Skip to content

🐛 Missing a space after create #3

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
rdenise wants to merge 1 commit into
base: main
Choose a base branch
from
Open

🐛 Missing a space after create #3

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
10 changes: 5 additions & 5 deletions scripts/master_set_up_env.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -91,23 +91,23 @@ 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:
logger.info("ViWrap-iPHoP conda env path is not present!")
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:
logger.info("ViWrap-GTDBTk conda env path is not present!")
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:
Expand All @@ -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:
Expand All @@ -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)")
logger.info(f"The total running time is {duration} (in \"hr:min:sec\" format)")