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
2260 responses
Rating Distribution
By topic
Assembly galaxy_instance
80 responses
Rating Distribution
5 responses
Rating Distribution
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. |
22 responses
Rating Distribution
Detailed feedback
Date | What did you like? | What could be improved? |
---|---|---|
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 |
7 responses
Rating Distribution
Detailed feedback
Date | What did you like? | What could be improved? |
---|---|---|
Apr 16, 2019 | easy to follow, step by step |
1 responses
Rating Distribution
Detailed feedback
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
Rating Distribution
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 |
27 responses
Rating Distribution
Detailed feedback
Date | What did you like? | What could be improved? |
---|---|---|
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...) |
4 responses
Rating Distribution
Detailed feedback
Date | What did you like? | What could be improved? |
---|---|---|
Jul 8, 2021 | the lessons | not sure |
1 responses
Rating Distribution
Detailed feedback
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 |
2 responses
Rating Distribution
Detailed feedback
Date | What did you like? | What could be improved? |
---|---|---|
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) |
2 responses
Rating Distribution
Detailed feedback
Date | What did you like? | What could be improved? |
---|---|---|
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. |
2 responses
Rating Distribution
Detailed feedback
Date | What did you like? | What could be improved? |
---|
Climate galaxy_instance
7 responses
Rating Distribution
3 responses
Rating Distribution
Detailed feedback
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
Rating Distribution
Detailed feedback
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
Rating Distribution
Detailed feedback
Date | What did you like? | What could be improved? |
---|
1 responses
Rating Distribution
Detailed feedback
Date | What did you like? | What could be improved? |
---|
1 responses
Rating Distribution
Detailed feedback
Date | What did you like? | What could be improved? |
---|
Computational chemistry galaxy_instance
28 responses
Rating Distribution
3 responses
Rating Distribution
Detailed feedback
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
Rating Distribution
Detailed feedback
Date | What did you like? | What could be improved? |
---|---|---|
Nov 18, 2019 | The feeling of creating something on my own | Nothing |
6 responses
Rating Distribution
Detailed feedback
Date | What did you like? | What could be improved? |
---|---|---|
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. |
4 responses
Rating Distribution
Detailed feedback
Date | What did you like? | What could be improved? |
---|---|---|
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 |
11 responses
Rating Distribution
Detailed feedback
Date | What did you like? | What could be improved? |
---|---|---|
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 |
2 responses
Rating Distribution
Detailed feedback
Date | What did you like? | What could be improved? |
---|
Contributing to the Galaxy Training Material galaxy_instance
23 responses
Rating Distribution
5 responses
Rating Distribution
Detailed feedback
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
Rating Distribution
Detailed feedback
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
Rating Distribution
Detailed feedback
Date | What did you like? | What could be improved? |
---|
6 responses
Rating Distribution
Detailed feedback
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
Rating Distribution
Detailed feedback
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. |
5 responses
Rating Distribution
Detailed feedback
Date | What did you like? | What could be improved? |
---|---|---|
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 :) |
2 responses
Rating Distribution
Detailed feedback
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
5 responses
Rating Distribution
4 responses
Rating Distribution
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 `<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`) |
1 responses
Rating Distribution
Detailed feedback
Date | What did you like? | What could be improved? |
---|---|---|
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 |
Ecology galaxy_instance
7 responses
Rating Distribution
3 responses
Rating Distribution
Detailed feedback
Date | What did you like? | What could be improved? |
---|
1 responses
Rating Distribution
Detailed feedback
Date | What did you like? | What could be improved? |
---|
2 responses
Rating Distribution
Detailed feedback
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
Rating Distribution
Detailed feedback
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
52 responses
Rating Distribution
1 responses
Rating Distribution
Detailed feedback
Date | What did you like? | What could be improved? |
---|
8 responses
Rating Distribution
Detailed feedback
Date | What did you like? | What could be improved? |
---|---|---|
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 ?? |
9 responses
Rating Distribution
Detailed feedback
Date | What did you like? | What could be improved? |
---|---|---|
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 |
8 responses
Rating Distribution
Detailed feedback
Date | What did you like? | What could be improved? |
---|---|---|
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? |
23 responses
Rating Distribution
Detailed feedback
Date | What did you like? | What could be improved? |
---|---|---|
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 |
2 responses
Rating Distribution
Detailed feedback
Date | What did you like? | What could be improved? |
---|---|---|
Jul 1, 2021 | update is required |
1 responses
Rating Distribution
Detailed feedback
Date | What did you like? | What could be improved? |
---|
Evolution galaxy_instance
4 responses
Rating Distribution
3 responses
Rating Distribution
Detailed feedback
Date | What did you like? | What could be improved? |
---|---|---|
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. |
1 responses
Rating Distribution
Detailed feedback
Date | What did you like? | What could be improved? |
---|
Foundations of Data Science galaxy_instance
28 responses
Rating Distribution
17 responses
Rating Distribution
Detailed feedback
Date | What did you like? | What could be improved? |
---|---|---|
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. |
7 responses
Rating Distribution
Detailed feedback
Date | What did you like? | What could be improved? |
---|---|---|
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 |
1 responses
Rating Distribution
Detailed feedback
Date | What did you like? | What could be improved? |
---|
1 responses
Rating Distribution
Detailed feedback
Date | What did you like? | What could be improved? |
---|
2 responses
Rating Distribution
Detailed feedback
Date | What did you like? | What could be improved? |
---|---|---|
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 |
Galaxy Server administration galaxy_instance
169 responses
Rating Distribution
20 responses
Rating Distribution
Detailed feedback
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
Rating Distribution
Detailed feedback
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
Rating Distribution
Detailed feedback
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. |
34 responses
Rating Distribution
Detailed feedback
Date | What did you like? | What could be improved? |
---|---|---|
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. |
17 responses
Rating Distribution
Detailed feedback
Date | What did you like? | What could be improved? |
---|---|---|
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
Rating Distribution
Detailed feedback
Date | What did you like? | What could be improved? |
---|---|---|
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
Rating Distribution
Detailed feedback
Date | What did you like? | What could be improved? |
---|
7 responses
Rating Distribution
Detailed feedback
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
Rating Distribution
Detailed feedback
Date | What did you like? | What could be improved? |
---|---|---|
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
Rating Distribution
Detailed feedback
Date | What did you like? | What could be improved? |
---|
4 responses
Rating Distribution
Detailed feedback
Date | What did you like? | What could be improved? |
---|---|---|
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. |
Tutorial "Use Singularity containers for running Galaxy jobs" is not available anymore.
9 responses
Rating Distribution
Detailed feedback
Date | What did you like? | What could be improved? |
---|---|---|
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
Rating Distribution
Detailed feedback
Date | What did you like? | What could be improved? |
---|---|---|
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 |
Tutorial "Mapping Jobs to Destinations" is not available anymore.
Tutorial "Recording Job Metrics" is not available anymore.
2 responses
Rating Distribution
Detailed feedback
Date | What did you like? | What could be improved? |
---|---|---|
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
Rating Distribution
Detailed feedback
Date | What did you like? | What could be improved? |
---|---|---|
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 |
1 responses
Rating Distribution
Detailed feedback
Date | What did you like? | What could be improved? |
---|---|---|
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
Rating Distribution
Detailed feedback
Date | What did you like? | What could be improved? |
---|---|---|
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). |
1 responses
Rating Distribution
Detailed feedback
Date | What did you like? | What could be improved? |
---|---|---|
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. |
1 responses
Rating Distribution
Detailed feedback
Date | What did you like? | What could be improved? |
---|
1 responses
Rating Distribution
Detailed feedback
Date | What did you like? | What could be improved? |
---|
1 responses
Rating Distribution
Detailed feedback
Date | What did you like? | What could be improved? |
---|
Genome Annotation galaxy_instance
55 responses
Rating Distribution
15 responses
Rating Distribution
Detailed feedback
Date | What did you like? | What could be improved? |
---|---|---|
Nov 24, 2022 | Short and precise, not more or less than what the title promises | One setting in the JBrowse step isn't congruent with the most recent Prokka version anymore: can't configure "Produce Standalone Instance”: "Yes" maybe you can update this :) |
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?) |
8 responses
Rating Distribution
Detailed feedback
Date | What did you like? | What could be improved? |
---|---|---|
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! |
13 responses
Rating Distribution
Detailed feedback
Date | What did you like? | What could be improved? |
---|---|---|
Apr 17, 2023 | chart explanation | language can be made more simple |
Aug 5, 2022 | List elements identified during the process of genome annotation. | |
May 23, 2022 | proper description and arrangement. | Results |
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 |
3 responses
Rating Distribution
Detailed feedback
Date | What did you like? | What could be improved? |
---|---|---|
Aug 23, 2022 | everything.. thanks for this | i cant find bowtie tools.. only bowtie 2, but the parameters described here are for bowtie. |
Aug 4, 2021 | very clear | r code |
4 responses
Rating Distribution
Detailed feedback
Date | What did you like? | What could be improved? |
---|---|---|
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
Rating Distribution
Detailed feedback
Date | What did you like? | What could be improved? |
---|---|---|
Jul 11, 2021 | Thanks for the detail explanation. |
2 responses
Rating Distribution
Detailed feedback
Date | What did you like? | What could be improved? |
---|---|---|
Oct 11, 2022 | What I liked most about this tutorial was the existence of explanations that helped in the interpretation of the various outputs produced by the software. | The tutorial could be updated because I found that there are discrepancies between the tutorial and the Galaxy platform. Namely, the name of some of the tools and their location on the website differ between the tutorial and the current platform. |
6 responses
Rating Distribution
Detailed feedback
Date | What did you like? | What could be improved? |
---|---|---|
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. |
3 responses
Rating Distribution
Detailed feedback
Date | What did you like? | What could be improved? |
---|---|---|
Mar 16, 2022 | good explanation why masking is done |
Imaging galaxy_instance
6 responses
Rating Distribution
4 responses
Rating Distribution
Detailed feedback
Date | What did you like? | What could be improved? |
---|
2 responses
Rating Distribution
Detailed feedback
Date | What did you like? | What could be improved? |
---|
Introduction to Galaxy Analyses galaxy_instance
796 responses
Rating Distribution
127 responses
Rating Distribution
Detailed feedback
Date | What did you like? | What could be improved? |
---|---|---|
May 13, 2023 | It is very clear and easy to follow. The video also helps sooo much! Thank you. | |
Apr 4, 2023 | more screenshots can be added. | |
Mar 5, 2023 | It included in the end the possibility of using it to analyze repeats instead of SNPs, leading us to realize that it can easily be done. | |
Feb 23, 2023 | All steps were clearly explained (besides one) and the screenshots and extra info was very helpful! | With the Hands on: Extract workflow I found the end of step 4 a bit confusing in the sense that I wasn't sure if the tutorial required me to run the workflow. Immediately after it was said the Exon box was named ok. I didn't immediately realize we were to rename the box in the workflow editor. |
Feb 23, 2023 | Syntax improved version of Galaxy | |
Feb 22, 2023 | It explained every steps in a basic manner! | The result of work flow application (for the student to check whether their workflow work or not) |
Feb 15, 2023 | Very clear and detailed. Great for the first-time user. | A few suggestions to try after 101 |
Nov 30, 2022 | The tutorial is broken up into sections, and it's in a step-by-step format. | Some of the tools, like the "compare two datasets" tool, were hard to find even with the search bar. Some of the tutorials need an update because the instructions are unclear, or the method of doing something has changed. |
Nov 29, 2022 | all of this tutorial | nothing, everything is so cool |
May 18, 2022 | Easy to follow. Helpful examples. | |
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! |
77 responses
Rating Distribution
Detailed feedback
Date | What did you like? | What could be improved? |
---|---|---|
May 24, 2023 | Everything! | |
May 23, 2023 | Things were clearly explained. It was a comprehensive introduction to Galaxy. I really learnt a lot. | I think for an introduction to Galaxy, everything was covered really well. |
May 22, 2023 | the try one and see approach | a little more time on the USC graphic--juat a little, I know its a whole course alone,but a little more time spent in the different lines available and options would be nice. |
May 22, 2023 | The explanation and details | It's awesome |
Jan 21, 2023 | My first time working with genomic tools. | |
Aug 30, 2022 | Biological explanations after a command. | I think its great, but one improviment is add more image from Galaxy. |
Aug 25, 2022 | Most of the explanations and step were explained well but many icons in Galaxy have changed . An update will be appreciated. If USC browser is the main source , please have a detailed tutorial what all that stuff means . Thanks | |
May 25, 2022 | It explained everything in simple language!! | |
Apr 29, 2022 | interactive | |
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 |
76 responses
Rating Distribution
Detailed feedback
Date | What did you like? | What could be improved? |
---|---|---|
Mar 3, 2023 | One of the initial steps, the one involving getting the RefSeq list of genes from UCSC genome browser is flawed and should be updated. I had to use a different list of genes and make some modifications in the input file. | |
Feb 21, 2023 | Everything is clear and understandable | I was satisfied with everything |
Jan 12, 2023 | Very well detailed | nothing special |
May 7, 2022 | topic is very important | some steps are not cleared explained, workflow for this specific task and visualization tool is not working showing loading error |
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. |
43 responses
Rating Distribution
Detailed feedback
Date | What did you like? | What could be improved? |
---|---|---|
May 7, 2023 | Simple and easy-to-understand language of the hands-on-tutorial | Some of the hyperlinks are not functional; please update those. For example, the hyperlink for alignment tools does not open. |
Jun 18, 2022 | it can be more better how do you get the end result was not clearly explained | |
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 |