FINEMAP

“As long as you live, shine;
let nothing grieve you at all!
Life lasts only a little while,
and time demands its due!”
— “The Song of Seikilos” (Ὅσον ζῇς, φαίνου / Seikilos Epitaph)

Install & Calling

mamba create -y -n FM   --override-channels   -c conda-forge   -c bioconda   python=3.11   jupyterlab   notebook   ipykernel   numpy   pandas   scipy   matplotlib   pyarrow   openpyxl   r-base=4.4   r-data.table   r-matrix   r-ggplot2   r-irkernel   finemap=1.4.2   plink2   gcta
mamba activate FM
R

# install.packages("remotes")
remotes::install_github("stephenslab/susieR")
# Rscript -e 'IRkernel::installspec(name="ir-fm", displayname="R (FM: SuSiE)")'
IRkernel::installspec(user = TRUE, name = "r-fm", displayname = "R453 Finemapping")

python -m ipykernel install --user --name FM --display-name "Py311 Finemapping"

GCTB_HOME="/cpfs01/projects-HDD/cfff-afe2df89e32e_HDD/public/czh_data/Tanzimat/software/gctb/2.5.5"
GCTB_BIN="${GCTB_HOME}/bin"
readlink -f "${GCTB_BIN}/gctb"
# /cpfs01/projects-HDD/cfff-afe2df89e32e_HDD/public/czh_data/Tanzimat/software/gctb/2.5.5/dist/gctb_2.5.5_Linux/gctb

mkdir -p \
  "${CONDA_PREFIX}/etc/conda/activate.d" \
  "${CONDA_PREFIX}/etc/conda/deactivate.d"

cat > "${CONDA_PREFIX}/etc/conda/activate.d/gctb.sh" <<'EOF'
export _FM_PATH_BEFORE_GCTB="${PATH}"
export GCTB_HOME="/cpfs01/projects-HDD/cfff-afe2df89e32e_HDD/public/czh_data/Tanzimat/software/gctb/2.5.5"
export PATH="${GCTB_HOME}/bin:${PATH}"
EOF

cat > "${CONDA_PREFIX}/etc/conda/deactivate.d/gctb.sh" <<'EOF'
if [[ -n "${_FM_PATH_BEFORE_GCTB:-}" ]]; then
  export PATH="${_FM_PATH_BEFORE_GCTB}"
fi

unset _FM_PATH_BEFORE_GCTB
unset GCTB_HOME
EOF

我的建议是直接建立软链接：

GCTB_REAL="/cpfs01/projects-HDD/cfff-afe2df89e32e_HDD/public/czh_data/Tanzimat/software/gctb/2.5.5/dist/gctb_2.5.5_Linux/gctb"
ln -s \
  "${GCTB_REAL}" \
  "${CONDA_PREFIX}/bin/gctb"
readlink -f "${CONDA_PREFIX}/bin/gctb"

mamba env export -n FM --no-builds > /cpfs01/projects-HDD/cfff-afe2df89e32e_HDD/zy_22111220045/Env/FM_environment.yml

FINEMAP原理

FINEMAP:

FINEMAP 是一种基于贝叶斯变量选择的局部精细定位方法，