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usegalaxy-no / galaxyadmin

A repository for managing the work of the usegalaxy.no GalaxyAdmin team
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Add category labels from usegalaxy.eu to the tools menu #11

Closed torfinnnome closed 3 years ago

torfinnnome commented 3 years ago

Have added to https://test.usegalaxy.no/ now.

kjetilkl commented 3 years ago

I notice that several categories appear twice, either within the same section or in multiple sections. Including, e.g.: Get Data, Send Data, FASTA/FASTQ, Operate on genomic intervals, and Phenotype association.

I also feel that the section headers could stand out more, since they are difficult to distinguish from the category labels at first glance. And if you point the mouse at a category, it will look almost like a section header. Here is an example with more prominent section headers, but maybe that is too much: tools_panel

torfinnnome commented 3 years ago

Yeah, trying to solve those duplicates. Not very obvious where they come from (cleaning var/cache/ did not help).

torfinnnome commented 3 years ago

OK, I have finally added labels on test.usegalaxy.no. Please help me with checking that they all make sense.

torfinnnome commented 3 years ago

Modifications should be pushed here: https://github.com/usegalaxy-no/infrastructure-playbook/blob/master/env/common/files/galaxy/config/tool_conf.xml

kjellp commented 3 years ago

Looks good to me, and a very nice improvement!

Getting issue #2 fixed with Get/Send from/to NeLS tools at the top (Get most important) would really be a nice icing of the cake, and have ready for the first online NeLS/usegalaxy.no course 23/3 :)

K.

On 10/03/2021 20.30, Torfinn Nome wrote:

OK, I have finally added labels on test.usegalaxy.no. Please help me with checking that they all make sense.

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ehj000 commented 3 years ago

The labels looks good, but I see that there are some tool categories that are misplaced or duplicated. Here are a few examples:

SAM/BAM MANIPULATION under Miscellaneous Tools should go under Genomic File Manipulation label, but there is a SAM/BAM category there already. This has more tools, but older versions. Ok to leave, or could tools be moved?

Statistics under Miscellaneous Tools should go under Statistics and Visualisation label, but there is a Statistics there already with different tools. Could tool from Statistics under Miscellaneous Tools be moved to Statistics under Statistics and Visualisation label?

Graph/Display Data under Miscellaneous Tools should go under Statistics and Visualisation label, but there is a Graph/Display Data there already with different tools. Could tools be moved as above?

I am not sure how to edit this as I don't understand the structure in tool_conf.xml

torfinnnome commented 3 years ago

Getting issue #2 fixed with Get/Send from/to NeLS tools at the top (Get most important) would really be a nice icing of the cake, and have ready for the first online NeLS/usegalaxy.no course 23/3 :) K.

FIxed! (Permanently, I hope...)

torfinnnome commented 3 years ago

The labels looks good, but I see that there are some tool categories that are misplaced or duplicated. Here are a few examples:

Great! Exactly the feedback I needed. Have updated now. Looks better?

ehj000 commented 3 years ago

Looks better, but the SAMTOOLS under SAM/BAM seem to be an additional "sub-label".

Don't want to be picky and I am not sure if it is worth the effort, but there are still some tool categories under Miscellaneous Tools that could be moved (e.g. Genome diversity could go under Genomic analysis and Filter and sort under Genomic File Manipulation)

Still there are many tool categories such as Apollo, Imaging, Phenotype Association, Fetch sequences/alignments and more that are duplicated (they are both under Miscellaneous Tools and elsewhere), They don't not contain the same tools both places. Maybe merging?

torfinnnome commented 3 years ago

Thanks. Have modified it now. (I had to synchronize the section IDs in tool_conf.xml with shed_tool_conf.xml to get rid of the duplicates.)

torfinnnome commented 3 years ago

Implemented in prod now. Labels can be modified here (and tools moved around): https://github.com/usegalaxy-no/infrastructure-playbook/blob/master/env/common/files/galaxy/config/tool_conf.xml