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widdowquinn / find_differential_primers

Code for design of diagnostic PCR primers, and metabarcoding markers.
https://widdowquinn.github.io/find_differential_primers/
MIT License
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is pdp still available? #48

Closed AlexGaithuma closed 4 years ago

AlexGaithuma commented 4 years ago

I could not install pdp with conda or pip following the instructions in the manual (https://pdp.readthedocs.io/en/diagnostic_primers/quickstart.html) I tried finding pdp in anaconda packages and in pypi to no success..

my command:

conda install -c bioconda pdp
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: failed with initial frozen solve. Retrying with flexible solve.

PackagesNotFoundError: The following packages are not available from current channels:
  - pdp
Current channels:
  - https://conda.anaconda.org/bioconda/linux-64
  - https://conda.anaconda.org/bioconda/noarch
  - https://repo.anaconda.com/pkgs/main/linux-64
  - https://repo.anaconda.com/pkgs/main/noarch
  - https://repo.anaconda.com/pkgs/r/linux-64
  - https://repo.anaconda.com/pkgs/r/noarch

To search for alternate channels that may provide the conda package you're looking for, navigate to
https://anaconda.org and use the search bar at the top of the page.

I also tried pip

 pip install pdp
 Requirement already satisfied: pdp in ./anaconda3/lib/python3.7/site-packages (0.3.0)

running the command pdp:

 pdp
 No command 'pdp' found, but there are 24 similar ones
 pdp: command not found

I found out that the pdp that was installed was an interface package to organize pipelines of data processing.

widdowquinn commented 4 years ago

Hi Alex,

Thanks for trying pdp/find_differential_primers.

pdp is available, but there is a stable version (find_differential_primers) and a development version (pdp).

I don't know where Dan's comment went (I got an email notification but can't see it here) but he was correct: pdp is not currently available via conda, and you have to install from source. As noted here pdp is on the development branch, not the stable version. It has new features, but isn't ready for formal release, yet. It does work well enough to design diagnostic primers, though.

If you need to install via conda, then the older, stable version is available, and the relevant documentation for usage is here.

I hope this helps, but please do raise further questions as issues.

L.