From e7ec4339ffdeb2d78c0285aabfec668e648de5cc Mon Sep 17 00:00:00 2001 From: Kevin Stanford Liao Date: Thu, 25 Apr 2024 10:25:47 -0400 Subject: [PATCH 1/2] Update README.md Updated text to 1.4.0 manually for now. --- README.md | 14 +++++--------- 1 file changed, 5 insertions(+), 9 deletions(-) diff --git a/README.md b/README.md index 8d2f13a5..07560fc9 100755 --- a/README.md +++ b/README.md @@ -41,10 +41,10 @@ docker run -v $(pwd):/home/data -i -t gwas_qc_pipe snakemake -k --use-conda -npr # Installing GwasQcPipeline on ccad2 - Install miniconda and then create GwasQcPipeline production environment ``` -$ mkdir /scratch/myfolder/GwasQcPipeline_v1.2 -$ cd /scratch/myfolder/GwasQcPipeline_v1.2 +$ mkdir /scratch/myfolder/GwasQcPipeline_v1.4.0 +$ cd /scratch/myfolder/GwasQcPipeline_v1.4.0 $ wget https://repo.anaconda.com/miniconda/Miniconda3-py39_4.12.0-Linux-x86_64.sh -$ bash Miniconda3-py39_4.12.0-Linux-x86_64.sh -p /scratch/myfolder/GwasQcPipeline_v1.2/conda -b +$ bash Miniconda3-py39_4.12.0-Linux-x86_64.sh -p /scratch/myfolder/GwasQcPipeline_v1.4.0/conda -b $ source conda/bin/activate base (base) $ conda update -n base -c defaults conda (base) $ conda install -n base -c conda-forge mamba @@ -54,14 +54,10 @@ $ source conda/bin/activate base - Install GwasQcPipeline source code ``` $ source /scratch/myfolder/GwasQcPipeline_v1.2/conda/bin/activate GwasQcPipeline -(GwasQcPipeline) $ pip install https://github.com/NCI-CGR/GwasQcPipeline/releases/download/v1.2.0/cgr_gwas_qc-1.2.0-py3-none-any.whl +(GwasQcPipeline) $ pip install https://github.com/NCI-CGR/GwasQcPipeline/releases/download/v1.4.0/cgr_gwas_qc-1.4.0-py3-none-any.whl (GwasQcPipeline) $ cgr --help (GwasQcPipeline) $ cgr version -v1.2.0 +v1.4.0 ``` ## Usage ```cgr submit --ccad2 --local-mem-mb 8000``` - -### LOG v1.2.0 -- add ccad2-slurm profile - From e30044355c826ea43e9c4a8e6fd04bfb9858c06d Mon Sep 17 00:00:00 2001 From: Kevin Stanford Liao Date: Thu, 25 Apr 2024 10:26:50 -0400 Subject: [PATCH 2/2] Update README.md fixed typo --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 07560fc9..932dc89b 100755 --- a/README.md +++ b/README.md @@ -53,7 +53,7 @@ $ source conda/bin/activate base ``` - Install GwasQcPipeline source code ``` -$ source /scratch/myfolder/GwasQcPipeline_v1.2/conda/bin/activate GwasQcPipeline +$ source /scratch/myfolder/GwasQcPipeline_v1.4.0/conda/bin/activate GwasQcPipeline (GwasQcPipeline) $ pip install https://github.com/NCI-CGR/GwasQcPipeline/releases/download/v1.4.0/cgr_gwas_qc-1.4.0-py3-none-any.whl (GwasQcPipeline) $ cgr --help (GwasQcPipeline) $ cgr version