Data intensive science for everyone. https://galaxyproject.org | https://usegalaxy.org | https://help.galaxyproject.org
Docker on windows should work well, and there's a ready-to-go image for you with Galaxy preinstalled.
thanks
https://github.com/bgruening/docker-galaxy-stable This is a link to the repository with some more information in the README file, about how it runs, etc.
Definitely ping us here, though, if you run into more trouble.
You can also check out https://www.lifewire.com/run-ubuntu-within-windows-virtualbox-2202098 for how to run an ubuntu VM, Galaxy can be installed there easily.
if you want to just try Galaxy, try the docker solution. If you want to develop Galaxy tools and get more familiar with Linux - try the VM.
There is also a virtualbox image with ubuntu and Galaxy preinstalled at https://images.galaxyproject.org/planemo/latest.ova
Good luck.
[gronke] I am getting this error in the galaxy.log when I try to send a file to Jbrowse. The error in Galaxy is "Exit code 1" https://pastecode.xyz/view/8a47f3f0
[gronke] Any idea what is causing it?
[gronke] Actually hold on, I have more information, here is the error from jbrowse right before, from the log
[gronke] https://pastecode.xyz/view/2a59bad4
Hi Everyone!
I would like to remind everyone that the 2019 Galaxy Admin Training will be offered January 28 through February 1 at Penn State University (where the Galaxy Project got started over ten years ago). The workshop offers a 2 day introductory session followed by a 3 day advanced topics session. Participants can register for one or both sessions.
Registration is open and starts at $40 / day for participants from non-profits and academia. Early registration ends TODAY October 31, register now before rates increase.
The 2016 and 2018 admin trainings were both full, so you are strongly encouraged to register now.
@martenson @mvdbeek Interesting question about BAM indexes. Any ideas for a solution? In main distro or tuning their local: https://biostar.usegalaxy.org/p/29884/
I assume the issue is mostly that metadata setting doesn't work for that genome ?
hi all, thanks for quick response. What I do in most of the custom/adjusted tools is to load the SAM header and check if there is any coordinate beyond 2^30. If there is, then I create the index using "-c -m 14". Many users use Galaxy to map their *seq data to the genome and upload the data in the genome browser to viewing. However, since Galaxy tries to create the bai index automatically, the tools fail and I had to define a custom data format "unsorted.bam" to prevent the default behavior
then it gets really messy, since I can create tools that sort the unsorted bam files, but the type should again be "unsorted.bam", which is misleading and won't allow me to discriminate between the sorted and unsorted bams any more.
[gronke] The three ones that fail have this in common: MarkDuplicatesWithMateCigar and AddOrReplaceReadGroups. Both of those run fine, but the jbrowse afterwards fail
Thanks for the report @SergejN, i've opened galaxyproject/galaxy#6956 for this. Do you know if .crai index for cram files have the same limitation ?
Depending on what type of sequencing data you have that might be another option. Cram files use a different compression scheme to bam files and are interconvertible for short read sequencing (you might loose some information on very long reads if converting from cram to bam). Galaxy supports these as well, and you can switch minimap2 for instance to produce cram files
But it isn't clear from the samtools manual whether they'd have the same limitation
Is there a way to (or a way planned to) add help text to workflow parameters that shows up with the parameter entry boxes at the top of a "run workflow" form? I try to make my variables verbose, but I can't exactly put an equation in there for the user to know how to calculate the value that should be entered...
Hello! We are attempting to improve the performance of our compute cluster, and are exploring ways to offload stuff that usually occurs in the job_working_dir (on the shared portion of the filesystem) to compute node local scratch space. Does anyone have suggestions regarding Galaxy configuration that can help us achieve this?
Good afternoon,
I wanted to perform the cgSNVanalysis for 925 genomes, but my data can't be analysed in one history. So, I put them in 4 separated histories and I created a list of datasets pairs for each of them. In this case, SNVphyl works for each list separately. However, when I merged all these lists using Merge Collections into single list of datasets tool (Galaxy Version 1.0.0), SNVphyl doesn't work on this collection. Could you, please, tell me how I can analyse more than 250 isolates using SNVphyl in Galaxy? Because when we have more than 250 genomes they are usually distributed on the separate pages of the same history and we can't create a list of datasets pairs.
Thanks,
Best regards,
I wanted to perform the cgSNVanalysis for 925 genomes, but my data can't be analysed in one history. So, I put them in 4 separated histories and I created a list of datasets pairs for each of them. In this case, SNVphyl works for each list separately. However, when I merged all these lists using Merge Collections into single list of datasets tool (Galaxy Version 1.0.0), SNVphyl doesn't work on this collection. Could you, please, tell me how I can analyse more than 250 isolates using SNVphyl in Galaxy? Because when we have more than 250 genomes they are usually distributed on the separate pages of the same history and we can't create a list of datasets pairs.
Thanks,
Best regards,
[gronke] or rather the bam jbrowse finishes, the vcf snps jbrowse crashes
[gronke] I am hoping someone out there can help me figure out what the heck is wrong here.