Checking the /microbiology.usegalaxy.eu/ landing page for issues

[teresa-m]

I am collecting everything that looks incorrect to me on the https://microbiology.usegalaxy.eu/ lab page.

Section: Wellcome test on top:

1. link of 'How does this page relate to Galaxy Europe?' links to: https://labs.usegalaxy.org.au/?content_root=https://github.com/galaxyproject/galaxy_codex/blob/main/communities/microgalaxy/lab/usegalaxy.eu.yml# , which holds the same context. Link may be wrong?
2. For people who are not sure what Galaxy is maybe include a sentence that explains what you can do with the subdomain. Maybe something like: This is the space where you can conduct your microbiology analyses using a carefully curated selection of tools and workflows. Below, you’ll find an introduction to help you get started and guide you toward the type of analysis you aspire to achieve.

Section:
Getting started:
Downloade:

1. For Download data from NCBI GenBank/RefSeq: change 'by accession' to accession number (But it is always only called accession, also in the galaxy tool, so maybe leave it)
2. Download run Data from EBI SRA: This is linking ot the EBI SRA, will this automaticly integratble into galaxy or do they need to downloade and uploade to Galaxy. To me this is not clear. Maybe explain this time how the data comes to galaxy as this link is not opening a 'tool'.
3. Download run data from EBI Metagenomics database (MGnify): Is the EBI Metagenomics database well know to the community? Is this MGnify data? The tool help description is not so clear on this and by a quick google search is was also not sure. It would be great if the help text of this tool would explain a bit more.
   Highlighte Tolls
4. SPAdes: looks a bit confusing to me. The decription mentions for steps but mor then 4 tools are linked below. It is also missing the input data if you want to make it equal for all of the tools. Maybe you could mention the very first input?
5. FastqP: Should this tool maybe go on top as this will likely be the first step?
6. dada2: Again a lot of tools are linked. Maybe a bit of more explanation how to navigate the links. Are the links in an meaningfull order, if there is one? And if possible mention the input data
   Interactive tools
7. Phinch: 'A framework for visualizing bio data' -> should be biom data?
8. ** Phyloseq**: When opening the tool I saw that there is only one input parameter and this one is optional. Should it really be optional?
9. RStudio: Is it really also for python code? If not remove Python from the description
10. Interactive Jupyter Notebook: The description sounds very generic. I would e.g. remove 'Uses include: data cleaning and transformation, numerical simulation, statistical modeling, data visualization, machine learning, and much more.' As hopefully people who are opening a notebook know what they are doing. But people who do not know will not get this functionality without coding.

Section: Microbial isolates
Tools:

1. This time there is no input section for the tools.
2. ** Bakta** has a different desctiption than the one in the Highlited tools above. Just if you want to have it in sync.
3. Bowtie: Links Bowtie2 tool
4. ** featureCounts**: Do you want to link FastqP here instead?
5. DEseq: Links to DEseq2
   Interactive tools:
6. RStudio delet python if it is not included
   Databases:
7. They are all linking outside of Galaxy. Maybe mention in the text above if all of them have a direct Galaxy integration or how to link data to Galaxy
8. RESFinder: Is it a Database or a tool? In the texte it says tool
9. ARG-ANNOT: Links to 'not found'
   Workflows
10. All links are working. The descriptions are mostly very short, but I guess its ok
    Tutorials
11. Descriptions seem to be very genaric and I can not check if they are correct. All links are correct. So I guess this section is good.
    Learning Pathways
    -> All good

Section: Microbiome
From here I only check the links
Tools:

1. dada2 and PICRUSt2 only little description and lots of links to different tools
2. no input data for all tools
3. metabat2 metabat2_jgi_summarize_bam_contig_depths link not working
4. concoct: concoct_coverage_table, concoct_cut_up_fasta, concoct_extract_fasta_bins, concoct_merge_cut_up_clustering link not working
5. checkm: all links are not working
6. OpenMS links to a tool called XTandemAdapter
   Database:
7. GreenGenes: links to page not found
8. ChocoPhlAn 404

Starting from section Community curated tools

[EngyNasr]

Thank you so much @teresa-m <3 <3 <3 for such careful testing, I passed through all your points. Please let me know if you found anything else

[teresa-m]

Yes, sorry think it is not clearly written above. I did not finish, and 'only' came until the section 'Community curated tools'.
Not sure if I'll find the time to check the rest this week.

[EngyNasr]

Yes, sorry think it is not clearly written above. I did not finish, and 'only' came until the section 'Community curated tools'. Not sure if I'll find the time to check the rest this week.

they were really clear I understood them all, and I will continue with the remaining sections same way <3