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run_threshold_pipeline.slurm
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#!/bin/bash
#SBATCH --job-name=threshold
#SBATCH --output=celltyping_threshold.out
#SBATCH --gres=gpu:1
#SBATCH --cpus-per-task=10
source ~/.bashrc
PROJECT_PATH=""
ENV_PATH=""
conda activate $ENV_PATH/celltyping
cd $PROJECT_PATH
## 1. PBMC_batch1_indS1_to_indS5
task="PBMC_batch1_ind"
train="1154"
test="1085"
python -m pipelines.threshold_pipeline $task --train $train --test $test --leaveout 2
## 2. PBMC_batch1_A_to_B
task="PBMC_batch1_ABC"
train="A"
test="B"
python -m pipelines.threshold_pipeline $task --train $train --test $test --leaveout 2
## 3. PBMC_downsampled_batch1_A_to_indS5
task="PBMC_batch1_batchtoind"
train="A"
test="1085"
python -m pipelines.threshold_pipeline $task --train $train --test $test --leaveout 2
## 4. PBMC_batch2_control_to_stimulated
task="PBMC_batch2"
train="control"
test="stimulated"
python -m pipelines.threshold_pipeline $task --train $train --test $test --leaveout 2
## 5. PBMC_protocols_Smart-seq2_to_CEL-Seq2
task="PBMC_protocols_pbmc1"
train="Smart-seq2"
test="CEL-Seq2"
python -m pipelines.threshold_pipeline $task --train $train --test $test --leaveout 2
## 6. PBMC_protocols_CEL-Seq2_to_10X
task="PBMC_protocols_pbmc1"
train="CEL-Seq2"
test="10x-v2"
python -m pipelines.threshold_pipeline $task --train $train --test $test --leaveout 2
## 7. PBMC_protocols_10X_to_CEL-Seq2
task="PBMC_protocols_pbmc1"
train="10x-v2"
test="CEL-Seq2"
python -m pipelines.threshold_pipeline $task --train $train --test $test --leaveout 2
## 8. PBMC_protocols_Smart-Seq2_PBMC1_to_PBMC2
task="PBMC_protocols_batch_smart"
train="pbmc1"
test="pbmc2"
python -m pipelines.threshold_pipeline $task --train $train --test $test --leaveout 2
## 9. Seg_to_Muraro
task="pancreas"
train="seg"
test="muraro"
python -m pipelines.threshold_pipeline $task --train $train --test $test --leaveout 2
## 10. Muraro_to_Seg
task="pancreas"
train="muraro"
test="seg"
python -m pipelines.threshold_pipeline $task --train $train --test $test --leaveout 2
## 11. Seg_Xin_to_Muraro
task="pancreas_multi_to_multi"
train="seg_xin"
test="muraro"
python -m pipelines.threshold_pipeline $task --train $train --test $test --leaveout 2
## 12. Seg_Healthy_to_T2D
task="pancreas_seg_cond"
train="Healthy"
test="T2D"
python -m pipelines.threshold_pipeline $task --train $train --test $test --leaveout 2
## 13. Seg_Healthy_to_Muraro
task="pancreas_custom"
train="Healthy"
test="muraro"
python -m pipelines.threshold_pipeline $task --train $train --test $test --leaveout 2
## 14. Seg_6Healthy3T2D_to_Seg_1T2D
task="pancreas_seg_mix"
train="Healthy"
test="T2D"
python -m pipelines.threshold_pipeline $task --train $train --test $test --leaveout 2
## 15. Seg_5Healthy4T2D_to_Seg_1Healthy
task="pancreas_seg_mix"
train="T2D"
test="Healthy"
python -m pipelines.threshold_pipeline $task --train $train --test $test --leaveout 2
## 16. Wholebrain_FC_ind1_to_ind2_major_celltypes
task="mousebrain_FC"
train="P60FCRep1"
test="P60FCCx3cr1Rep1"
python -m pipelines.threshold_pipeline $task --train $train --test $test --leaveout 2
## 17. Wholebrain_FC_ind1_to_ind2_sub_celltypes
task="mousebrain_FC_sub"
train="P60FCRep1"
test="P60FCCx3cr1Rep1"
python -m pipelines.threshold_pipeline $task --train $train --test $test --leaveout 2
## 18. Wholebrain_HC_ind1_to_ind2_major_celltypes
task="mousebrain_HC"
train="P60HippoRep1"
test="P60HippoRep2"
python -m pipelines.threshold_pipeline $task --train $train --test $test --leaveout 2
## 19. Wholebrain_HC_ind1_to_ind2_sub_celltypes
task="mousebrain_HC_sub"
train="P60HippoRep1"
test="P60HippoRep2"
python -m pipelines.threshold_pipeline $task --train $train --test $test --leaveout 2
## 20. Wholebrain_FC_to_HC_major_celltypes, cannot run no-feature because CUDA out of memory
task="mousebrain_region"
train="FC"
test="HC"
python -m pipelines.threshold_pipeline $task --train $train --test $test --leaveout 2
## 21. pFC_Adult_to_P21_major_celltypes
task="mousebrain_FC_stage"
train="Adult"
test="P21"
python -m pipelines.threshold_pipeline $task --train $train --test $test --leaveout 2
## 22. pFC_Adult_to_P21_sub_celltypes
task="mousebrain_FC_stage_sub"
train="Adult"
test="P21"
python -m pipelines.threshold_pipeline $task --train $train --test $test --leaveout 2
## 23. Wholebrain_FC_adult_to_pFC_adult_major_celltypes, cannot run no-feature because CUDA out of memory
task="mousebrain_FC_datasets"
train="FC"
test="Adult"
python -m pipelines.threshold_pipeline $task --train $train --test $test --leaveout 2
## 24. Wholebrain_FC_ind1_to_pFC_ind1
task="mousebrain_FC_datasets_multiinds"
train="FC_P60FCRep1"
test="Adult_PFCSample1"
python -m pipelines.threshold_pipeline $task --train $train --test $test --leaveout 2
## 25. Wholebrain_FC_exclude_ind2_to_ind2_major_celltypes
task="mousebrain_FC_multiinds"
train="ALL"
test="P60FCCx3cr1Rep1"
python -m pipelines.threshold_pipeline $task --train $train --test $test --leaveout 2
## 26. Wholebrain_FC_exclude_ind2_to_ind2_sub_celltypes
task="mousebrain_FC_multiinds_sub"
train="ALL"
test="P60FCCx3cr1Rep1"
python -m pipelines.threshold_pipeline $task --train $train --test $test --leaveout 2
## 27. Wholebrain_FC_downsampled_exclude_ind2_to_ind2_major_celltypes
task="mousebrain_FC_multiinds_sample"
train="P60FCRep1"
test="P60FCCx3cr1Rep1"
python -m pipelines.threshold_pipeline $task --train $train --test $test --leaveout 2
## 28. Wholebrain_FC_downsample_exclude_ind2_to_ind2_sub_celltypes
task="mousebrain_FC_multiinds_sub_sample"
train="P60FCRep1"
test="P60FCCx3cr1Rep1"
python -m pipelines.threshold_pipeline $task --train $train --test $test --leaveout 2
## 29. Wholebrain_FC_downsample_adult_to_pFC_ind1
task="mousebrain_FC_datasets_multiinds_sample"
train="FC_P60FCRep1"
test="Adult_PFCSample1"
python -m pipelines.threshold_pipeline $task --train $train --test $test --leaveout 2