diff --git a/Run_GeVarLi.sh b/Run_GeVarLi.sh index 6394d45ddf0348b718500e9771b3038f3cbad0b0..68b3332772e684e8abce60d0dfddf74cbc68739d 100755 --- a/Run_GeVarLi.sh +++ b/Run_GeVarLi.sh @@ -16,7 +16,7 @@ # Aim ____________________ Bash script running gevarli.smk snakefile # Date ___________________ 2021.10.12 # Latest modifications ___ 2025.01.08 (Prepare for Snakedeploy) -# Use ____________________ 'bash Run_GeVarLi.sh' +# Use ____________________ '. Run_GeVarLi.sh' ############################################################################### ### COLORS ### @@ -46,7 +46,7 @@ ${blue}Affiliation${nc} ____________ IRD_U233_TransVIHMI ${blue}Aim${nc} ____________________ Bash script for ${red}Ge${nc}nome assembling, ${red}Var${nc}iant calling and ${red}Li${nc}neage assignation ${blue}Date${nc} ___________________ 2021.10.12 ${blue}Latest modifications${nc} ___ 2025.01.08 (Prepare for Snakedeploy) -${blue}Use${nc} ____________________ '${ylo}bash Run_GeVarLi.sh${nc}' +${blue}Use${nc} ____________________ '${ylo}. Run_GeVarLi.sh${nc}' " ############################################################################### @@ -157,10 +157,6 @@ else # If yes, print informations conda config --show channels # channels fi -############################################################################### -### CONDA INIT ### -################## - # Intern shell source conda source ~/miniforge3/etc/profile.d/conda.sh 2> /dev/null # local user with miniforge3 source ~/mambaforge/etc/profile.d/conda.sh 2> /dev/null # local user with mambaforge ¡ Deprecated ! @@ -191,6 +187,7 @@ ${ylo}Workflow-Core${nc} conda environment will be create, with: > ${red}GraphViz${nc}${blue} ____ drawing graph${nc} " conda env create --file ${workdir}/workflow/envs/workflow-core.yaml > /dev/null 2>&1 +fi echo -e " You can remove old depreciated environements such as: 'gevarli-base', 'snakemake-base' or 'workflow-base'. @@ -198,7 +195,7 @@ To list all your conda environments, you can run: '${ylo}conda env list${nc}'. To remove old conda environments, you can run: '${ylo}conda remove --all --yes --name <ENV_NAME>${nc}'. " -# Active workflow-core conda environment +# Active workflow-core conda environment. echo -e "Activate ${ylo}Workflow-Core${nc} conda environment." conda activate workflow-core @@ -583,7 +580,7 @@ Affiliation ____________ IRD_U233_TransVIHMI Aim ____________________ Bash script for GeVarLi Date ___________________ 2021.10.12 Latest modifications ___ 2025.01.08 (Prepare for Snakedeploy) -Run ____________________ 'bash Run_GeVarLi.sh' +Run ____________________ '. Run_GeVarLi.sh' Operating System _______ ${os} Shell __________________ ${shell} @@ -641,5 +638,4 @@ echo -e " ${green}------------------------------------------------------------------------${nc} " - ###############################################################################