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Nicola Soranzo
@nsoranzo
@Ter-lab Have a look at https://galaxyproject.org/admin/config/windows/
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
galaxybot
@galaxybot

[unknown]
Galaxy Admin Training, January 25-29 [Uncategorized] admin, events, training
Online, global and free. Apply by December 18.

The next Galaxy Admin Training will be offered online and asynchronously January 25-29.

Thi…

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
@aivndv_twitter https://stackoverflow.com/a/61082642
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
galaxybot
@galaxybot
[unknown]
Thiết bị nhà bếp giá rẻ [usegalaxy.be support] admin, galaxy-local, error
http://camnangnhabep.info/
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 (…
galaxybot
@galaxybot
[unknown]
cannot add tools in local Galaxy [Uncategorized]
I installed the local Galaxy in Ubuntu subsystem in my Windows 10 computer. I used “nano galaxy.yml” to enter galaxy yml file and added my e…
galaxybot
@galaxybot

[unknown]
Tool error with STAR aligner [usegalaxy.org support] error, rna-star
STAR aligner encountered following errors in all available versions.

"

tool error

An error occurred with this dataset:

Encountered an un…

tensionhead
@tensionhead
Hello, I am developing a galaxy tool which produces an html report to summarize the results. However when looking at this report within galaxy, all the CSS styles get ignored and hence it looks horrible. However if I download that very same html and open it via file:/// it looks as it should.
Apparently that happened before: https://biostar.galaxyproject.org/p/12025/index.html but there is no solution/answer?!
Björn Grüning
@bgruening
@tensionhead please look at this Galaxy setting https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/config/sample/galaxy.yml.sample#L1194 and the following.
HTML can be portnatially harmful, so Galaxy disables the "harful" parts. If you trust the tool you can whitelist the HTML output from a particual tool
tensionhead
@tensionhead
ah, great thx @bgruening !
Björn Grüning
@bgruening
Your welcome!
tensionhead
@tensionhead
little follow up question, on my local testing galaxy instance I see: ./test/unit/config/config_manage/embedded/config/galaxy.yml and
./test/unit/config/config_manage/simple/config/galaxy.yml I could whitelist my tool in one of these?
Björn Grüning
@bgruening
Please look into ./config/galaxy.yml
it might be called ./config/galaxy.yml.sample. In this case copy the file so that you have a galaxy.yml file.