From 99b22d33f2100a7e4cf2d080a2272959a712d055 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Wed, 30 Mar 2022 11:44:50 +0200 Subject: [PATCH] fix: obtaining conda prefix when using in combination with singularity (#1535) --- snakemake/deployment/conda.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/snakemake/deployment/conda.py b/snakemake/deployment/conda.py index 956be88f0..869bb70ef 100644 --- a/snakemake/deployment/conda.py +++ b/snakemake/deployment/conda.py @@ -564,7 +564,9 @@ def __init__(self, container_img=None, prefix_path=None): if prefix_path is None or container_img is not None: self.prefix_path = json.loads( - shell.check_output(self._get_cmd("conda info --json")) + shell.check_output( + self._get_cmd("conda info --json"), universal_newlines=True + ) )["conda_prefix"] else: self.prefix_path = prefix_path