Problems with use of pdp

[aiqubo]

Dear developer,
I was installed pdp as following step :

_1

[aiqubo@aiqubo find_differential_primers]$ conda create --name pdp python=3.7
Proceed ([y]/n)? y
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
To activate this environment, use
conda activate pdp
To deactivate an active environment, use
conda deactivate

_2

(pdp) [aiqubo@aiqubo find_differential_primers]$ conda activate pdp

_3

(pdp) [aiqubo@aiqubo find_differential_primers]$ cd find_differential_primers/

_4

(pdp) [aiqubo@aiqubo find_differential_primers]$ conda install --file requirements.txt
Collecting package metadata (current_repodata.json): done
.......
Proceed ([y]/n)? y
Preparing transaction: done
Verifying transaction: done
Executing transaction: done

_5

(pdp) [aiqubo@aiqubo find_differential_primers]$ conda install --file requirements-thirdparty-primer3_237.txt
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): done
Solving environment: done
......
Proceed ([y]/n)? y
Preparing transaction: done
Verifying transaction: done
Executing transaction: done

_ 6##

(pdp) [aiqubo@aiqubo find_differential_primers]$ python setup.py install
/home/aiqubo/anaconda3/envs/pdp/lib/python3.7/site-packages/setuptools/dist.py:458: UserWarning: Normalizing '0.2.0.dev' to '0.2.0.dev0'
warnings.warn(tmpl.format(**locals()))
running install
running bdist_egg
running egg_info
writing diagnostic_primers.egg-info/PKG-INFO
writing dependency_links to diagnostic_primers.egg-info/dependency_links.txt
writing entry points to diagnostic_primers.egg-info/entry_points.txt
writing requirements to diagnostic_primers.egg-info/requires.txt
writing top-level names to diagnostic_primers.egg-info/top_level.txt
reading manifest file 'diagnostic_primers.egg-info/SOURCES.txt'
writing manifest file 'diagnostic_primers.egg-info/SOURCES.txt'
installing library code to build/bdist.linux-x86_64/egg
running install_lib
running build_py
........
Using /home/aiqubo/anaconda3/envs/pdp/lib/python3.7/site-packages
Searching for numpy==1.19.2
Best match: numpy 1.19.2
Adding numpy 1.19.2 to easy-install.pth file
Installing f2py script to /home/aiqubo/anaconda3/envs/pdp/bin
Installing f2py3 script to /home/aiqubo/anaconda3/envs/pdp/bin
Installing f2py3.7 script to /home/aiqubo/anaconda3/envs/pdp/bin
Using /home/aiqubo/anaconda3/envs/pdp/lib/python3.7/site-packages
Searching for pytz==2020.4
Best match: pytz 2020.4
Adding pytz 2020.4 to easy-install.pth file
Using /home/aiqubo/anaconda3/envs/pdp/lib/python3.7/site-packages
Searching for python-dateutil==2.8.1
Best match: python-dateutil 2.8.1
Adding python-dateutil 2.8.1 to easy-install.pth file
Using /home/aiqubo/anaconda3/envs/pdp/lib/python3.7/site-packages
Finished processing dependencies for diagnostic-primers==0.2.0.dev0
(pdp) [aiqubo@aiqubo find_differential_primers]$ conda install -c bioconda biopython=1.77
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): done
Solving environment: done
Package Plan
environment location: /home/aiqubo/anaconda3/envs/pdp
added / updated specs:
- biopython=1.77
The following packages will be DOWNGRADED:
biopython 1.78-py37h8f50634_1 --> 1.77-py37h8f50634_1
Proceed ([y]/n)? y
Preparing transaction: done
Verifying transaction: done
Executing transaction: done

_7##

(pdp) [aiqubo@aiqubo find_differential_primers]$ pdp -help
Traceback (most recent call last):
File "/home/aiqubo/anaconda3/envs/pdp/bin/pdp", line 33, in
sys.exit(load_entry_point('diagnostic-primers==0.2.0.dev0', 'console_scripts', 'pdp')())
File "/home/aiqubo/anaconda3/envs/pdp/lib/python3.7/site-packages/pkg_resources/init.py", line 488, in load_entry_point
return get_distribution(dist).load_entry_point(group, name)
File "/home/aiqubo/anaconda3/envs/pdp/lib/python3.7/site-packages/pkg_resources/init.py", line 2872, in load_entry_point
return ep.load()
File "/home/aiqubo/anaconda3/envs/pdp/lib/python3.7/site-packages/pkg_resources/init.py", line 2472, in load
return self.resolve()
File "/home/aiqubo/anaconda3/envs/pdp/lib/python3.7/site-packages/pkg_resources/init.py", line 2478, in resolve
module = import(self.module_name, fromlist=['name'], level=0)
File "/home/aiqubo/anaconda3/envs/pdp/lib/python3.7/site-packages/diagnostic_primers-0.2.0.dev0-py3.7.egg/diagnostic_primers/scripts/pdp_script.py", line 48, in
ImportError: cannot import name 'parsers' from 'diagnostic_primers.scripts'(/home/aiqubo/anaconda3/envs/pdp/lib/python3.7/site-packages/diagnostic_primers-0.2.0.dev0-py3.7.egg/diagnostic_primers/scripts/init.py)

is something wrong?

qubo

[widdowquinn]

Hi @aiqubo - thank you for your interest in pdp.

I don't see from your issue how you acquired pdp. Did you clone the repository? If so, what is the most recent commit in your version of the repository (you can discover this with the command git log).

Please note that pdp is the development branch and should not be considered to be stable. The stable version (which should be installable using conda install -c bioconda find_differential_primers, see https://github.com/widdowquinn/find_differential_primers/tree/master) may be more reliable for you.

L.

[aiqubo]

Hi Leighton - thank you for feedback,
I'm more interested in the new version
I download pdp use 'git clone https://github.com/widdowquinn/find_differential_primers'

qubo

[widdowquinn]

Hi Leighton - thank you for feedback,
I'm more interested in the new version
I download pdp use 'git clone https://github.com/widdowquinn/find_differential_primers'

qubo

Apologies for the delayed response - I missed your reply.

Please could you try installing in a clean environment with:

conda install --file requirements.txt -y
conda install --file requirements-thirdparty-primer3_237.txt -y
pip install -e .

and then try pdp -h?