Is there any galaxy site that has the kraken2 nt-database 719 GB installed?? I keep running into problems where the databases are missing some of the species in my samples. Also, I see that kraken2 can work similar to Diamond where it can translate to protein and search against a protein database.…

Hi @Jon_Colman We just added EUPathDB to UseGalaxy.org for Kraken2 this week. Would you want to try that one? EuPathDB

Hi @mycojon You can search text files with tools that are similar to what is used command line. Are you familiar with that? Even if not, this is a powerful way to use Galaxy and not that different from spreadsheet/text editing programs. This is a short cheat sheet and guide with examples. It is fo…

Hi Jennifer, The new EuPathDB definitely works better to identify the Plasmodium species, thanks!!! I found that Galaxy EU had a new Kraken2 database Mycobacterium V1, do you have any information on this one??? I would like to be able to see the list of the species that it includes. I knew that I …

Hi Jennifer, Since it seems the two Kraken2 databases that I need to use are on either Galaxy.org or Galaxy EU, and my files are quite large. I had heard that I can move histories to other Galaxy servers?? So can I move them between the two Galaxy sites without having to download/upload???

Hi Jennifer, I finally figured out how to transfer my files between servers, this was a HUGE help. It took me a while to figure that I had to share the file first. A question regarding the EuPathDB, I noticed that this database does not include a human reference. For this type of database, should …

[image] mycojon: I found that Galaxy EU had a new Kraken2 database Mycobacterium V1, do you have any information on this one??? Look at the full description of that new database. It contains a link, which leads to a zenodo record with exact details about how the db has been built. Specificall…

Thanks Wolfgang, I found it!!! It looks like a great database, so many of those species aren’t represented in other databases.

Hi Jennifer, Is Galaxy.org working properly??? It was working great, then it seemed like nearly all programs were running very slowly. It took hours even to move files between servers. Just running de-interlace on a relatively small file didn’t even complete after running all night. Thanks

Hi @mycojon It has been working for me all day today. I’m starting another test in a different account. Meanwhile, if you want to post back a share link to a history that seems stalled, I can take a look. Thanks! :slight_smile: Update: I just launched a workflow and a bunch of job ran nearly immedi…

Is a share link the same link I would use to copy to a different server?

HI Jennifer, Here is one of the histories. I tried to de-interlace this same file that ran last night, which I deleted and restarted. Same issue with other histories on galaxy.org as well. https://usegalaxy.org/u/squidly/h/mandy

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Kraken2 database

reference-index, metagenomics

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