From 30843d3c61c68800de08ff582cb52770152f7aa8 Mon Sep 17 00:00:00 2001 From: Remi Denise Date: Fri, 3 Feb 2023 12:39:32 +0000 Subject: [PATCH] :bug: Missing a space after create In the original script, for iphop, gtdbtk, vs2 and mapping a space was missing between create and -c --- scripts/master_set_up_env.py | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/scripts/master_set_up_env.py b/scripts/master_set_up_env.py index 9be9502..9522323 100644 --- a/scripts/master_set_up_env.py +++ b/scripts/master_set_up_env.py @@ -91,7 +91,7 @@ def main(args): time_current = f"[{str(datetime.now().replace(microsecond=0))}]" logger.info(f"{time_current} | ViWrap-Tax conda env has been installed") - os.system(f"mamba create-c bioconda -c conda-forge -p {os.path.join(args['conda_env_dir'], 'ViWrap-iPHoP')} python=3.8 iphop=1.2.0 -y >/dev/null 2>&1") + os.system(f"mamba create -c bioconda -c conda-forge -p {os.path.join(args['conda_env_dir'], 'ViWrap-iPHoP')} python=3.8 iphop=1.2.0 -y >/dev/null 2>&1") if os.path.exists(os.path.join(args['conda_env_dir'], 'ViWrap-iPHoP/bin')): logger.info("ViWrap-iPHoP conda env path has been checked") else: @@ -99,7 +99,7 @@ def main(args): time_current = f"[{str(datetime.now().replace(microsecond=0))}]" logger.info(f"{time_current} | ViWrap-iPHoP conda env has been installed") - os.system(f"mamba create-c bioconda -c conda-forge -p {os.path.join(args['conda_env_dir'], 'ViWrap-GTDBTk')} gtdbtk=2.1.1 numpy=1.20.0 -y >/dev/null 2>&1") + os.system(f"mamba create -c bioconda -c conda-forge -p {os.path.join(args['conda_env_dir'], 'ViWrap-GTDBTk')} gtdbtk=2.1.1 numpy=1.20.0 -y >/dev/null 2>&1") if os.path.exists(os.path.join(args['conda_env_dir'], 'ViWrap-GTDBTk/bin')): logger.info("ViWrap-GTDBTk conda env path has been checked") else: @@ -107,7 +107,7 @@ def main(args): time_current = f"[{str(datetime.now().replace(microsecond=0))}]" logger.info(f"{time_current} | ViWrap-GTDBTk conda env has been installed") - os.system(f"mamba create-c bioconda -c conda-forge -p {os.path.join(args['conda_env_dir'], 'ViWrap-vs2')} python=3.8 virsorter=2.2.3 numpy=1.20.0 -y >/dev/null 2>&1") + os.system(f"mamba create -c bioconda -c conda-forge -p {os.path.join(args['conda_env_dir'], 'ViWrap-vs2')} python=3.8 virsorter=2.2.3 numpy=1.20.0 -y >/dev/null 2>&1") # Add " - numpy=1.20.0" to the conda env yaml file vs2_yaml_file = os.path.join(args['conda_env_dir'], 'ViWrap-vs2', 'lib/python3.8/site-packages/virsorter/envs/vs2.yaml') with open(vs2_yaml_file, 'a') as f: @@ -119,7 +119,7 @@ def main(args): time_current = f"[{str(datetime.now().replace(microsecond=0))}]" logger.info(f"{time_current} | ViWrap-vs2 conda env has been installed") - os.system(f"mamba create-c bioconda -c conda-forge -p {os.path.join(args['conda_env_dir'], 'ViWrap-Mapping')} python=3.8 pysam bowtie2=2.4.5 coverm pandas pyfastx minimap2=2.24 consent -y >/dev/null 2>&1") + os.system(f"mamba create -c bioconda -c conda-forge -p {os.path.join(args['conda_env_dir'], 'ViWrap-Mapping')} python=3.8 pysam bowtie2=2.4.5 coverm pandas pyfastx minimap2=2.24 consent -y >/dev/null 2>&1") if os.path.exists(os.path.join(args['conda_env_dir'], 'ViWrap-Mapping/bin')): logger.info("ViWrap-Mapping conda env path has been checked") else: @@ -138,4 +138,4 @@ def main(args): end_time = datetime.now().replace(microsecond=0) duration = end_time - start_time - logger.info(f"The total running time is {duration} (in \"hr:min:sec\" format)") \ No newline at end of file + logger.info(f"The total running time is {duration} (in \"hr:min:sec\" format)")