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Marius
@mvdbeek:matrix.org
[m]
@kaneja123: you might be logged out, try logging back in
Kawalpreet K Aneja
@kaneja123
I tried even then I don't see my second upload file.
Brad Langhorst
@bwlang
looks like fastp on a 30M fastq is taking many hours… maybe something is misconfigured?
some ids in case they are helpful:
History Content API ID
bbd44e69cb8906b5e1cab7810cd8d913
History API ID
4a7330af5174f9d7
UUID 446d5819-7ef8-4a10-a31c-4f237482452f
bgruening
@bgruening:matrix.org
[m]
Which Galaxy server is that @bwlang ?
Brad Langhorst
@bwlang
@bgruening:matrix.org : sorry to assume… thats on usegalaxy.org. I plan to share this with some folks in dusseldorf when the analysis is complete so it’s probably better to do it on usegalaxy.eu anyway. Trying there now.
Jonathan Manning
@pinin4fjords

Morning all, easy question to ask: what's the simplest way of selecting named columns from a tabular file in Galaxy, without prior knowledge of column indices?

@pcm32 points at https://github.com/galaxyproject/tools-devteam/blob/master/tools/cut_columns and suggest I might PR there to add the feature, but it seems like something someone would have done ages ago so don't want to reinvent the wheel if it exists somewhere already.

wm75 (Wolfgang Maier)
@wm75:matrix.org
[m]

A tool that does that directly is:
toolshed.g2.bx.psu.edu/repos/bgruening/column_arrange_by_header/bg_column_arrange_by_header/0.2

However, that's only available on usegalaxy.eu and .org.au, not .org.

As a workaround you could use toolshed.g2.bx.psu.edu/repos/iuc/column_order_header_sort/column_order_header_sort/0.0.1
avaiable on .org and .eu, but not org.au ;)
to first bring your columns into predictable order to then cut by column indices.

Jonathan Manning
@pinin4fjords
Ahh good- thanks @wm75:matrix.org . We're running our own instance so I'll just grab column_arrange_by_header
akankshabafna
@akankshabafna
@bgruening @gmauro:matrix.org @beatrizserrano My jobs have stopped due to lack of disk space. I have filled the quota request form and also emailed the same but have not received any reply. Please can you help.
shirleynelson
@shirleynelson
There is a bug in the galaxy aws cloud install. I deleted the galaxy instance on the aws side. Now galaxy side record of the instance refuses to giving an error. Tried deleting it from the galaxy side before deleting it from AWS and it gave an error. I need someone to either delete the record on the galaxy side that says I have an instance of Galaxy on aws or delete my account so everything gets reset and I can recreate the account with the same name and that will get rid of the galaxy AWS cloud Galaxy instance record on the Galaxy side.
shirleynelson
@shirleynelson

Galaxy isn't allowing the AWS cloud Galaxy aka galaxy_cloudman record to be deleted on the side that is outside of aws cloud. I have removed the instance of galaxy on the aws cloud side. But the installer will not allow another install of the instance because it has a record of an install even though that instance didn't work, doesn't work and isn't working and now is deleted.

What was the problem?

Tried to ssh to the system on aws that held the instance of galaxy and initially it did allow for a password entry which means it was up but maybe not running galaxy. It wouldn't take the password. So after a few attempts it stopped allowing a password entry and then the instance of galaxy on aws didn't respond to a ping timing out. At that point the instance on the AWS cloud of galaxy was completely broken. Tried rebooting. Tried stop and restart. Finally I terminated the instance on the AWS galaxy side and then tried to re-initiate the install on of Galaxy_cloudman but it wouldn't allow it cause it showed a record that there was already an install so it wouldn't allow a re-install. The only solution may be to delete my account on usegalaxy and create a new account on use galaxy to reset everything. But I want to keep my same login.

Is there anyone here that is an administrator who can remove the instance record of AWS cloud from my UseGalaxy account? Or delete my account so I can recreate it and reset everything which would basically get rid of the record of the instance on AWS of Galaxy cause there is no instance at this point on AWS cloud of galaxy_cloudman.

Also AmazonS3FullAccess as a permission policy no longer exists.
Or someone needs to fix the bug on the usegalaxy where one has the option to delete the record of the instance of Aws cloud galaxy_cloudman. Cause it doesn't work at the moment, doesn't allow a delete of the record. Gives an error when you try.
joaodias-bioinf
@joaodias-bioinf
Hi everyone, i am trying to upload a tool to toolshed but the databases reach the size limit. Is there a way to upload the tool and the databases required ? Thank you.
2 replies
Edward Chen
@DwardEE
Hi I'm been trying to use goseq and obtain the KEGG pathways. However, when I run my data, I get this error:
Warning message:
In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") :
OS reports request to set locale to "en_US.UTF-8" cannot be honored
Error in file(file, "rt") : cannot open the connection
Calls: read.delim -> read.table -> file
Warning message:
In file(file, "rt") :
cannot open file '/galaxy-repl/main/files/058/010/dataset_58010972.dat': No such file or directory
2 replies
orcunhacariz
@orcunhacariz
Hello. How can I terminate queued jobs in an in-house Galaxy Server using command line? Thanks.
wm75 (Wolfgang Maier)
@wm75:matrix.org
[m]
with bioblend and assuming you know the job ID: gi.jobs.cancel_job(job_id)
orcunhacariz
@orcunhacariz
OK. Many thanks, Wolfgang. Yes, I know the job ID. I will try that.
ntillquist
@ntillquist
Hi, I am trying to obtain a reference genome that is not listed. I have downloaded the FASTA sequence from NCBI but the file downloads as a fasta.tar file so I cannot use it in galaxy. Is there any way to get a specific reference genome added? Or does anyone know how to change this file type to just fasta?
orcunhacariz
@orcunhacariz
After I cancel all queued jobs, I try to upload a file (e.g. reference transcriptome file) to a Galaxy instance (which is connected to an in-house Galaxy Server). However, it remains queued again. Any suggestions? Many thanks in advance.
mostafaf
@mostafaf
hi every body ..
how to disable automatic update from galaxy
and
mostafaf
@mostafaf
How to grant deleting to someone without permission deleting shared data from library
Melisa Magallanes
@Melisa-Magallanes
Hi there, Can I install a package in galaxy as a regular user?
Martin Cech
@martenson
@Melisa-Magallanes usually not on a public instance that is hosted by somebody else. However you can set up your own Galaxy (https://getgalaxy.org/)
And install in it whatever you'd like.
Melisa Magallanes
@Melisa-Magallanes
@martenson thanks!!
Martin Cech
@martenson
@mostafaf Galaxy does not automatically update. And admins usually grant data library permissions, including deletion.
sosani2007
@sosani2007
hi
how to hidden upload and upload button on the galaxy ?
Björn Grüning
@bgruening
What do mean @sosani2007 ?
baczer
@baczer
Dear Galaxy,
I put the analysis yesterday evening and so far it is not producing output. Normally, it was taking an overnight. Previously it was working fine (trimming step was OK and stacked on alignment). I do not see any errors, just all tasks has the "clock" sign and . Do you know what might be an issue? What can I do?
bgruening
@bgruening:matrix.org
[m]
There is probably no issue. Be patient.
baczer
@baczer
Thx! So you are saying it happens that the analysis got stacked for days and then will be suddenly launched?
baczer
@baczer
It happens to me for the first time, although I am using Galaxy for more than a half a year now.
Margot Otto
@MargotOtto5_twitter
Dear Galaxy, can you please upload the following genome for me for alignment of my sequencing reads? The Botrytis genome: ASM14353v4 (NCBI). Or where can I ask for a genome upload? Thank you
bgruening
@bgruening:matrix.org
[m]
@MargotOtto5_twitter: which tool do you want o use?
you can always download the genome (FASTA) into your history
and use that for the mapping tool
Margot Otto
@MargotOtto5_twitter
Hi! Yes thank you I just figured that out. I am busy uploading the fasta and associated gtf file.....I will use Hisat2 for alignment of reads to a reference genome.
bgruening
@bgruening:matrix.org
[m]
Awesome! Sorry for late response but glad you figured it out :)
muscle_body
@tepodone_twitter
Hi! Now, I'm trying to use 'X!tandem' at Galaxy. However, it does not work well and following error message is indicated: Error executing tool with id 'proteomics_search_tandem_1': cannot find 'has_key' while searching for 'has_key'. What dose it mean? What can I solve the problem? @baczer
Melisa Magallanes
@Melisa-Magallanes
Dear Galaxy could you please install rcorrercor tool? thanks
bgruening
@bgruening:matrix.org
[m]
Which Galaxy instance are you on?
Melisa Magallanes
@Melisa-Magallanes
at the server, usegalaxy.org
bgruening
@bgruening:matrix.org
[m]
@Melisa-Magallanes I can install the tool on usegalaxy.eu in a few hours.
Melisa Magallanes
@Melisa-Magallanes
@bgruening:matrix.org thank you very much, here's the link https://github.com/mourisl/Rcorrector