search

arpcard / rgi

Resistance Gene Identifier (RGI). Software to predict resistomes from protein or nucleotide data, including metagenomics data, based on homology and SNP models.
Other
314 stars 75 forks source link

Collectors Not Found Error in test.sh in RGI Using pytest #261

Closed mainakbioinfo closed 6 months ago

mainakbioinfo commented 7 months ago

Hi, I am getting this error while trying to run test.sh script in RGI using Pytest (base) admin1@admin:~/miniconda3/rgi/rgi-master/tests$ cd .. (base) admin1@admin:~/miniconda3/rgi/rgi-master$ pytest test.sh -v

platform linux -- Python 3.11.0, pytest-7.4.3, pluggy-1.3.0 -- /home/admin1/miniconda3/bin/python cachedir: .pytest_cache rootdir: /home/admin1/miniconda3/rgi/rgi-master collected 0 items
=========================================================== no tests ran in 0.00s ERROR: found no collectors for /home/admin1/miniconda3/rgi/rgi-master/test.sh

Kindly suggest what should be done.. Thanks in anticipation!

raphenya commented 6 months ago

@mainakbioinfo you will need to have all the dependencies installed before running the tests. Maybe create an environment before running the tests. something like so: 


# make directory for rgi-analysis
mkdir rgi-analysis

# change into the directory
cd rgi-analysis

# create env
python3 -m venv rgi603

# activate 
source rgi603/bin/activate

# download rgi version 6.0.3 tarball
wget https://github.com/arpcard/rgi/archive/refs/tags/6.0.3.tar.gz

# decompressed tarball
tar -xvf 6.0.3.tar.gz

# change into decompressed directory
cd rgi-6.0.3/

# install rgi
pip install .

# run tests
bash test.sh

# deactivate environment
deactivate
mainakbioinfo commented 6 months ago

Did it. it worked.. Thanks a lot..! MAINAK BHATTACHARJEE DEPTT.OF BIO-TECHNOLOGY, HIT-K

On Thu, Jan 4, 2024 at 10:22 PM amos @.***> wrote:

Closed #261 https://github.com/arpcard/rgi/issues/261 as completed.

— Reply to this email directly, view it on GitHub https://github.com/arpcard/rgi/issues/261#event-11392491615, or unsubscribe https://github.com/notifications/unsubscribe-auth/BETFR73TSU4BLWUC7VRDF4LYM3M3PAVCNFSM6AAAAABAQ3OWFOVHI2DSMVQWIX3LMV45UABCJFZXG5LFIV3GK3TUJZXXI2LGNFRWC5DJN5XDWMJRGM4TENBZGE3DCNI . You are receiving this because you were mentioned.Message ID: @.***>

--

Disclaimer: This e-mail contains confidential information belonging to Heritage Institute of Technology & is intended solely for the Addressee. The unauthorized disclosure, use dissemination or copying (either whole or partial of this e-mail, or any information it contains), is prohibited. E-mail is susceptible to alteration and their integrity cannot be guaranteed. Heritage Institute of Technology shall not be liable for this e-mail if modified or falsified. If you are not the intended recipient of this e-mail, please delete it immediately from your system & notify the sender of the wrong delivery and the mail deletion.