From 80362f8fd576141120cd946b1aaa165e364e01b0 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Nicolas=20FERNANDEZ=20NU=C3=91EZ?=
<nicolas.fernandez@ird.fr>
Date: Fri, 10 Jan 2025 16:41:06 +0100
Subject: [PATCH] Fix: close test condition fi line 190
---
Run_GeVarLi.sh | 14 +++++---------
1 file changed, 5 insertions(+), 9 deletions(-)
diff --git a/Run_GeVarLi.sh b/Run_GeVarLi.sh
index 6394d45..68b3332 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}
"
-
###############################################################################
--
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