Where communities thrive


  • Join over 1.5M+ people
  • Join over 100K+ communities
  • Free without limits
  • Create your own community
People
Activity
bgruening
@bgruening:matrix.org
[m]
Possible, but I would really discourage you from using this tool :-(
Colby Gekko
@ColbyGekko_twitter
I've had this error with other tools so I was trying to see if it was just a problem with the things I was trying to use. Do I just need to install python2 instead of python3?
Nicola Soranzo
@nsoranzo:matrix.org
[m]
No, it's that the TopHat Galaxy wrapper is unmaintained, given that use of TopHat itself is discouraged from its own authors.
Colby Gekko
@ColbyGekko_twitter
Okay great, thanks.
Havshxjdnaggz
@ASQWZXED
Hello
I want to run ClustalO but I want to change the value of k in k-tuple to 6
How can I change this value ?
5 replies
firat kurt
@firat.kurt.usa_gitlab
This message was deleted
2 replies
Helena
@hexylena:matrix.org
[m]
no worries :)
Matthias De Smet
@matthdsm
Hi everyone. I was wondering if there's support for secrets in galaxy tools? e.g. we're writing an in house tool that need a secret API key in the config. How would be go about this?
bgruening
@bgruening:matrix.org
[m]
The answer depends a bit of how secure you want to be
For example you can store secrets in the user preference and access this during tool scheduling and pass it as an env bar to the tool
Matthias De Smet
@matthdsm
The idea is that the admin would be able to set the API key for the tool. Our users shouldn't have to handle those
Are there docs somewhere about the user preferences?
bgruening
@bgruening:matrix.org
[m]
Oh then it's easier
Just assume an ENV bar in your tool and bail out if the ENV bar is not set
The admin then just needs to set the VAR
Or assume a file with the secret, the path passed via ENV
Matthias De Smet
@matthdsm
oh, awesome, thanks!
Anatolii
@Anatolii1002_twitter
hi
can u help me
i have a problem
i cant verify to get a galaxe passport
i tried 1000 times and nothing
thanks a lot for help
dannon
@dannon:matrix.org
[m]
Hi @Anatolii1002_twitter, you may be on the wrong community channel here. This is for the Galaxy scientific analysis platform.
Anatolii
@Anatolii1002_twitter
@dannon:matrix.org sorry, thanks
AntonioBaeza
@AntonioBaeza
Hi! Any chance you can add rnammer to Galaxy. Installation is painful and the web server is not working anymore
2 replies
martinzx13
@martinzx13
Hi there, can someone advise me in which galaxy server can I use for antibiotic resistance analysis, but I need large storage, also security data requirements and the option to work remotely with the team. I was thinking in AnVIL. But I am not sure yet, any help will be really appreciated
Sindhuprava Rana
@Sindhuprava
I had been working in this ID, but now when login in my user ID and valid password, was not allowed. When I tried for "forgotten password "system reverted with msg saying this user ID doesn't exist. Later I tried to make a ney account with the same user ID, I received a msg saying user ID is already in use. So, I here re-confirm that this user ID- sindhu.sahoo@gmail.com belongs to me, so I here request you to resolve the issue with my user ID and allow me to access my user ID in galaxy.
plz. help me to login
Nicola Soranzo
@nsoranzo:matrix.org
[m]
Given rnammer license and support status, I doubt it's worth spending time on wrapping it for Galaxy.
16svale
@16svale
Hi can someone help with generating the .tree files from the .biom1 files obstained from NG.Tax 2.0? I can only generate the fasta files and I get this error : ERROR App:46 - clustalo not found, createTree option ignored. Please install clustalo in the path..
1 reply
Peter Montso
@Peter_1_gitlab
Hi all.
I am the new user of galaxy. I was trying to detect PhagePromoters in my phage genome dataset using galaxy. However, the run finished with error message. ... File"/export/tool_deps/_conda/envs/mulled-v1-d7e02de4dc8cf90bc17a8fc1486d04e19f03edb0d6e7cd4de5385beda6b9903e/lib/python3.7/site-packages/Bio/SeqIO/InsdcIO.py", line 598, in _write_the_first_line
raise ValueError("Locus identifier %r is too long" % locus)
ValueError: Locus identifier 'vB_EcoM_366V_SA_NWU_length_6638_cov_6.442311' is too long. Please assist. I thank you.
1 reply
mmotoc
@mmotoc
Has anyone else had problems with funannotate?
M Bernt
@bernt-matthias:matrix.org
[m]
@mmotoc: what kind of problems?
eilyn
@eilyn_mena_twitter

Hello,

I am trying to run FEELnc_codpot, and I am getting two types of errors. The first error occurs after parsing the genome annotation file. I get the following message:

--------------------- WARNING ---------------------
MSG: Got a sequence without letters. Could not guess alphabet
I think this message is coming up because of short sequences that BioPerl can't decipher as DNA, RNA, or protein. However, I'm not sure what I need to edit to manually input that the alphabet should be set as DNA.
In case this information is relevant, the genome annotation file was converted from gff to gtf using "gffread -T", However, I noticed that the resulting output file is missing any attribute information other than gene_id, transcript_id, and some gene_name. So, all exon_number and other information were lost.

Cristóbal Gallardo
@gallardoalba:matrix.org
[m]
I'll install it also in usegalaxy.org
vikash yadav
@Vikash0208_twitter
Dear Galaxy Support team,
First, thank you for helping millions of students across the world. I am trying to use the ORFipy tool. There are many options which user can set to get the desire ORF including the size of ORF. In the usegalaxy.org tool the option for minimum length is available but Maximum length of ORFs is missing which is available in the ORFipy. I wonder if it is possible to include the option for maximum length of ORFs. Thank you
Sincerely
2 replies
Kayla Conner
@kaylaconner
Hi! Is anyone else having issues with getting jobs to run? I have six jobs lined up (all FeatureCounts) that have been stuck since yesterday.
ktian811
@ktian811
I'm stuck with jobs waiting to run for hours since this morning (FastQC). I hope there no problems with the server.
1 reply
Henrik Eckermann
@HenrikEckermann
Hi there, I get the following error. If anyone could help me out how to fix it that would be amazing: "ERROR App:46 - clustalo not found, createTree option ignored. Please install clustalo in the path."
eilyn
@eilyn_mena_twitter

Dear Galaxy Support team,
I am trying to run FEELnc, and I am getting this error :

--------------------- WARNING ---------------------
MSG: Got a sequence without letters. Could not guess alphabet

I have the hisat bam result, i used Stringtie or cufflinks to obtain gtf of the transcriptome annotation, but the data income (gtf of transcriptome annotation, reference gtf and reference genome) in FEELnc ocuurs this error
-------------------- WARNING ---------------------
MSG: Got a sequence without letters. Could not guess alphabet
Arushi Arora
@Arora155_twitter
hi I have a problem. I uploaded my rna seq data file. Tried fastaq and trimmomatic but it comes waiting for job to run for hours. Please help
1 reply
مزنة العقلا
@Maloqalaa_twitter
Hi, I am asking if there is a way to view a BioCompute Object, as a json file , in Galaxy platform ?
Nicola Soranzo
@nsoranzo:matrix.org
[m]
@Maloqalaa_twitter: You can export a workflow invocation (i.e. the result of running a workflow) as a BioCompute Object
Cristóbal Gallardo
@gallardoalba:matrix.org
[m]
Hi @ktian811, which Galaxy instance are you using?
3 replies