SEA-PHAGES | PDM utils on a Mac M1

Link to this post \| posted 07 Feb, 2024 01:10
debbie	Hi all, If you are looking how to instal PDM utils on a M1 mac, you can follow this: On a series of MacBook Pro computers, including most recently an M1 mac, I have only ever done native installs of pdm_utils. The hardest part for me is MySQL – use an installer for 8.0.18 or later (earlier versions had funky bugs related to cascaded deletes!). Choose “Legacy Password” when prompted, and you’ll be forced to choose an 8-character or longer password (no more ‘phage’). Make sure you add mysql to the $PATH (export PATH=’/usr/local/mysql/bin:$PATH’) in your ~/.zshrc file. Other than that, if you use some flavor of conda to manage the third-party dependencies (Aragorn, trnascan-se, mmseqs2, blast) pdm_utils should be just fine. –Christian Gauthier Edited 07 Feb, 2024 01:21

Link to this post | posted 07 Feb, 2024 01:10

Hi all,
If you are looking how to instal PDM utils on a M1 mac, you can follow this:

On a series of MacBook Pro computers, including most recently an M1 mac, I have only ever done native installs of pdm_utils. The hardest part for me is MySQL – use an installer for 8.0.18 or later (earlier versions had funky bugs related to cascaded deletes!). Choose “Legacy Password” when prompted, and you’ll be forced to choose an 8-character or longer password (no more ‘phage’). Make sure you add mysql to the $PATH (export PATH=’/usr/local/mysql/bin:$PATH’) in your ~/.zshrc file. Other than that, if you use some flavor of conda to manage the third-party dependencies (Aragorn, trnascan-se, mmseqs2, blast) pdm_utils should be just fine.
–Christian Gauthier

Edited 07 Feb, 2024 01:21

Link to this post \| posted 09 Feb, 2024 16:32
cdshaffer	there is one more important difference in the installation for Arm based mac's. once you get mysql installed and are setting up conda { see here } you need to change the conda create command by adding some bits at the beginning. So you want to change the create command from `> conda create –name pdm_utils curl python pip biopython==1.77 networkx paramiko pymysql sqlalchemy tabulate urllib3` to `CONDA_SUBDIR=osx-64 conda create –name pdm_utils ….etc.` Then activate the conda environment the first time add this second command: `conda activate pdm_utils conda env config vars set CONDA_SUBDIR=osx-64` You should only have to run the "conda env config…." line one time to set things up. From then on you can just use `conda activate` and `conda deactivate` as outlined in the instructions.

Link to this post | posted 09 Feb, 2024 16:32

cdshaffer

there is one more important difference in the installation for Arm based mac's. once you get mysql installed and are setting up conda { see here } you need to change the conda create command by adding some bits at the beginning. So you want to change the create command from

> conda create –name pdm_utils curl python pip biopython==1.77 networkx paramiko pymysql sqlalchemy tabulate urllib3

CONDA_SUBDIR=osx-64 conda create –name pdm_utils ….etc.

Then activate the conda environment the first time add this second command:

conda activate pdm_utils
conda env config vars set CONDA_SUBDIR=osx-64

You should only have to run the "conda env config…." line one time to set things up. From then on you can just use

conda activate

and

conda deactivate

as outlined in the instructions.

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PDM utils on a Mac M1