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Nuwan Goonasekera
@nuwang
Hope the tests don’t use it because there’s still a reference to it there
FiReTiTi
@FiReTiTi
@nuwang @natefoo Thank you for your answers. I didn't see any file config/tool_conf.xml contrary to what was indicated in http://https://galaxyproject.org/admin/tools/add-tool-tutorial/, that's why I tried first to modify the main, and as my test was not found, I tried to modify sample, and decided to ask my question as I found it a little bit confusing.
Glad it ends up being a PR.
natefoo
@natefoo:matrix.org
[m]
Ah yes somewhere we document that you should create tool_conf.xml by copying from the sample if it does not yet exist, but it is missing from that page.
I would recommend using the Galaxy Training Network (training.galaxyproject.org) over that guide, we should probably just remove that page as it's fairly out of date.
Jeevan Karloss
@ajkarloss

I am trying to install galaxy in my MacBook Pro and Getting below errors. Any Tips?

WARNING: The candidate selected for download or install is a yanked version: 'cheetah3' candidate (version 3.2.6.post2 at https://files.pythonhosted.org/packages/7f/ff/d6eebd29ce2d55ce903a268b830302acb05f22f94dff941859776ab79382/Cheetah3-3.2.6.post2-cp36-cp36m-macosx_10_9_x86_64.whl#sha256=62fb67ad64dbe7ec45cf4256745fe4db18245ad335c157c6c788cc3ed24bc6a2 (from https://pypi.org/simple/cheetah3/) (requires-python:>=2.7, !=3.0., !=3.1., !=3.2., !=3.3.))
Reason for being yanked: Failed
Building wheels for collected packages: mercurial
Building wheel for mercurial (setup.py) ... error
ERROR: Command errored out with exit status 1:
command: /Users/jeevka/IRIDA/galaxy/.venv/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/z4/598z4x912_d17v8k299nqtkw0000gn/T/pip-install-k18hs8so/mercurial_da207d2ad9e74fa3b16c10e7785513ba/setup.py'"'"'; file='"'"'/private/var/folders/z4/598z4x912_d17v8k299nqtkw0000gn/T/pip-install-k18hs8so/mercurial_da207d2ad9e74fa3b16c10e7785513ba/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(file) if os.path.exists(file) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' bdist_wheel -d /private/var/folders/z4/598z4x912_d17v8k299nqtkw0000gn/T/pip-wheel-vrmt_824
cwd: /private/var/folders/z4/598z4x912_d17v8k299nqtkw0000gn/T/pip-install-k18hs8so/mercurial_da207d2ad9e74fa3b16c10e7785513ba/

nsoranzo
@nsoranzo:matrix.org
[m]
@ajkarloss: That error traceback is not very readable, can you paste it on a gist ( https://gist.github.com/ ), please?
Jeevan Karloss
@ajkarloss
Thanks a lot
nsoranzo
@nsoranzo:matrix.org
[m]
@ajkarloss: I think your issue would be solved by galaxyproject/starforge-recipes#81 , which is unfortunately stuck at the moment.
Jeevan Karloss
@ajkarloss
:(
Nate Coraor
@natefoo:matrix.org
[m]
Blech, can we not just remove mercurial at this point? I thought all Galaxy-side usage of mercurial had switched to hgutil
Nate Coraor
@natefoo:matrix.org
[m]
Ah, hg_util still relies on hg on the command line.
FiReTiTi
@FiReTiTi
Hi, I'm a new user, and I'm trying to integrate a pipeline of mine into Galaxy, but I'm having issues with I/Os. The input is a directory, and the outputs are 3 different directories, plus a lot of text going to the stdout and a log file. I read in the documentation how to define the input using <param format="directory".../>and the output with <data format="directory"... />, but is there a tutorial or even examples to help me improve what I have done?
nsoranzo
@nsoranzo:matrix.org
[m]
@ajkarloss The issue I mentioned is solved, you should be able to install now.
Christophe Antoniewski
@drosofff

Hi,
I recently noticed that our galaxy server instance (21.05) are failing to send error reports by email. It used to work before recently (I received some alerts in july).
We are using gmail smtp, so the parameters in our galaxy.yml conf files are these:

galaxy:
    error_email_to: ouradress@gmail.com
    smtp_password: google_app_auth_token
    smtp_server: smtp.gmail.com:587
    smtp_username: ouradress@gmail.com

and the uwsgi log file returns the following error (displayed in the web user interface):

galaxy.util DEBUG 2021-08-29 08:51:59,836 [pN:main.web.1,p:2325,w:1,m:0,tN:uWSGIWorker1Core1] Initiated SSL/TLS connection to SMTP server: smtp.gmail.com:587
galaxy.tools.error_reports DEBUG 2021-08-29 08:52:00,043 [pN:main.web.1,p:2325,w:1,m:0,tN:uWSGIWorker1Core1] Bug report plugin <galaxy.tools.error_reports.plugins.email.EmailPlugin object at 0x7f451875b1d0> generated response ("An error occurred sending the report by email: 'NoneType' object has no attribute 'strip'", 'danger')

I guess the error may come from changes in gmail smtp policy and/or an ssl/tls python module ?

any thought appreciated !

2 replies
Salvador1313
@Salvador1313
Я только начинал постигать азы этих дебрей... Прошу прощения если буду тупить.
kenza12
@kenza12
Hi all,
I’m using local galaxy with local tools. I executed a worklow with valid inputs, so I got complete and valid results. But then I tried with bad inputs to get failed results. So in some steps, jobs were paused because its input datasets are in an error state but in the next step which normally output a list of files (collection), I got an empty list but in « green » state, no error state or paused as expected. And I can’t see the details of the jobs or anything else. I just start using bioblend and I want to get all failed jobs « paused » because of bad inputs or «error» but I can’t in this case with state « ok » and empty list. Thanks for helping.
Khadijeh
@Khadijehsadegh_twitter
Hello everybody,
Khadijeh
@Khadijehsadegh_twitter
when I analyze different samples by Cutadapt. it get this error (This job was resubmitted to the queue because it encountered a tool detected error condition on its compute resource.
cutadapt: error: Error in FASTQ file at line 169629: Line expected to start with '@', but found '\n')
2 replies
so, I can't continue my job. how can I resolve my problem?
MelonaT
@MelonaT
Hi everybody, do things also take really really long for you? I have not that big datasets, but they're already being processed for approximately 24 hours ...
Nate Coraor
@natefoo:matrix.org
[m]
@MelonaT: which Galaxy server, what tools, and what state are they in (gray, yellow, what message is displayed when you expand the dataset)?
6 replies
kenza12
@kenza12
Hello, I was wondering if someone has an idea about the problem that I encountered
yesterday, I posted it at 10:58. Thanks a lot.
metabolomika
@metabolomika
Hi everybody! I have just started with Galaxy. I am interested in GCMS data processing. Today I converted a file form GCMS to mzda.xml file but after trying to generate workflow the file was designated as unknown. Could you please refer me to some helpful resources related to this issue. Many thanks.
bwlang
@bwlang:matrix.org
[m]
i've been strugging to try to combine lanes for a nextseq run using a nested collection in galaxy (hundreds of libraries). I need to run cat on these to form one file for R1 and one for R2 for each library. Anybody know how to do this?
2 replies
Greg Von Kuster
@gregvonkuster
Uploading to the TS seems broken. Does it need a reboot or something?
Greg Von Kuster
@gregvonkuster
Just worked. Maybe just a hiccup somewhere.
Simon Gene Gottlieb
@SGSSGene
Is the testtoolshed down, or is it just me? https://testtoolshed.g2.bx.psu.edu/
4 replies
jt008
@jt008
hi
I would like to download directly from medgenome sequencing center. I pasted the URL and it says that it Warning: Unsupported Media Type (415)
4 replies
Marius
@mvdbeek:matrix.org
[m]
@kenza12: I'd recommend checking the job status for the individual steps in the invocation, you can do that under User -> Workflow invocations
For mapped over outputs we have to precreate a structure, that's why this is green
kenza12
@kenza12
@mvdbeek:matrix.org : Ok thanks for the advise.
Matúš Kalaš
@matuskalas
image.png
image.png
Hi👋🏽 What happened to Galaxy that the tools panel is covered by the middle panel? 😢 (latest Firefox on Win10)
My students are supposed to use it tomorrow morning 😭
(looks normally in a Chromium-based browser)
Helena Rasche
@hexylena:matrix.org
[m]
looks normal in firefox on linux
Björn Grüning
@bgruening
hu?
but you have usegalaxy.eu and org
is that an EU problem? or a FF problem?
Helena Rasche
@hexylena:matrix.org
[m]
I reckon it's a browser version issue
dannon
@dannon:matrix.org
[m]
@matuskalas: I'm looking at FF 92.0 on Win10 and it looks fine to me. Is there maybe an addon or something misbehaving? Is your monitor gigantic, or are you using something to zoom the contents, perhaps?
Matúš Kalaš
@matuskalas
W10, single screen 1280x720, FF92.0 all add-ons disabled except the fb container, same behavior. But if it's only a problem on my setup, then it's not that much of an issue 😅 I'll report back if any of my students experience it too...
image.png
Dannon
@dannon
Very weird. And, yes, please do let me know if you see any other occurrences of this and we can dig deeper.
Matúš Kalaš
@matuskalas
👍🏽 Many thanks! 🙏🏽
Jessica Conway
@jessicaconway__twitter
Hi, I am having problems running the summary.seqs after executing the make.contigs. It keeps displaying an error message and I am unsure how to fix this
It keeps displaying: