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Makefile
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executable file
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.PHONY: install_seuratv5
# * neuron + 10xv3 integration
.PHONY: neuron_10xv3 neuron_10xv3_encoder
snakemake := /home/szu/mambaforge/envs/seurat/bin/snakemake
neuron_10xv3: src/main/pipeline/Seurat.Intgn.Snakefile
-mkdir -p build/$@
cp $< build/$@/Snakefile
cd build/$@ && \
${snakemake} --snakefile Snakefile -R -c 32 \
--config \
gp=neuron \
debug=0 \
intgn_method='rpca' \
allen_techs='10xv3' \
feature='TF,markers,k8' \
--rerun-triggers mtime \
--skip-script-cleanup \
--profile pbs-torque-conda
# * neuron 10xv3 transfer data
## encoder
.PHONY: neu_tf_ds50_encoder
neu_tf_ds50_encoder: src/main/pipeline/Seurat.TransferLabel.Snakefile
-mkdir -p build/$@
cp $< build/$@/Snakefile
cd build/$@ && \
${snakemake} --snakefile Snakefile -R -c 1 \
--config \
gp=neuron \
sys=encoder \
queue=encoder\
debug=0 \
intgn_method='cca' \
allen_techs='10xv3' \
feature='k8' \
k_anchors='50,70,100' \
allen_as_ref=1\
ds_seu=1\
atac_ds_min=150\
atac_ds_max=151\
allen_ds_min=50\
allen_ds_max=51\
--keep-incomplete \
--rerun-triggers mtime \
--skip-script-cleanup
## tscc
.PHONY: neu_tf_ds50_tscc
neu_tf_ds50_tscc: src/main/pipeline/Seurat.TransferLabel.Snakefile
-mkdir -p build/$@
cp $< build/$@/Snakefile
cd build/$@ && \
${snakemake} --snakefile Snakefile -R -c 64 \
--config \
gp=neuron \
sys=tscc \
queue=home \
debug=0 \
intgn_method='cca' \
allen_techs='allen' \
feature='k8' \
k_anchors='100,150,200' \
allen_as_ref=1\
ds_seu=1\
atac_ds_min=150\
atac_ds_max=151\
allen_ds_min=50\
allen_ds_max=51\
--keep-incomplete \
--rerun-triggers mtime \
--skip-script-cleanup \
--profile pbs-torque-conda
.PHONY: imnneu_tf_ds50_tscc
# only neuronal cells from both data in Allen IMN top regions
# no IMN from nn involved
imnneu_tf_ds50_tscc: src/main/pipeline/Seurat.TransferLabel.Snakefile
-mkdir -p build/$@
cp $< build/$@/Snakefile
cd build/$@ && \
${snakemake} --snakefile Snakefile -R -c 50 \
--config \
gp=imneuron \
sys=tscc \
queue=glean \
debug=0 \
intgn_method='cca' \
allen_techs='allen' \
feature='k8' \
k_anchors='50' \
allen_as_ref=1\
ds_seu=1\
atac_ds_min=150\
atac_ds_max=151\
allen_ds_min=50\
allen_ds_max=51\
--keep-incomplete \
--rerun-triggers mtime \
--skip-script-cleanup
# --profile pbs-torque-conda
.PHONY: imnneu2_tf_ds50_tscc
# due to the bug of Seuratv5 merge
# https://github.com/satijalab/seurat/issues/7191
# only data.1 are used, so equals to the one above
imnneu2_tf_ds50_tscc: src/main/pipeline/Seurat.TransferLabel.Snakefile
-mkdir -p build/$@
cp $< build/$@/Snakefile
cd build/$@ && \
${snakemake} --snakefile Snakefile -R -c 50 \
--config \
gp=imneuron \
sys=tscc \
queue=glean \
debug=0 \
intgn_method='cca' \
allen_techs='nneuronallen' \
feature='k8' \
k_anchors='50' \
allen_as_ref=1\
ds_seu=1\
atac_ds_min=150\
atac_ds_max=151\
allen_ds_min=50\
allen_ds_max=51\
--keep-incomplete \
--rerun-triggers mtime \
--skip-script-cleanup
# --profile pbs-torque-conda
.PHONY: imnneu3_tf_ds50_tscc
# due to memory issue, directly downsample data
# and both IMN and neuronal cells are included from allen
# in total, about 200K cells are used
# needs > 167G RAM in CCA
# about 2 - 3 hours to finish on a 61 cores node
# it sometimes use 10 CPUs or more sometimes during CCA
# but usually 1 CPUs
imnneu3_tf_ds50_tscc: src/main/pipeline/Seurat.TransferLabel.Snakefile
-mkdir -p build/$@
cp $< build/$@/Snakefile
cd build/$@ && \
${snakemake} --snakefile Snakefile -R -c 50 \
--config \
gp=imneuron \
sys=tscc \
queue=glean \
debug=0 \
intgn_method='cca' \
allen_techs='dp50allen' \
feature='k8' \
k_anchors='50' \
allen_as_ref=1\
ds_seu=1\
atac_ds_min=150\
atac_ds_max=151\
allen_ds_min=50\
allen_ds_max=51\
--keep-incomplete \
--rerun-triggers mtime \
--skip-script-cleanup
# --profile pbs-torque-conda
.PHONY: nn_tf_ds200_tscc
nn_tf_ds500_tscc: src/main/pipeline/Seurat.TransferLabel.Snakefile
-mkdir -p build/$@
cp $< build/$@/Snakefile
cd build/$@ && \
${snakemake} --snakefile Snakefile -R -c 20 \
--config \
gp=nn \
sys=tscc \
queue=glean \
debug=0 \
intgn_method='cca' \
allen_techs='allen' \
feature='k8' \
k_anchors='49,100,150' \
allen_as_ref=1\
ds_seu=1\
atac_ds_min=300\
atac_ds_max=301\
allen_ds_min=500\
allen_ds_max=501\
--keep-incomplete \
--rerun-triggers mtime \
--skip-script-cleanup \
--profile pbs-torque-conda
.PHONY: dotplot_neu_tf dotplot_nn_tf
#dotplot_neu_tf: src/main/R/analyzetf.R
# parallel -j 5 Rscript --vanilla $< \
# ::: 5 30 ::: vf markers k8 TF ::: 10xv3 allen ::: rpca cca
dotplot_neu_tf: src/main/R/analyzetf.R
parallel -j 2 Rscript --vanilla $< ::: 50 70 ::: k8 ::: allen ::: cca ::: neuron
dotplot_nn_tf: src/main/R/analyzetf.R
parallel -j 2 Rscript --vanilla $< ::: 49 100 150 ::: k8 ::: allen ::: cca ::: nn
dotplot_imn_tf: src/main/R/analyzetf.R
Rscript --vanilla $< 50 k8 dp50allen cca imneuron
lightsum_neu_tf: src/main/R/lightSummaryOfTransferLabel.R
parallel -j 2 Rscript --vanilla $< ::: 30 50 ::: neuron ::: allen
lightsum_nn_tf: src/main/R/lightSummaryOfTransferLabel.R
parallel -j 2 Rscript --vanilla $< ::: 49 50 ::: nn ::: allen
lightsum_imn_tf: src/main/R/lightSummaryOfTransferLabel.R
Rscript --vanilla $< 50 imneuron dp50allen
# * test
.PHONY: test_tf
test_tf: src/main/pipeline/Seurat.TransferLabel.Snakefile
-mkdir -p build/$@
cp $< build/$@/Snakefile
cd build/$@ && \
${snakemake} --snakefile Snakefile -R -c 4 \
--config \
gp=nn \
sys=tscc \
queue=glean \
debug=0 \
intgn_method='cca' \
allen_techs='10xv3' \
feature='vf' \
allen_as_ref=1\
ds_seu=1\
atac_ds_min=20\
atac_ds_max=21\
allen_ds_min=10\
allen_ds_max=11\
--keep-incomplete \
--rerun-triggers mtime \
--skip-script-cleanup \
--profile pbs-torque-conda
# * clean up
clean_script:
-rm build/*/.snakemake/scripts/*
clean:
-rm -rf build/test_tf