very clear explanations
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 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
11 responses
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Date What did you like? What could be improved?
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
2 responses
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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!
3 responses
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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. , 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
1 responses
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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?
1 responses
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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).

Genome Annotation galaxy_instance

42 responses
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13 responses
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Oct 10, 2021 quick and simple none
Apr 3, 2021 It seemed clear - just didn't work. I read the tutorial as I tried to duplicate it in Galaxy with a phage genome sequence. The tutorial did not correspond with what was in Galaxy. JBrowse did not work - no indication why.
Mar 10, 2021 It doesn't show you where to begin. It gives you steps but doesn't show you how to get to each step. Very frustrating
Feb 18, 2021 Simple and easy to demonstrate gene annotation using contigs
Jan 29, 2021 Concise and clear. Thank you!
Jan 8, 2021 The explaination about how to use Prokka JBrowse doesn't work with this parameters, you should update this tutorial
Sep 21, 2018 I am doing this tutorial 09/2018 -> the step using the JBrowse tool works only (at least in my hands) with this version: (Galaxy Version 1.12.5+galaxy0) i had troubles finding it (maybe the search does not work properly?)
Sep 21, 2018 I am doing this tutorial 09/2018 -> the step using the JBrowse tool works only (at least in my hands) with this version: (Galaxy Version 1.12.5+galaxy0) i had troubles finding it (maybe the search does not work properly?)
7 responses
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Jan 26, 2022 nothing nothing
Oct 20, 2021 This tutorial is very helpful After the functional annotation how to recognise genes related
Nov 13, 2019 nothing everything no vid
May 12, 2019 Analysis for tutorial should be done on large datasets like genome from population rather than on individual genome.
Feb 27, 2019 The first steps of the tutorial are great, described in a simple and objective way. I was unable to continue from the "Hands-on: Run I look for the genome" stage. I looked for the BUSCO tool on the Galaxy platform but nothing was found. For this reason I could not complete the tutorial. It would be good to evaluate the availability of this tool or change this step of the tutorial so that we can finish successfully, thank you!
9 responses
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Feb 17, 2022 The clear steps and explanation attached Some tools have not been found in Galaxy such as antiSMASH.
Apr 8, 2019 good description of what annotation is did not tell me how to do annotation using tools present here, would like a step by step instruction on how to do an annotation if I have a genome sequence
2 responses
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Aug 4, 2021 very clear r code
4 responses
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Mar 31, 2022 the sharing link is not working, so i couldnt share and create the group
Mar 15, 2022 super interesting ! especially the sharing part !
Jul 2, 2021 nice talk and gives a rly good overview of apollo/galaxy interface. thank you! explain what are all the data you add as input inthefirst step, do u rly need that much? in the tutorial we only use some of them
1 responses
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Jul 11, 2021 Thanks for the detail explanation.
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4 responses
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Apr 3, 2022 A demo with a cripsr pool set who works (so many online pool screen CRIPSR tools do not work). so many command based installation do not work. Simply starting with MAGECK installation on python is just a nightmare, it does not install smoothly, and it seems thatthe original authors move on and do not care at deploying this smoothly to the community(only expert can use these code lines). I really appreciate the work here. It seems more applicable from any machine without all the dependancies, environments, expertise in coding and languages bug...... Should make mageck available in global galaxy and not just australia one. Could provide other datasets such as cripsrI or cripsA pool set to extend the range of trial for users to get accustomed with the pipeline.
Mar 25, 2022 everything because all was new for me Add more information in the lecture (describe more meticulously the CRISPR analysis)
Mar 15, 2022 It was super clear, and combine nice tools For me was not "intuitive" to have a test with two p-values (for negative/positive selection). That I do not know if it is pretty common in transcriptomic (and I missed it) or if it is non so commonly used and it was speciffically developed on MAGeCK test. If it is not commonly use I think that can be nice to include a brief description of the statistical test in the tutorial of the course.
1 responses
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Mar 16, 2022 good explanation why masking is done

Imaging galaxy_instance

6 responses
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4 responses
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2 responses
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Introduction to Galaxy Analyses galaxy_instance

641 responses
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111 responses
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Apr 1, 2022 it's was more clear and more relating than others i think a pdf explaining some notes would be ok
Mar 21, 2022 easy to understand and the tips are really usefull no idea
Mar 18, 2022 I never have even coded before! so easy to use
Mar 8, 2022 Easy to follow, user friendly for someone without background
Feb 9, 2022 very clear tutorial!
Feb 7, 2022 I liked the step by step follow up of results while doing the analysis
Feb 7, 2022 the simple and easy demonstration
Feb 2, 2022 The educational aspect and questions asked The last question has no answer
Oct 14, 2021 I love that you have to pay close to every little details for now nothing
Oct 11, 2021 How it shows you that you to make adaptable workflows
Oct 11, 2021 I especially loved how simplified the tutorial was, even as a beginner I was able to run my analysis and publish it. Thank You! It is fine as it is...maybe extra datasets to practice with.
Sep 1, 2021 good explaination difficult to say
Aug 12, 2021 the easy step by step guide nothing
Aug 11, 2021 Systematic Excellent
Aug 11, 2021 Automating workflows Add more analysis
Aug 10, 2021 Easy to follow. To the point!
Aug 10, 2021 training format
Aug 10, 2021 great organizing and illustrations more practice
Aug 10, 2021 clarity, information packed
Aug 10, 2021 It was very clear It is perfect!
Aug 9, 2021 The hands-on manual is very interactive More pictures on how to carry out the steps
Aug 9, 2021 It was very clearly explained. So even someone without experience, as myself, could go through this very easily. No suggestions
Jun 29, 2021 Completness
Jun 25, 2021 All Nothing
Jun 17, 2021 The explanation to implement each step nothing
May 23, 2021 clear and to the point
Mar 22, 2021 Easy to follow steps Where to go next button to jump into another training session
Jan 6, 2021 In a previous version of this tutorial a join was performed to add exon info to the number of snps. This step was removed in a later version of the tutorial.
Sep 11, 2020 I like the Galaxy tools and how well the tutorial explained what the purpose of the tools were in terms of the science itself. The tutorital should be upgraded and edited to ensure its correct. For example, telling reading to type "Column: 4" caused errors; should have only typed in "4" for it to work. This was addressed, but WELL after that part of the tutorial.
Jul 23, 2020 Everything :) this is incredibly illustrative and I feel so much more confident to use Galaxy now
Jun 29, 2020 Easy to follow. The comments were very helpfull
Apr 15, 2020 very easy to follow
Mar 30, 2020 failed at step of either join or count. column drop down was not available in count, so entered manually. when count applied, error on column sepecification
Mar 12, 2020 Explanation how to use UCSC browser to see user track
Feb 14, 2020 I appreciated that this tutorial used a smaller data set, so that the analysis went much faster. I also appreciated comments on what to look for if the analysis didn't work. I am a genetics instructor at a PUI, so this tutorial was at a good level for me to think about what I want to teach my students. At the section on "recovering exon info" it would be nice to prompt the audience to consider which data sets they should compare, and which columns should be used (maybe as a side activity). When viewing results at UCSC main, ideally it would be nice to direct audience something in particular to look for. There is a lot of data, which will definitely overwhelm my students. This is a meta suggestion....I'm going through the introductory tutorials one by one and found this one to be more introductory than the "peaks to genes" tutorial. I wonder if considering reordering tutorials (make this one the second on the list?) or naming tutorials would help audience. Great tutorial - I definitely appreciate your work on this!
Jan 28, 2020 The fact that it had a task in mind A bit more clarity on how to correctly indicate the column names would have saved me a lot of time trying different variations when "Column: 4" was not recognized as an input
Jan 2, 2020 Repeatable workflow for fresh man to this server. Further clarification to the function input parameter maybe need.
Dec 5, 2019 In general, it is good. For first time user, some instruction should include more details. Some guides are not clear.
Nov 29, 2019 very clear instructions
Nov 21, 2019 Easy Maybe automattically update to gencode updates, there is no genecode v29 anymore
Oct 16, 2019 Informative and easy to follow
Oct 9, 2019 Useful and easy to follow
Oct 8, 2019 details other cases
Sep 6, 2019 Very easy to follow Ability to zoom on the graphics
Aug 28, 2019 Easy to follow and useful
Aug 28, 2019 it was sufficient
Aug 28, 2019 Screenshots and clear colour coding made it extremely easy to follow Nothing - I thought it was great! :)
Aug 2, 2019 I liked how easily it flows, some concepts of biology are briefly explained, it helps a lot! Maybe add more examples, more explanations on the datasets used.
Jun 11, 2019 Good introduction to Galaxy. I like the worklflow function the most. Couldn´t really see what the results in the genome browser would tell me and how I apply this for my work.
May 30, 2019 The instructions were very clear and easy to follow It would be nice if there is more explanations on the significance of each step and what exactly is being performed when selecting different tools.
May 16, 2019 Ease of understanding Adding more examples of its applications and how it is used in real time
May 1, 2019 Instructive I do not know - I know only Biopython
Apr 25, 2019 explanations were very clear ! this is a bit too long
Apr 18, 2019 Fatal error: Exit code 1 () Error running sorter.py Command '(grep '^#' /galaxy-repl/main/files/030/998/dataset_30998511.dat) >> /galaxy-repl/main/files/030/998/dataset_30998729.dat' returned non-zero exit status 1
Feb 25, 2019 Very simple to follow and learn on my own
Jan 31, 2019 Very good explanations, good demonstration of Galaxy potential for begginer
Jan 14, 2019 Galaxy at usegalaxy.org ends up showing "the white screen of death" extremely often (10s of times during following this tutorial).
Nov 28, 2018 Easy to follow, but the task is not trivial! update some of the options and screenshots to be consistent with the latest version of Galaxy
Nov 28, 2018 Easy to follow Including some assignment or home work
Nov 4, 2018 One could add a section describing the use of multiple datasets, tags, etc.
Sep 27, 2018 easy to follow
Sep 27, 2018 I found it interesting and user friendly nothing for now
Sep 26, 2018 The presentation of the tutorial and the practicality of it The rate of update of the tutorial
Sep 14, 2018 very detailed and easy to follow, even for a complete beginner - great!
61 responses
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Date What did you like? What could be improved?
Apr 7, 2022 It's easy, indexing and saving history is great tool Maybe, in this tutorial, using colors for different strand genes would be more easy to see in genome browser later
Apr 6, 2022 the fact that it gave definitions for things that could be unknown not really much. maybe make similar tutorials but for larger jobs
Mar 26, 2022 It was written clearly One place I think it could be improved would be on Create a reusable workflow from a history, under the Test Workflow part 2 (Examine the workflow run form) wasn't clear as the others and found it to be confusing.
Mar 22, 2022 Detailed description All are ecxellent
Mar 19, 2022 The detailed description I think that all are perfect
Mar 19, 2022 very simple and basics mode of explanation
Mar 19, 2022 User friendly and really hepful for novices like me
Mar 17, 2022 Explanations
Mar 16, 2022 The final percentage overlap could be provided so students can compare to make sure the results are the same
Mar 16, 2022 The practical easy-to-use guide
Mar 16, 2022 everything was so interesting, but workflow part is more fascinating. I think there is no need of the improvement every thing is so perfectly fine and easily understandable.
Mar 15, 2022 Ease of understanding and depth of explanation The videos are old and out of sync of the tutorial material in some cases. There is need for new videos to be developed
Mar 14, 2022 saving and re using the workflow more hand on activities
Mar 14, 2022 intuitive nothing
Mar 14, 2022 A single tutorial teaches to get information from UCSC, analyze them, view it in genome browser and asks us to use the pipeline to work on similar biological problems.
Feb 24, 2022 Nice Step by Step Tutorial Finding the tools was a bit difficult with the search bar. Somethings are a bit outdated.
Feb 22, 2022 Very detailed explained steps, which made the analysis very easy
Jan 27, 2022 An example full of information no
Nov 15, 2021 Detailed Explanation
Oct 15, 2021 Basically the fact that you can always get your way around None for now
Aug 3, 2021 Tools Detailed Explanation: how to use and details about the tool. Nill
Jul 15, 2021 Update to the newer version of Galaxy (new style)
Jul 1, 2021 Expaination from Dave was Fantastic, and I was able to have the Hands-on without any problem :D Nothing in my oppinion.
Jul 1, 2021 explanations which were easy to understand, explaining concepts well without going into overwhelming amounts of detail; defined any foreign terms clearly
Mar 11, 2021 It was clear and well structured. Nothing! Galaxy is awesome
Feb 26, 2021 The tutorial is hands-on, straight forward and easy to follow
Feb 26, 2021 The hands-on tutorial which is straight forward and easy to follow
Feb 16, 2021 Practical Error of concept of nucleotides vrs amino acids
Feb 16, 2021 The tutorial and the goals were clear
Feb 15, 2021 Overall good structure It is rather specific, a short introduction ahead on the tools and ideas might be helpful
Feb 15, 2021 Very clear presentation, the results are clearly explained helping bioinformatician/biologist to understand the output Some tools were not in the right column, maybe use 'search tools' instead of looking for tools in a specific section (when the tool is actually in another section). Especially for Galaxy beginners
Feb 15, 2021 Very informative.
Aug 3, 2020 Simple introductions to bioinformatics with easy to understand (for a non-biologist) explanation of gene/chromosome and other concepts. Nothing. This was great!
Jun 30, 2020 Easy to follow Nowadays the tool Intersect, it's no longer in the Operate on Genomic Intervals toolbox.
Jun 12, 2020 Very clear Slightly outdated, some tool locations seem to have changed
Jun 11, 2020 I like the brief but detailed and easy to understand instructions with explanations the section on Visualize the overlapping genes could do with some improvement. I struggled to understand what scale track was and how to click it at the begining but eventually got around it. Maybe other users found it easy but that was my challenge.
Mar 17, 2020 Steps are clearly explained
Feb 20, 2020 I really liked how this tutorial encourages its audience to try to figure out which tools to use and how to use them to address the question. Just before the section on "Examine the data" there is a [TODO] line that has been left in. Oops!
Feb 15, 2020 this .bed file contain more row than number of genes on chr22 ?!
Aug 23, 2019 Update the intersect phase since that tool is no more available
Feb 28, 2019 Broke down the concepts well. Introduced ideas one step at a time with good explanations that minimized jargon. And worked to make concepts tangible with hands on use of Galaxy.
Jan 16, 2019 Galaxy says it has ran the workflow, but nothing happens.
Sep 15, 2018 very detailed and easy to follow, thank you
70 responses
Rating Distribution
Detailed feedback
Date What did you like? What could be improved?
Apr 1, 2022 detailing make an upgrage to server and do a video if possible
Mar 30, 2022 it was engaging to use of terms and examples so a first time contributor could follow along
Mar 15, 2022 The hands-on material is really well thought and it really gives us confidence in doing this type of analysis. It is very easy to follow through. There were two steps where I fumbled, one was when I tried importing the genes from UCSC browser it opened in the new history, I feel one link to paste that to current history tab would be beneficial, secondly, I was literally searching for Group tool under the workflow, then when I expanded the list then I could find it.
Mar 10, 2022 easy to understand with easy steps
Jan 20, 2022 How the each and every step is shwon with the screenshots. Just what an beginner needs. :)
Jan 5, 2022 guidelines are clear / no questions are left unanswered
Jan 3, 2022 Not yet completed This is how the output of get flanks are stated in the tutorial: For regions on the negative strand e.g. chr1 8349819 9289958 this gives chr1 9279958 9291958. However what I am getting is similar to the results of the + strand; the promoter regions lies between 8347819 and 8359819; it seems to me that get flanks did not recognize between the + and - strands
Nov 24, 2021 the concept. multiple issues with platform - loosing (they are not on the screen) history buttons, tag buttons, Once I brought the UCSC file in, I no longer can find the gz file - maybe it is supposed to be merged, but that is not what the tutorial showed. There was a disclaimer that said 'results might be different' but there were no Chr 21 to rename on the file. A little video showing what to expect might be more helpful than the icons in the description. I see it was updated in early November, but as a real beginner, this isn't any fun at all and very frustrating.
Oct 18, 2021 learning of workflows
Oct 13, 2021 It was well detailed only a few to crack about. some illustration needs to be more detailed
Sep 7, 2021 Great introduction to Galaxy, simple, easy to follow Clearer explanation of why something is done. Perhaps similar to the 'tips', added detail for those that want to delve deeper. Also more up-to-date visuals of the steps involved The final output is a little lack-lustre. maybe a nicer visualisation option to cap off the tutorial (kind of like a nice 'reward' for effort)
May 11, 2021 It is a very clear step by step, well defined tutorial. The difference between method 1 and 2. The peak summit concept may need more explanation.
Mar 12, 2021 Part1, the Repeat workflow is not working. The manual is different from for actual workflow in galaxy.
Jan 22, 2021 I think it's supposed to be an introductory course, but it got too complicated and theoretical. I am familiar with sequencing terminologies but I didn't understand what do you mean bye peak and broadness of the peaks!! Thanks BTW I think the theoretical part of this tutorial should be explained in details
Jan 1, 2021 everything excellent as is
Dec 1, 2020 the easyness and biological meaning of the data some data import, from UCSC for example, some times fail and ends up in a different history and logges me out
Nov 27, 2020 The tutorial should probably be updated to use the latest versions of tools
Nov 18, 2020 This was confusingly written. It's use of jargon and short cuts limits its access to those not trained in bioinformatics and coding. The presence of multiple authors on this piece may have led to this confusion, as the person that wrote the first two was very clear.
Sep 28, 2020 everything hardly
Jun 29, 2020 very easy to follow
Jun 24, 2020 everything
Jun 11, 2020 Very little Incredibly hard to follow
Apr 7, 2020 Building more complex workflow from small steps. Hands-on: Count genes on different chromosomes - needs to be updated, instead of Column 1 only 1 should be used. Otherwise the analysis fails.
Feb 25, 2020 it was easy to understand how to do it why do i do it?
Feb 25, 2020 detailed explanations; step for step -
Feb 14, 2020 The format of the tutorial is easy to follow and the instructions are clear. The organization is such that it was easy to find where I had left off from the day before. I ran into technical difficulties that I cannot resolve; it's hard to say whether this is due to the tutorial itself (visualizations hasn't worked yet; the first analysis went fine, but the second yielded an empty data set). Also, it took FAR longer than 3 hours; I do wonder if having a smaller mock data set would have helped this problem. I'm trying to learn galaxy in order to incorporate an activity into my undergraduate course. This tutorial seemed more relevant for training people who will use galaxy for their research. A toned-down version with a smaller data set, perhaps without so many necessary file preparation steps would have been appreciated for my particular goals. Having said that, I am guessing I am not the target audience, so I can see how this tutorial would be very useful for another audience.
Feb 12, 2020 in Hands-on: Adjust chromosome names incolumn must be just number not Column:1 first part could explain more about chip seq and input data
Sep 29, 2019 Clear and easy to follow More results illustrations
Sep 28, 2019 The easy to follow structure of the guide plus the additional links provided in the Tips sections. I recommend adding more images of the data being analysed for part 2 section Repeat workflow, 'Run a workflow with changed settings'. This would have been helpful to be able to compare my results with the guides.
Aug 21, 2019 not working with the bedtools intersect intervals (the other tool is currently not working) Update
Aug 15, 2019 I didn't have the time to like it since the intersect command is not working :( I would love it to work, the tools changed in the meanwhile and it need to be updated cause it is not working anymore for some not clear reason . Most probably there is a problem with the UCSC file (I changed any kind of parameter on the interval file and i get always the same error).
Mar 5, 2019 most but if the files that need to be downloaded do not exist at UCSC, this tutorial is useless go through the process and correct
Feb 25, 2019 Very clear instruction and step-by-step explanation some small exercises or quizes
Jan 8, 2019 Step by step introduction and repetition of features
Nov 22, 2018 Easy to follow tutorial We did not realize the 00000000rik names were also gene names, so we spent some time thinking we did something wrong...
Nov 22, 2018 easy to follow individual steps Chipseq data seems a little more complex than more 1-dimensional seq reads (DNA/RNAseq), so would seem to me that starting with e.g. RNAseq analysis could be more logical
Oct 17, 2018 Nice clear , very informative airconditioning less cold
Oct 17, 2018 it is clear would like to have example outputs for important steps, so if i made a mistake in step 7 i don't have to find out in step 19 and go back to revise everything. I can just use the dummy dataset for step 19 to continue and finish the practice
Oct 17, 2018 scope, topic and clarity of tutorial
Oct 8, 2018 More visual examples
Oct 2, 2018 simplicity pick a relevant induction based on your needs
Sep 17, 2018 Well-structured and helpful More information on the flanking region tool (how it works)
Sep 17, 2018 well explained maybe by adding more pictures next to the explanations?
Sep 17, 2018 Well structured, easy to understand.
39 responses
Rating Distribution
Detailed feedback
Date What did you like? What could be improved?
Mar 28, 2022 The tutorial was instructive and easy to follow. I loved the variant calling and annotation.
Jan 6, 2022 I am getting an error : Warning unsupported media type (415) while trying to upload the reference genome using the link "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/009/858/895/GCF_009858895.2_ASM985889v3/GCF_009858895.2_ASM985889v3_genomic.fna.gz". And I am not sure which file type to pick when trying to download from NCBI using the accession number "NC_045512.2" provided.
Dec 23, 2021 Step by step nature More explanation of what i am actually doing at each step
Aug 21, 2021 Good for beginners More explanation and examples
Aug 17, 2021 The simplicity of the step by step guide If the tool needed for each step is clearly listed
Aug 12, 2021 The step-by-step analysis Clear sound/tone of presenter
Aug 12, 2021 Clear and systematic Instructions can be more specific (e.g. names of tools)
Aug 11, 2021 The way Galaxy is able to bring all these bioinformatics data possible to the public.
Aug 9, 2021 There was so much info about FLAG and CIGAR which was not relevant for the exercise. I would have rather learn more about VCF which was important as well as all the meanings behind the headers of the final dataset like DP, AF, SB, DP4, EFF.IMPACT etc. How was read group information relevant for this exercise? I did not understand this. Please state it more clearly in the process if it is relevant. The search did not often find the specific tools but gave 100 options if the name was not specific. Sometimes the full description of the tool was added at the end of instruction but in some cases it was absent which made it more difficult to find the correct tool. The info about duplicates is messy and confusing. Either leave it our or explain/link the info about duplicates more clearly and more in relevance to the excercise. State the point of the final outputs. What can we do with this data, how can this information be used in relation to the covid pandemic? What are the downstream analysis options after this etc.
Aug 3, 2021 detailed explanation of the steps for analysis Also provide information of other tools for the same type of analysis
Jul 8, 2021 good and clear explanation of formats and data -
Jul 8, 2021 protocol Analysis part can be explained a bit detailed
Feb 22, 2021 Very good material
Feb 15, 2021 Complex but very interesting!! All steps are clearly explained. As i said, the data analysis was complex. So detailing the results would have helped to better understand.
Feb 3, 2021 Background information about NGS data progressing and file types Perhaps could includes some information about how to view or check the SAM/BAM file.
Oct 19, 2020 clarity
Mar 24, 2020 Video are difficult to follow
Aug 27, 2019 Please date this content. Is it out of date? It does not mention kallisto, sleuth or salmon. Are these available in a cloud somewhere? Are they better?
May 24, 2019 all of it add example with bowtie2
Apr 30, 2019 I liked the videos. I would suggest to make the videos longer and theory shorter.
Jan 22, 2019 awesome and answered many of the questions in my head nothing I can think of
Jan 17, 2019 Explanation of theoretical basics. Links to additional resources. Mark Duplicates step fails: Fatal error: Exit code 1 () Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/galaxy-repl/main/jobdir/022/055/22055178/_job_tmp -Xmx7g -Xms256m 11:37:37.876 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/cvmfs/main.galaxyproject.org/deps/_conda/pkgs/picard-2.18.2-py36_0/share/picard-2.18.2-0/picard.jar!/com/intel/gkl/native/libgkl_compression.so [Thu Jan 17 11:37:37 CST 2019] MarkDuplicates INPUT=[Filter_on_data_7__Filtered_BAM] OUTPUT=/galaxy-repl/main/files/029/341/dataset_29341054.dat METRICS_FILE=/galaxy-repl/main/files/029/341/dataset_29341053.dat REMOVE_DUPLICATES=true ASSUME_SORTED=true DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true ADD_PG_TAG_TO_READS=true PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Thu Jan 17 11:37:37 CST 2019] Executing as g2main@roundup55.tacc.utexas.edu on Linux 3.10.0-693.21.1.el7.x86_64 amd64; OpenJDK 64-Bit Server VM 1.8.0_152-release-1056-b12; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: 2.18.2-SNAPSHOT INFO 2019-01-17 11:37:38 MarkDuplicates Start of doWork freeMemory: 248936480; totalMemory: 259588096; maxMemory: 7265714176 INFO 2019-01-17 11:37:38 MarkDuplicates Reading input file and constructing read end information. INFO 2019-01-17 11:37:38 MarkDuplicates Will retain up to 26325051 data points before spilling to disk. [Thu Jan 17 11:37:38 CST 2019] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=382373888 To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Exception in thread "main" htsjdk.samtools.SAMFormatException: SAM validation error: ERROR: Record 262, Read name M01368:16:000000000-A3M99:1:2114:3862:13382, bin field of BAM record does not equal value computed based on alignment start and end, and length of sequence to which read is aligned at htsjdk.samtools.SAMUtils.processValidationErrors(SAMUtils.java:454) at htsjdk.samtools.BAMFileReader$BAMFileIterator.advance(BAMFileReader.java:812) at htsjdk.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.java:797) at htsjdk.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.java:765) at htsjdk.samtools.SamReader$AssertingIterator.next(SamReader.java:576) at htsjdk.samtools.SamReader$AssertingIterator.next(SamReader.java:548) at picard.sam.markduplicates.MarkDuplicates.buildSortedReadEndLists(MarkDuplicates.java:495) at picard.sam.markduplicates.MarkDuplicates.doWork(MarkDuplicates.java:232) at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:282) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:98) at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:108)
Nov 27, 2018 The explanation is very clear and concise, thanks!
Nov 17, 2018 Clear and consise
Sep 27, 2018 makes life easy very good
303 responses
Rating Distribution
Detailed feedback
Date What did you like? What could be improved?
Apr 8, 2022 Detailed and accurate. I have no suggestions
Apr 7, 2022 clear directions. screen shots help
Apr 4, 2022 It was straigthforward and had animations to guide you. I think it's missing some basics of Galaxy.
Mar 31, 2022 Maybe if you in "Convert your analysis history into a workflow" change the photo for how it should looks - where you write what, I was bit confused. This could be better for me.
Mar 30, 2022 Simple explanation with helpful images to provide guidance
Mar 29, 2022 It was simple and easy to follow It would be great to have some real examples of how this can be applied to your data
Mar 28, 2022 i like the fact that it took me from a newbie to having some level of knowledge on how the galaxy interface works. As much as i really enjoyed this article, i actually struggled with understanding the "Convert your analysis history into a workflow" part, as it needed more pictures or more specific descriptions at number 4 and 5 guide steps. i had to read it over and over, and do some brain work to figure out what the author meant. if this could be improved for upcoming readers like me, it would be much appreciated and will lead to more productivity on our end.
Mar 28, 2022 I loved the workflow aspect of the platform.
Mar 27, 2022 All the steps were clear and precise. Somewhere I found video demonstrations too, which was unexpected. The concept of collapse and expand features were eyecatching. Yes, at the end if we have a video covering the entire steps, it could be used as a quick revision of the steps we did above.
Mar 24, 2022 hands on run everything is perfect
Mar 23, 2022 Easy to follow and grasp concept Not sure
Mar 20, 2022 it was understandable
Mar 17, 2022 Step by Step learning
Mar 16, 2022 The hand one are very easy and clear. Allow students to answer the questions whithin the hand on then they can compare with the available answers
Mar 7, 2022 It is really hands on
Mar 7, 2022 It is very detailed tutorial and easy to follow also for beginners like me
Mar 7, 2022 Step wise instruction It was perfect for me.
Mar 7, 2022 Easy to follow and focused on the basics
Feb 21, 2022 every step was clear to follow follow-up video for people who have network issues so that they can watch and catch-up fast
Feb 18, 2022 It was very precise and easy to follow. I think it's excellent as it is.
Jan 14, 2022 The way they teached us. Very Short tutorial, needs to add some other tools alo.
Dec 20, 2021 Muy claras las explicaciones Todo está bien en este tutorial
Nov 30, 2021 How easy is to follow the instructions Probably adding more languages, but the english it's totally understandable
Nov 29, 2021 Very well explained, very visual Maybe add some more information about the type of analysis we're running
Nov 28, 2021 It is very clear and easy to follow anything, it is what it states: a short introduction :)
Nov 6, 2021 Ease of explanation Nothing I think
Nov 2, 2021 Everything More Videos
Nov 1, 2021 La facilidad de interfaz que tiene la pagina, se entiende muy rápido y claramente los pasos que se deben realizar para cargar un documento, y el como se visualizan, analizan e interpretación de los diferentes datos. Aun me toca explorar la pagina por el momento este tutorial introductorio es bastante útil y fácil para quien apenas esta escudriñando con el programa.