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Hi folks! I'm deploying a self-hosted Galaxy instance & trying to connect to CockroachDB, which is similar to Postgres but can automatically scale & backup data. But since CockroachDB is relatively new, the Galaxy data definitions require some SQL features not yet implemented in that dialect.
sqlalchemy.exc.NotSupportedError: (psycopg2.errors.FeatureNotSupported) at or near "if": syntax error: unimplemented: this syntax
DETAIL: source SQL:
DROP TRIGGER IF EXISTS trigger_history_dataset_association_bir
^
HINT: You have attempted to use a feature that is not yet implemented.
See: https://go.crdb.dev/issue-v/28296/v21.2Does anyone know where the data definitions for Galaxy are? I can't find a clear reference in documentation or within the galaxy-docker repo. I'll try to workaround these SQL triggers (and any other SQL that may not be implemented) if possible.
galaxy.model.triggers should have those for ya; trying to think of what other things might be slightly less compatible.
Ahh, that error there looks like it's actually in the migrations though. One sec.
Actually it looks like the migration code is consolidated there, too; note there are
postgres_install, sqlite_install; guess you need to work out a cockroach_install.
Hi! I'm trying to make a galaxy wrapper for a tool (bcl-convert) that takes a directory as input. Specifically, users will need to specify a network path. Is there a way to specify this as an input parameter, e.g.
<param name="bcldir" type="directory" /> where the user can browse to a path on the network and select a folder as as a parameter?
@mcmero: Galaxy works with an object store model, there are no filename or directories in that sense.
You have you data in Galaxy for example as a collection. You can then iterate over them put them in your CWD in a directory during runtime and run your tool on top of it.
In doing so I noticed that I should probably mention that we only allow one account per user.
I do agree that I have two accounts but it happened because for some reasons I was unable to access my previous account so I created a new account....Now I can access both the accounts but I am using only one at present.. Please guide me with a solution to resolve this issue
Make really sure it's permanently deleted. Maybe sent us a screenshot.
Good day, I'm doing an analysis with Kraken to do a taxonomic classification for viruses. Whenever I do the kraken mpa report I choose "viral_2020", the results show fungus. Whenever I select "Virus", the results also show fungus.
The same thing happens whenevr I choose "Plasmid" and "Archaea". Everything that I choose gives fungus as the results. What do I have to do to get the resuts that I need?
The same thing happens whenevr I choose "Plasmid" and "Archaea". Everything that I choose gives fungus as the results. What do I have to do to get the resuts that I need?
2 replies
Hi, I am working with dUTP bases stranded RNA-Seq paired end data. After aligning with STAR , I would like to convert my bam files to bigwig.
Traceback (most recent call last):
File "/shed_tools/testtoolshed.g2.bx.psu.edu/repos/george-weingart/lefse/a6284ef17bf3/lefse/format_input.py", line 435, in <module>
feats = numerical_values(feats,params['norm_v'])
File "/shed_tools/testtoolshed
File "/shed_tools/testtoolshed.g2.bx.psu.edu/repos/george-weingart/lefse/a6284ef17bf3/lefse/format_input.py", line 435, in <module>
feats = numerical_values(feats,params['norm_v'])
File "/shed_tools/testtoolshed
i am getting this error in Lefse
can anyone help me out resolve this issue
...just see it: RSEM it is already integrated.
I want to understand cuff diff
it alwys gives me error
Using something like deseq2 if you can
please help me in that i checked my data file but nowhere is missing value or any other character but still this error is coming in galaxy
It seems not to be on the toolshed. I remember that there was a pull request, but I can't find it.
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Hello everyone, I'm new to galaxy. I'm following a tutorial to analyse differential expressed genes. There a few steps that requires the use of the cut tool. When I run it, it says in the description that it breaks the column assignments and to click on the pencil to re-establish them after. However I don't know what I have to click? Anyone knows? I have the same issue with Change case tool
1 reply
Dear All, I was using DESeq2 to perform differential expression between 7 different cell-lines, however, I just saw that the DE genes are listed by just using the first two cell-lines that I input in the factor, does anyone have any idea on how can I perform pairwise comparison and extract differentially expressed genes across all 7 cell-lines like we can do in limma? IT would be of great help! Thank you! :)
3 replies
