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

1427 responses
Rating Distribution

By topic

Assembly

48 responses
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3 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.
14 responses
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Detailed feedback
Date What did you like? What could be improved?
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
13 responses
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Detailed feedback
Date What did you like? What could be improved?
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...)
2 responses
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Date What did you like? What could be improved?
Jul 8, 2021 the lessons not sure

Climate

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

Computational chemistry

11 responses
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3 responses
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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
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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
1 responses
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Date What did you like? What could be improved?
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.
1 responses
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Date What did you like? What could be improved?
May 21, 2020 Analysis of Rg, Hydrogen bonds can also be explained
3 responses
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Date What did you like? What could be improved?
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

15 responses
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4 responses
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Detailed feedback
Date What did you like? What could be improved?
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
2 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.
1 responses
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Detailed feedback
Date What did you like? What could be improved?
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 :)

Development in Galaxy

1 responses
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1 responses
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Date What did you like? What could be improved?
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

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

37 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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Detailed feedback
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 ??
6 responses
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Date What did you like? What could be improved?
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
4 responses
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Detailed feedback
Date What did you like? What could be improved?
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?
18 responses
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Detailed feedback
Date What did you like? What could be improved?
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

Galaxy Server administration

129 responses
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14 responses
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Detailed feedback
Date What did you like? What could be improved?
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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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
11 responses
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Detailed feedback
Date What did you like? What could be improved?
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.
24 responses
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Detailed feedback
Date What did you like? What could be improved?
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.
13 responses
Rating Distribution
Detailed feedback
Date What did you like? What could be improved?
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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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
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4 responses
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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.
11 responses
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Date What did you like? What could be improved?
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.
8 responses
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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
8 responses
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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
10 responses
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Detailed feedback
Date What did you like? What could be improved?
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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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!
2 responses
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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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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?

Genome Annotation

26 responses
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10 responses
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Detailed feedback
Date What did you like? What could be improved?
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?)
4 responses
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Date What did you like? What could be improved?
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!
8 responses
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Date What did you like? What could be improved?
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
1 responses
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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.

Imaging

6 responses
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4 responses
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2 responses
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Date What did you like? What could be improved?

Introduction to Galaxy Analyses

524 responses
Rating Distribution
91 responses
Rating Distribution
Detailed feedback
Date What did you like? What could be improved?
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!
34 responses
Rating Distribution
Detailed feedback
Date What did you like? What could be improved?
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
59 responses
Rating Distribution
Detailed feedback
Date What did you like? What could be improved?
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.
34 responses
Rating Distribution
Detailed feedback
Date What did you like? What could be improved?
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
253 responses
Rating Distribution
Detailed feedback
Date What did you like? What could be improved?
Sep 1, 2021 Steps were clear and friendly
Aug 27, 2021 the instructions were detailed and precise i think it was fine
Aug 17, 2021 It is reproducable
Aug 5, 2021 The explanation was clear The example file does not work
Jul 30, 2021 Really easy to follow and understand what I was doing. Very up to date also. Better than many online tutorials that I have done. More explanation of what the outputs mean.
Jul 11, 2021 clarity and simple
Jul 8, 2021 step by step explanation for each task
Jul 6, 2021 All the instruction provided were user friendly, even students without the knowledge of computer can easily learn the tool just by follwing instructions
Jun 26, 2021 Simple and Elegant
Jun 25, 2021 Clear and concise; had images to show where things are; I got a little confused at the end where it said to click on Analyze Data in the top panel (step 3 in the "Look at all your histories") and could not find a way back without clicking the home button again.
Jun 19, 2021 It helps me to understand about the basic of data type -
Jun 2, 2021 very clear and complete
May 22, 2021 well explained!
May 21, 2021 It was clear and easy to follow
May 12, 2021 The trimming and filtering part is the most important stage of RNA-seq data analysis. Generally, adapter sequences are not given with SRA data in NCBI . Therefore, I was shot in the dark while using the trimmomatic, cuadapt and other tools whose results are not that much satisfactory. The information given in the tutorial seems to work for one of the messiest data. I think it would be great to see usage of filtering and trimming tools on one or two messy data. It will give us insights about how to deal with such data
Apr 20, 2021 Good for a beginner
Apr 14, 2021 It was easy and great with visuals as well
Apr 9, 2021 All aspects: clear, step by step illustration.
Mar 22, 2021 easy to follow
Mar 11, 2021 It's very precise and explain the most important characteristics of how to use the platform
Feb 23, 2021 Easy to follow and clear
Feb 18, 2021 How easy and friendly is the tutorial Nothing
Feb 17, 2021 Easy to follow We use FastQC. it would be nice to have some information about "Contaminant list ", "Adapter list", "Submodule and Limit specifing file" etc
Jan 29, 2021 Each part was beside its example. Add more images to each part and more questions to assure learning.
Jan 19, 2021 it's cleanness and clarity and simplicity. it is ideal for start
Dec 28, 2020 Excellent step by step instructions
Dec 27, 2020 Yes, but I needed more of NGS data analysis and interpretation Include thoughrough analysis of sequencing data eg finding a gene of interest, SNP, QTLs, marker trait associations etc
Dec 21, 2020 Everything was perfect! Nothing specific.
Dec 2, 2020 It was very visual and easy to follow
Nov 29, 2020 Hands on training Hands on training
Nov 29, 2020 Very clear step by step instructions with good visual cues and tests along the way to verify I'm doing everything correctly. I can tell this is going to reinforce good habits and logical thinking later on in your students. Really nice job.
Nov 28, 2020 Everything was clearly mentioned, making it very easy for beginners
Nov 25, 2020 very simple Thank you
Nov 18, 2020 Clarity of screen shots, simplicity of instructions, very little jargon Define what the quality of the reads means and why it's important
Oct 30, 2020 simple and clear no more
Oct 24, 2020 easy to follow more info on how to search for tools among the thousands of results
Oct 9, 2020 clear step-by-step the filter by quality tool does not appear in galaxy, unless I run it from the workflow associated to this training
Oct 2, 2020 Easy to follow
Sep 29, 2020 Very easy to follow Nothing
Sep 29, 2020 Simple to follow The link to the data is not owrking
Sep 11, 2020 Its comprehensive
Aug 20, 2020 The detailed step-by-step commands
Aug 10, 2020 Easy to follow
Jul 28, 2020 So clear
Jul 28, 2020 So clear
Jul 20, 2020 Easy to follow. Good use of pictures as a guide. Maybe include a video at the end doing all this.
Jul 11, 2020 Simple to follow I used the docker image and forgot to login, so I couldn't find the history rename / add new history options
Jul 8, 2020 Simple and clear!
Jul 6, 2020 I couldn't find "filter on quality" in the tools
Jul 3, 2020 Very easy to follow because of images with screen shots
Jun 29, 2020 easy to follow
Jun 25, 2020 It was helpful to learn to upload data. The tools no longer are found, that could be improved/
Jun 25, 2020 very detailed
Jun 24, 2020 It's a very simple and objective tutorial Images (prints of screen) of the tool parameters configuration screen would be of great help. Only the name of parameters is placed that we must changed, but, I believe that the screen print with these parameter and de value whould much more interesting mainly for very novice users like me.
Jun 19, 2020 Being able to follow through. Some links with good explanations to what these new bioinformatic terms are for beginners . Overall, it was great, thank you!
Jun 9, 2020 It was a very good explanation!
Jun 7, 2020 it includes a lot of details it will be better to include more exercises
Jun 1, 2020 Hands-on
Jun 1, 2020 Well explained/detailed
Jun 1, 2020 everything works as expected
May 15, 2020 questions and answers not sure
May 15, 2020 It's easy to understand.
May 8, 2020 clarity of the text improving my knowledge about galaxy panel
May 5, 2020 Having comprehension questions after each part of the lessons
Apr 25, 2020 It is simple and easy to follow.
Apr 17, 2020 Very easy to follow and good reinforcement
Apr 17, 2020 Very easy to follow and good reinforcement
Apr 15, 2020 Great that a URL was provided in case of not having a dataset to analyse yet. That made it possible to get "hands on". But also nice visualizations with pictures and the video, and good examples of how to search for the tools, how the three windows are arranged and how to navigate between the different histories. On the top of my head, nothing.
Apr 9, 2020 step by step approach adding more pictorial description of for example the exact place of the tool in the tool search, it took me long to find the tool I needed, and they didn't have that monkey-wrench image next to them
Apr 5, 2020 Clear and easy explanation with exercise.
Apr 4, 2020 the detailed descreption using a power point or video to visualize the steps in galaxy
Mar 24, 2020 The picture examples were very helpful. Information could be described more thoroughly.
Mar 23, 2020 simple, informative, easy first step by step guide
Mar 23, 2020 easy to follow, great visual aids
Mar 18, 2020 very basic. I need that How do you get back to a single history showing and the other two panels
Mar 3, 2020 The clear and short convenient characteristics nothing
Feb 21, 2020 every bit of it it was cool, and the best I think
Feb 18, 2020 Very easy to follow the instructions
Feb 11, 2020 Very Informative. Looking forward to it. Even for beginner as i am, i can using a galaxy without any problem. Thank you guys :) More analysis. Like whenever we'are using a tools, and it has a data view in it in the middle viewing panel, like QC, what is the number mean by all the statistic coming. Youre the best!
Feb 10, 2020 I liked the well-labeled comments/questions/hands on sections. Great level for beginners. There were some very slight differences between my window and the windows shown here, but honestly, I think this problem is unavoidable, and also it is good practice for people to struggle a tiny bit to figure out exactly what to click on. So...no improvements!
Feb 8, 2020 clearness a brief intro to IPython
Feb 7, 2020 logical flow of info what types of data can be processed having what type extension?
Feb 3, 2020 It's simplicty, I will use the images for my presentation as it's much faster than the slideshow.
Jan 27, 2020 Easy to follow and helpful Maybe more tips about what's important in setting criteria to filter the data; reasons, general practices...etc.
Jan 15, 2020 Very clear
Jan 14, 2020 detailed explanations and easy to follow
Jan 13, 2020 The variety in options when it comes to software
Jan 8, 2020 It is easy to understand and I hope I can start this tool easily.
Jan 2, 2020 The questions, pictures, easy explanations, AMAZING!! Update for updated version of Galaxy?
Dec 31, 2019 simple, informative and straightforward
Dec 27, 2019 all of the web
Nov 28, 2019 Straightforward and easy to follow
Nov 28, 2019 very good step by step instructions explain what the each step is doing to my data in this particular example
Nov 28, 2019 Quick and easy to follow!
Nov 25, 2019 easy to follow some guidance on the graphs that are generated and what they mean
Nov 19, 2019 C'est très bien expliqué
Oct 17, 2019 very helpful visualizations for tools inputs and outputs Not that I know of
Oct 10, 2019 for some reason the filter by quality tool did not appear :( but the tutorial was fab!
Sep 19, 2019 The step by step
Sep 11, 2019 The step-by-step guidance with explanations.
Sep 11, 2019 The simplicity and practicality of the tutorial More exploration of the data analysis to aid those who are not familiar with biological data (e.g. brief explanation of FASTQ and how to interpret it)
Sep 1, 2019 The step by step teaching More publicity to make this fantastic site more popular to bioinformatic field
Aug 19, 2019 thorough
Aug 14, 2019 Simple and clear
Aug 14, 2019 User friendly multiple ways of importing data in the introduction
Aug 7, 2019 Super simple and interactive
Jul 28, 2019 a very clear and concise introduction. The history names in fig 1 could be showing as the next-analysis and my-analysis.
Jun 23, 2019 the layout was great will not know until I work on my own data
Jun 14, 2019 almost all of it worked like the tutorial, very helpful the Filter by quality function was not on the program
May 31, 2019 simple and easy to learn
Apr 27, 2019 It was easy to follow and very clear
Apr 22, 2019 Very straight forward and convenient to catch up! None
Apr 22, 2019 Very graphical and easy to follow If you make a question, include always the answer with an appropiate explanation to make everything clear. Why in the case you use the 36 filter there are so many reads discarded? Do not Forget most of people is the first time they work with this online tool.
Apr 21, 2019 The detailed explanation
Apr 16, 2019 Tutorials are up to the point as the interface is user friendly If the tutorials could be downloadable, it could be a great help
Apr 10, 2019 everything
Apr 6, 2019 It is simple, clear and has materials for training.
Mar 22, 2019 the way it presented
Feb 13, 2019 Simple and easy to follow
Feb 12, 2019 Clear and concise instructions Nothing really,
Jan 23, 2019 Images with arrows, and short answer questions (made sure I was on the right path). The icons in the text were also a nice touch. I found the boxes around each of the big steps a little distracting. They are not necessary for the transition between the steps. The large headings are enough.
Jan 16, 2019 Easy to follow and use
Jan 13, 2019 No ambiguity and it showed some basics. Liked the labelled images.
Nov 19, 2018 Simplicity Nothing
Nov 1, 2018 This made using Galaxy very simple. This should be the first tutorial that shows up, even before the longer version as now I would feel more comfortable doing the long one whereas that one was overwhelming at first.
Oct 29, 2018 Easiness, You could link to short description of what a fastq format is, etc... and warn that Filterbyquality sometimes is not present. I could not find it. I use FilterFASTQ instead
Oct 18, 2018 explorations, explanations
Oct 18, 2018 Intuitive and well executed. Images were useful in following the flow of the tutorial. There is no answer to the question under the section entitled 'Re-run that tool with changed settings'. A 'Done' button does not appear in the view history screen as well.
Oct 18, 2018 Detailed explanation with screenshots!
Oct 18, 2018 Easy to follow with great pictures and arrows and labels none
Oct 18, 2018 Easy to follow and understand
Oct 10, 2018 step by step introduction, everything is very clear and easy to find some buttons do not exist (anymore)? Like in "Look at all your histories" under 3. at the top line there is a "done" button - this was not displayed when I did it. That is not a tragedy but it can be confusing....
Oct 8, 2018 The good explanation and visual help
Oct 8, 2018 Very straight forward Nothing
7 responses
Rating Distribution
Detailed feedback
Date What did you like? What could be improved?
May 7, 2021 It is not clear which files to choose, because "C2C12" clearly isnt available.
Feb 12, 2020 It is easy to follow and summurazing many tools features as much as possible. A real-life and frequently performed case tutorial could be shown for demonstrating what could be done in IGV.
Aug 22, 2019 RNASeq of C2C12 not available
Feb 25, 2019 Cannot find C2C12 file
Jan 15, 2019 Actually show some use-cases (there is only one and i am unable to load ENCODE data)
14 responses
Rating Distribution
Detailed feedback
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.
25 responses
Rating Distribution
Detailed feedback
Date What did you like? What could be improved?
Sep 9, 2021 Easy to follow step-by-step instructions
Sep 9, 2021 Hands on tutorial, that makes learning easier Can probably expand the training to involved more complicated thing. Maybe saperate training
Jul 1, 2021 Its a quite good tutorial nothing feld sofar
Mar 4, 2021 The instructions are very detailed and clearly presented. Some pictures in the tutorial are not up-to-date.
Mar 2, 2021 Very good guiding cant think of something..
Nov 19, 2020 Very clearly written and helpful. I didn't see the advanced options for graphing until i played with the versions.
Nov 12, 2020 Nice and quick introductory course to Galaxy. I also really liked the breakout room idea.
Oct 8, 2020 Easy to follow steps and control examples. Sometimes locating certain tools/features on the web interface was like looking for the needle in a hay stack - especially true for the "upload data" button.
Jul 29, 2020 Well written explanations, easy to follow, highlights value of the project well Sometimes different tool versions available with identical names but different input options, that was slightly confusing.
Jul 27, 2020 I had problems with rerunning the dataset (diamond). Please further specify the parameters that should be used (It was asking me to insert column parameters in the "unique" part of the last task)
Jun 30, 2020 Very easy to follow tutorial. With usefull tips
Jun 22, 2020 Clear directions for execution and correlation of results.
Mar 26, 2020 Error when I followed instructions When I set “Data point options”: User defined point options “relative size of points” to 2.0, I got an error "Error in alpha * 255 : non-numeric argument to binary operator Calls: ggsave ... validGP -> numnotnull -> alpha -> -> encode_c"
Mar 26, 2020 Error when I followed instructions When I set “Data point options”: User defined point options “relative size of points” to 2.0, I got an error "Error in alpha * 255 : non-numeric argument to binary operator Calls: ggsave ... validGP -> numnotnull -> alpha -> -> encode_c"
Mar 23, 2020 extensive, simple, step by step in section "Visualize Iris dataset with Scatterplot w ggplot2" using the Data point options as user defined point options (relative size of points”: 2.0") originates error. Leaving default parameters corrects error.
Mar 16, 2020 Learn how to run statistics
Feb 7, 2020 introduce the tutorial with a statement of what type of data is being processed. Only when I saw a picture did I realize that your processing a flower called iris.
Feb 7, 2020 It was more advanced than the other introductory tutorial I had read.
Nov 11, 2019 The hands on exercises The images about the diamonds are not very legible
6 responses
Rating Distribution
Detailed feedback
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
Rating Distribution
Detailed feedback
Date What did you like? What could be improved?

Metabolomics

6 responses
Rating Distribution
5 responses
Rating Distribution
Detailed feedback
Date What did you like? What could be improved?
Oct 14, 2020 Well explained and simple to follow Include a workflow for GCMS analysis
Oct 30, 2019 Comprehensive in terms of breadth; hands-on
Sep 29, 2019 All the careful and detailed explanations make the training easy to follow
Sep 18, 2019 The detailed explanation behind the steps. It was awesome
Jul 6, 2019 This format is much more approachable (esp. for hands-on) than the PDFs at W4M.org. I'm not saying that the PDFs are not helpful or informative (they are), but this is much more suitable for walking through the steps. Also, because it is a "living document", you can improve it in place, and we do not need to look for an updated document somewhere else. We can always link to one URL when referencing the tutorial. Document every axis of every panel of Quality_Metrics_figure.pdf, e.g., what are deciles and missing values in the bottom left panel? Put into the description the rationale behind the parameters chosen in Data Filtering (you presented it wonderfully verbally, but I don't find it written into the tutorial).
1 responses
Rating Distribution
Detailed feedback
Date What did you like? What could be improved?

Metagenomics

57 responses
Rating Distribution
34 responses
Rating Distribution