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Eric Mockler
@mocklee

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/v21.2

Does 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.

dannon
@dannon:matrix.org
[m]
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.
Eric Mockler
@mocklee
@dannon:matrix.org Thanks for the pointer!
Marek Cmero
@mcmero
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?
bgruening
@bgruening:matrix.org
[m]
@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.
anoopanandmalik
@anoopanandmalik
The disk quota remains full even after deleting files permanently from the history. I need help to refresh my disk quota
bgruening
@bgruening:matrix.org
[m]
please log out and in again to reset the quota meter
anoopanandmalik
@anoopanandmalik
I tried but nothing is happening .. earlier it was 22% and then after using it for sometime it came to 94% now even after deleting the files permanently the quota meter is still at 94%
dannon
@dannon:matrix.org
[m]
I recalculated your disk usage manually and it remains at 235.5GB.
In doing so I noticed that I should probably mention that we only allow one account per user.
anoopanandmalik
@anoopanandmalik
Hi, but earlier it was 22 GB and then I executed a command with which my disk quota reached to 235.5 GB....I deleted the results permanently from my history. But still the disk quota remain the same
anoopanandmalik
@anoopanandmalik
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
bgruening
@bgruening:matrix.org
[m]
Make really sure it's permanently deleted. Maybe sent us a screenshot.
anoopanandmalik
@anoopanandmalik
Where should I send the screenshot. Please provide me email Id to share the screenshot
image.png
anoopanandmalik
@anoopanandmalik
Before job no 77 my disk quota was showing 22% but after running job no 77 it was showing 94%. Although I have permanently deleted job 77 from my workflow
Davia Peart
@PeartDavia_twitter
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?
2 replies
akankshabafna
@akankshabafna
Hi,
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.
akankshabafna
@akankshabafna
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. I am trying to use bamCoverage but cannot use the --filterRNAstrand in Galaxy. Please can anyone help . Thanks
5 replies
anitatiknaik
@anitatiknaik
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
i am getting this error in Lefse
can anyone help me out resolve this issue
kriskris99
@kriskris99
Could anyone please help: I cant find bamCompare, bamCoverage tools on usegalaxy.org.
3 replies
HHerlyn
@HHerlyn
Hi, I would like to use the RSEM program within Galaxy, but that option doesn't seem to exist yet. Can someone tell me how I can make RSEM be integrated into the Galaxy framework?
...just see it: RSEM it is already integrated.
Hossam Shawki
@HossamShawki6_twitter
hello
I want to understand cuff diff
it alwys gives me error
bgruening
@bgruening:matrix.org
[m]
Please do not use cuffdiff anymore
Using something like deseq2 if you can
jamietamie123
@jamietamie123
Anyone know how to solve this problem? I keep getting "Uncaught exception in exposed API method:" while logging into my galaxy account online at usegalaxy.org
anitatiknaik
@anitatiknaik

Number of significantly discriminative features: 54 ( 63 ) before internal wilcoxon
/galaxy_venv/local/lib/python2.7/site-packages/rpy2/rinterface/init.py:185: RRuntimeWarning: Error in svd(X, nu = 0L) : infinite or missing values in 'x'

warnings.

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
Sukanya Sahu
@SukanyaSahu5_twitter
I want to use picrust2. It says that it is available online in galaxy, but I couldn't find it.
M Bernt
@bernt-matthias:matrix.org
[m]
It seems not to be on the toolshed. I remember that there was a pull request, but I can't find it.
91425101212
@91425101212
Hello. I am using cuffdiff by galaxy but in my output I don't have isoforms differential expression file. how can i get that. please help me.
3 replies
Hossam Shawki
@HossamShawki6_twitter
Do we must trim the fastq files made by illumina HiSeq before alignment with Hisat2 for deferential expression ?
1 reply
Anna Syme
@AnnaSyme
Welcome to all for the GTN CoFest & Galaxy Papercuts CoFest Day
https://galaxyproject.org/events/2022-05-papercuts/
Nadeen
@nadeen_khaled19_twitter
please i need help. My account has been marked deleted.
bgruening
@bgruening:matrix.org
[m]
@nadeen_khaled19_twitter: do you have maybe multiple accounts?
Nadeen
@nadeen_khaled19_twitter
@bgruening:matrix.org No, i have just created a new one, because i have an exam tomorrow and i need my workflows as soon as possible...
1 reply
Federica Moda
@federica96_gitlab
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
shwetagodbole
@shwetagodbole
Dear All,
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
Gurpreet Dhaliwal
@g_dhaliwal1_twitter
Hi, I accidentally purged one of my histories thinking that this would free up space from deleted datasets rather than delete the whole thing. Is there anyway to retrieve this?