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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.
tensionhead
@tensionhead
Got it and it works.. phew, that makes for a good start of the week thanks again!
Björn Grüning
@bgruening
hehe :)
galaxybot
@galaxybot
[fubar] @bgruening: does this kind of "papercut" make a galaxy configuration gui worthwhile? Plenty of help text in the yml - could be a Galaxy tool :)
tensionhead
@tensionhead
Hi, I uploaded a tool to https://testtoolshed.g2.bx.psu.edu/repository?repository_id=0a3480fb2f5eb710&changeset_revision=5e07fe722e0e However in my local galaxy instance, it apparently doesn't get listed/found
Ha, actually nevermind sorry.. it just took like 30min, now it's there :)
Hugo Jiménez Hernández
@HugoJH
Hello folks. I just got slurm backend runner working with two worker nodes (tested with very simple sbatch file ) on my local galaxy. The thing is once I tried to execute a tool from galaxy interface it crashed with the following message: "This job failed for reasons that could not be determined."
Took a peek into the logs and nothing really helpful (at least for me): https://pastebin.com/DQi01C2G
Any suggestions?
Nicola Soranzo
@nsoranzo
@HugoJH You may want to ask this on https://gitter.im/galaxyproject/admins
Hugo Jiménez Hernández
@HugoJH
Thank you @nsoranzo. :D
Dave Clements
@tnabtaf
@olesya749 Just saw your post from 3 days ago. (With apologies). I don't know of anyone who does one on one training. However, there is a wealth of training material here, and there is a dedicated Gitter Channel for the Galaxy Training Network. Those are good places to start.
We also list any trainings we know about here. The next intro training is see is this one, which is free. It will be in your evening (9pm-midnight).
galaxybot
@galaxybot

[unknown]
Data Usage and Job Processing Issues [usegalaxy.org support]
I’m having an issue that I think is related to my disk usage.

I accidentally permanently deleted a huge number of files from the history I’…

galaxybot
@galaxybot
[unknown]
Abundance of OTU's [usegalaxy.org support]
Is Mothur the only metagenomic toolset that provides the number of sequences/OTU? I would love to use map with BWA-MEM/Bowtie2 and get abund…
galaxybot
@galaxybot

[unknown]
Determining the haplotype [usegalaxy.eu support] vcf
Hello everyone,

we just started sequencing bloodgroups by using ngs. We are using the MiSeq from Illumina and our reads are 150 bp long.

I…