Tutorial Feedback

This issue will collect all feedback submitted via the feedback form at the end of each tutorial

Results have been aggregated and pro/cons per tutorial

New GTN feedback received
How much do you like this tutorial?: 5
What do you like?: just testing
What would you change?: more test
Tutorial: mothur
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New GTN feedback received
Which GTN tutorial did you complete?: test
How did you use this tutorial?: I took the tutorial on my own.
**Usefulness **: 3
Quality: 3
Length: Too short
Level of detail: Perfect
If you used this material to teach, how many students/participants attended?: 42
What did you like?: good things
What would you change?: bad things
Please provide any feedback you have on your experience with this tutorial.:
Your institution:: bla
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New GTN feedback received
Which GTN tutorial did you complete?: assembly with velvet
How did you use this tutorial?: I took the tutorial on my own.
Usefulness: 3
Quality: 3
Length: Too short
Level of detail: Not enough details
If you used this material to teach, how many students/participants attended?:
What did you like?:
What would you change?:
Please provide any feedback you have on your experience with this tutorial.: I want to use velvet for genome assembly but I am unable to find it on Galaxy. Is the application removed from galaxy?
Your institution: Okayama University
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New GTN feedback received
How much did you like this tutorial?: 5
What did you like?: very detailed and easy to follow, even for a complete beginner - great!
What could be improved?:
Tutorial: Galaxy 101 (Introduction to Galaxy Analyses)
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New GTN feedback received
How much did you like this tutorial?: 2
What did you like?:
What could be improved?:
Tutorial: Identification of the binding sites of the Estrogen receptor (ChIP-Seq data analysis)
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New GTN feedback received
What did you like?:
What could be improved?:
Tutorial: NGS data logistics (Introduction to Galaxy Analyses)
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New GTN feedback received
How much did you like this tutorial?: 5
What did you like?: Well structured, easy to understand.
What could be improved?:
Tutorial: From peaks to genes (Introduction to Galaxy Analyses)
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New GTN feedback received
How much did you like this tutorial?: 5
What did you like?: The data clean-up was thoroughly covered. Every step was well explained
What could be improved?: Using the mock community. More light on rationale
Tutorial: 16S Microbial Analysis with Mothur (Metagenomics)
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New GTN feedback received
How much did you like this tutorial?: 5
What did you like?:
What could be improved?:
Tutorial: From peaks to genes (Introduction to Galaxy Analyses)
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New GTN feedback received
How much did you like this tutorial?: 5
What did you like?: Very detailed, thank you
What could be improved?:
Tutorial: Mapping (Sequence analysis)
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New GTN feedback received
How much did you like this tutorial?: 5
What did you like?: perfect step by step !!!!
What could be improved?: maybe use human data ??
Tutorial: Hi-C analysis of Drosophila melanogaster cells using HiCExplorer (Epigenetics)
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New GTN feedback received
How much did you like this tutorial?: 4
What did you like?: Everything works with provided data and the scale is good for use in class
What could be improved?: 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.
Tutorial: De Bruijn Graph Assembly (Assembly)
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New GTN feedback received
How much did you like this tutorial?: 5
What did you like?: İts explanatory feature
What could be improved?:
Tutorial: Reference-based RNA-Seq data analysis (Transcriptomics)
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New GTN feedback received
How much did you like this tutorial?: 5
What did you like?:
What could be improved?:
Tutorial: DNA Methylation data analysis (Epigenetics)
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New GTN feedback received
How much did you like this tutorial?: 3
What did you like?:
What could be improved?: Not clear that Trim Galore and FastQ are integrated into Galaxy. Uncertain how obtained 97,644 sequences after trim galore of bad data (I got 99,341).
Tutorial: Quality Control (Sequence analysis)
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New GTN feedback received
How much did you like this tutorial?: 5
What did you like?:
What could be improved?:
Tutorial: Galaxy 101 (Introduction to Galaxy Analyses)
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New GTN feedback received
How much did you like this tutorial?: 5
What did you like?:
What could be improved?:
Tutorial: Quality Control (Sequence analysis)
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New GTN feedback received
How much did you like this tutorial?: 5
What did you like?:
What could be improved?:
Tutorial: Galaxy 101 (Introduction to Galaxy Analyses)
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New GTN feedback received
How much did you like this tutorial?: 4
What did you like?: The presentation of the tutorial and the practicality of it
What could be improved?: The rate of update of the tutorial
Tutorial: Galaxy 101 (Introduction to Galaxy Analyses)
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New GTN feedback received
How much did you like this tutorial?: 5
What did you like?: I found it interesting and user friendly
What could be improved?: nothing for now
Tutorial: Galaxy 101 (Introduction to Galaxy Analyses)
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New GTN feedback received
How much did you like this tutorial?: 5
What did you like?: makes life easy
What could be improved?: very good
Tutorial: NGS data logistics (Introduction to Galaxy Analyses)
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New GTN feedback received
How much did you like this tutorial?: 5
What did you like?: interesting and user friendly
What could be improved?: very good
Tutorial: Reference-based RNAseq data analysis (long) (Transcriptomics)
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New GTN feedback received
How much did you like this tutorial?: 4
What did you like?: The tutorial was very interesting and easy to follow
What could be improved?: Naming of the output files
Tutorial: Reference-based RNA-Seq data analysis (Transcriptomics)
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New GTN feedback received
How much did you like this tutorial?: 4
What did you like?: Many details and background information
What could be improved?: Fasta merging parameter How are sequences judged to be unique? should be set to 'Accession only'
Tutorial: Protein FASTA Database Handling (Proteomics)
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New GTN feedback received
How much did you like this tutorial?: 5
What did you like?: Well explained, great background information - my favourite was the greedy group resolution
What could be improved?:
Tutorial: Peptide and Protein ID using OpenMS tools (Proteomics)
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New GTN feedback received
How much did you like this tutorial?: 5
What did you like?:
What could be improved?:
Tutorial: Introduction to Genome Assembly (Assembly)
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New GTN feedback received
How much did you like this tutorial?: 5
What did you like?: simplicity
What could be improved?: pick a relevant induction based on your needs
Tutorial: From peaks to genes (Introduction to Galaxy Analyses)
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New GTN feedback received
How much did you like this tutorial?: 5
What did you like?: Background info such as: The explanation of 'doubtful' for all levels
What could be improved?: SearchGui crashed with the database containing mycoplasma, with human and crap database it worked
Tutorial: Peptide and Protein ID using SearchGUI and PeptideShaker (Proteomics)
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New GTN feedback received
How much did you like this tutorial?: 5
What did you like?:
What could be improved?:
Tutorial: A short introduction to Galaxy (Introduction to Galaxy Analyses)
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New GTN feedback received
How much did you like this tutorial?: 5
What did you like?:
What could be improved?:
Tutorial: Protein FASTA Database Handling (Proteomics)
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New GTN feedback received
How much did you like this tutorial?: 3
What did you like?:
What could be improved?:
Tutorial: Galaxy 101 (Introduction to Galaxy Analyses)
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New GTN feedback received
How much did you like this tutorial?: 5
What did you like?:
What could be improved?:
Tutorial: IGV Introduction (Introduction to Galaxy Analyses)
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New GTN feedback received
How much did you like this tutorial?: 5
What did you like?: Very straight forward
What could be improved?: Nothing
Tutorial: A short introduction to Galaxy (Introduction to Galaxy Analyses)
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New GTN feedback received
How much did you like this tutorial?: 5
What did you like?:
What could be improved?:
Tutorial: Galaxy 101 (Introduction to Galaxy Analyses)
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New GTN feedback received
How much did you like this tutorial?: 5
What did you like?: The good explanation and visual help
What could be improved?:
Tutorial: A short introduction to Galaxy (Introduction to Galaxy Analyses)
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New GTN feedback received
How much did you like this tutorial?: 4
What did you like?: Examples and questionaries with solutions :-)
What could be improved?: More details regarding others output sections of FastQC tool
Tutorial: Quality Control (Sequence analysis)
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New GTN feedback received
How much did you like this tutorial?: 5
What did you like?:
What could be improved?:
Tutorial: Ansible (Galaxy Server administration)
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New GTN feedback received (extended form)
Which GTN tutorial did you complete?: Reference-based RNA-Seq data analysis (Transcriptomics)
How did you use this tutorial?: I took the tutorial on my own.
Usefulness: 4
Quality: 4
Length: Perfect
Level of detail: Not enough details
If you used this material to teach, how many students/participants attended?:
What did you like?: I like how this tutorial was laid out. It was easy to follow and execute the program.
What could be improved?:
Please provide any feedback you have on your experience with this tutorial.: I did not understand why abs(c3)>1 was used to sort absolute fold change above 2 (FC>2). Will it not be abs(c3)>2 instead? Furthermore, when I select first 100 genes with fold change above 2, it also selects data with fold change below 2.
Do you have suggestions for additional topics or tutorials?:
Your institution: IIT Guwahati, India
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New GTN feedback received
How much did you like this tutorial?: 5
What did you like?:
What could be improved?:
Tutorial: From peaks to genes (Introduction to Galaxy Analyses)
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New GTN feedback received
How much did you like this tutorial?: 5
What did you like?: step by step introduction, everything is very clear and easy to find
What could be improved?: 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....
Tutorial: A short introduction to Galaxy (Introduction to Galaxy Analyses)
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New GTN feedback received
What did you like?:
What could be improved?:
Tutorial: Hi-C analysis of Drosophila melanogaster cells using HiCExplorer (Epigenetics)
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New GTN feedback received
How much did you like this tutorial?: 5
What did you like?: scope,  topic and clarity of tutorial
What could be improved?:
Tutorial: From peaks to genes (Introduction to Galaxy Analyses)
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New GTN feedback received
How much did you like this tutorial?: 5
What did you like?: Nice clear , very informative
What could be improved?: airconditioning less cold
Tutorial: From peaks to genes (Introduction to Galaxy Analyses)
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New GTN feedback received
How much did you like this tutorial?: 4
What did you like?:
What could be improved?:
Tutorial: From peaks to genes (Introduction to Galaxy Analyses)
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New GTN feedback received (extended form)
Which GTN tutorial did you complete?: Network analysis with Heinz (Transcriptomics)
How did you use this tutorial?: At a workshop.
Usefulness: 5
Quality: 5
Length: Perfect
Level of detail: Perfect
If you used this material to teach, how many students/participants attended?:
What did you like?:
What could be improved?: maybe some interpretation of the results.  ie what genes are involbved, what might this mean?  The tutorial mentions that this can be done, but some more discussion of what would be done with the resulting optimal subnetwrk would help pull it all together.
Please provide any feedback you have on your experience with this tutorial.:
Do you have suggestions for additional topics or tutorials?:
Your institution:
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New GTN feedback received
How much did you like this tutorial?: 3
What did you like?: It was well structured and simply explained
What could be improved?: It would be very helpful if the parameter setting on the tools was discussed a bit more and explain the reason why to certain choices
Tutorial: Network analysis with Heinz (Transcriptomics)
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New GTN feedback received
How much did you like this tutorial?: 5
What did you like?: Topic and clarity (DIY is easy)
What could be improved?:
Tutorial: Network analysis with Heinz (Transcriptomics)
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New GTN feedback received
How much did you like this tutorial?: 5
What did you like?: Nice clear and good to start a bit further down for speed so it fits the program.
What could be improved?: note that the use of build list is unclear, perhaps good to move description of how to solve this  up so to prevent questions.
Tutorial: Network analysis with Heinz (Transcriptomics)
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New GTN feedback received
How much did you like this tutorial?: 5
What did you like?: Easy to follow and understand
What could be improved?: N/A
Tutorial: A short introduction to Galaxy (Introduction to Galaxy Analyses)
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New GTN feedback received
How much did you like this tutorial?: 5
What did you like?: Easy to follow with great pictures and arrows and labels
What could be improved?: none
Tutorial: A short introduction to Galaxy (Introduction to Galaxy Analyses)
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New GTN feedback received
How much did you like this tutorial?: 5
What did you like?: Detailed explanation with screenshots!
What could be improved?: N/A
Tutorial: A short introduction to Galaxy (Introduction to Galaxy Analyses)
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New GTN feedback received
How much did you like this tutorial?: 5
What did you like?: Intuitive and well executed. Images were useful in following the flow of the tutorial.
What could be improved?: 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.
Tutorial: A short introduction to Galaxy (Introduction to Galaxy Analyses)
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New GTN feedback received
How much did you like this tutorial?: 5
What did you like?:
What could be improved?:
Tutorial: A short introduction to Galaxy (Introduction to Galaxy Analyses)
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New GTN feedback received
How much did you like this tutorial?: 5
What did you like?: explorations, explanations
What could be improved?: N/A
Tutorial: A short introduction to Galaxy (Introduction to Galaxy Analyses)
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New GTN feedback received
How much did you like this tutorial?: 5
What did you like?:
What could be improved?:
Tutorial: A short introduction to Galaxy (Introduction to Galaxy Analyses)
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New GTN feedback received
How much did you like this tutorial?: 3
What did you like?: Clarity and background details
What could be improved?: Need a step on how to remove barcodes, adapters and primers from raw FASTAq sequences
Tutorial: 16S Microbial Analysis with Mothur (Metagenomics)
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New GTN feedback received
How much did you like this tutorial?: 5
What did you like?: Topic and completeness of the scope
What could be improved?: I think there is an error:
Join two Datasets tool

with (output of the last Filter tool)
--> Should be with (output of Concatenate tool)

Tutorial: Reference-based RNA-Seq data analysis (Transcriptomics)
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What could be improved?: I think there is an error:
Join two Datasets tool

with (output of the last Filter tool)
--> Should be with (output of Concatenate tool)

Tutorial: Reference-based RNA-Seq data analysis (Transcriptomics)

@pvanheus I think this is a valid remark, right?

New GTN feedback received
How much did you like this tutorial?: 5
What did you like?:
What could be improved?:
Tutorial: From peaks to genes (Introduction to Galaxy Analyses)
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New GTN feedback received
How much did you like this tutorial?: 5
What did you like?: Very very straightforward !
What could be improved?: Nothing...
Tutorial: Running the Galaxy Training material website locally (Contributing to the Galaxy Training Material)
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New GTN feedback received
How much did you like this tutorial?: 5
What did you like?:
What could be improved?:
Tutorial: RNA-seq counts to genes and pathways (Transcriptomics)
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New GTN feedback received
How much did you like this tutorial?: 1
What did you like?:
What could be improved?:
Tutorial: Calling variants in diploid systems (Variant Analysis)
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New GTN feedback received
How much did you like this tutorial?: 2
What did you like?: Krona
What could be improved?: It needs to be updated, some returns error and some is missing. Be more detail and specific
Tutorial: Analyses of metagenomics data - The global picture (Metagenomics)
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New GTN feedback received
How much did you like this tutorial?: 4
What did you like?: "Easiness",
What could be improved?: 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
Tutorial: A short introduction to Galaxy (Introduction to Galaxy Analyses)
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New GTN feedback received
How much did you like this tutorial?: 1
What did you like?: Some instructions were not clear at all, please be more specific as i encounter errors very likely despite following the steps
What could be improved?: Please review the protocol and revise some segments
Tutorial: Analyses of metagenomics data - The global picture (Metagenomics)
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New GTN feedback received
How much did you like this tutorial?: 5
What did you like?: It's easy to follow.
What could be improved?: 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.
Tutorial: Ansible (Galaxy Server administration)
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New GTN feedback received
How much did you like this tutorial?: 5
What did you like?:
What could be improved?:
Tutorial: Mapping (Sequence analysis)
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New GTN feedback received
How much did you like this tutorial?: 5
What did you like?: all of it!
What could be improved?: how to rmemeber steps....
Tutorial: Quality Control (Sequence analysis)
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New GTN feedback received
How much did you like this tutorial?: 1
What did you like?:
What could be improved?:
Tutorial: Galaxy 101 (Introduction to Galaxy Analyses)
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New GTN feedback received
How much did you like this tutorial?: 5
What did you like?: This made using Galaxy very simple.
What could be improved?: 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.
Tutorial: A short introduction to Galaxy (Introduction to Galaxy Analyses)
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New GTN feedback received
How much did you like this tutorial?: 5
What did you like?: excellent intro, thanks!
What could be improved?:
Tutorial: Ansible (Galaxy Server administration)
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New GTN feedback received
How much did you like this tutorial?: 5
What did you like?:
What could be improved?: One could add a section describing the use of multiple datasets, tags, etc.
Tutorial: Galaxy 101 (Introduction to Galaxy Analyses)
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New GTN feedback received
How much did you like this tutorial?: 2
What did you like?:
What could be improved?: I'm still in the middle of it.  But when doing snpEFF there is no refernece genome available.  This tutorial does not say to download one.  Other variant analyses say to download hg19.  this is not available in the shared data folders.  When using an hg19 fasta from another source freeBayes fails because it isn't indexed.  Not sure how to index it.  SnpEFF calls for a database.  I downloaded one and am trying it now.  But it would be good to include this step in the tutorial
Tutorial: Calling variants in diploid systems (Variant Analysis)
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New GTN feedback received
How much did you like this tutorial?: 2
What did you like?: I like the idea
What could be improved?: After running the FreeBayes I ended up with 2 variants instead of 30.  And so got stuck there.  Also it's not clear why the filtering and subsequent steps would be done on the markduplicates output, rather than the left align output.  Why do the leftalign if we don't use that output again?  I did both and got the same results.
Overall I am finding the galaxy experience to be rather frustrating.  I'm trying to decide whether to incorporate these tutorials in my class, but often I can't find the necessary input data, get unexplained errors, or get output different from the tutorial
Tutorial: Calling variants in non-diploid systems (Variant Analysis)
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New GTN feedback received
How much did you like this tutorial?: 5
What did you like?:
What could be improved?:
Tutorial: A short introduction to Galaxy (Introduction to Galaxy Analyses)
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New GTN feedback received
How much did you like this tutorial?: 5
What did you like?:
What could be improved?:
Tutorial: Galaxy 101 (Introduction to Galaxy Analyses)
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New GTN feedback received
How much did you like this tutorial?: 4
What did you like?:
What could be improved?:
Tutorial: IGV Introduction (Introduction to Galaxy Analyses)
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New GTN feedback received (extended form)
Which GTN tutorial did you complete?: IGV Introduction (Introduction to Galaxy Analyses)
How did you use this tutorial?: I took the tutorial on my own.,To teach a workshop.
Usefulness: 4
Quality: 4
Length: Too short
Level of detail: Perfect
If you used this material to teach, how many students/participants attended?: 10
What did you like?: Image wise explanation on using a particular tool.
What could be improved?: More content according to case studies and some video output as well.
Please provide any feedback you have on your experience with this tutorial.: Very nicely presented the data, just the content addition needs to be little more; showing examples relatively till data interpretation with conclusion & future aspects as well.
Do you have suggestions for additional topics or tutorials?: Metagenomic Data Analysis with visualization tutorial how to upload, view and data interpretation; other than that, 5C-Seq Analysis, RIP-Seq Analysis, Mnase-Seq Analysis and FAIRE-Seq Analysis should also be available including few interesting topics like ribosome profiling, epigenomic sequencing, miRNA/ncRNA sequencing data analysis.
Your institution: RASA Life Science Informatics, Pune, Maharashtra, India.
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New GTN feedback received
How much did you like this tutorial?: 4
What did you like?: The overview of all the tools available.
What could be improved?: The time for the processes on Galaxy.
Tutorial: Analyses of metagenomics data - The global picture (Metagenomics)
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New GTN feedback received
How much did you like this tutorial?: 4
What did you like?: clear step by step module
What could be improved?:
Tutorial: Analyses of metagenomics data - The global picture (Metagenomics)
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New GTN feedback received
How much did you like this tutorial?: 4
What did you like?:
What could be improved?:
Tutorial: Galaxy 101 (Introduction to Galaxy Analyses)
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New GTN feedback received
How much did you like this tutorial?: 5
What did you like?: Thorough step by step directions. Does not assume you know stuff already.
What could be improved?: Naming the output files was a little confusing, especially when I was left on my own to continue to name all the rest of them. Why doesn't the new name show up in the workflow boxes after you name them?
Tutorial: Workflows: Extracting Workflows from Histories (User Interface and Features)
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New GTN feedback received
Tutorial: Ansible (Galaxy Server administration)
How much did you like this tutorial?: 3
What did you like?: TEST
What could be improved?: TEST
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New GTN feedback received
Tutorial: NGS data logistics (Introduction to Galaxy Analyses)
How much did you like this tutorial?: 5
What did you like?: Clear and consise
What could be improved?: N/A
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New GTN feedback received
Tutorial: A short introduction to Galaxy (Introduction to Galaxy Analyses)
How much did you like this tutorial?: 5
What did you like?:
What could be improved?:
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New GTN feedback received
Tutorial: From peaks to genes (Introduction to Galaxy Analyses)
How much did you like this tutorial?: 5
What did you like?: easy to follow individual steps
What could be improved?: 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
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New GTN feedback received
Tutorial: From peaks to genes (Introduction to Galaxy Analyses)
How much did you like this tutorial?: 4
What did you like?: Easy to follow tutorial
What could be improved?: We did not realize the 00000000rik names were also gene names, so we spent some time thinking we did something wrong...
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New GTN feedback received
Tutorial: Mapping (Sequence analysis)
How much did you like this tutorial?: 5
What did you like?:
What could be improved?:
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New GTN feedback received
Tutorial: Galaxy 101 (Introduction to Galaxy Analyses)
How much did you like this tutorial?: 5
What did you like?:
What could be improved?:
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New GTN feedback received
Tutorial: Galaxy 101 (Introduction to Galaxy Analyses)
How much did you like this tutorial?: 5
What did you like?: Easy to follow
What could be improved?: Including some assignment or home work
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New GTN feedback received (extended form)
Which GTN tutorial did you complete?: Differential abundance testing of small RNAs (Transcriptomics)
How did you use this tutorial?: I took the tutorial on my own.
Usefulness: 4
Quality: 2
Length: Perfect
Level of detail: Not enough details
If you used this material to teach, how many students/participants attended?:
What did you like?:
What could be improved?: Clarity of the files
Please provide any feedback you have on your experience with this tutorial.: Input of the given blank/simplekin files did not align to the expected outputs shown in the tutorial. For example, running a FASTQC report on the blank_rep1 did not detect Illumina universal adaptors featured in the screen shot example on your tutorial. I am unsure whether the files have been changed since the tutorial has initially made. Using the last tool DeSeq2 would not work despite following instructions very carefully. I am unsure what the final output of this tutorial is meant to be.
Do you have suggestions for additional topics or tutorials?:
Your institution:
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New GTN feedback received
Tutorial: A short introduction to Galaxy (Introduction to Galaxy Analyses)
How much did you like this tutorial?: 5
What did you like?:
What could be improved?:
Note: this comment was autogenerated

New GTN feedback received
Tutorial: Galaxy 101 (Introduction to Galaxy Analyses)
How much did you like this tutorial?: 5
What did you like?:
What could be improved?:
Note: this comment was autogenerated

New GTN feedback received
Tutorial: Galaxy 101 (Introduction to Galaxy Analyses)
How much did you like this tutorial?: 5
What did you like?:
What could be improved?:
Note: this comment was autogenerated

New GTN feedback received (extended form)
Which GTN tutorial did you complete?: Reference-based RNA-Seq data analysis (Transcriptomics)
How did you use this tutorial?: I took the tutorial on my own.
Usefulness: 4
Quality: 4
Length: Perfect
Level of detail: Perfect
If you used this material to teach, how many students/participants attended?:
What did you like?:
What could be improved?: bool function with compute option is NOT working for some reasons. I could not obtain True/False result  from DESeq result file.
Please provide any feedback you have on your experience with this tutorial.: bool function with compute option is NOT working for some reasons. I could not obtain True/False result  from DESeq result file.
Do you have suggestions for additional topics or tutorials?: Please include a tutorial for human genome
Your institution:
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New GTN feedback received
Tutorial: De novo transcriptome reconstruction with RNA-Seq (Transcriptomics)
How much did you like this tutorial?: 4
What did you like?: The explanations and solutions to check our output
What could be improved?: Explanations of the plots
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New GTN feedback received
Tutorial: 16S Microbial Analysis with Mothur (Metagenomics)
How much did you like this tutorial?: 5
What did you like?:
What could be improved?:
Note: this comment was autogenerated

New GTN feedback received
Tutorial: Reference-based RNA-Seq data analysis (Transcriptomics)
How much did you like this tutorial?: 4
What did you like?: step-by-step configuration
What could be improved?: colors to enhance instructions clarity
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New GTN feedback received
Tutorial: Visualization of RNA-Seq results with CummeRbund (Transcriptomics)
How much did you like this tutorial?: 1
What did you like?:
What could be improved?:
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New GTN feedback received
Tutorial: Quality Control (Sequence analysis)
How much did you like this tutorial?: 4
What did you like?: Nice explanation, really easy!
What could be improved?: what is the next step?
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New GTN feedback received
Tutorial: A short introduction to Galaxy (Introduction to Galaxy Analyses)
How much did you like this tutorial?: 5
What did you like?:
What could be improved?:
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New GTN feedback received
Tutorial: Deploying a compute cluster in OpenStack via Terraform (Galaxy Server administration)
How much did you like this tutorial?: 5
What did you like?: Really detailed, could use it for my project for creating my project
What could be improved?: maybe go deeper and show a template for a project
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New GTN feedback received (extended form)
Which GTN tutorial did you complete?: De novo transcriptome reconstruction with RNA-Seq (Transcriptomics)
How did you use this tutorial?: As an assignment for a class.
Usefulness: 5
Quality: 5
Length: Perfect
Level of detail: Too many details
If you used this material to teach, how many students/participants attended?:
What did you like?: How many transcripts have a significant change in expression between these conditions?
To filter, use “c7<0.05”. And we get 249 transcripts with a significant change in gene expression between the G1E and megakaryocyte cellular states.
Please check if your answer is correct? Are you using a P value of 0.5 and not 0.05?
What could be improved?:
Please provide any feedback you have on your experience with this tutorial.:
Do you have suggestions for additional topics or tutorials?:
Your institution: Johns Hopkins
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New GTN feedback received
Tutorial: A short introduction to Galaxy (Introduction to Galaxy Analyses)
How much did you like this tutorial?: 5
What did you like?:
What could be improved?:
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New GTN feedback received
Tutorial: Exome sequencing data analysis (Variant Analysis)
How much did you like this tutorial?: 1
What did you like?:
What could be improved?: unfortunately in compare with others tutorial, this is very unclear and o'm not satisfied please improve this very important tutorial with clear and accurate dive.
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New GTN feedback received
Tutorial: Visualization of RNA-Seq results with Volcano Plot (Transcriptomics)
How much did you like this tutorial?: 5
What did you like?:
What could be improved?:
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New GTN feedback received
Tutorial: Reference-based RNA-Seq data analysis (Transcriptomics)
How much did you like this tutorial?: 5
What did you like?: Nothing :)
What could be improved?: I think it's already good and clear as it is
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New GTN feedback received
Tutorial: A short introduction to Galaxy (Introduction to Galaxy Analyses)
How much did you like this tutorial?: 5
What did you like?:
What could be improved?:
Note: this comment was autogenerated

New GTN feedback received
Tutorial: From peaks to genes (Introduction to Galaxy Analyses)
How much did you like this tutorial?: 5
What did you like?:
What could be improved?:
Note: this comment was autogenerated

New GTN feedback received
Tutorial: Quality Control (Sequence analysis)
How much did you like this tutorial?: 5
What did you like?:
What could be improved?:
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New GTN feedback received
Tutorial: Formation of the Super-Structures on the Inactive X (ChIP-Seq data analysis)
How much did you like this tutorial?: 5
What did you like?:
What could be improved?:
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New GTN feedback received
Tutorial: RNA-Seq reads to counts (Transcriptomics)
How much did you like this tutorial?: 5
What did you like?:
What could be improved?:
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New GTN feedback received
Tutorial: Running the Galaxy Training material website locally (Contributing to the Galaxy Training Material)
How much did you like this tutorial?: 2
What did you like?: Clear wording.
What could be improved?: As a Windows user, I was not able to install requirements successfully.
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New GTN feedback received (extended form)
Which GTN tutorial did you complete?: Running the Galaxy Training material website locally (Contributing to the Galaxy Training Material)
How did you use this tutorial?: I took the tutorial on my own.,At a workshop.
Usefulness: 4
Quality: 5
Length: Perfect
Level of detail: Not enough details
If you used this material to teach, how many students/participants attended?:
What did you like?: Clear wordings.
What could be improved?: Windows-compatibility.
Please provide any feedback you have on your experience with this tutorial.: Installing packages requires make, which Windows does not have. The make package which can be installed via conda does not work.
Do you have suggestions for additional topics or tutorials?:
Your institution:
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New GTN feedback received
Tutorial: A short introduction to Galaxy (Introduction to Galaxy Analyses)
How much did you like this tutorial?: 2
What did you like?:
What could be improved?:
Note: this comment was autogenerated

New GTN feedback received
Tutorial: Galaxy 101 (Introduction to Galaxy Analyses)
What did you like?:
What could be improved?:
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New GTN feedback received
Tutorial: Mapping (Sequence analysis)
How much did you like this tutorial?: 5
What did you like?:
What could be improved?:
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New GTN feedback received
Tutorial:
How much did you like this tutorial?: 5
What did you like?:
What could be improved?:
Note: this comment was autogenerated

New GTN feedback received
Tutorial: A short introduction to Galaxy (Introduction to Galaxy Analyses)
How much did you like this tutorial?: 5
What did you like?: Clear and concise instructions
What could be improved?: Nothing really,
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New GTN feedback received
Tutorial: A short introduction to Galaxy (Introduction to Galaxy Analyses)
How much did you like this tutorial?: 4
What did you like?: Simple and easy to follow
What could be improved?:
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New GTN feedback received
Tutorial: Creating a new tutorial (Contributing to the Galaxy Training Material)
How much did you like this tutorial?: 5
What did you like?: the option to automatically extract all steps of my workflow instead of typing them all is sooooo increadibly helpful!!!
What could be improved?:
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New GTN feedback received
Tutorial: Introduction to Genome Assembly (Assembly)
What did you like?:
What could be improved?:
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New GTN feedback received
Tutorial: De novo transcriptome reconstruction with RNA-Seq (Transcriptomics)
How much did you like this tutorial?: 5
What did you like?: The explanation and description is easy to understand.
What could be improved?:
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New GTN feedback received
Tutorial: From peaks to genes (Introduction to Galaxy Analyses)
How much did you like this tutorial?: 5
What did you like?: Very clear instruction and step-by-step explanation
What could be improved?: some small exercises or quizes
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New GTN feedback received
Tutorial: From peaks to genes (Introduction to Galaxy Analyses)
How much did you like this tutorial?: 5
What did you like?:
What could be improved?:
Note: this comment was autogenerated

New GTN feedback received
Tutorial: Galaxy 101 (Introduction to Galaxy Analyses)
How much did you like this tutorial?: 5
What did you like?: Very simple to follow and learn on my own
What could be improved?:
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New GTN feedback received
Tutorial: IGV Introduction (Introduction to Galaxy Analyses)
How much did you like this tutorial?: 3
What did you like?:
What could be improved?: Cannot find C2C12 file
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New GTN feedback received
Tutorial: GO Enrichment Analysis (Transcriptomics)
How much did you like this tutorial?: 5
What did you like?:
What could be improved?:
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New GTN feedback received
Tutorial: Genome annotation with Maker (Genome Annotation)
How much did you like this tutorial?: 2
What did you like?: The first steps of the tutorial are great, described in a simple and objective way.
What could be improved?: 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!
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New GTN feedback received
Tutorial: Introduction to Genomics and Galaxy (Introduction to Galaxy Analyses)
How much did you like this tutorial?: 4
What did you like?: 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.
What could be improved?:
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New GTN feedback received
Tutorial: Hi-C analysis of Drosophila melanogaster cells using HiCExplorer (Epigenetics)
How much did you like this tutorial?: 4
What did you like?:
What could be improved?:
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New GTN feedback received
Tutorial: Hi-C analysis of Drosophila melanogaster cells using HiCExplorer (Epigenetics)
How much did you like this tutorial?: 4
What did you like?: Nothing bad, just I do not have sufficient background knowledge to comprehend everything. Nevertheless, very well-structured for a beginner to learn.
What could be improved?:
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New GTN feedback received
Tutorial: Deploying a compute cluster in OpenStack via Terraform (Galaxy Server administration)
What did you like?:
What could be improved?:
Note: this comment was autogenerated

New GTN feedback received
Tutorial: Genome Annotation (Genome Annotation)
How much did you like this tutorial?: 5
What did you like?:
What could be improved?:
Note: this comment was autogenerated

New GTN feedback received
Tutorial: Galaxy 101 (Introduction to Galaxy Analyses)
How much did you like this tutorial?: 5
What did you like?:
What could be improved?:
Note: this comment was autogenerated

New GTN feedback received
Tutorial: Galaxy 101 (Introduction to Galaxy Analyses)
What did you like?:
What could be improved?:
Note: this comment was autogenerated

New GTN feedback received
Tutorial: Formation of the Super-Structures on the Inactive X (ChIP-Seq data analysis)
How much did you like this tutorial?: 4
What did you like?:
What could be improved?:
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New GTN feedback received
Tutorial: Basics of machine learning (Statistics and machine learning)
How much did you like this tutorial?: 5
What did you like?: very straightforward tutorial
What could be improved?:
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New GTN feedback received
Tutorial: 16S Microbial Analysis with mothur (Metagenomics)
How much did you like this tutorial?: 5
What did you like?: Step-by-step guidance to complete tutorial, comprehensive and easy to understand and follow along
What could be improved?:
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New GTN feedback received
Tutorial: 16S Microbial Analysis with mothur (Metagenomics)
How much did you like this tutorial?: 4
What did you like?: that it went right from the beginning (fastq) with explanations at each point of what I was looking at
What could be improved?: the galaxy biom1 file output does not open successfully in Phinch, preventing the final visualisation
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New GTN feedback received
Tutorial: 16S Microbial Analysis with mothur (Metagenomics)
How much did you like this tutorial?: 5
What did you like?:
What could be improved?:
Note: this comment was autogenerated

New GTN feedback received
Tutorial: 16S Microbial Analysis with Mothur (Metagenomics)
What did you like?:
What could be improved?:
Note: this comment was autogenerated

New GTN feedback received
Tutorial: 16S Microbial Analysis with Mothur (Metagenomics)
How much did you like this tutorial?: 5
What did you like?: Clear explanations of the tools; helpful workflow; I think the Hand On opportunities and prompt questions are really beneficial.
What could be improved?: Descriptions of which files to use were not always clear enough for me to determine which one to use. The justification of some selections for tool options could be expanded on, or additional links to papers noted where appropriate.
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New GTN feedback received
Tutorial: Unicycler Assembly (Assembly)
How much did you like this tutorial?: 5
What did you like?:
What could be improved?:
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New GTN feedback received
Tutorial: Deploying a compute cluster in OpenStack via Terraform (Galaxy Server administration)
How much did you like this tutorial?: 4
What did you like?:
What could be improved?:
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New GTN feedback received
Tutorial: Identification of somatic and germline variants from tumor and normal sample pairs (Variant Analysis)
How much did you like this tutorial?: 1
What did you like?:
What could be improved?:
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New GTN feedback received
Tutorial: Differential abundance testing of small RNAs (Transcriptomics)
How much did you like this tutorial?: 3
What did you like?:
What could be improved?:
Note: this comment was autogenerated

New GTN feedback received
Tutorial: A short introduction to Galaxy (Introduction to Galaxy Analyses)
How much did you like this tutorial?: 3
What did you like?:
What could be improved?:
Note: this comment was autogenerated

New GTN feedback received
Tutorial: Basics of machine learning (Statistics and machine learning)
How much did you like this tutorial?: 4
What did you like?: This was a helpful example for how machine learning can be applied to a real-world dataset.
What could be improved?: Add more info on how to access the SVM Classifier tool. This tool does not seem to be available in the US Galaxy instance, but it is available in the EU Galaxy instance.
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New GTN feedback received
Tutorial: Quality Control (Sequence analysis)
How much did you like this tutorial?: 4
What did you like?: very clear
What could be improved?: specificity of quality check regarding the type of data (16S, whole genome)
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New GTN feedback received
Tutorial: A short introduction to Galaxy (Introduction to Galaxy Analyses)
How much did you like this tutorial?: 5
What did you like?: the way it presented
What could be improved?:
Note: this comment was autogenerated

New GTN feedback received
Tutorial: Quality Control (Sequence analysis)
How much did you like this tutorial?: 4
What did you like?:
What could be improved?:
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New GTN feedback received (extended form)
Which GTN tutorial did you complete?: Galaxy Installation with Ansible (Galaxy Server administration)
How did you use this tutorial?: I took the tutorial on my own.
Usefulness: 5
Quality: 5
Length: Too short
Level of detail: Not enough details
If you used this material to teach, how many students/participants attended?: NA
What did you like?: the step by step material on these major areas:- deployment and configuration of nginx, certificate for SSL from certbot
What could be improved?: add more details on the certbot configuration for cluster production environment. Also notice some error in the section on the configuration of the certbot certificate
Please provide any feedback you have on your experience with this tutorial.:
Do you have suggestions for additional topics or tutorials?:
Your institution: Medical research council The Gambia
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New GTN feedback received
Tutorial: A short introduction to Galaxy (Introduction to Galaxy Analyses)
How much did you like this tutorial?: 4
What did you like?:
What could be improved?:
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New GTN feedback received
Tutorial: De Bruijn Graph Assembly (Assembly)
How much did you like this tutorial?: 5
What did you like?: Easy to follow
What could be improved?:
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New GTN feedback received
Tutorial: Unicycler Assembly (Assembly)
How much did you like this tutorial?: 3
What did you like?:
What could be improved?:
Note: this comment was autogenerated

New GTN feedback received
Tutorial: Quality Control (Sequence analysis)
How much did you like this tutorial?: 4
What did you like?:
What could be improved?:
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New GTN feedback received
Tutorial: GO Enrichment Analysis (Transcriptomics)
How much did you like this tutorial?: 4
What did you like?: Nicely explained and easy to follow even with own data.
What could be improved?: There is no explanation of the graph (colours, %, arrows) and meaning of columns in tabular output (Study#, pvalue, qvalue). Would be nice to shortly describe this with one example GO term.
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New GTN feedback received
Tutorial: Galaxy 101 (Introduction to Galaxy Analyses)
How much did you like this tutorial?: 5
What did you like?:
What could be improved?:
Note: this comment was autogenerated

New GTN feedback received
Tutorial: A short introduction to Galaxy (Introduction to Galaxy Analyses)
How much did you like this tutorial?: 4
What did you like?:
What could be improved?:
Note: this comment was autogenerated

New GTN feedback received
Tutorial: Unicycler Assembly (Assembly)
How much did you like this tutorial?: 4
What did you like?:
What could be improved?:
Note: this comment was autogenerated

New GTN feedback received
Tutorial: A short introduction to Galaxy (Introduction to Galaxy Analyses)
How much did you like this tutorial?: 5
What did you like?: It is simple, clear and has materials for training.
What could be improved?:
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New GTN feedback received
Tutorial: A short introduction to Galaxy (Introduction to Galaxy Analyses)
How much did you like this tutorial?: 5
What did you like?:
What could be improved?:
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New GTN feedback received
Tutorial: Genome Annotation (Genome Annotation)
How much did you like this tutorial?: 1
What did you like?: good description of what annotation is
What could be improved?: 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
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New GTN feedback received
Tutorial: A short introduction to Galaxy (Introduction to Galaxy Analyses)
How much did you like this tutorial?: 5
What did you like?:
What could be improved?:
Note: this comment was autogenerated

New GTN feedback received
Tutorial: A short introduction to Galaxy (Introduction to Galaxy Analyses)
How much did you like this tutorial?: 5
What did you like?: everything
What could be improved?:
Note: this comment was autogenerated

New GTN feedback received
Tutorial: Reference-based RNA-Seq data analysis (Transcriptomics)
How much did you like this tutorial?: 5
What did you like?:
What could be improved?:
Note: this comment was autogenerated

New GTN feedback received
Tutorial: 16S Microbial Analysis with mothur (Metagenomics)
How much did you like this tutorial?: 4
What did you like?:
What could be improved?:
Note: this comment was autogenerated

New GTN feedback received
Tutorial: Reference-based RNA-Seq data analysis (Transcriptomics)
What did you like?:
What could be improved?:
Note: this comment was autogenerated

New GTN feedback received
Tutorial: Reference-based RNA-Seq data analysis (Transcriptomics)
How much did you like this tutorial?: 5
What did you like?: Most complete tuto with lot of aspect.
What could be improved?: Maybe add so MULTIQC (for inferexperiment for example) for an easiest visualisation.
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New GTN feedback received
Tutorial: Set up a Galaxy for Training (Teaching and Hosting Galaxy training)
How much did you like this tutorial?: 5
What did you like?:
What could be improved?:
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New GTN feedback received
Tutorial: Analyses of metagenomics data - The global picture (Metagenomics)
How much did you like this tutorial?: 3
What did you like?:
What could be improved?:
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New GTN feedback received
Tutorial: Analyses of metagenomics data - The global picture (Metagenomics)
How much did you like this tutorial?: 4
What did you like?: step by step very well described
What could be improved?: data analysis with OTU / phylotype
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New GTN feedback received
Tutorial: Visualization of RNA-Seq results with Volcano Plot (Transcriptomics)
How much did you like this tutorial?: 5
What did you like?:
What could be improved?:
Note: this comment was autogenerated

New GTN feedback received
Tutorial: A short introduction to Galaxy (Introduction to Galaxy Analyses)
How much did you like this tutorial?: 5
What did you like?:
What could be improved?:
Note: this comment was autogenerated

New GTN feedback received
Tutorial: Genome annotation with Prokka (Genome Annotation)
How much did you like this tutorial?: 4
What did you like?:
What could be improved?:
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New GTN feedback received
Tutorial: A short introduction to Galaxy (Introduction to Galaxy Analyses)
How much did you like this tutorial?: 5
What did you like?: Tutorials are up to the point as the interface is user friendly
What could be improved?: If the tutorials could be downloadable, it could be a great help
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New GTN feedback received
Tutorial: Unicycler Assembly (Assembly)
How much did you like this tutorial?: 4
What did you like?: easy to follow, step by step
What could be improved?:
Note: this comment was autogenerated

New GTN feedback received
Tutorial: Reference-based RNA-Seq data analysis (Transcriptomics)
What did you like?:
What could be improved?:
Note: this comment was autogenerated

New GTN feedback received
Tutorial: Genome Annotation (Genome Annotation)
How much did you like this tutorial?: 4
What did you like?:
What could be improved?:
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New GTN feedback received
Tutorial: Collections: Using dataset collection (Data Manipulation)
How much did you like this tutorial?: 5
What did you like?:
What could be improved?:
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New GTN feedback received
Tutorial: Galaxy 101 (Introduction to Galaxy Analyses)
How much did you like this tutorial?: 4
What did you like?:
What could be improved?: 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
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New GTN feedback received
Tutorial: Visualization of RNA-Seq results with Volcano Plot (Transcriptomics)
How much did you like this tutorial?: 5
What did you like?:
What could be improved?:
Note: this comment was autogenerated

New GTN feedback received
Tutorial: RNA-seq counts to genes (Transcriptomics)
How much did you like this tutorial?: 5
What did you like?: Clear, comprehensive, great screenshots
What could be improved?: Nothing so far
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New GTN feedback received
Tutorial:
How much did you like this tutorial?: 5
What did you like?: Everything
What could be improved?: In  "Hands-on: Format the sample information file" it should be mentioned that neither sample names nor categories should start with a number. eg MCG1 is ok., but 1MCG is not. I had this problem, which causes limma/voom to throw an error.
Also with the sample information file, it is unclear if more than two columns can be created.
It would be great to mention in more detail how to include batch effects as a factor - unless I missed it, or it is included in a more advanced tutorial.
Thanks for the great work (from a bioinformatician, who is enjoying getting away from the console and or Rstudio for a bit)
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New GTN feedback received
Tutorial: Galaxy 101 (Introduction to Galaxy Analyses)
How much did you like this tutorial?: 5
What did you like?:
What could be improved?:
Note: this comment was autogenerated

New GTN feedback received
Tutorial: A short introduction to Galaxy (Introduction to Galaxy Analyses)
How much did you like this tutorial?: 5
What did you like?: The detailed explanation
What could be improved?:
Note: this comment was autogenerated

New GTN feedback received
Tutorial: A short introduction to Galaxy (Introduction to Galaxy Analyses)
How much did you like this tutorial?: 4
What did you like?:
What could be improved?:
Note: this comment was autogenerated

New GTN feedback received
Tutorial: A short introduction to Galaxy (Introduction to Galaxy Analyses)
How much did you like this tutorial?: 5
What did you like?: Very graphical and easy to follow
What could be improved?: 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.
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New GTN feedback received
Tutorial: A short introduction to Galaxy (Introduction to Galaxy Analyses)
How much did you like this tutorial?: 5
What did you like?: Very straight forward and convenient to catch up!
What could be improved?: None
Note: this comment was autogenerated

New GTN feedback received
Tutorial: A short introduction to Galaxy (Introduction to Galaxy Analyses)
How much did you like this tutorial?: 5
What did you like?:
What could be improved?:
Note: this comment was autogenerated

New GTN feedback received
Tutorial: 16S Microbial Analysis with mothur (Metagenomics)
How much did you like this tutorial?: 5
What did you like?: Everything
What could be improved?:
Note: this comment was autogenerated

New GTN feedback received
Tutorial: A short introduction to Galaxy (Introduction to Galaxy Analyses)
How much did you like this tutorial?: 5
What did you like?:
What could be improved?:
Note: this comment was autogenerated

New GTN feedback received
Tutorial: Galaxy 101 (Introduction to Galaxy Analyses)
How much did you like this tutorial?: 3
What did you like?: explanations were very clear !
What could be improved?: this is a bit too long
Note: this comment was autogenerated

New GTN feedback received
Tutorial: Reference-based RNA-Seq data analysis (Transcriptomics)
What did you like?:
What could be improved?:
Note: this comment was autogenerated

New GTN feedback received
Tutorial: Detection and quantitation of N-termini (degradomics) via N-TAILS (Proteomics)
How much did you like this tutorial?: 1
What did you like?:
What could be improved?: still to complex to make sense
Note: this comment was autogenerated

New GTN feedback received
Tutorial: Unicycler Assembly (Assembly)
How much did you like this tutorial?: 4
What did you like?:
What could be improved?:
Note: this comment was autogenerated

New GTN feedback received
Tutorial: Label-free versus Labelled - How to Choose Your Quantitation Method (Proteomics)
How much did you like this tutorial?: 5
What did you like?:
What could be improved?:
Note: this comment was autogenerated

New GTN feedback received
Tutorial: 16S Microbial Analysis with mothur (Metagenomics)
How much did you like this tutorial?: 5
What did you like?:
What could be improved?:
Note: this comment was autogenerated

New GTN feedback received
Tutorial: A short introduction to Galaxy (Introduction to Galaxy Analyses)
How much did you like this tutorial?: 5
What did you like?:
What could be improved?:
Note: this comment was autogenerated

New GTN feedback received
Tutorial: A short introduction to Galaxy (Introduction to Galaxy Analyses)
How much did you like this tutorial?: 5
What did you like?: It was easy to follow and very clear
What could be improved?:
Note: this comment was autogenerated

New GTN feedback received
Tutorial: Downstream Single-cell RNA analysis with RaceID (Transcriptomics)
How much did you like this tutorial?: 5
What did you like?:
What could be improved?:
Note: this comment was autogenerated

New GTN feedback received
Tutorial: NGS data logistics (Introduction to Galaxy Analyses)
How much did you like this tutorial?: 3
What did you like?: I liked the videos.
What could be improved?: I would suggest to make the videos longer and theory shorter.
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New GTN feedback received
Tutorial: Galaxy 101 (Introduction to Galaxy Analyses)
How much did you like this tutorial?: 5
What did you like?: Instructive
What could be improved?: I do not know - I know only Biopython
Note: this comment was autogenerated

New GTN feedback received
Tutorial: 16S Microbial Analysis with mothur (Metagenomics)
How much did you like this tutorial?: 5
What did you like?: easy step by step guide to analysing 16s rRNA data
What could be improved?: When you say skip mock test if time retrain, skip whole section to OTU step? More information of the choice of databases used and do we use all etc?
Note: this comment was autogenerated

New GTN feedback received
Tutorial: Antibiotic resistance detection (Metagenomics)
How much did you like this tutorial?: 5
What did you like?:
What could be improved?:
Note: this comment was autogenerated

New GTN feedback received
Tutorial: A short introduction to Galaxy (Introduction to Galaxy Analyses)
How much did you like this tutorial?: 5
What did you like?:
What could be improved?:
Note: this comment was autogenerated

New GTN feedback received
Tutorial: Visualization of RNA-Seq results with Volcano Plot (Transcriptomics)
What did you like?:
What could be improved?: Tutorial doesn't have any public servers listed. Maybe a tool version conflict? Latest version is 0.0.3 and is installed at EU (and I made a request to add it to ORG). Are probably more tutorials like this -- seems the lists of "instances" is decreasing overall (bigger project, maybe good for the GTN or GCC co-fests)
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New GTN feedback received
Tutorial: Reference-based RNA-Seq data analysis (Transcriptomics)
How much did you like this tutorial?: 5
What did you like?: the "step by step "
What could be improved?:
Note: this comment was autogenerated

New GTN feedback received
Tutorial: Genome annotation with Maker (Genome Annotation)
What did you like?: Analysis for tutorial should be done on large datasets like genome from population rather than on individual genome.
What could be improved?:
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New GTN feedback received
Tutorial: Quality Control (Sequence analysis)
How much did you like this tutorial?: 5
What did you like?: solid logic and small amount of valuable information
What could be improved?: Probably as we are not trimming any adaptors in this tutorial, Trimmomatic can also be used on datasets provided.
Note: this comment was autogenerated

New GTN feedback received
Tutorial: RNA-Seq reads to counts (Transcriptomics)
How much did you like this tutorial?: 5
What did you like?:
What could be improved?:
Note: this comment was autogenerated

New GTN feedback received
Tutorial: A short introduction to Galaxy (Introduction to Galaxy Analyses)
How much did you like this tutorial?: 5
What did you like?:
What could be improved?:
Note: this comment was autogenerated

New GTN feedback received
Tutorial: 16S Microbial Analysis with mothur (extended) (Metagenomics)
How much did you like this tutorial?: 4
What did you like?:
What could be improved?:
Note: this comment was autogenerated

New GTN feedback received
Tutorial: 16S Microbial Analysis with mothur (extended) (Metagenomics)
How much did you like this tutorial?: 4
What did you like?:
What could be improved?:
Note: this comment was autogenerated

New GTN feedback received
Tutorial: Galaxy 101 (Introduction to Galaxy Analyses)
How much did you like this tutorial?: 5
What did you like?: Ease of understanding
What could be improved?: Adding more examples of its applications and how it is used in real time
Note: this comment was autogenerated

Workshop Feedback
Topics:

Day 1: Intro, QC, Mapping (@erasche)
Day 2: Annotation with MAKER (@abretaud)
Day 3: 16S with Mothur (@shiltemann)

Audience: Fungal annotation people
What did you like?
Day 1:

Easy to follow, nice atmosphere
Good intro for someone with very little knowledge
Material used was good/clear/easy to follow
I like galaxy as a package no doubt, especially after command line in Linux, this is a relief
"clean" information
Slides are easy to read and process (not too many words per slide)

Day 2:

More complex assignment, very straightforward
great intro to annotation

Day 3:

Really well explained
Lots of resources
Super convenient to design workflows
Great introduction and also resource for general steps and procedures
Was very nice to know about these tools from galaxy, today I enjoy more because it is more related to my project
Thanks, I'll start using Galaxy much more in the coming weeks, months, years
Very well done! Thank you very much!
Overall a good course, provided much hope and leads!!

What could be improved?
Day 1:

Could you please point to cove genome trees / snp based trees
Please spend more time on parameter selection / critera / instrument application / optimum reasoning behind executing certain steps
We had quite a bit of spare time, without reading a lot into what/how each tool does, which parameters it uses, etc. But galaxy is pretty strightforward
I missed a bit more explanation about why we do these steps, more than how to do them. Also interpretation of the outputs
Lot of information in a short time, but that is something that can't be avoided
Improvement, more information on "pitfalls", e.g. mistakes people make when running analyses
More info about diff parameters
Longer introduction on: errors with examples (QC), different tools for diff sequencing techniques
Explain in detail the different tools, specially those that are not familiar with the program/genomics
How to extract for methods section

Day 2:

For galaxy dev, would it be possible to group items in the history? That would enable collapsing reports or part that will become less relevant, e.g. group all the QC steps (responded with: collections the next day)
Version bug in tutorial (@erasche fixed on .eu)
Including assembly before annotation would be great
less repetitive tutorials, e.g. same tools used too many times

Day 3:

More varied tutorials / less repetitive
Fungal versions would be nice (but understand due to the "numbers game")
Would be nice if there is a little more background of the subject before start with all the tools.
Although the overall topics are a lot, I would like to have a dedicated course on nanopore

@erasche great idea!
Here's our workshop feedback from last week.
Intro to Galaxy and RNA-seq
2 x 3hr sessions
Material used
(tried this format for first time, previously tried 4 x 2hr)
Audience: Cancer biologists
What did you like about this workshop?

Hands on and approachable
it is practical
Really well presented and explained, extra resources (pdfs, training material) very helpful
Day 2!! Day 1 was a disaster for me as it went too quick and I wasn't prepared, and had a few minor technical issues. Overall the content and content level was appropriate
I liked that fact that some theories was explained behind the data representation and what all the Figures mean and implying it to. I like that it was explained in very detail and step by step so that it could be followed.
Hand on Experience
Very clear explanation of theory and application methods. Well supported by the team when problems are encountered.
Very direct tutorial of the actual tools we would use, rather than just generic discussion

What could be improved?

Help understand some of the data
More training courses are needed
Although we already covered quite a lot in a short amount of time, would be good if we had more time to discuss the different tools and different options for different types of data in more detail. This would probably require more sessions
Difficult to follow at the beginning.
Will be better if you can send out the course materials earlier.
Pre-reading the Galaxy Introduction document should be suggested to the next group
The number of sessions should be more. In particular the pathway analysis could have been shown in much more detail with the increased number of sessions.
Can include more analysis
Perhaps reducing speed when processing the more complex demonstration data. As with many technical courses, things moving too fast can make people fall behind and become frustrated. I don't see an easy way around this though as it is all important and needed.
If you get people to read/familiarise themselves with some basic principals/terms first (ahead of the course) it would save time (P-value/multiple testing corrections, GO terms).

Any further comments or suggestions?

Get Galaxy to improve their interface! For some actions its impossible to know what to do
Yes, the future workshops may be considered running as multiple short sessions. It would have been great to give an option to researchers to come along in future workshops just for the day they are interested to learn. In that way we can only attend the part we are not familiar with or we are interested on. It also would be helpful for the lab scientists since it is hard to find time to learn new bioinformatics skill.

Myself and helper's thoughts on improving
General

Send some material (at least the Introduction tutorial) before the course as pre-reading
Try sessions of 2hr with addtional optional 1 hr Q&A for people to hang around to ask questions, get more details, ask about own data
Create histories and share with user emails in advance. As trying to share histories during the session to help people catch up caused us issues during the course, as tried initially sharing histories by link but then any new datasets created were locked to users (permissions) so had to reshare, share individually with emails
See if can get a mouse highlighter app to make more obvious where the cursor is pointing (suggested by attendee) e.g. https://itunes.apple.com/us/app/mypoint-light-s/id518658487?mt=12

Material
Introduction

Send out in advance

Reads to Counts

Only run one MultiQC to demo as too confusing when have multiple MultiQCs in history, they all look the same
Focus on the main steps Trim > Align > Count (and then show info/workflow for QCs)
Maybe get people to load in data from Shared History instead of Rule Builder to make more straightforward (put Rule Builder method in More details box?) as the majority were new users just getting used to Galaxy. As then they'd be no need to strip header, assign columns, build etc, they could just start working with the data. Also may avoid some issues, as if data is pre-loaded could have datatype and genome preselected, as some users selected wrong datatype (fastqcsanger) or genome (mm10Strains1).

Counts to genes material

Drop the beginning, formatting data, part (or put in a More details box) and provide the data already formatted so all they have to do is run the annotatemyids tools and limma, as it takes a while to run that part and they could (and likely will) format in Excel.
Add in part on batch effects

Genes to pathways

Needed more time, was too squished in at the end. Go back to running as a separate module.

UI Feedback

If sharing histories with email address it works ok, if sharing by link, need to make sure to tick to make the datasets accessible so people don't get permissions errors when the try to run. But then if run more tools the new datasets are locked so have to unshare and reshare the link (or share with emails). That caused a lot of confusion!
Multiple people tried to rename a history using the history search box which then caused them confusion because it filtered their history datasets and they couldn't see any data in their history. One user said they tried to rename using the search box because "Unnamed history" did not look editable (we had covered renaming histories but it was a lot of new info for them to remember). If you mouse over "Unamed history" it does say "Click to rename history" but they had already made the assumption that it was the search box that was the history name so the mouse over didn't help. If it was possible to make it more obvious that "Unamed history" is editable that could be good.
Having something like an "Import" button for importing histories would be good if possible, instead of the "+" button that's over on the right side when viewing a shared history, as it wasn't obvious to them that + was the way to import.
The rerun button on collections was reported as hard to find
A user asked if there was a way to view a history like in the workflow editor e.g. so can see what steps are orphan? Said yes would be great but not possible at the moment.
Having a way to edit bulk edit datatypes and database would be useful for users that make mistakes selecting those when importing data, will try to work around that by pre-loading data into Shared History. Btw this is one reason we ran into the history sharing issues as tried to share histories with users who had made errors with importing but who didn't realise til after they had run a few tools on the data.

New GTN feedback received
Tutorial: Reference Data with CVMFS (Galaxy Server administration)
How much did you like this tutorial?: 5
What did you like?:
What could be improved?:
Note: this comment was autogenerated

New GTN feedback received
Tutorial: A short introduction to Galaxy (Introduction to Galaxy Analyses)
How much did you like this tutorial?: 5
What did you like?:
What could be improved?:
Note: this comment was autogenerated

New GTN feedback received
Tutorial: Differential abundance testing of small RNAs (Transcriptomics)
How much did you like this tutorial?: 5
What did you like?:
What could be improved?: Needs another step after "BAM-to-Fastq" is run. Tool outputs "fastq", not "fastqsanger". Redetecting the datatype will work. Other option is to modify the tool to try to assign "fastqsanger" (if the data matches that type, cannot be assume, I'll open an IUC request). See discussion/confusion from a tutorial user here: https://help.galaxyproject.org/t/convert-from-bam-to-fastq/1318
Note: this comment was autogenerated

New GTN feedback received
Tutorial: Reference-based RNA-Seq data analysis (Transcriptomics)
How much did you like this tutorial?: 1
What did you like?:
What could be improved?:
Note: this comment was autogenerated

New GTN feedback received
Tutorial: RNA-Seq reads to counts (Transcriptomics)
How much did you like this tutorial?: 4
What did you like?:
What could be improved?:
Note: this comment was autogenerated

New GTN feedback received
Tutorial: NGS data logistics (Introduction to Galaxy Analyses)
How much did you like this tutorial?: 5
What did you like?: all of it
What could be improved?: add example with bowtie2
Note: this comment was autogenerated

New GTN feedback received
Tutorial: Quality Control (Sequence analysis)
What did you like?:
What could be improved?:
Note: this comment was autogenerated

New GTN feedback received
Tutorial: Galaxy 101 (Introduction to Galaxy Analyses)
How much did you like this tutorial?: 5
What did you like?: The instructions were very clear and easy to follow
What could be improved?: 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.
Note: this comment was autogenerated

New GTN feedback received
Tutorial: Reference-based RNA-Seq data analysis (Transcriptomics)
How much did you like this tutorial?: 5
What did you like?: Clearly stated.
What could be improved?: I can not say for sure.
Note: this comment was autogenerated

New GTN feedback received
Tutorial: A short introduction to Galaxy (Introduction to Galaxy Analyses)
How much did you like this tutorial?: 5
What did you like?: simple and easy to learn
What could be improved?:
Note: this comment was autogenerated

New GTN feedback received
Tutorial: Label-free versus Labelled - How to Choose Your Quantitation Method (Proteomics)
How much did you like this tutorial?: 5
What did you like?: Detailed of both technique are very concise and helpful
What could be improved?:
Note: this comment was autogenerated

New GTN feedback received
Tutorial: Galaxy 101 (Introduction to Galaxy Analyses)
How much did you like this tutorial?: 5
What did you like?:
What could be improved?:
Note: this comment was autogenerated

New GTN feedback received
Tutorial: De novo transcriptome reconstruction with RNA-Seq (Transcriptomics)
How much did you like this tutorial?: 5
What did you like?:
What could be improved?:
Note: this comment was autogenerated

New GTN feedback received
Tutorial: Introduction to Genome Assembly (Assembly)
How much did you like this tutorial?: 4
What did you like?: the real data analysis
What could be improved?: provide links to the tool side by side
Note: this comment was autogenerated

New GTN feedback received
Tutorial: Introduction to Genome Assembly (Assembly)
What did you like?:
What could be improved?:
Note: this comment was autogenerated

New GTN feedback received
Tutorial: Visualization of RNA-Seq results with heatmap2 (Transcriptomics)
How much did you like this tutorial?: 5
What did you like?:
What could be improved?:
Note: this comment was autogenerated

New GTN feedback received
Tutorial: A short introduction to Galaxy (Introduction to Galaxy Analyses)
How much did you like this tutorial?: 5
What did you like?:
What could be improved?:
Note: this comment was autogenerated

New GTN feedback received
Tutorial: Galaxy 101 (Introduction to Galaxy Analyses)
How much did you like this tutorial?: 5
What did you like?:
What could be improved?:
Note: this comment was autogenerated

New GTN feedback received
Tutorial: Galaxy 101 (Introduction to Galaxy Analyses)
How much did you like this tutorial?: 4
What did you like?: Good introduction to Galaxy. I like the worklflow function the most.
What could be improved?: Couldn´t really see what the results in the genome browser would tell me and how I apply this for my work.
Note: this comment was autogenerated

New GTN feedback received
Tutorial: A short introduction to Galaxy (Introduction to Galaxy Analyses)
How much did you like this tutorial?: 5
What did you like?:
What could be improved?:
Note: this comment was autogenerated

New GTN feedback received
Tutorial: Reference-based RNA-Seq data analysis (Transcriptomics)
How much did you like this tutorial?: 4
What did you like?:
What could be improved?: waiting time during analyses
Note: this comment was autogenerated

New GTN feedback received
Tutorial: Reference-based RNA-Seq data analysis (Transcriptomics)
How much did you like this tutorial?: 4
What did you like?: You can work only on the tutorial and if you follow the descriptions carefully, you will get the result you expect to get.
What could be improved?: Explaining how to get the featureCounts data from another history (drag and drop and say it should be taken from another history in the first place).
Note: this comment was autogenerated

New GTN feedback received
Tutorial: A short introduction to Galaxy (Introduction to Galaxy Analyses)
How much did you like this tutorial?: 2
What did you like?: almost all of it worked like the tutorial, very helpful
What could be improved?: the Filter by quality function was not on the program
Note: this comment was autogenerated

New GTN feedback received
Tutorial: Galaxy 101 (Introduction to Galaxy Analyses)
How much did you like this tutorial?: 5
What did you like?:
What could be improved?:
Note: this comment was autogenerated

New GTN feedback received
Tutorial: Galaxy 101 (Introduction to Galaxy Analyses)
How much did you like this tutorial?: 5
What did you like?:
What could be improved?:
Note: this comment was autogenerated

New GTN feedback received
Tutorial: A short introduction to Galaxy (Introduction to Galaxy Analyses)
How much did you like this tutorial?: 5
What did you like?:
What could be improved?:
Note: this comment was autogenerated

New GTN feedback received (extended form)
Which GTN tutorial did you complete?: Differential abundance testing of small RNAs (Transcriptomics)
How did you use this tutorial?: for using it in my thesis
Usefulness: 5
Quality: 1
If you used this material to teach, how many students/participants attended?:
What did you like?:
What could be improved?:
Please provide any feedback you have on your experience with this tutorial.: its a great tutorial but it has a problem. in "hands_on Hands-on: Hierarchical alignment to rRNA and miRNA reference sequences (2)" step , when i use "Convert bam to fastQ", the result file has 0 byte and it makes impossible to continue the tutorial. i need cut contaminant of my data and need this tutorial to work. please help me. p.s i used the tutorials Data, So my Data isnt the problem
Do you have suggestions for additional topics or tutorials?:
Your institution: Golestan university of medical school
Note: this comment was autogenerated

New GTN feedback received
Tutorial: RNA-Seq reads to counts (Transcriptomics)
How much did you like this tutorial?: 5
What did you like?:
What could be improved?:
Note: this comment was autogenerated

New GTN feedback received
Tutorial: Running the Galaxy Training material website locally (Contributing to the Galaxy Training Material)
How much did you like this tutorial?: 5
What did you like?: Clearly explained.
What could be improved?: In the first step (install requirements) - does there need to be an extra step before step 5, that says "conda activate galaxy_training_material" ?
Note: this comment was autogenerated

New GTN feedback received
Tutorial: A short introduction to Galaxy (Introduction to Galaxy Analyses)
How much did you like this tutorial?: 4
What did you like?:
What could be improved?:
Note: this comment was autogenerated

New GTN feedback received
Tutorial: Visualization of RNA-Seq results with Volcano Plot (Transcriptomics)
How much did you like this tutorial?: 5
What did you like?: complete, with examples (questions+solutions)
What could be improved?:
Note: this comment was autogenerated

New GTN feedback received
Tutorial: 16S Microbial Analysis with mothur (extended) (Metagenomics)
How much did you like this tutorial?: 5
What did you like?:
What could be improved?:
Note: this comment was autogenerated


Links

I have made links for the tutorials relative. The remaining links are to yet to be fixed similarly.

I am planning to make all the absolute links relative before this weekend.

Done


Try release finish with push changes

When I finish the release and try push changes to the remote repository (check Push changes in dialog), I get an error:
> git checkout master
Your branch is up-to-date with 'origin/master'.
Switched to branch 'master'
> git pull
Already up-to-date.
> git merge --no-ff release/0.1.0
Merge made by the 'recursive' strategy.
 Solution/General.txt  |  1 +
 Solution/Solution.sln | 15 +++++++++++++++
 2 files changed, 16 insertions(+)
 create mode 100644 Solution/General.txt
 create mode 100644 Solution/Solution.sln
> git tag v0.1.0
> git checkout develop
Your branch is up-to-date with 'origin/develop'.
Switched to branch 'develop'
> git pull
Already up-to-date.
> git merge --no-ff release/0.1.0
Already up-to-date.

Succes (10720 ms @ 07.06.2017 12:44:10)
> git push origin develop
Everything up-to-date
> git push origin master
To bitbucket.org:<repo_path>git
   59363df..5461daf  master -> master
> git push origin 0.1.0
error: src refspec 0.1.0 does not match any.
error: failed to push some refs to 'git@bitbucket.org:<repo_path>.git'

What is git push origin 0.1.0?
Am I doing something wrong?
Thanks.

Probably, there should be git push origin v0.1.0.
I have [gitflow "prefix"] versiontag = v

Yup I made a mistake :(
Will fix :D

Very fast. Nice.


Could not connect to server

🐞 bug report
Description
Tried running scully on an angular 9 app, got an error.
🔬 Minimal Reproduction
Run scully
💻Your Environment
Angular CLI: 9.0.0-rc.6
Node: 12.8.1
OS: darwin x64
🔥 Exception or Error

started servers in background
Could not connect to server

Can you give me more info?
Can you create a repo for try? i need more description about your environment!

I get the same error in the scully branch of this repo:
https://github.com/isaacplmann/nx-monorepo-sample/tree/scully
I'm trying to get scully working in an nx monorepo, so maybe there's some hard-coded path that is expecting a default Angular CLI set up?
yarn run v1.19.1
$ scully
Cleaned up /Users/isaac/Documents/code/nx-monorepo-sample/dist/static/ folder.
 ☺   new Angular build imported
started servers in background
Could not connect to server
✨  Done in 17.08s.

Could be related to lazy-loading routes with tsconfig path aliases.
yarn scully:serve gives this error:
$ scully serve
starting static server...
Could not start Scully serve Error: Scully could not traverse routes

And AppModule loads its routes like this:
  {
    path: 'home',
    loadChildren: () => import('@ng-cli-app/home/ui').then(m => m.HomeUiModule),
    canActivate: [AuthGuard]
  },

Possibly related to https://github.com/scullyio/scully/issues/31 as I saw this first before I saw the extra info from the errors in that issue.

Oops, I missed the first line of getting started that says you need Angular 9.x.  I'll upgrade and report back

I've updated that repo to angular 9 and am still getting the same error.  I think guess is having trouble with the lazy loaded routes.
I added a console.log to<EMAIL_ADDRESS>var collectRoutingModules = function (root, registry, result, parentPath, currentPath) {
    if (parentPath === void 0) { parentPath = root; }
    if (currentPath === void 0) { currentPath = ''; }
    console.log('root', root);
    var declaration = registry[root];
    var process = function (r) {
        if (r.module) {

And modified<EMAIL_ADDRESS>exports.traverseAppRoutes = async (appRootFolder = config_1.scullyConfig.projectRoot) => {
    try {
        const routes = guess_parser_1.parseAngularRoutes(appRootFolder).map(r => r.path);
        return routes;
    }
    catch (e) {
        console.log('e',e)
        throw new Error('Scully could not traverse routes');
    }
};

And this is what shows up when I run yarn scully:serve:
root /Users/isaac/Documents/code/nx-monorepo-sample/apps/ng-cli-app/src/app/app.module.ts
root<EMAIL_ADDRESS>e TypeError: Cannot read property 'eagerRoutes' of undefined
    at collectRoutingModules (/Users/isaac/Documents/code/nx-monorepo-sample/node_modules/@scullyio/scully/node_modules/guess-parser/dist/guess-parser/index.js:464:17)
    at processLazyRoute (/Users/isaac/Documents/code/nx-monorepo-sample/node_modules/@scullyio/scully/node_modules/guess-parser/dist/guess-parser/index.js:462:9)
    at Array.forEach (<anonymous>)

This line<EMAIL_ADDRESS>is obviously not a valid file path.

could be a problem with host (like at angular cli). I had the same.  I created a feature request for this:
https://github.com/scullyio/scully/issues/87
If you try to manually change the host here in your node_modules, does it work then? https://github.com/scullyio/scully/blob/8ce6c13c06e07f0082a2d75936f232e03efb3a98/scully/utils/waitForServerToBeAvailable.ts#L13
Do you have an alternative host then localhost on your machine?

I had the same issue,  I thought the problem was the port 1864 but after some debugging this is what I encountered.
It seems like npm run scully (sometimes?) is giving the following error, and because of this some spawned processes are not being shut down correctly and will stay alive.
C:\Users\tdeschryver\dev\throw-aways\bloggy\node_modules\.bin\scully:2
basedir=$(dirname "$(echo "$0" | sed -e 's,\\,/,g')")
          ^^^^^^^

SyntaxError: missing ) after argument list
    at Module._compile (internal/modules/cjs/loader.js:872:18)
    at Object.Module._extensions..js (internal/modules/cjs/loader.js:947:10)
    at Module.load (internal/modules/cjs/loader.js:790:32)
    at Function.Module._load (internal/modules/cjs/loader.js:703:12)

lala at Function.Module.runMain (internal/modules/cjs/loader.js:999:10)
    at internal/main/run_main_module.js:17:11

The next time I run scully the express servers are not spawned because the port is already in use. I would have expected this error to be caught by https://github.com/scullyio/scully/blob/master/scully/utils/staticServer.ts#L64, but this is not the case. By listening to errors, the error showed me that the port was already in use.
 ☺   new Angular build imported
Error: listen EADDRINUSE: address already in use
    at Server.setupListenHandle [as _listen2] (net.js:1228:14)
    at listenInCluster (net.js:1276:12)
    at Server.listen (net.js:1364:7)
    at Function.listen (C:\Users\tdeschryver\dev\throw-aways\bloggy\node_modules\express\lib\application.js:618:24)         at Object.staticServer (C:\Users\tdeschryver\dev\throw-aways\bloggy\node_modules\@scullyio\scully\bin\utils\staticServer.js:31:45)
    at processTicksAndRejections (internal/process/task_queues.js:85:5) {
  code: 'EADDRINUSE',
  errno: 'EADDRINUSE',
  syscall: 'listen',
  address: '::',

After I modified the port to another port (in the bin files) I got it up and running again. After a while I had to repeat this because I was in the same scenario.
I think not swallowing these errors and logging them might be useful,
For spawned processes:
const child = spawn('node', [join(scullyConfig.homeFolder, './node_modules/.bin/scully'), 'serve'], {
          detached: true,
        })

child.stderr.on('data', err => {
  console.log(err.toString())
})

For express:
angularServerInstance = angularDistServer.listen(scullyConfig.appPort, x => {
      log(
        `Angular distribution server started on "${yellow(
          `http://localhost:${scullyConfig.appPort}/`
        )}" `
      );
    }).on('error', err => {
		console.log(err)
	});

Environment:

Windows 10
Node.js v12.9.1
Angular v9 rc6

I've updated that repo to angular 9 and am still getting the same error. I think guess is having trouble with the lazy loaded routes.
I added a console.log to<EMAIL_ADDRESS>var collectRoutingModules = function (root, registry, result, parentPath, currentPath) {
    if (parentPath === void 0) { parentPath = root; }
    if (currentPath === void 0) { currentPath = ''; }
    console.log('root', root);
    var declaration = registry[root];
    var process = function (r) {
        if (r.module) {

And modified<EMAIL_ADDRESS>exports.traverseAppRoutes = async (appRootFolder = config_1.scullyConfig.projectRoot) => {
    try {
        const routes = guess_parser_1.parseAngularRoutes(appRootFolder).map(r => r.path);
        return routes;
    }
    catch (e) {
        console.log('e',e)
        throw new Error('Scully could not traverse routes');
    }
};

And this is what shows up when I run yarn scully:serve:
root /Users/isaac/Documents/code/nx-monorepo-sample/apps/ng-cli-app/src/app/app.module.ts
root<EMAIL_ADDRESS>e TypeError: Cannot read property 'eagerRoutes' of undefined
    at collectRoutingModules (/Users/isaac/Documents/code/nx-monorepo-sample/node_modules/@scullyio/scully/node_modules/guess-parser/dist/guess-parser/index.js:464:17)
    at processLazyRoute (/Users/isaac/Documents/code/nx-monorepo-sample/node_modules/@scullyio/scully/node_modules/guess-parser/dist/guess-parser/index.js:462:9)
    at Array.forEach (<anonymous>)

may be guess-parser need app-routing.module.ts to parser. nx monorepo embed routes in  app.module.ts !

@isaacplmann @vsavkin   here is a workaround for   nx monorepo  compatibility issue
https://github.com/xmlking/yeti/commit/7daffcd02de62a69686f053c79d30660633233d3
may be @mgechev  can help making guess-parser compatible with  nx monorepos

@isaacplmann yes, the Guess.js parser does not know how to handle path mappings currently.
@chrisguttandin did some work towards support for Nx monorepos for his angular-prerender.

Hi everyone, the changes that I made to guess-parser a while ago to support nx monorepos were related to that line: https://github.com/guess-js/guess/blob/master/packages/guess-parser/src/angular/index.ts#L50.
It is using TypeScript's own module resolution and should therefore respect path prefixes like @my-app. We also added a library with a prefix to the test fixture which is why I'm optimistic that it still works.
Right now I don't know of any issues related to nx monorepos when using angular-prerender. But that does of course not guarantee that there are none. :-)
I hope this somehow helps.

@mgechev is there a new version of guess-parser released that includes this fix?

@SanderElias yes, 0.4.12 includes the fix.

I opened a PR to handle path mappings in lazy routes here. The integration test is from the repro that @isaacplmann provided.
Feel free to check this out and tell me if it solves the main problem.


Unhandled Docs exception

There is some missing exception handling in the parsing logic of the !docs get command.
Here is one example, exact cause is still TBD:

Looking into this


Issues with date format on hscic.raw_prescribing_normalised

I attempted to write a new measure definition using hscic.raw_prescribing_normalised as the numerator, and list_size as the denominator, and it threw the following error:
No matching signature for operator = for argument types: TIMESTAMP, DATE. Supported signature: ANY = ANY at [86:15], with line 86 being AND practices_with_months.month = num.month
On investigation I found a stackoverflow discussion on the same issue.
Looking at how we create the SQL for the view, we have this line:
PARSE_DATETIME("%F", REGEXP_REPLACE(raw_prescribing._FILE_NAME, "^.+/(20\\d\\d)_(\\d\\d)/[^/]+$", "\\1-\\2-01")) AS month, which creates a DATETIME field type.
Other views, such as hscic.normalised_prescribinghave a TIMESTAMP field type.
As a temporary workaround, I have created a new view hscic.raw_prescribing_normalised_date which replaced the line above with PARSE_TIMESTAMP("%F", REGEXP_REPLACE(raw_prescribing._FILE_NAME, "^.+/(20\\d\\d)_(\\d\\d)/[^/]+$", "\\1-\\2-01")) AS month, which seems to work fine.
@evansd @inglesp should we replace the line in hscic.raw_prescribing_normalised with the PARSE_TIMESTAMP version, or is that likely to break anything?

I think we should update the existing view to use PARSE_TIMESTAMP as you suggest. As you say, the other views use this type and I can see quite a few places in the code where we explicitly cast dates to TIMESTAMP so we're obviously expecting that. My guess is that we used PARSE_DATETIME inadvertently when defining this view and then never noticed because we never attempted to a join on that column until you created that measure.

https://github.com/ebmdatalab/openprescribing/pull/5089


bpf: Skip policy enforcements for service loopback case

bpf: Skip policy enforcements for service loopback case

We should track the backport in the upstream original PR rather than in this one.
If we intend to merge this as the backport, then we will also want to update the description for the release note and mark that the original PR has a backport outstanding and link to that PR from here.
For what it's worth, I don't think you need to create an actual PR to kick off a hotfix build; I believe that it's enough to just push the PR and then look into the actions for the relevant image build job to get approved.

mark that the original PR has a backport outstanding

The original PR was submitted on the master branch so it should already be in 1.10 branch. It was only pending 1.9 backport, which this PR is addressing. @christarazi I think it might be better to convey this in the commit title?

Superseded by https://github.com/cilium/cilium/pull/15709.


type control fails with logical operator "||"

I'm not a expert of flow, but I think it's not a normal behaviour.
Please tell me!
Bug?
when doing form.valuesBadlyWritten || {}, it won't rise error for valuesBadlyWritten (search for  will NOT rise error in the link below)
Reproduce
see Link with a reproduced example

What is the question exactly? This looks alright to me.  Flow is correct when it says there is no proeprty valuesBadlyWritten.

@lll000111 sorry for the lack of clarity. Updated

Fixed in current version 0.132.0


Remove version: qBittorrent.qBittorrent version 4.5.1

[Automated] It returns code over 400 in all urls
Microsoft Reviewers: Open in CodeFlow

URL: https://sourceforge.net/projects/qbittorrent/files/qbittorrent-win32/qbittorrent-4.5.1/qbittorrent_4.5.1_lt20_qt6_x64_setup.exe/download
Status Code: 200
(Automated message - build 896)

Close with reason: Package still available.;