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Cristian
@cche
I could copy and undelete a dataset that wasn’t available anymore so I couldn’t show the content. We are using 17.09 though.
It could be that the user shared his history before purging the dataset. I will check with him tomorrow.
galaxybot
@galaxybot
[gronke] Hi, I administrate my own Galaxy server. When I am trying to import another user's history, I get the following error: "History could not be imported. Please contact a Galaxy administrator if the problem persists."
[gronke] and then on the details, it has the following: https://pastecode.xyz/view/5ef9faed
[gronke] Can someone help me figure out why this is happening and how to fix it? Thanks.
galaxybot
@galaxybot
[gronke] To give more info: I have a link to the user's history. And there's an "Import History" button, and that says "Make a copy of the history and switch to it." When I do that, the system works for about a minute and then that error comes up
[gronke] I should add that the user's history is 802.48 GB. Is it possible the server is just crashing under that load?
[gronke] If that's true, is there a way to share a specific file with a user instead of the entire history?
Jaime Lagunez
@lagunez
Hey there...I've been away for a while...anyone can help me recover my files and projects?
galaxybot
@galaxybot
[dannon] lagunez: This is at usegalaxy.org? Are you able to log in?
galaxybot
@galaxybot
[unknown]
Restore Deleted History. [Uncategorized]
how to recover deleted history?
galaxybot
@galaxybot

[unknown]
why my transcript doesnt had the pvalue adj or fold change [usegalaxy.org support] deseq2
i used Star and featureCounts and after that Deseq2 then download the data and put it on the exel to find my transcript which was the PER3…

…

galaxybot
@galaxybot

[unknown]
RNA-STAR Fatal Error [usegalaxy.org support]
Hi, I am getting this error when trying to run RNA-STAR, how can I resolve it? Thank you.

Fatal error: Matched on FATAL ERROR

Transcriptom…

galaxybot
@galaxybot

[unknown]
Trying to make batch runs with tool that takes single text entry [usegalaxy.org support] admin, tool-dev
Myself and a colleague have developed a Galaxy tool that runs Picard for a specific purpose. It works fine with a single SAM/BAM input.

How…

[gronke] I made a post for my issue, hoping for some help: https://help.galaxyproject.org/t/trying-to-make-batch-runs-with-tool-that-takes-single-text-entry/751
galaxybot
@galaxybot

[unknown]
htseq-count shows fatal error every time [usegalaxy.org support] htseq-count
Hello everyone.

I am trying to operate htseq-count in galaxy. I have used HISAT2 BAM files (I am using Arabidopsis WT and Double Knock Out)…

Carolin Ehlert
@AnnaEhlert_twitter
Does anyone else have problems with heatmap2?
Exit code 1?
Helena Rasche
@erasche
Hi @AnnaEhlert_twitter we received your bug report at .eu, it is not immediately clear why this error occurred, one of my colleagues will hopefully respond today. I'm sorry I don't have more information at this time
It appears that somewhere a NA/NaN value was passed through, but I'm not sure where/why this would be.
Carolin Ehlert
@AnnaEhlert_twitter
Thank you!
Gilda
@Gilda69372910_twitter
Hi all, I have another newbie question. I finished my alignment and tried to merge my file using merge SAM but I keep getting this error Fatal error: Exit code 1 () Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/galaxy-repl/main/jobdir/022/603/22603368/_job_tmp -Xmx7g -Xms256m 16:06:23.035 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/cvmfs/main.galaxyproject.org/d. From what I have understood I need to sort the inputs but I am not sure how to do it as our sequencing service named the files in a weird way and I guess the sorting tools can't do anything. Any tip?
galaxybot
@galaxybot

[unknown]
Fatal error: Exit code 1 () merge SAM [Uncategorized]
Hi, When I try to merge filtered SAM files I keep getting this error:

Fatal error: Exit code 1 ()

Picked up _JAVA_OPTIONS: -Djava.io.tmpdi…

Gilda
@Gilda69372910_twitter
yes thanks, I just posted it
galaxybot
@galaxybot
[gronke] I'm trying to write a tool that can take multiple names in a file and then apply them in order to a collection, is that possible?
Marius van den Beek
@mvdbeek
gronke: https://usegalaxy.org/?tool_id=__RELABEL_FROM_FILE__&version=1.0.0&__identifer=9kfnui017g
galaxybot
@galaxybot
[gronke] ahh thanks mvdbeek this will be a great guide, we have a picard tool that uses addreadgroups, but it uses a unique strain name for each bam/sam file. i was struggling to figure out how to take in a list and use them on each one in a collection
Nolan Woods
@innovate-invent
Where is galaxybot connecting to? Is there another chat?
Nate Coraor
@natefoo
The #galaxyproject IRC channel on Freenode
Nolan Woods
@innovate-invent
oh, cool
galaxybot
@galaxybot
[gronke] yeah i hang out in IR, i actually have no idea where you guys are all that post from g2roboto
[gronke] *IRC
Nate Coraor
@natefoo
gronke: https://gitter.im/galaxyproject/Lobby =)
galaxybot
@galaxybot
[gronke] whoaaaa yeah that makes more sense, I always thought there was like, really, really few people in this chat.
[gronke] There are 13 people in IRC and 680 in the glitter chat
[Ferris] oh wow I didn’t know there were so few here on ye olde IRC
[natefoo] I'm still here on IRC. =)
galaxybot
@galaxybot
[dannon] Same!
[[nas]peter] Same here
Nolan Woods
@innovate-invent
Does anyone know why galaxy would refuse to load a tool xml file after replacing it? I have watch tools enabled and I am patching a shed tool after install. Even restoring the old file won't load it.
this is 19.01
The log shows an error reading the xml file, presumably while I was swapping the files
Nate Coraor
@natefoo
Does the error message indicate a syntax error?
Nolan Woods
@innovate-invent
The permissions are identical on the files
no
even the original working xml file when swapped back wont reload
Restarting galaxy does nothing either
it is like it is flagging the tool as bad and ignoring it
Nate Coraor
@natefoo
What's the error message?
Nolan Woods
@innovate-invent
Error reading tool configuration file from path 'toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/a6f147a050a2/text_processing/awk.xml': [Errno 2] No such file or directory