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Nick Stoler
@NickSto
Thanks for confirming
Later than I'd expect
Maybe I'll hop on a Europe one before that
(And, the next call starts in ~40 minutes.)
Dave Clements
@tnabtaf
luke
@luke-c-sargent
Righto, the paper cuts call has concluded - thanks to those that joined! Next call is in a bit over 6 hours; in the interim, inquiries can be made here in this channel where operators are standing by
Ter-lab
@Ter-lab
Hi, is there any version Of galaxy I can install on windows pc?
Nolan Woods
@innovate-invent
@Ter-lab you could possibly find a way of making it work on windows. You are asking for pain though.
Actually, I think windows 10 has docker support
try docker run --rm -d -p 8080:80 quay.io/bgruening/galaxy:19.09
Nicola Soranzo
@nsoranzo
selten
@selten
I just noticed that 20.09 announcement isn't displayed in the docs: https://docs.galaxyproject.org/en/master/releases/20.09_announce.html
Nicola Soranzo
@nsoranzo
@selten Seems to be fixed now
galaxybot
@galaxybot
[unknown]
LEfSs uploded file looks different to 2018 – problem? [Uncategorized]
Hello everyone, I already used LEfSe in 2018 and have now a new dataset to analyse. I noticed when I upload my .tsv file that it looks diffe…
selten
@selten
@nsoranzo On master it's still not working well (https://docs.galaxyproject.org/en/master/releases/20.09_announce.html) but on release_20.09 it works fine (https://docs.galaxyproject.org/en/release_20.09/releases/20.09_announce.html). However, it's master that's referenced in e.g. emails.
Nicola Soranzo
@nsoranzo
@selten Yep, we discussed in another channel, I see the correct content on master too, it seems it may be an issue with the CDN.
selten
@selten
Alright! Then I'm probably just in the cache of the CDN
Dave Clements
@tnabtaf
Most recent PaperCuts call just wrapped up. Next one in a little under two hours.
Dave Clements
@tnabtaf
Hi all, Next Papercuts call starting in ~ 5 mins https://galaxyproject.org/events/2020-11-papercuts/
OK, more like 3 minutes
Dave Clements
@tnabtaf
Hi all, last Papercuts call starting in ~ 20 mins https://galaxyproject.org/events/2020-11-papercuts/
galaxybot
@galaxybot

[unknown]
How to merge to files [Uncategorized]
Dear all,

I am a very new galaxy user. I have 4 fastq files from the same organism, 2 forward reads and 2 reverse reads. I want to merge fo…

Dave Clements
@tnabtaf
And the final call of the November 2020 Galaxy Papercuts day is done. Thanks to everyone who participated by creating or addressing issues.
Dong-Hun Lee
@aivndv_twitter
Please help. I am trying to install local galaxy instance in my Macbook (Catalina), but have a problem. the first part of long error message as below. ....Running setup.py clean for pysam
Failed to build pysam
Installing collected packages: pysam, python-jose, python3-openid, pyuwsgi, tqdm, yacman, refgenconf, repoze.lru, routes, unidecode, social-auth-core, sortedcontainers, tempita, sqlalchemy, sqlparse, sqlalchemy-migrate, sqlalchemy-utils, sqlitedict, svgwrite, whoosh
Running setup.py install for pysam ... error
ERROR: Command errored out with exit status 1:
galaxybot
@galaxybot
[unknown]
uploading fa.gz file [Uncategorized]
why fa.gz file of 4.3Gb is failed to upload from my computer to galaxy history or any mapping tool?
galaxybot
@galaxybot

[unknown]
Galaxy doesn't allow Cloud Authorization - Save Key button deactivated [usegalaxy.org support] admin, galaxy-local, error
Hi,

I have a problem with the Cloud Authorization option on Galaxy.

I followed these steps:

I log in to my account at usegalaxy.org

I c…

Wolfgang Maier
@wm75
@aivndv_twitter This particular error with pysam should be fixed now. You should be able to just start your clone of Galaxy again and it should find a precompiled version of pysam this time. Hope the rest of the startup is going to work smoothly for you :) If not, keep reporting errors here. Thanks!
Dong-Hun Lee
@aivndv_twitter
@wm75 Thanks. the error with pysam is fixed! I see this error message now. The Galaxy client build is up to date and will not be rebuilt at this time.
Activating virtualenv at .venv
Executing: .venv/bin/uwsgi --module 'galaxy.webapps.galaxy.buildapp:uwsgi_app()' --virtualenv /Users/donghunlee/galaxy/.venv --static-safe /Users/donghunlee/galaxy/client/src/assets --pythonpath lib --threads 4 --buffer-size 16384 --http localhost:8080 --static-map /static=/Users/donghunlee/galaxy/static --static-map /favicon.ico=/Users/donghunlee/galaxy/static/favicon.ico --die-on-term --hook-master-start 'unix_signal:2 gracefully_kill_them_all' --hook-master-start 'unix_signal:15 gracefully_kill_them_all' --enable-threads --umask 027 --py-call-osafterfork
Traceback (most recent call last):
File ".venv/bin/uwsgi", line 5, in <module>
from pyuwsgi import run
ImportError: dlopen(/Users/donghunlee/galaxy/.venv/lib/python3.8/site-packages/pyuwsgi.cpython-38-darwin.so, 2): Symbol not found: _Py_GetArgcArgv
Referenced from: /Users/donghunlee/galaxy/.venv/lib/python3.8/site-packages/pyuwsgi.cpython-38-darwin.so
Expected in: flat namespace
in /Users/donghunlee/galaxy/.venv/lib/python3.8/site-packages/pyuwsgi.cpython-38-darwin.so
Nolan Woods
@innovate-invent
galaxybot
@galaxybot

[unknown]
DESeq2 error running htseq-count [Uncategorized]
Every time I run DESeq2 I get this fatal “undefined” error:

estimating size factors

Error in checkForExperimentalReplicates(object, modelM…

galaxybot
@galaxybot

[unknown]
edgeR error running htseq-count files [Uncategorized]
When I attempt to run edgeR under default conditions with successfully processed htseq-count files, I get fatal error: exit code 1 ():

Warn…

galaxybot
@galaxybot
[unknown]
Errors with makeblastdb & blastn on very large file sets [usegalaxy.org support] galaxy-local
I am trying to follow a procedure in the following link - detailed instructions are in supplementary. I believe I have everything working un…
Wolfgang Maier
@wm75
@aivndv_twitter hmm, this error has been reported before on the help forum here: https://help.galaxyproject.org/t/trying-to-get-local-galaxy-running-but-cant-open-localhost-8080-in-browser-err-connection-refused/4726 but for Python3.6. Can you add your report there please for further debugging?
galaxybot
@galaxybot

[unknown]
Trimmomatic Work Flow Issue [usegalaxy.eu support]
Hi All,

just new to galaxy and I am designing a workflow whenever I insert a Trimmomatic into the workflow I can not update the numbers of …

galaxybot
@galaxybot
[unknown]
To convert String tie GTF file to FASTA file [Uncategorized]
I have used tool String tie to prepare reference assembly and got output data as GTF file. For structural and functional annotation I need …
olesya749
@olesya749
please help me with SAM/BAM specification
Jennifer Hillman-Jackson
@jennaj
@olesya749 Common datatypes are listed here with help plus links to related resources/details https://galaxyproject.org/learn/datatypes/
galaxybot
@galaxybot
[unknown]
single cell barcode extraction [usegalaxy.eu support]
I have tried to run single cell pre-processing workflow.but its not available for my data. I think it has a special kind of data uploading, …
galaxybot
@galaxybot

[unknown]
Fatal error: Exit code 1 () using Shovill [usegalaxy.org support] error
Hi, When I try to Shovill I keep getting this error:

Fatal error: Exit code 1 ()

[kmc] Error: some error while reading fastq file, please …

olesya749
@olesya749
I am wondering if somebody knows a tutor who can teach me Galaxy on line face to face. I am going to pay that person. Please let me know. Thank you
I live in Chicago, IL,USA. My phone number is 773-814-5566
MaralQ
@MaralQ
Hello!
I'm trying to map my reads to human reference genome. But I don't know which build-in genome to use.
I would use Homo_sapiens.GRCh38.dna.toplevel.fa if I was using STAR.
RNA-seq single end library.
MaralQ
@MaralQ
Never mind. I'm just using hg38, the latest release.
galaxybot
@galaxybot
[unknown]
Version update for Galaxy environment [usegalaxy.org support] error
It is written " * Download and Extract Reads in FASTA/Q* format from NCBI SRA (Galaxy Version 2.10.8+galaxy0) ". But only Galaxy Version (…