sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
3a2db7320d43abe084147790ca028b2f3eb01b7c33f1c8e7c5deaaf9040f431e | Shell | 727 | 35 | #!/bin/bash
#SBATCH -p shared
#SBATCH --mem-per-cpu=5G
#SBATCH --job-name=10_DREAM_plots
#SBATCH -c 1
#SBATCH -o logs/10_DREAM_plots.txt
#SBATCH -e logs/10_DREAM_plots.txt
#SBATCH --mail-type=ALL
set -e
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${SLURM_JOB_ID}"
e... |
3dd768953b8075f332ba174cd8986ca7503eb99ddfda7f8242c44a2363b3efc6 | Shell | 727 | 35 | #!/bin/bash
#SBATCH -p shared
#SBATCH --mem-per-cpu=5G
#SBATCH --job-name=11_GO_analysis
#SBATCH -c 1
#SBATCH -o logs/11_GO_analysis.txt
#SBATCH -e logs/11_GO_analysis.txt
#SBATCH --mail-type=ALL
set -e
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${SLURM_JOB_ID}"
e... |
4a375d8591b394e83e20aa689244d9231ebca68c4e0a98115af3ed1c50fb26ab | Shell | 728 | 35 | #!/bin/bash
#SBATCH -p shared
#SBATCH --mem=5G
#SBATCH --job-name=04_get_est_prop
#SBATCH -c 1
#SBATCH -o logs/04_get_est_prop.txt
#SBATCH -e logs/04_get_est_prop.txt
#SBATCH --mail-type=ALL
set -e
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${SLURM_JOB_ID}"
echo "... |
c77c5e175227efc09c9429f232765534bd900dbbb9308192b171aa5b01b2e0ff | Shell | 728 | 35 | #!/bin/bash
#SBATCH -p shared
#SBATCH --mem=5G
#SBATCH --job-name=03_get_est_prop
#SBATCH -c 1
#SBATCH -o logs/03_get_est_prop.txt
#SBATCH -e logs/03_get_est_prop.txt
#SBATCH --mail-type=ALL
set -e
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${SLURM_JOB_ID}"
echo "... |
d54c7c6246e38c4854716a611f89bb822673cb996b4c9aebc022a6a46de8d63f | Shell | 728 | 32 | #!/bin/bash
#$ -cwd
#$ -l bluejay,mem_free=50G,h_vmem=50G,h_fsize=100G
#$ -N find_markers_broad
#$ -o logs/03_find_markers_broad.txt
#$ -e logs/03_find_markers_broad.txt
#$ -m e
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo... |
4c5a877daa42baa9f239f3d3924fa1494538b35c264d7128eca4372e99cf1a3a | Shell | 729 | 13 | #!/usr/bin/env bash
# ------------------------------------------------------------------------------------------------
# Deformable DETR
# Copyright (c) 2020 SenseTime. All Rights Reserved.
# Licensed under the Apache License, Version 2.0 [see LICENSE for details]
# -----------------------------------------------------... |
9b6a23e7ec2f5b0c9221394e76cb3648aaf758488d205dcc38543bfde947640d | Shell | 729 | 35 | #!/bin/bash
#SBATCH -p shared
#SBATCH --mem=25G
#SBATCH --job-name=00_pull_markers
#SBATCH -c 1
#SBATCH -o logs/00_pull_markers.txt
#SBATCH -e logs/00_pull_markers.txt
#SBATCH --mail-type=ALL
set -e
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${SLURM_JOB_ID}"
echo ... |
5051def38d60728fda985eb3f88fa4c20516c68a699256ce0d5820d087f73792 | Shell | 730 | 33 | #!/bin/bash
#Submit to the cluster, give it a unique name
#$ -S /bin/bash
#$ -cwd
#$ -V
#$ -l h_vmem=1.9G,h_rt=20:00:00,tmem=1.9G
#$ -pe smp 2
# join stdout and stderr output
#$ -j y
#$ -R y
if [ "$1" != "" ]; then
RUN_NAME=$1
else
RUN_NAME=$""
fi
FOLDER=$(date +"%Y%m%d%H%M")
WRITEFOLDER=submissions/$FOLDER... |
9a27d4aa385b07c857fbc5486c6f8acc56b2a3e6038b53243cb7107b5faa41af | Shell | 730 | 41 | # Apply registration to the denoised brain images (loop through all subjects)
#Author: Valeria Oliva
echo -n "session? 01 or 02 >"
read ses
cd ../../../data/BIDS/derivatives/
for subject in sub-NSPilot0??
do
(
cd ${subject}/ses-${ses}brain/func/feat_analyses/
for scan in FingerTap ForceAbs Fo... |
681eeda450a4a4985c9ca199a50601508e4b3b064fbbb86055cd131daddacb3c | Shell | 733 | 35 | #!/bin/bash
#SBATCH -p shared
#SBATCH --mem=50G
#SBATCH --job-name=00_PEC_data_prep
#SBATCH -c 1
#SBATCH -o logs/00_PEC_data_prep.txt
#SBATCH -e logs/00_PEC_data_prep.txt
#SBATCH --mail-type=ALL
set -e
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${SLURM_JOB_ID}"
ec... |
ee46daf0c720b7f0420b9ea00385bc04b5d9f67eb9dff07948d6558295b0c53a | Shell | 733 | 15 | #!/bin/sh
# DEVELOPER INSTALLATION SCRIPT
# You must have Java Development Kit (JDK) 8 (1.8). If higher (>8) then it must
# support --release flag to pin down the version when compiling.
# Always compile with 8 (1.8) to keep backward compatibility.
# In conda, you can get a JDK version that supports --release flag:
#... |
5adbe9332b52ce9bbf3be55bb411a37d69a1046af3cc222b471fa051ab6c820f | Shell | 734 | 32 | #!/bin/bash
#Submit to the cluster, give it a unique name
#$ -S /bin/bash
#$ -cwd
#$ -V
#$ -l h_vmem=1.9G,h_rt=20:00:00,tmem=1.9G
#$ -pe smp 2
# join stdout and stderr output
#$ -j y
#$ -R y
if [ "$1" != "" ]; then
RUN_NAME=$1
else
RUN_NAME=$""
fi
FOLDER=$(date +"%Y%m%d%H%M")
WRITEFOLDER=../submissions/$FOL... |
cc4454888f1bc1eb50cec52d105d647bd0c45b2bdd12cce7bd12dc5454ee8ffc | Shell | 734 | 31 | cuda=$1
dataset=$2
ft=$3
hidden_channels_lst=(64)
n_layers_lst=(4)
lr_lst=(0.001)
weight_decay_lst=(0. 0.0005 0.001 0.005)
dropout_lst=(0.2 0.5 0.6 0.7)
R_list=(10. 100.)
# R_list=(100.)
for n_layer in "${n_layers_lst[@]}"; do
for hidden in "${hidden_channels_lst[@]}"; do
for lr in "${lr_lst[... |
67c550dd46110353fefa0b7a6a406281a223ddcb80fcd30beea8a99c9905cf4b | Shell | 736 | 35 | #!/bin/bash
#SBATCH -p shared
#SBATCH --mem=80G
#SBATCH --job-name=06_find_markers_CMC
#SBATCH -c 1
#SBATCH -t 1-00:00:00
#SBATCH -o logs/06_find_markers_CMC.txt
#SBATCH -e logs/06_find_markers_CMC.txt
set -e
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${SLURM_JOB_... |
adb56b39beacec996eedc0af615de1ddb9fb65e280ce6b44d6f8a93b1c2936e5 | Shell | 737 | 35 | #!/bin/bash
#SBATCH -p shared
#SBATCH --mem=10G
#SBATCH --job-name=00_data_prep_Tran
#SBATCH -c 1
#SBATCH -o logs/00_data_prep_Tran.txt
#SBATCH -e logs/00_data_prep_Tran.txt
#SBATCH --mail-type=ALL
set -e
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${SLURM_JOB_ID}"... |
763ea62031c047293bda8ae6fb05a28ca694fe8de2222d177c5d8bc82691cfe2 | Shell | 738 | 32 | #!/bin/bash
#$ -cwd
#$ -l bluejay,mem_free=5G,h_vmem=5G,h_fsize=100G
#$ -N check_bulk_qc_metrics
#$ -o logs/01_check_bulk_qc_metrics.txt
#$ -e logs/01_check_bulk_qc_metrics.txt
#$ -m e
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME... |
49565af123bb5113c0485c783683fa0addb4a35d53d615c94bd7874a49e9b08b | Shell | 739 | 35 | #!/bin/bash
#SBATCH -p shared
#SBATCH --mem-per-cpu=5G
#SBATCH --job-name=04_DREAM_plots_sn
#SBATCH -c 1
#SBATCH -o logs/04_DREAM_plots_sn.txt
#SBATCH -e logs/04_DREAM_plots_sn.txt
#SBATCH --mail-type=ALL
set -e
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${SLURM_J... |
f490e05a31226c440a30a46ee46c2c69b35f99db4b5cd141bc685277756ce1c8 | Shell | 739 | 35 | #!/bin/bash
#SBATCH -p shared
#SBATCH --mem=50G
#SBATCH --job-name=07_prep_CIBERSORTx
#SBATCH -c 1
#SBATCH -o logs/07_prep_CIBERSORTx.txt
#SBATCH -e logs/07_prep_CIBERSORTx.txt
#SBATCH --mail-type=ALL
set -e
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${SLURM_JOB_I... |
c39c5483a7bf7af7a3fe73e0f95a5cebdee58ff1e9cebc3a35ffd21c6520cbfa | Shell | 740 | 35 | #!/bin/bash
#SBATCH -p shared
#SBATCH --mem-per-cpu=10G
#SBATCH --job-name=01_pseudobulk_sn
#SBATCH -c 1
#SBATCH -o logs/01_pseudobulk_sn.txt
#SBATCH -e logs/01_pseudobulk_sn.txt
#SBATCH --mail-type=ALL
set -e
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${SLURM_JOB... |
a2535e97a2dfe69a36458235f666325d6c84b5971123017e2fea413aff7bd25b | Shell | 742 | 20 | #!/bin/bash
# Step 1: Create the directory 'out' in the current working directory if it doesn't already exist
mkdir -p ./out
# Step 2: Move and rename *.bam files
for file in ./temp/*_output.sorted.reheaded.bam; do
# Construct the new file path in the 'out' directory with the new name
new_file="./out/$(basena... |
01594cf99a2701bdb683d6b0b408ad6abfa81f8568a4d0432fa77cb0ecd900d2 | Shell | 744 | 35 | #!/bin/bash
#SBATCH -p shared
#SBATCH --mem-per-cpu=10G
#SBATCH --job-name=03_DREAM_sn_v_bulk
#SBATCH -c 1
#SBATCH -o logs/03_DREAM_sn_v_bulk.txt
#SBATCH -e logs/03_DREAM_sn_v_bulk.txt
#SBATCH --mail-type=ALL
set -e
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${SLU... |
57a3c07603499f4748ac0285346516cd9f5c887feabbd91bc9ccb27a28175575 | Shell | 744 | 32 | #!/bin/bash -l
#SBATCH --output=logs/02_spatial_size_QC.txt
#SBATCH --error=logs/02_spatial_size_QC.txt
#SBATCH --partition=shared
#SBATCH --job-name=spatial_size_QC
#SBATCH --mem=5GB
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${SLURM_JOB_ID}"
echo "Job name: ${SL... |
e3f540993e19f331c6e61729313c19433434babd1c4d89820780c18fca868fdd | Shell | 744 | 23 | #!/bin/bash -l
#SBATCH --job-name="EEG_2_CoordsV"
#SBATCH --partition=prod
#SBATCH --nodes=1
#SBATCH -C clx
#SBATCH --cpus-per-task=2
#SBATCH --time=24:00:00
##SBATCH --mail-type=ALL
#SBATCH --account=proj85
#SBATCH --no-requeue
#SBATCH --output=EEG_2_CoordsV.out
#SBATCH --error=EEG_2_CoordsV.err
#SBATCH --exclusive
#S... |
031d361833f6d0920090b700ea921bb0db9bde4a453e64f2aa8d491f3709113c | Shell | 745 | 37 | #!/bin/bash
#Submit to the cluster, give it a unique name
#$ -S /bin/bash
#$ -cwd
#$ -V
#$ -l h_vmem=1.9G,h_rt=20:00:00,tmem=1.9G
#$ -pe smp 2
# join stdout and stderr output
#$ -j y
#$ -R y
WORKFLOW="workflows/${1}.smk"
if [ "$2" != "" ]; then
RUN_NAME="$1"_"$2"
else
RUN_NAME=$1
fi
FOLDER=submissions/$(da... |
0b23e7f254d837181ae337e26c2740dbb39183ca437cbf61dd0c12d6a43df8be | Shell | 745 | 35 | #!/bin/bash
#SBATCH -p shared
#SBATCH --mem=10G
#SBATCH --job-name=06_data_prep_Mathys
#SBATCH -c 1
#SBATCH -o logs/06_data_prep_Mathys.txt
#SBATCH -e logs/06_data_prep_Mathys.txt
#SBATCH --mail-type=ALL
set -e
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${SLURM_JO... |
91008091b4a0fb7ffaeb2f8a96e34f6002f2ecab65e633051a283ee7a658099c | Shell | 745 | 37 | #!/bin/bash
#Submit to the cluster, give it a unique name
#$ -S /bin/bash
#$ -cwd
#$ -V
#$ -l h_vmem=1.9G,h_rt=20:00:00,tmem=1.9G
#$ -pe smp 2
# join stdout and stderr output
#$ -j y
#$ -R y
WORKFLOW="workflows/${1}.smk"
if [ "$2" != "" ]; then
RUN_NAME="$1"_"$2"
else
RUN_NAME=$1
fi
FOLDER=submissions/$(da... |
0059af15c90165e47612390e084f932e86eae1eba3b4ebce685e1bc83416ff81 | Shell | 746 | 35 | #!/bin/bash
#SBATCH -p shared
#SBATCH --mem=200G
#SBATCH --job-name=01_find_markers_PEC
#SBATCH -c 1
#SBATCH -o logs/01_find_markers_PEC.txt
#SBATCH -e logs/01_find_markers_PEC.txt
#SBATCH --mail-type=ALL
set -e
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${SLURM_J... |
1e6f9f3352de019b1d028dfbe1a7d92cb28be10b170745ccd56d4cc54108b50b | Shell | 746 | 23 | #!/bin/bash
#SBATCH --job-name=spin_cf
#SBATCH --output=/data/p_02915/SPOT/logs/%x_%A_%a.out
#SBATCH --error=/data/p_02915/SPOT/logs/%x_%A_%a.err
#SBATCH --time=24:00:00
#SBATCH --cpus-per-task=16
#SBATCH --mem=32G
#SBATCH --array=0-5%2
RUN_GROUPS=(2nd 3rd preterm fullterm adolescent adult)
GROUP=${RUN_GROUPS[$SLURM_A... |
8b34d7522947005002834a3b9afe378db23584eba52360cb1b4afc39f7ea6615 | Shell | 746 | 28 | #!/bin/bash
source /data_st01/drug/itosho/.bash_profile
pyenv shell miniconda3-latest/envs/kmol
run_path="/data_st01/drug/itosho/kmol/"
cd $run_path
#train_base_path="/data_st01/drug/itosho/ADMET/configs/accuracy_drug/adme/multitask/train/*"
#for folder in $train_base_path; do
# if [ -d "$folder" ]; then
# ... |
536d2296792ff8cb07a1ca3ded0e707a27ae21c944eacd7e44a6f36c87496ae0 | Shell | 747 | 31 | #!/bin/bash -l
#SBATCH --output=logs/04_DE_library-type.txt
#SBATCH --error=logs/04_DE_library-type.txt
#SBATCH --partition=shared
#SBATCH --job-name=04_DE_library-type
#SBATCH --mem=75GB
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${SLURM_JOB_ID}"
echo "Job name: $... |
6489529f97637bc121c121bd7028833c426cced01ea0078aa5dca7f600e2764d | Shell | 747 | 31 | #!/bin/bash -l
#SBATCH --output=logs/05_DE_library-prep.txt
#SBATCH --error=logs/05_DE_library-prep.txt
#SBATCH --partition=shared
#SBATCH --job-name=05_DE_library-prep
#SBATCH --mem=75GB
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${SLURM_JOB_ID}"
echo "Job name: $... |
0af3b67f325adb9299e2d23e999a3f8db534da38b15e26168babe1b4c8d8f2d8 | Shell | 748 | 33 | #!/bin/bash -l
#SBATCH --job-name="EEG_1_CoordsV"
#SBATCH --partition=prod
#SBATCH --nodes=1
#SBATCH -C clx
#SBATCH --cpus-per-task=2
#SBATCH --time=24:00:00
##SBATCH --mail-type=ALL
#SBATCH --account=proj85
#SBATCH --no-requeue
#SBATCH --output=EEG_1_CoordsV.out
##SBATCH --error=EEG_1_CoordsV.err
#SBATCH --exclusive
#... |
57a8e6d209ddb2c8a95367f15919da489ebf3fea4910d2f6ab93f9532fe61ed8 | Shell | 749 | 35 | #!/bin/bash
#SBATCH -p shared
#SBATCH --mem=25G
#SBATCH --job-name=01_find_markers_Tran
#SBATCH -c 1
#SBATCH -o logs/01_find_markers_Tran.txt
#SBATCH -e logs/01_find_markers_Tran.txt
#SBATCH --mail-type=ALL
set -e
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${SLURM... |
8675b355659db51322119d68e57ab841f641daf860d4e0f8b56dbd23c4a0d62f | Shell | 749 | 14 | # RNAseq process
fastqc -t 20 -o "$output_folder/fastqc_output" "$FQ1" "$FQ2"
trim_galore -j 20 -q 25 --phred33 --length 36 -e 0.1 --stringency 3 --paired "$FQ1" "$FQ2" -o "$output_folder"
hisat2 -p 20 -x "$genome_index" -1 "${output_folder}/${Al_fq1}" -2 "${output_folder}/${Al_fq2}" -S "${output_folder}/${SampleName... |
2a69bcc2f01c6dd9101735f0a852cebc801eb8936e2a7e71e8f304a672e83e91 | Shell | 752 | 35 | #!/bin/bash
#SBATCH -p shared
#SBATCH --mem-per-cpu=10G
#SBATCH --job-name=01_import_HALO_data
#SBATCH -c 1
#SBATCH -o logs/01_import_HALO_data.txt
#SBATCH -e logs/01_import_HALO_data.txt
#SBATCH --mail-type=ALL
set -e
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${... |
c811e095e691caf04d810705b378681df2f8767c817226006599de869eb99c8d | Shell | 753 | 35 | #!/bin/bash
#SBATCH -p shared
#SBATCH --mem=25G
#SBATCH --job-name=05_deconvolution_hspe
#SBATCH -c 1
#SBATCH -o logs/05_deconvolution_hspe.txt
#SBATCH -e logs/05_deconvolution_hspe.txt
#SBATCH --mail-type=ALL
set -e
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${SL... |
5f0890a6165c997b7a92a7a5959b5cf41d166559832bd1a3d9c1982baca303af | Shell | 754 | 35 | #!/bin/bash
#SBATCH -p shared
#SBATCH --mem=400G
#SBATCH --job-name=04_deconvolution_DWLS
#SBATCH -c 1
#SBATCH -o logs/04_deconvolution_DWLS.txt
#SBATCH -e logs/04_deconvolution_DWLS.txt
#SBATCH --mail-type=ALL
set -e
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${S... |
df1fca5082be32221dde9f575065c615a568ad374d8c8f827cd2e707f5fc5581 | Shell | 754 | 21 | #!/bin/bash
# The code plotRelativeOccurrenceHeatmap.py takes the following arguments:
# PathToKmerOccurrenceTable (*5mer_distribution_whole_gene.tsv*)
# PathToKmerRtxnTable (*5mer_rtxn_whole_gene.tsv*)
# PathToOutputDirectory
# WindowAroundCrosslinkSite (plot n nucleotides up and downstream from crosslink)
# NumberOf... |
fe82a7e728db0bae1c1269908b2d618494ca9d8cbc9ea0f71f979cd01bdb803b | Shell | 754 | 32 | #!/bin/bash -l
#SBATCH --output=logs/06_DE_library-combo.txt
#SBATCH --error=logs/06_DE_library-combo.txt
#SBATCH --partition=shared
#SBATCH --job-name=06_DE_library-combo
#
#SBATCH --mem=75GB
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${SLURM_JOB_ID}"
echo "Job n... |
446dff35317fd24fd6614a469df038893aa5928db17fa53d509329d69404c3e2 | Shell | 756 | 35 | #!/bin/bash
#SBATCH -p shared
#SBATCH --mem-per-cpu=10G
#SBATCH --job-name=08_DREAM_library-type
#SBATCH -c 1
#SBATCH -o logs/08_DREAM_library-type.txt
#SBATCH -e logs/08_DREAM_library-type.txt
#SBATCH --mail-type=ALL
set -e
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job ... |
7590b58d61e29fee26cd2d687fd1f88d7a91ea0f12ebf5242f5bc36fd2485cd7 | Shell | 756 | 35 | #!/bin/bash
#SBATCH -p shared
#SBATCH --mem-per-cpu=10G
#SBATCH --job-name=09_DREAM_library-prep
#SBATCH -c 1
#SBATCH -o logs/09_DREAM_library-prep.txt
#SBATCH -e logs/09_DREAM_library-prep.txt
#SBATCH --mail-type=ALL
set -e
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job ... |
9dd5b22b2a37e71166311791bb2ef80f15a7e427880a17e8539a1bd968d4fbe2 | Shell | 756 | 18 | #!/bin/bash
# Orftcr.sh
export NA=$1
export TF=$2
export LEN=$3
export NORM=$4
cd ${NA}
printf "${NA}_dipy_bk_inbetween_plot.txt\n${LEN}\n${TF}\n${NA}_dipy_inbetween_bk_plus.wig\n${NA}_dipy_inbetween_bk_minus.wig\n\n" | perl ../motifplot_yeastbs_inbetween.pl
fastaFromBed -s -fi ../saccer3_genome.fa -bed ${NA}_dipy_b... |
a2498d5b23b373b6ce37eb80f8ad7e0a26a0ab2ab8d74aa3094ece796aa3daac | Shell | 756 | 33 | #!/bin/bash
#SBATCH -p transfer
#SBATCH -c 1
#SBATCH --mem=3G
#SBATCH -t 3-00:00:00
#SBATCH --job-name=05_upload_fastq
#SBATCH -o ../../processed-data/11_raw_data_upload/05_upload_fastq.log
#SBATCH -e ../../processed-data/11_raw_data_upload/05_upload_fastq.log
#SBATCH --open-mode=append
set -e
echo "**** Job starts ... |
ba56593b2a579ed91d67117295b8267455abb905b8b0b17168519c251cd52a12 | Shell | 756 | 35 | #!/bin/bash
#SBATCH -p shared
#SBATCH --mem-per-cpu=10G
#SBATCH --job-name=05_broad_registration
#SBATCH -c 1
#SBATCH -o logs/05_broad_registration.txt
#SBATCH -e logs/05_broad_registration.txt
#SBATCH --mail-type=ALL
set -e
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job ... |
ede32ca126d191caac7fe47a05cda0166c572e904532b06418f95ac608b8f3c8 | Shell | 756 | 35 | #!/bin/bash
#SBATCH -p shared
#SBATCH --mem=5G
#SBATCH --job-name=05_deconvo_input_plots
#SBATCH -c 1
#SBATCH -o logs/05_deconvo_input_plots.txt
#SBATCH -e logs/05_deconvo_input_plots.txt
#SBATCH --mail-type=ALL
set -e
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${... |
143d1b38fc8d9c50c9ecb0009fca4125f0971fab688bb43d5968c49891965cf7 | Shell | 757 | 35 | #!/bin/bash
#SBATCH -p shared
#SBATCH --mem=10G
#SBATCH --job-name=10_get_est_prop_subset
#SBATCH -c 1
#SBATCH -o logs/10_get_est_prop_subset.txt
#SBATCH -e logs/10_get_est_prop_subset.txt
#SBATCH --mail-type=ALL
set -e
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: $... |
5f733bae3d1075a2678cb8e62a19a3d1b7681731a2e260c3b6d42fbdc76add6d | Shell | 757 | 35 | #!/bin/bash
#SBATCH -p shared
#SBATCH --mem=25G
#SBATCH --job-name=07_find_markers_Mathys
#SBATCH -c 1
#SBATCH -o logs/07_find_markers_Mathys.txt
#SBATCH -e logs/07_find_markers_Mathys.txt
#SBATCH --mail-type=ALL
set -e
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: $... |
2d4b72f5f53bdf5788e14013e0c56928e99e77e303a9953834e3f2c544d16293 | Shell | 759 | 31 | #!/bin/bash -l
#SBATCH --output=logs/08_explore_proportions.txt
#SBATCH --error=logs/08_explore_proportions.txt
#SBATCH --partition=shared
#SBATCH --job-name=explore_proportions
#SBATCH --mem=5GB
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${SLURM_JOB_ID}"
echo "Job... |
887959575a5f516a835c5c1de32e105c92a4ad7a06f210af14dc0796c06e5a34 | Shell | 759 | 31 | #!/bin/bash -l
#SBATCH --output=logs/09_compare_proportions.txt
#SBATCH --error=logs/09_compare_proportions.txt
#SBATCH --partition=shared
#SBATCH --job-name=compare_proportions
#SBATCH --mem=5GB
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${SLURM_JOB_ID}"
echo "Job... |
2f217bfa16c1e87f22ed3dea37478ed687ce7c8f05553e10aca2bdcb4312b875 | Shell | 760 | 35 | #!/bin/bash
#SBATCH -p shared
#SBATCH --mem-per-cpu=10G
#SBATCH --job-name=06_marker_gene_heatmap
#SBATCH -c 1
#SBATCH -o logs/06_marker_gene_heatmap.txt
#SBATCH -e logs/06_marker_gene_heatmap.txt
#SBATCH --mail-type=ALL
set -e
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "J... |
c2cba56e3b1ff46ec125c503ff1f6c19926110ef25017fb9ae81b0445c3f0f0e | Shell | 760 | 21 | #! /bin/bash
# get rid of offset in niftis, as they are currently not in the reconstructed images
for f in *nii.gz; do
base=${f%%.nii.gz}
stir_math $base.hv $base.nii.gz
sed -i -e '/first pixel offset/ d' \
-e '/!INTERFILE/a !imaging modality := PT' \
$base.hv
# patient position is currently not i... |
69f4267f7af44648b522de8d6997ade613885fb8aedaecb53bb9caba91871316 | Shell | 761 | 29 | torchrun --rdzv-backend=c10d --rdzv-endpoint=localhost:0 repl/scripts/cli.py \
--dataset mnist \
--grayscale \
--flatten_images \
--seq_len 64 \
--num_sequences 10000 \
--mnist_seqtype triplets \
--encoder mlp \
--enc_output_dim 64 \
--enc_n_layers 2 \
--integrator rnn \
--ct... |
d8ea9281339dfe5bde42fddb0f2506888d75fa508f9099d144ae3832a887fe71 | Shell | 761 | 18 | ### 1. need to run in the spatial environment
### 2. need to put spatial.txt file in the same directory
in_image="Spnb70_ROI.png" # png image file
img_resolution_smaller=1300 # change this based on image resolutions, use smaller resolution
###
block_size_threshold=35 # default value is 35. block size for adaptiv... |
773cb02d24c2c4e87b7ccda62f94082f41d323f63c163a0c75ab68b52da14032 | Shell | 762 | 27 | # runVignette01.sh - Forward simulation
# --------------------------------------------------
# This vignette demonstrates forward simulation of
# blood flow through a vascular network.
# The ESL viscosity model is used, hematocrit is
# uniform throughout the network, and prescribed pressure
# bundary conditions are use... |
242b5d78163b929d4f73a66e6bff729ad2722415c4068a84b276ee6fc97f16b0 | Shell | 763 | 32 | #!/bin/bash
#$ -cwd
#$ -l mem_free=150G,h_vmem=150G,h_fsize=100G
#$ -N DLPFC-n3_step03_markerDetxn_LAH
#$ -o logs/DLPFC-n3_step03_markerDetxn_LAH.txt
#$ -e logs/DLPFC-n3_step03_markerDetxn_LAH.txt
#$ -m e
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "... |
3947831b7a622f7accca7f4ff68c497737ca5eb55214397436dde1d312d988b8 | Shell | 763 | 35 | #!/bin/bash
#SBATCH -p shared
#SBATCH --mem=50G
#SBATCH --job-name=04_get_expression_cutoff
#SBATCH -c 1
#SBATCH -o logs/04_get_expression_cutoff.txt
#SBATCH -e logs/04_get_expression_cutoff.txt
#SBATCH --mail-type=ALL
set -e
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job... |
4ace758dc2378db5c5f067f779909ae7b257ecd9f04865573ad0e0112c130948 | Shell | 764 | 24 | #!/bin/bash
chr_num="X"
dx login --token TOKEN
my_cmd="plink2 --bfile chr${chr_num}_hqc \
--chr X \
--out chr${chr_num}_hqc_nopar --output-chr chrMT \
--make-bed --threads 32"
bed_file="/notebooks/wes/sample_qc/high_quality_variants/chr${chr_num}/chr${chr_num}_hqc.bed"
bim_file="/notebooks... |
e65bde90a2f65f4111b6fa9e2ca2a92cae01666a7aef2d5153c7c5912f88fcbf | Shell | 764 | 23 | #!/bin/bash -l
#SBATCH --job-name="EEG_2_CoordsV"
#SBATCH --partition=prod
#SBATCH --nodes=1
#SBATCH -C clx
#SBATCH --cpus-per-task=2
#SBATCH --time=24:00:00
##SBATCH --mail-type=ALL
#SBATCH --account=proj85
#SBATCH --no-requeue
#SBATCH --output=EEG_2_CoordsV.out
#SBATCH --error=EEG_2_CoordsV.err
#SBATCH --exclusive
#S... |
34d6ec5da248049ac2e38bfe2cafef5412faf6b4f208453fbed00430de301690 | Shell | 766 | 40 | # Install/unInstall package files in LAMMPS
# mode = 0/1/2 for uninstall/install/update
mode=$1
# enforce using portable C locale
LC_ALL=C
export LC_ALL
# arg1 = file, arg2 = file it depends on
action () {
if (test $mode = 0) then
rm -f ../$1
elif (! cmp -s $1 ../$1) then
if (test -z "$2" || test -e ../... |
182c491c4fd61881f0387cc937c7398f82dd09797c83c4b228ae14cffd6baf71 | Shell | 768 | 22 | #!/bin/bash
dx login --token TOKEN
my_cmd="wget https://www.kingrelatedness.com/Linux-king.tar.gz && tar -xzvf Linux-king.tar.gz && \
./king -b autosome_hqc.bed --kinship --degree 2 --cpus 44"
bed_file="/notebooks/wes/sample_qc/high_quality_variants/autosomes/autosome_hqc.bed"
bim_file="/notebooks/wes/samp... |
1d83b3f8234f9a30e2236066fd5ac1ba799168cac5dd0e28e752afa554085126 | Shell | 769 | 20 | #!/bin/bash
echo "Fixing input data permissions"
sudo chown $USER -R /$WORKFLOW_DIR/$BATCH_NAME
echo "Starting MTIK Flow"
/mitk-flow/MitkFlowBench.sh /$WORKFLOW_DIR/$BATCH_NAME/tasklist.json &
PID=$!
# Wait for the main MITK FlowBench window ('Segmentation - MITK FlowBench ...') to map, then make
# it fullscreen. Pol... |
0d943b59c77d0e444b3a94be6e609e1a9b7d8758ec89e3e4155add3632d78d81 | Shell | 770 | 33 | #!/bin/bash -l
#SBATCH --job-name="EEG_1_CoordsV"
#SBATCH --partition=prod
#SBATCH --nodes=6
#SBATCH -C clx
#SBATCH --cpus-per-task=2
#SBATCH --time=24:00:00
##SBATCH --mail-type=ALL
#SBATCH --account=proj85
#SBATCH --no-requeue
#SBATCH --output=EEG_1_CoordsV.out
##SBATCH --error=EEG_1_CoordsV.err
#SBATCH --exclusive
#... |
091fbed1505d2a47f75b6f89774c5b4d3143d37e11f50bb5a766cafc61838e56 | Shell | 772 | 36 | #!/bin/bash
#SBATCH -p shared
#SBATCH --mem=25G
#SBATCH --job-name=07_prep_CIBERSORTx_HVG
#SBATCH -c 1
#SBATCH -t 1-00:00:00
#SBATCH -o logs/07_prep_CIBERSORTx_HVG.txt
#SBATCH -e logs/07_prep_CIBERSORTx_HVG.txt
#SBATCH --mail-type=ALL
set -e
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${... |
2891814c17b08678f44ab4131f1c509d14256ee8530c2c2959aefc25ecdbbb4a | Shell | 772 | 31 | #!/bin/bash
# test 1: damping and exchange
cd validation_damped_exchange/
./run-test-exchange.sh
rm dump.data res_lammps.dat res_llg.dat
cd ..
# test 2: damping and Zeeman
cd validation_damped_precession/
./run-test-prec.sh
rm res_lammps.dat res_llg.dat
cd ..
# test 3: langevin, damping and Zeeman, low damping (0.0... |
72bec428bdc1fa2e7a477fade859c31a8118894397b7cd8c18fab685ec46919a | Shell | 773 | 35 | #!/bin/bash
#SBATCH -p shared
#SBATCH --mem=25G
#SBATCH --job-name=05_deconvolution_hspe_FULL
#SBATCH -c 1
#SBATCH -o logs/05_deconvolution_hspe_FULL.txt
#SBATCH -e logs/05_deconvolution_hspe_FULL.txt
#SBATCH --mail-type=ALL
set -e
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
ech... |
78d90ee3690930e05e530a4d3421ecc24683c2cae3f99faa693a3a861fbd09ee | Shell | 773 | 11 | s="sample-prefix"
mm10="path-to-mm10-STAR-ref"
mm10_rna="path-to-your-mm10-annotation-reference"
trim_galore ${s}_BC_cov.fq.gz
trim_galore -a AAAAAAAAAAAAAAAACCTGCAGGNNNNACGAATGCTCTGGCCTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN ${s}_BC_cov_trimmed.fq.gz ### trim oligo-dT primer
trim_galore -a CCTGCAGGNNNNACGAATGCTCTGGCCTNNNNNNNNN... |
b0328e9ba0348fed5ffa258cf7267bbc1f144f011e0748612108779630698a33 | Shell | 774 | 33 | #!/bin/bash -l
#SBATCH --job-name="EEG_1_CoordsV"
#SBATCH --partition=prod
#SBATCH --nodes=8
#SBATCH -C clx
#SBATCH --cpus-per-task=2
#SBATCH --time=24:00:00
##SBATCH --mail-type=ALL
#SBATCH --account=proj85
#SBATCH --no-requeue
#SBATCH --output=EEG_1_CoordsV.out
##SBATCH --error=EEG_1_CoordsV.err
#SBATCH --exclusive
#... |
219f983f0c8e7ce74c9d92427eb7305a17338114624af24314cf5bcbd2a1c63e | Shell | 775 | 35 | #!/bin/bash
#SBATCH -p caracol
#SBATCH --mem=300G
#SBATCH --job-name=04_deconvolution_DWLS_FULL
#SBATCH -c 1
#SBATCH -o logs/04_deconvolution_DWLS_FULL.txt
#SBATCH -e logs/04_deconvolution_DWLS_FULL.txt
#SBATCH --mail-type=ALL
set -e
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
e... |
28dcf136aa0b19df3d272c81e2c6191c5eec9f2b7878805934b7f9e931d853b4 | Shell | 775 | 35 | #!/bin/bash
#SBATCH -p shared
#SBATCH --mem=25G
#SBATCH --job-name=02_deconvolution_MuSiC_FULL
#SBATCH -c 1
#SBATCH -o logs/02_deconvolution_MuSiC_FULL.txt
#SBATCH -e logs/02_deconvolution_MuSiC_FULL.txt
#SBATCH --mail-type=ALL
set -e
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
... |
94a586a3e479406888a03fa3a336925f7a288fa01106e08372a32ac573e0dc0e | Shell | 777 | 22 | #!/bin/bash
# STAR v2.7.9a
# Generate count matrices from filtered BAM files
STAR --runThreadN 6 \
--genomeDir /path/to/GENOME/mm10_cellranger_2020-A/star/ \
--readFilesType SAM SE \
--readFilesIn Aligned_unique.bam,Aligned_multi_primary_n1.bam \
--readFilesPrefix /path/to/mmCortex_scRNA-seq/alignments_AllBestScore/SA... |
e74b655a39c5c8c6abd4bdee68a61349889a672504c18ab35d93cb0594a339b0 | Shell | 778 | 33 | #!/bin/bash -l
#SBATCH --job-name="EEG_1_CoordsV"
#SBATCH --partition=prod
#SBATCH --nodes=142
#SBATCH -C clx
#SBATCH --cpus-per-task=2
#SBATCH --time=24:00:00
##SBATCH --mail-type=ALL
#SBATCH --account=proj85
#SBATCH --no-requeue
#SBATCH --output=EEG_1_CoordsV.out
##SBATCH --error=EEG_1_CoordsV.err
#SBATCH --exclusive... |
24c6742ecf7853a09b932587247810bc47898a0af9cfe6a8a9a7a05656410c8f | Shell | 779 | 20 | dx login --token TOKEN
subset_num=$1
my_cmd="plink2 --bfile autosome_hqc --keep-col-match subsets.txt ${subset_num} \
--make-bed --out subset${subset_num} --threads 32"
bed_file="/notebooks/wes/sample_qc/high_quality_variants/autosomes/autosome_hqc.bed"
bim_file="/notebooks/wes/sample_qc/high_quality_variants... |
d22ee1752b4fd629cd0bf0c176d44c555bf35ac49eacd0fb961b761e33548fa1 | Shell | 781 | 28 | #!/bin/bash
LMP_BIN="$1"
NP="${2:-1}"
echo "MPI over $NP procs:"
for feat in conp etypes tf
do
echo "Using base input file in.$feat:"
echo "mat_inv, log excerpts:"
logfile="log.algo_test.$NP.$feat"
mpirun -np $NP $LMP_BIN -i in.$feat -l $logfile > /dev/null 2>&1
grep -A2 'Per MPI rank' $logfile
grep -B1 'L... |
6c367f2386bdcfd704684637772d7945f658cef71b75618f1d248c5928287b53 | Shell | 782 | 35 | #!/bin/bash
#SBATCH -p shared
#SBATCH --mem=100G
#SBATCH --job-name=01_deconvolution_Bisque_FULL
#SBATCH -c 1
#SBATCH -o logs/01_deconvolution_Bisque_FULL.txt
#SBATCH -e logs/01_deconvolution_Bisque_FULL.txt
#SBATCH --mail-type=ALL
set -e
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USE... |
c115bcd46137f60f8ba3d5f1884e3a2e0bbbeeb0e6762164db06f8e9dad1f6a2 | Shell | 787 | 33 | #!/bin/bash -l
#SBATCH --job-name="EEG_1_CoordsV"
#SBATCH --partition=prod
#SBATCH --nodes=20
#SBATCH -C clx
#SBATCH --cpus-per-task=2
#SBATCH --time=24:00:00
##SBATCH --mail-type=ALL
#SBATCH --account=proj85
#SBATCH --no-requeue
#SBATCH --output=EEG_1_CoordsV.out
##SBATCH --error=EEG_1_CoordsV.err
#SBATCH --exclusive
... |
a13b15c0e50934d7b08ad5bf82c16fe444be979b5144faf76a26ec08c8661318 | Shell | 788 | 31 | #!/bin/bash
# Siwei 04 Jul 2023
# reorder all previous bams that are mapped using 1000G hg38 fasta
# to the chr order of 10x hg38 fasta
picard_jar="/home/zhangs3/Data/Tools/gatk-4.2.6.1/picard.jar"
GRCh38_10x_ref="/home/zhangs3/Data/Databases/Genomes/CellRanger_10x/refdata-cellranger-arc-GRCh38-2020-A/fasta/genome.fa... |
b65c0e3d79889717784f622f92c1fbeb4605918a50325d9e648991318944775a | Shell | 789 | 17 | #!/bin/bash -ef
# Datasets the test suite needs. Downstream projects that reuse this script (e.g.
# MNE-BIDS) can override it to fetch only what they actually use; whatever is
# listed here must also be reflected in the actions/cache key of the caller.
MNE_CI_DATASETS="${MNE_CI_DATASETS:-testing misc}"
if [ "${MNE_CI... |
6ecd42438d1b5d2dd8e6a7ec3eb57ca192e5ffbecd1008d95c35af36acc92f5f | Shell | 790 | 45 | #!/bin/bash
# Siwei 04 Jul 2023
# merge and downsample rs10792832 het bams to 100M reads for peak plotting
cell_type="DN"
temp_folder="/home/zhangs3/NVME/package_temp/downsample_100M_"$cell_type
if [[ -d $temp_folder ]]
then
rm -r $temp_folder
fi
mkdir -p $temp_folder
mkdir -p output
echo $temp_folder
samtools ... |
40e553f0adb77e0b1f7bd4f6b4a4cdf4665de84e1ba0508f0671f754c6eadec8 | Shell | 792 | 14 | perl /home/yli4/bin/customizedDB/RDT/readQC_IDshort.pl $1.fq $2 $1-QC.fas
perl /home/yli4/bin/customizedDB/RDT/fas_tr6.pl $1-QC.fas $1-QC
perl /home/yli4/bin/customizedDB/RDT/tryptic_digest.pl $1-QC_peptide.fas KR P $1-QC_peptide_digested.fas
perl /home/yli4/bin/customizedDB/RDT/uniq_digested_peptides.pl $1-QC_peptide_... |
53e828ef268dbcac5bf686ed9725166ca1b47b5ae33c6eb0473b3d71c6d7628a | Shell | 792 | 16 | #!/bin/bash
# SetBackground.sh
#Code adapted from code on Taylor lab github site
export NA=$1
cd ${NA}
# calculate inbetween position for wig
perl ../intersect_UV_wig_files.pl ../initial_bothstrands_inbetween_CC.wig ${NA}_dipy_leftinbetween_bk_bothstrands.wig >${NA}_CC_leftinbetween_bk_bothstrands.wig
perl ../inter... |
6055a78f6272b008f45cb8074dc736bfe21717ba25bba8dd6f7c7fa085b6ad1f | Shell | 793 | 35 | #!/bin/bash
#SBATCH -p shared
#SBATCH --mem=10G
#SBATCH --job-name=12_get_est_prop_MuSiC_cell_size
#SBATCH -c 1
#SBATCH -o logs/12_get_est_prop_MuSiC_cell_size.txt
#SBATCH -e logs/12_get_est_prop_MuSiC_cell_size.txt
#SBATCH --mail-type=ALL
set -e
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "Use... |
cb165abf5eb1e861877368a0ccf2e452ed410fd82a7be59d2c81560eeacc6aeb | Shell | 796 | 36 | #! /bin/bash
# collect BAM insert size (1 txt for eachfile)
[[ -d ./insert_sumstat ]] &&
rm -r insert_sumstats
mkdir -p insert_sumstats
# find all WASPed.bam files
mapfile -d $'\0' BAMs_to_count < <(find . -type f -name "*WASPed.bam" -print0)
for ((i=0; i<${#BAMs_to_count[@]}; i++))
do
echo ${BAMs_to_count[$i]}
... |
e6263e31ba206e86b2827071348367df1ba0336b0f7556fbade6f0ee0b5be9bf | Shell | 797 | 35 | #!/bin/bash
#SBATCH -p shared
#SBATCH --mem=10G
#SBATCH --job-name=13_deconvo_plots_MuSiC_cell_size
#SBATCH -c 1
#SBATCH -o logs/13_deconvo_plots_MuSiC_cell_size.txt
#SBATCH -e logs/13_deconvo_plots_MuSiC_cell_size.txt
#SBATCH --mail-type=ALL
set -e
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "... |
6a01b51d64015c327140b86025d7805addb077e87f41b695ea2c681e8a7d550f | Shell | 798 | 34 | cuda=$1
dataset=$2
ft=$3
gnn=$4
heads_lst=(4)
hidden_channels_lst=(64)
n_layers_lst=(4)
lr_lst=(0.001 0.001)
weight_decay_lst=(0. 0.0005 0.001 0.005)
dropout_lst=(0.2 0.5 0.7)
R_list=(10. 100.)
for n_layer in "${n_layers_lst[@]}"; do
for head in "${heads_lst[@]}"; do
for hidden in "${hidden_... |
f6fa28132a3830707a879fca02fa14bec27f7f9d27eb76e7d36e3722b00a7e31 | Shell | 800 | 36 | #!/bin/bash
#SBATCH -p caracol
#SBATCH --mem=300G
#SBATCH --job-name=06_deconvolution_BayesPrism_FULL
#SBATCH -c 1
#SBATCH -o logs/06_deconvolution_BayesPrism_FULL.txt
#SBATCH -e logs/06_deconvolution_BayesPrism_FULL.txt
#SBATCH --mail-type=ALL
set -e
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo... |
46394f68b2742d65e985658c6b7965cfdb1cb366a8e1e215e5c74eb1c91b49d6 | Shell | 801 | 35 | #!/bin/bash
#SBATCH -p shared
#SBATCH --mem=25G
#SBATCH --job-name=05_deconvolution_hspe_1vALL_top25
#SBATCH -c 1
#SBATCH -o logs/05_deconvolution_hspe_1vALL_top25.txt
#SBATCH -e logs/05_deconvolution_hspe_1vALL_top25.txt
#SBATCH --mail-type=ALL
set -e
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
ech... |
f94361a68d1d4938b3780c084b7464098870384fe70d898cdb919d23b9464e30 | Shell | 805 | 28 | # runVignette04.sh - Forward simulation
# --------------------------------------------------
# This vignette demonstrates forward simulation of
# blood flow through a vascular network.
# The ESL viscosity model is used, hematocrit is
# non-uniform throughout the network (the phase separation
# effect is included), and ... |
a31f2341589506fb76d528aef262ecdabe2f11fe84eb131c92124174e557d47a | Shell | 807 | 25 | #!/bin/bash
### Install the package with a given type in a defined conda environment with a define python version,
### and call it to check if it works
### example usage:
### ./pip_install.sh stable my_env 3.9
set -e -u
INSTALL_TYPE=$1 # stable, loose, etc..
ENV_NAME=${2:-alphabase}
PYTHON_VERSION=${3:-3.9}
conda cre... |
c84276a082fb2ee1eb7a4740a25be87e1c03a186535de09a161c6b1ba7c0826a | Shell | 809 | 32 | #!/bin/bash
#$ -cwd
#$ -l bluejay,mem_free=50G,h_vmem=50G,h_fsize=100G
#$ -N R-batchJob_DLPFC-n3_optimalPCselxn_LAH2021
#$ -o logs/R-batchJob_DLPFC-n3_optimalPCselxn_LAH2021.txt
#$ -e logs/R-batchJob_DLPFC-n3_optimalPCselxn_LAH2021.txt
#$ -m e
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: $... |
9f48ae3d5aabba36c372d310501d1a97eb345cd727f24b9e2862e630a1ddd8e8 | Shell | 811 | 27 | #!/bin/bash
# STAR v2.7.9a
# Generate count matrices from filtered BAM files
STAR --runThreadN 6 \
--genomeDir /path/to/GENOME/mm10_cellranger_2020-A/star/ \
--readFilesType SAM SE \
--readFilesIn Aligned_unique.bam,Aligned_multi_primary_n1.bam \
--readFilesPrefix /path/to/mmCortex_snRNA-seq/alignments_AllBestScore/SA... |
daf5ba21168455b6c041032d4ccba6c16ea7475ffd5d4f8630ce5d749b489c3a | Shell | 811 | 32 | #!/bin/bash
#SBATCH --partition=GPU-a100s
#SBATCH --gres=gpu:a100s:1
#SBATCH --nodes=1
#SBATCH --job-name=train_tsdiff
#SBATCH --array=0-2
cd /home/leonard.galustian/projects/tsdiff-master || exit
mamba activate tsdiff
splits=(
"data/RDB7/splits/rxn_core_split.pkl"
"data/RDB7/splits/barrier_split.pkl"
"... |
111a509de248efb7972cc861ee033574f65d0bc723da9ed8cbc5f11695a113c9 | Shell | 812 | 18 | #!/bin/zsh
# set refrernaces to map to.
referance="Drosophila_melanogaster.BDGP6.32_combined.fa"
for read_set in *.fastq.gz;do
echo "Mapping and sorting $read_set"
#minimap2 -ax map-ont -N 20 -t 11 /Volumes/big_dog/Direct_RNA_Sequencing/referance/ensembl/$referance $read_set | /Users/paulramirez/samtools-1.14/sam... |
20194c1e60450cf4ceea3c1eb8ec31464febdf310c5872919253668f88d6ce50 | Shell | 812 | 35 | #!/bin/bash
#SBATCH -p shared
#SBATCH --mem=5G
#SBATCH --job-name=05_deconvolution_hspe_MeanRatio_MAD3
#SBATCH -c 1
#SBATCH -o logs/05_deconvolution_hspe_MeanRatio_MAD3.txt
#SBATCH -e logs/05_deconvolution_hspe_MeanRatio_MAD3.txt
#SBATCH --mail-type=ALL
set -e
echo "**** Job starts ****"
date
echo "**** JHPCE info *... |
3526b17065a861f5ff54c1213a46c8e31b196ddcc6a06b8a2a4948879ef3526f | Shell | 812 | 22 | #!/usr/bin/env bash
# Regenerate the robumeta reference values PyMARE's alignment test reads.
#
# Run from the repository root:
#
# validation/robumeta/regenerate.sh
#
# Rewrites pymare/tests/data/robumeta_reference.json in place. The alignment
# workflow runs this script and then compares the result numerically ag... |
6d181e9bf6f5427f663d5599dadbeaf5a6e13e73bbf772143cf4e80892ea7d43 | Shell | 814 | 33 | #!/bin/bash
tempi=0.0
tempf=20.0
rm res_*.dat
# compute Lammps
N=20
for (( i=0; i<$N; i++ ))
do
temp="$(echo "$tempi+$i*($tempf-$tempi)/$N" | bc -l)"
sed s/temperature/${temp}/g test-prec-spin.template > \
test-prec-spin.in
# test standard Lammps
./../../../../src/lmp_serial -in test-prec-spin.in
... |
798dbbc598b11becd808b8ff0b634d1d2e0f4ff341090681c406e1b11f22ace0 | Shell | 816 | 35 | #!/bin/bash
#SBATCH -p shared
#SBATCH --mem=5G
#SBATCH --job-name=05_deconvolution_hspe_MeanRatio_over2
#SBATCH -c 1
#SBATCH -o logs/05_deconvolution_hspe_MeanRatio_over2.txt
#SBATCH -e logs/05_deconvolution_hspe_MeanRatio_over2.txt
#SBATCH --mail-type=ALL
set -e
echo "**** Job starts ****"
date
echo "**** JHPCE inf... |
9fd95bd4796841601a1990d5fb55c6259e85df19d5a7840fc3d84214af2adc91 | Shell | 817 | 35 | #!/bin/bash
#SBATCH -p shared
#SBATCH --mem=25G
#SBATCH --job-name=05_deconvolution_hspe_MeanRatio_top25
#SBATCH -c 1
#SBATCH -o logs/05_deconvolution_hspe_MeanRatio_top25.txt
#SBATCH -e logs/05_deconvolution_hspe_MeanRatio_top25.txt
#SBATCH --mail-type=ALL
set -e
echo "**** Job starts ****"
date
echo "**** JHPCE in... |
a0e30ea194020c206cc10dbe5ee1dff3b136489f7826eb86a189d1fe7fb90378 | Shell | 817 | 35 | #!/bin/bash
#SBATCH -p shared
#SBATCH --mem=10G
#SBATCH --job-name=03_deconvolution_hspe_MeanRatio_top25
#SBATCH -c 1
#SBATCH -o logs/03_deconvolution_hspe_MeanRatio_top25.txt
#SBATCH -e logs/03_deconvolution_hspe_MeanRatio_top25.txt
#SBATCH --mail-type=ALL
set -e
echo "**** Job starts ****"
date
echo "**** JHPCE in... |
6d075c93da774ec9b9d8f711b6d40aa9891fe77451f33754771f2c8ed3a8f895 | Shell | 818 | 25 | #!/bin/bash
#BSUB -J random_baseline # Job name
#BSUB -n 20 # number of processors
#BSUB -q long # Select queue
#BSUB -o logs_shpc/output-PC3-%J.out # Output file
#BSUB -e logs_shpc/output-PC3-%J.err # Error file
#BSUB -M 5G #... |
1f9a772931535c78bc8d1f463656ed512629ecfde8d769ce6dc8ba60863ad1dc | Shell | 821 | 37 | # Install/unInstall package files in LAMMPS
# mode = 0/1/2 for uninstall/install/update
mode=$1
# enforce using portable C locale
LC_ALL=C
export LC_ALL
action () {
if (test $mode = 0) then
rm -f ../$1
fi
}
# all package files with no dependencies
for file in *.cpp *.h; do
test -f ${file} && action $file... |
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