How to cogfigure work environment

[androidpifu]

Hi， When I executed the command "snakemake --cores all --software-deployment-method conda", the following error occurred：

$ snakemake --cores all --software-deployment-method conda
Assuming unrestricted shared filesystem usage for local execution.
Building DAG of jobs...
Your conda installation is not configured to use strict channel priorities. This is however crucial for having robust and correct environments (for details, see https://conda-forge.org/docs/user/tipsandtricks.html). Please consider to configure strict priorities by executing 'conda config --set channel_priority strict'.
Creating conda environment workflow/envs/prioritization.yml...
Downloading and installing remote packages.
Environment for /mnt/work/zhumc/software/ScanNeo2/ScanNeo2/workflow/rules/../envs/prioritization.yml created (location: .snakemake/conda/a99ab8a671d44afcc6467ae776e816b0_)
Creating conda environment workflow/envs/manipulate_vcf.yml...
Downloading and installing remote packages.
Environment for /mnt/work/zhumc/software/ScanNeo2/ScanNeo2/workflow/rules/../envs/manipulate_vcf.yml created (location: .snakemake/conda/f986b795f4b2b540d4018e92198dbd13_)
Failed to open source file https://github.com/snakemake/snakemake-wrappers/raw/v2.2.1/bio/star/align/environment.yaml
ConnectionError: HTTPSConnectionPool(host='raw.githubusercontent.com', port=443): Max retries exceeded with url: /snakemake/snakemake-wrappers/v2.2.1/bio/star/align/environment.yaml (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f818b1b7e90>: Failed to establish a new connection: [Errno 111] Connection refused')), attempt 1/3 failed - retrying in 3 seconds...
Failed to open source file https://github.com/snakemake/snakemake-wrappers/raw/v2.2.1/bio/star/align/environment.yaml
ConnectionError: HTTPSConnectionPool(host='raw.githubusercontent.com', port=443): Max retries exceeded with url: /snakemake/snakemake-wrappers/v2.2.1/bio/star/align/environment.yaml (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f818b1b4350>: Failed to establish a new connection: [Errno 111] Connection refused')), attempt 2/3 failed - retrying in 6 seconds...
Failed to open source file https://github.com/snakemake/snakemake-wrappers/raw/v2.2.1/bio/star/align/environment.yaml
ConnectionError: HTTPSConnectionPool(host='raw.githubusercontent.com', port=443): Max retries exceeded with url: /snakemake/snakemake-wrappers/v2.2.1/bio/star/align/environment.yaml (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f818b2debd0>: Failed to establish a new connection: [Errno 111] Connection refused')), attempt 3/3 failed - giving up!
WorkflowError:
Failed to open source file https://github.com/snakemake/snakemake-wrappers/raw/v2.2.1/bio/star/align/environment.yaml
ConnectionError: HTTPSConnectionPool(host='raw.githubusercontent.com', port=443): Max retries exceeded with url: /snakemake/snakemake-wrappers/v2.2.1/bio/star/align/environment.yaml (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f818b2debd0>: Failed to establish a new connection: [Errno 111] Connection refused'))

What steps should I take to resolve this issue?

[riasc]

Hi, It seems that your installation is unable to download/create the conda environments defined. In principle, each rule has its own conda environment to avoid conflicts. Just to be sure, is the system you are executing this on capable of using HTTPS? Or is port 443 open? Or is GitHub blocked?

Also, you could set the strict mode to conda, as the strict mode is more robust and required by snakemake

conda config --set channel_priority strict

[riasc]

So once you set up the strict mode and have a working network connection (w/ access to Github) this should work. Let us know if you are still encountering this issue - feel free to reopen the issue.