I've been in a discussion with @nekrut about the newick data format in Galaxy. Unfortunately, this format uses the nhx extension instead of just using newick. @nekrut would like me to submit a PR to the Galaxy core to change this extension to be newick. Although nhx is based on newick, it seems to have become deprecated, and phyloxml is advised, at least based on this link: https://sites.google.com/site/cmzmasek/home/software/forester/nhx. But changing the extension in Galaxy will affect tools in both the tools-devteam and tools-iuc repos. My understanding is that support for a new PhyloTree viz is soon coming to the Galaxy core. This viz will be used in the HIV research with which Galaxy is involved, and it will be using the newick format as well. What does the iuc advise here?
I'm not sure I understand what the problem is, is it just a change of name?
Hiya there... I'm working on a tool that merges BLAST XML outputs... this tool takes either multiple datasets as input or a list collection, and outputs a single output (i.e. it is a "reduce" step) - is there any way to unify this or must I just use a conditional for switching between the two input modes?
If you use a data parameter with multiple=true you will be able to run it on individual datasets or a collection. You’d need a conditional if you wanted to either (1) have more control of the order of the datasets (use a repeat) or (2) you want to be able to map over a collection instead of reduce it (less likely in this case it sounds like)
@nsoranzo @bgruening I think @nekrut just wants to change the "nhx" extension defined by Galaxy to be "newick". This came up because I have been trying to get the PlantTribes tools installed on Galaxy main and this tool https://toolshed.g2.bx.psu.edu/view/greg/plant_tribes_gene_family_phylogeny_builder/c088c185f63f produces outputs that have the "nhx" extension.
Ah, @nekrut was hoping we could do this. But how does that work? Is there now support for multiple file extensions per datatype class where I can add another extension here https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/datatypes/data.py#L935? Or is there another way?
I've been away from this long enough that I'm a bit rusty, so bear with me ;). Would it be as simple as
<datatype extension="newick" type="galaxy.datatypes.data:Newick" display_in_upload="true"/> <datatype extension="nhx" type="galaxy.datatypes.data:Newick" subclass="true" display_in_upload="true"/>
@nsoranzo I have wondered about dropping testing against master in place of testing on a couple of release branches (which would require periodic updating when a new release happens). I had been assuming master would be a reasonable substitute for the latest release branch, but that does not seem to be quite the case?
@peterjc Most of the times
master is updated when a new release is tagged, but not kept in sync with the corresponding release_XX.XX branch until someone asks for it. We could do a better job here (e.g. automate syncing), but for the time being my suggestion above should give you a smoother experience.
can you provide more data?
@/all any idea how we can review this: galaxyproject/tools-iuc#1905 galaxyproject/tools-iuc#1897
I have ask the EDAM people and ELIXIR people and hope they will help as well.
how does it fare with edam-hand-annotated tools?
Would it be enough if everyone of us takes 5 tools and checks if they are coorect.
Random tools?
What is the risk if it is wrongly annotated? It has no impact on Galaxy's functionality now, does it?
Problem report when installing samtools from MTS with certain versions of ubunto as the OS. Known? Could someone help troubleshoot? https://biostar.usegalaxy.org/p/28213/
@nsoranzo The user replied at https://biostar.usegalaxy.org/p/28213/. They are trying to install an older version that is required by other tools as a dependency. Would you be able to help with a reply?
I'm running the test command on a tool I've been working on but it fails each time saying "History item different than expected, difference (using diff):". My output when I execute the command myself appears to have an extra space at the beginning of each line so I'm fairly certain that's what's causing my issue. Is there a way I can tell the test to ignore the spaces?
for example searching with a regex in your expected output