Created
February 2, 2018 12:27
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Snakemake with s3 and custom profile
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| import boto3 | |
| # set the profile name based on ~/.aws/credentials entry | |
| boto3.setup_default_session(profile_name='s3') | |
| from snakemake.remote.S3 import RemoteProvider as S3RemoteProvider | |
| s3 = S3RemoteProvider() | |
| # This simply copies the file from local storage to s3 | |
| rule all: | |
| input: "Snakefile" | |
| output: s3.remote("big_rna/Snakefile.fun") | |
| shell: "cp {input} {output}" |
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