Dear, Martin. Thank you for your advises. I have uploaded files what I use in X!tandem on Galaxy. Can you check them on the following GitHub URL?
Additionally, I also indicated the error messages what I received when I executed the X!tandem on Galaxy.
I'm not still familiar with GitHub. So, I'm worry about whether you can check my files and error codes. If you could not check them, please contact me again. Thank you.
Don't mean to be bothering you, but could you check my trouble mentioned above ?
tool_conf.xml.mainto make Galaxy aware of the tool, it was not found, however, when I modified
tool_conf.xml.sampleit worked. Why?
tool_config_file) then you can
cp config/tool_conf.xml.sample config/tool_conf.xmland make your modifications there.
config/tool_conf.xmlcontrary 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.
tool_conf.xmlby copying from the sample if it does not yet exist, but it is missing from that page.
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 = '"'"'/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
<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?
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: email@example.com smtp_password: google_app_auth_token smtp_server: smtp.gmail.com:587 smtp_username: firstname.lastname@example.org
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 !