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sabrinbashar1234
@sabrinbashar1234
Hi, I am trying to upload my excel file in Huttenhower lab Galaxy server for LefSe analysis but server is showing failed to upload every time. How can I upload my file?
I also tried with tabular format but each time it is showing internal server error
ifubar (ross lazarus)
@ifubar:matrix.org
[m]
@sabrinbashar1234: Sorry, but you will need to contact them directly using the contact details on that site - I don't think anyone from that lab reads this list?
amelielegare1
@amelielegare1
Hi! I think there is a bug with the cutadapt tool on Galaxy. For some reason, the Execute button is not working. When I click on it, it brings me back to the top of the page.
M Bernt
@bernt-matthias:matrix.org
[m]
@amelielegare1: Is there any parameter that is highlighted after hitting execute?
amelielegare1
@amelielegare1
No, it just brings me to the top :/
image.png
Now, when I try it the strip suffix is popping up
M Bernt
@bernt-matthias:matrix.org
[m]
Is this happening on a usegalaxy server?
And which tool version is this?
amelielegare1
@amelielegare1
Yes! On usegalaxy.org
Cutadapt Remove adapter sequences from FASTQ/FASTA (Galaxy Version 3.5+galaxy1)
amelielegare1
@amelielegare1
Just to put you in context, the strip suffix bug happened to me yesterday and it was quickly corrected. A little bit after, the execute button stopped working. And now the strip suffix bug is back ahaha
M Bernt
@bernt-matthias:matrix.org
[m]
OK. I can reproduce this on usegalaxy.org .. on usegalaxy.eu it is not happen with cutadapt 3.5 and 3.7
amelielegare1
@amelielegare1
Is there anything I can do?
amelielegare1
@amelielegare1
@bernt-matthias:matrix.org I found out that cutadapt is working when I write anything in the Strip suffix tab, erase it right away, and press execute. Thank you for your help! :)
M Bernt
@bernt-matthias:matrix.org
[m]
Might be a Galaxy bug. Good that you have a workaround. I opened an issue galaxyproject/galaxy#13516
amelielegare1
@amelielegare1
Thanks so much! @bernt-matthias:matrix.org
M Bernt
@bernt-matthias:matrix.org
[m]
@amelielegare1: Can you check if just clicking in the text box also allows you to submit the tool (i.e. do not enter text and delete it again)?
1 reply
eleo23
@eleo23
Is galaxy down right now
I cant seem to open the website
amelielegare1
@amelielegare1
Looks like there is an internal server error
Vir
@Virginia95Perez_twitter
Anyone having trouble uploading files to 'https://huttenhower.sph.harvard.edu/galaxy/' using the 'Upload data from your computer'?
1 reply
Srikanth Reddy
@Srikant22619033_twitter
Hi I have a issue with the VCF dataset to filter Why its specifically asking me ''Specify a region on which to target the filtering'', I don't want to use this command. Any help would be much appreciated.
Srikanth Reddy
@Srikant22619033_twitter
Hi I have a issue with the VCF dataset to filter Why its specifically asking me ''Specify a region on which to target the filtering'', I don't want to use this command. Any help would be much appreciated
1 reply
Nicola Soranzo
@nsoranzo:matrix.org
[m]
Tool tests can be run locally planemo test --biocontainers PATH/TO/TOOL/DIRECTORY
But the Continuous Integration on GitHub does also other tests (e.g. tool linting, Python and R code linting).
Arthur Eschenlauer
@eschen42
@nsoranzo right, CI what I'm getting at. For example, I have learned that flake8 is not enough; right how I'm working in an environment constructed with conda create -n lint r-lintr black flake8 flake8-import-order python=3.7.12 (Python 3.7 because that is the version that is running flake8). Any other suggestions would be welcome!
Manasi Apte, Ph.D
@Manasiapte_twitter
hello, I am looking to use S.cerevisiae (sacCer3) genome directory. is there any way to add that?
1 reply
Komal Chaurasia
@komalchrs_twitter
hello, can anyone tell me how to use the FTP server for galaxy Europe? I was trying to connect but it is not happening.
1 reply
although connected with main server
Manoj
@mbrahmane1
RNASeq samples quality check does not produce output
Charles Strittmatter
@charesredhat
Hi all for updating a tools in planemo now does it not except email and password do you also need the API key?
Marius
@mvdbeek:matrix.org
[m]
either email+password or api key, not both
Charles Strittmatter
@charesredhat
Ok thanks I am using email and password are correct so I need " around the password?
Marius
@mvdbeek:matrix.org
[m]
You'll have to make sure the password is shell-safe, so maybe ? Why don't you use the API key ? It is meant for that purpose
1 reply
amelielegare1
@amelielegare1
Hi, I have some problems with the FeatureCounts tool in the EU server. In fact, I can not select the built-in genome. The scrolling menu is not active. Here's a picture :
image.png
M Bernt
@bernt-matthias:matrix.org
[m]
@amelielegare1: have you selected a reference genome for Alignment file?
For usegalaxy.eu you should ask at https://gitter.im/usegalaxy-eu/Lobby .. maybe you can ask there which options are installed if any
amelielegare1
@amelielegare1
@bernt-matthias:matrix.org I'll ask the EU lobby, sorry for that!
pooh07
@pooh07
Hi All, I have uploaded the files for RNA-seq data analysis and I had performed Trimmomatic on my paired end fastq files but it looks like the pairing is different that is it paired with different sample. I am wondering if while selecting the R1 and R2 files it should be in same order or what. If yes, then how I can do that beacuse I had 48 files for each R1 and R2 reads. Please suggest me how I can figure out this situation.
Eman Koosehlar
@namia47
Hello everyone,
How can I find config/galaxy.yml file?
dannon
@dannon:matrix.org
[m]
@namia47: On a brand new instance you won't have one by default -- in the config directory there will be a galaxy.yml.sample containing the default settings that you can copy to galaxy.yml as a starting point.
Sara Victoria Good
@saravictoriagood
Hi, I am wondering if the galaxy server is down?
My job is taking longer than usual to run
Matt Chambers
@chambm
Why would repos show up in a local toolshed but not in a Galaxy connected to it? I've got one repo that shows up that was the first one I created on that shed, but new repos I create don't.
3 replies
Srikanth Reddy
@Srikant22619033_twitter
is anyone could use ANNOVAR Annotate VCF, I assume it's not working. Is it anyone?
Protalous
@Protalous
hi saw this in a thread. im setting up an iontorrent for endusers. saw gatk with this might be useful. any input?