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gem-pasteur / Integron_Finder

Bioinformatics tool to find integrons in bacterial genomes
GNU General Public License v3.0
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installing Integron_Finderv2 on conda #57

Closed mhyleung closed 5 years ago

mhyleung commented 5 years ago

Dear all

I have been trying to grab hold of IntegronFinderV2 because of the multi-fasta capability. I am trying to install it using the most updated version of conda by the instructions shown on README.md. However, it shows that:

conda install integron_finder

Solving environment: failed

PackagesNotFoundError: The following packages are not available from current channels:

  - integron_finder

Then I checked the bioconda website, and Integron_Finder is actually not one of the available packages?

Thanks!

Marc

bneron commented 5 years ago

The conda package is not yet officially released, we will release it when the final version 2 will be out. for now the you can install integron_finder from pip package or directly from the github repository.

but be careful the pip package is available only from testpypi.org

from testpypi

pip install --index-url https://pypi.python.org/simple --extra-index-url https://test.pypi.org/simple/ integron_finder==2.0rc5

from the git repository

pip install git+https://github.com/gem-pasteur/Integron_Finder/#egg=integron_finder

note that integron_finder v2 work with python3 only and support virtualenv

Regards

Bertrand Néron

On 11/15/18 9:06 AM, Marcus H Y Leung wrote:

Dear all

I have been trying to grab hold of IntegronFinderV2 because of the multi-fasta capability. I am trying to install it using the most updated version of conda by the instructions shown on README.md. However, it shows that:

conda install integron_finder

Solving environment: failed

PackagesNotFoundError: The following packages are not available from current channels:

  • integron_finder

Then I checked the bioconda website, and Integron_Finder is actually not one of the available packages?

Thanks!

Marc

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Bertrand Néron Software Engineer https://research.pasteur.fr/en/member/bertrand-neron/ Bioinformatics and Biostistics Hub https://research.pasteur.fr/en/team/bioinformatics-and-biostatistics-hub/ Institut Pasteur 28 rue du Dr Roux 75724 Paris cdex 15

mhyleung commented 5 years ago

Dear Bertrand

Thank you for that. I managed to get v2 based on what you indicated above. Appreciate it! However, I have encountered another issue in which I will make a separate post. Thanks again!