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@bgruening:matrix.org : Thank you for your reply. I provide you the URL(https://xgf.nu/m8RM) at which you can download the MS word file describing whole error messages. Could you mind to checking the word file? I use ".mzML" file, which was converted from ".mgf" file, as MSMS file; and I use "crap.fasta.pro" file, which was automatically provided at the time of downloading of "X!tandem", as FASTA format in Galaxy. If you need more information, please contact me again.
@tepodone_twitter from security perspective please try to avoid sharing msword docs especially on unknown url domains. Just plain text error information shared on something like https://gist.github.com/ would serve better
Another question: What is the best way to "package" tools that require two-steps. E.g. read mapper that first build an
index and then do some operations on it. I have seen bwa that offers two modes, build on the fly or use a pre-existing one (managed by galaxy).
Would it be also okay to split those two steps into two nodes where the index will be re-usable? Is there an example tool that uses that approach?
Indices we offer usually pre-build in Galaxy
and we have an entire subsystem for that
so an Galaxy admin can offer the same prebuild indices for all Galaxy user
and this is exactly also what BWA is doing. If there is a system-wide index available it will use that, if not you can provide a FASTA file.
But the assumption is that the Galaxy Admin is providing those indices
we have a shared index pool that the Galaxy community is maintaining with 6TB of all kinds of indices that we share with all admins
As a side-step the user can provide a FASTA file. (but this wastes storage and compute - we would like to share that, also to be reproducible )
Hi all, it looks like the Trinity tool have a trouble! it diddn't work on my account anymore. Does it still work on your project?
@martenson @bgruening:matrix.org
Dear, Martin. Thank you for your advises. I have uploaded files what I use in X!tandem on Galaxy. Can you check them on the following GitHub URL?
https://github.com/m-and-o138/m-and-o138/compare/main...m-and-o138-patch-1?expand=1#diff-c0256b69eda82032850603f4263167eb8bdeee0ed8eb7a35a17b65c59115e95b
Additionally, I also indicated the error messages what I received when I executed the X!tandem on Galaxy.
m-and-o138/m-and-o138#1
I'm not still familiar with GitHub. So, I'm worry about whether you can check my files and error codes. If you could not check them, please contact me again. Thank you.
It's a good idea to back up the database before doing a large upgrade if you're worried about it. Otherwise, a manual upgrade is generally as simple as stopping galaxy, pulling the new version you want, and running
sh manage_db.sh upgrade in galaxy directory, then restarting.
Here's a link for 21.05, from the release notes: https://docs.galaxyproject.org/en/master/releases/21.05_announce.html#get-galaxy
Hi all, I'm trying to annotate my vcf file with snpeff in the galaxy but there are no available database for Arabidopsis thaliana. Did someone also experience the same issue? I tried to download the database for snpeff from SourceForge but the snpeff tool in the galaxy is not recognizing the file as a database file. It would be really nice if someone could help me with this issue. Thanks.
May I know how to cite galaxy based on this sentence "variants calling was then performed using SAMtools mpileup v2.1.4 (Danecek et al. 2021) obtained from Galaxy Europe (https://usegalaxy.eu/). "
the citing galaxy information not quite clear to me
im using galaxy europe in this case. can it consider as public server and the citation to be used is "The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update, Enis Afgan, Dannon Baker, Marius van den Beek, Daniel Blankenberg, Dave Bouvier, Martin Čech, John Chilton, Dave Clements, Nate Coraor, Carl Eberhard, Björn Grüning, Aysam Guerler, Jennifer Hillman-Jackson, Greg Von Kuster, Helena Rasche, Nicola Soranzo, Nitesh Turaga, James Taylor, Anton Nekrutenko, and Jeremy Goecks. Nucleic Acids Research (2016) 44(W1): W3-W10 doi:10.1093/nar/gkw343", is it>
@wcc-new: Yes, that's the citation users are asked to use according to https://galaxyproject.org/use/usegalaxy-eu/
@wcc-new: please cite the Galaxy paper (https://pubmed.ncbi.nlm.nih.gov/29790989/) and use some acknowledgement along those lines: https://galaxyproject.eu/about
The latest version in the ToolShed is 3.2.1. The same for the development repository. https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate -- Looks like the wrapper itself needs an update. Once sec -- I'll make the request and post back the link
@jennaj https://github.com/Trinotate/Trinotate/releases, take a look here in the releases, there's a 3.2.2. Thanks again
Yes, the underlying tool needs an update or the current wrapper. The developers can decide the best path. This is the issue ticket: galaxyproject/tools-iuc#3875
Xref to IUC chat is here: https://gitter.im/galaxy-iuc/iuc?at=611417989484630efa324585
Thanks Melisa!
Hello, I meet some problem about module loading like above, need some help thanks
@MelonaT Hi -- please try at least one rerun. If the same error is reported, there is likely some problem with the inputs, tool choices, or workflow design. Try opening the workflow in the editor and check for warning messages. If you cannot resolve the problem, where are you running the workflow? URL if a public server or describe otherwise. Thanks!
@taikongrenren The tool is not finding a required dependency. This can be due to several reasons. Did you install Galaxy following the instructions here, with the latest release? https://galaxyproject.org/admin/get-galaxy/ Or by some other method?
@jennaj thanks for your answer! I already did several reruns on different days, but I always got the same message. I can't find any warnings in the editor either. The point is, that when using every tool separately, everything works.... Here is the link to my workflow: https://usegalaxy.org/u/malena_trost/w/ba
I give an NCBI SRR number as input to the "Download and Extract Reads in FASTA/Q", than execute MEGAHIT and finally ABRicate.
I give an NCBI SRR number as input to the "Download and Extract Reads in FASTA/Q", than execute MEGAHIT and finally ABRicate.
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