sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
26bf2d130e3baa82ef4cd9f0861304bfaf94fa9e5ece5af0fbb55d8e1bccdb1c | Shell | 1,638 | 75 | #!/bin/bash
# Run feature selection experiments across a few genes, with selected cancer
# types held out (either partially or completely)
# keep all the genes in the gene set, otherwise scripts default to 8000
MAD_PRESELECT=16042
genes=(
"KRAS"
)
sgd_lasso_penalties=(
"1.00e-07"
"3.16e-07"
"1.00e-06"
"3.... |
922b054e24d65c799c2e537a94e092e4968f68178d5500d2b86253071c956536 | Shell | 1,638 | 37 | #!/bin/bash
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable ... |
2db89373346c7cfe07f9582773d20fad188aa8af36c48b6f2bc485af60024ec0 | Shell | 1,643 | 42 | # for Hubbers
#install conda via miniconda :
follow this tuto : https://docs.conda.io/en/latest/miniconda.html#linux-installers
#create your conda env
conda create -n snakemake
conda activate snakemake
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
c... |
0a49d9d4f1d137827ebec28a6ce2e73f0559d658b558b3ddce6ae0da9030c1d7 | Shell | 1,645 | 61 | #!/bin/bash
set -ex
# This function installs protobuf 2.6
install_protobuf_26() {
pb_dir="/usr/temp_pb_install_dir"
mkdir -p $pb_dir
# On the nvidia/cuda:9-cudnn7-devel-centos7 image we need this symlink or
# else it will fail with
# g++: error: ./../lib64/crti.o: No such file or directory
ln -s /usr/l... |
2643491d7ed0c91c16b84bfd907a2993440e6c6726557e82c92cefe27fe0b0a7 | Shell | 1,648 | 57 | #!/usr/bin/env bash
set -x
export MASTER_PORT=$((12000 + $RANDOM % 20000))
export OMP_NUM_THREADS=1
OUTPUT_DIR='YOUR_PATH/work_dir/vit_g_hybrid_pt_1200e_k710_it_k600_ft'
DATA_PATH='YOUR_PATH/data/k600'
MODEL_PATH='YOUR_PATH/model_zoo/vit_g_hybrid_pt_1200e_k710_ft.pth'
JOB_NAME=$1
PARTITION=${PARTITION:-"video"}
# 8 ... |
f3183674c2b469921ea48aecb2d4854a58960cdcf34605e5af6205af83bf77fc | Shell | 1,649 | 57 | #!/usr/bin/env bash
set -x
export MASTER_PORT=$((12000 + $RANDOM % 20000))
export OMP_NUM_THREADS=1
OUTPUT_DIR='YOUR_PATH/work_dir/vit_g_hybrid_pt_1200e_k710_it_k400_ft'
DATA_PATH='YOUR_PATH/data/k400'
MODEL_PATH='YOUR_PATH/model_zoo/vit_g_hybrid_pt_1200e_k710_ft.pth'
JOB_NAME=$1
PARTITION=${PARTITION:-"video"}
# 8 ... |
88d0a83ef8e65651e494d446303a4e2e0d3c8f9ba723a4c6b1d4e1be04d0f726 | Shell | 1,650 | 54 | #!/bin/bash
# =============================================================================
# Author: Gerard Martí
# Description: Apply FastSurfer pipeline to a T1 image
# adapted from TVB-pipeline by Schirner et al
# =============================================================================
# Input
subID=$1
t1=$2... |
8c17da63e485bc0b7433bbb656008d347ae68be12bbb3134bd95f56fc42ba39a | Shell | 1,650 | 44 | #!/bin/bash
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable ... |
bbd3999ff29b00930d9513db21ea5eebd5b53382268a0c93aa0ad05237657621 | Shell | 1,650 | 53 | #!/bin/bash
#AWS_SSH_PRIVATE_KEY_FILE=''
echo $AWS_SSH_PRIVATE_KEY_FILE
set -e
if [ -z ${AWS_SSH_PRIVATE_KEY_FILE} ]
then
echo "ERROR: You must set AWS_SSH_PRIVATE_KEY_FILE in the environment."
exit 1
fi
# Adjust based on the build of H2O you want to download.
h2oBranch=rel-turchin
echo "Fetching latest bui... |
d9f01956b49c8e7c92fe5b32a0b380e33c048cf2d4b08f3b6c47ff78921a0823 | Shell | 1,653 | 56 | #!/bin/bash
# Written by Xiuming Zhang and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
###########################################
# Usage and Reading in Parameters
###########################################
# Usage
usage() { echo "
Usage: $0 -g <GMToNonlinTmpList> -o <outDir... |
f9697d185c30820934084dcf2ac9c37311c18339eaa33953473665bfe1f412e1 | Shell | 1,653 | 59 | #!/bin/bash
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable ... |
f52bc2e71fa4b33f493f3865b9013e245aa9a3cdda8fb517131aaecf5d5d7960 | Shell | 1,659 | 58 | #!/usr/bin/env bash
set -x
export MASTER_PORT=$((12000 + $RANDOM % 20000))
export OMP_NUM_THREADS=1
OUTPUT_DIR='YOUR_PATH/work_dir/vit_g_hybrid_pt_1200e_k710_ft'
DATA_PATH='YOUR_PATH/data/k710'
MODEL_PATH='YOUR_PATH/model_zoo/vit_g_hybrid_pt_1200e.pth'
JOB_NAME=$1
PARTITION=${PARTITION:-"video"}
# 8 for 1 node, 16 f... |
2f007736de9075b865912f713971bfb4a29be3606f8c7275044a678503fd9146 | Shell | 1,669 | 58 | #!/usr/bin/env bash
set -x
export MASTER_PORT=$((12000 + $RANDOM % 20000))
export OMP_NUM_THREADS=1
OUTPUT_DIR='YOUR_PATH/work_dir/vit_g_hybrid_pt_1200e_pt_1200e_k400_ft'
DATA_PATH='YOUR_PATH/data/k400'
MODEL_PATH='YOUR_PATH/model_zoo/vit_g_hybrid_pt_1200e.pth'
JOB_NAME=$1
PARTITION=${PARTITION:-"video"}
# 8 for 1 n... |
32ff31f1589b880a7eef195c071fe346cbed862a2f2dbde62fc7cab512397d32 | Shell | 1,672 | 58 | #!/usr/bin/env bash
set -x
export MASTER_PORT=$((12000 + $RANDOM % 20000))
export OMP_NUM_THREADS=1
OUTPUT_DIR='YOUR_PATH/work_dir/vit_h_hybrid_pt_1200e_k600_ft'
DATA_PATH='YOUR_PATH/data/k600'
MODEL_PATH='YOUR_PATH/model_zoo/vit_h_hybrid_pt_1200e.pth'
JOB_NAME=$1
PARTITION=${PARTITION:-"video"}
# 8 for 1 node, 16 f... |
160be91ab83e45af8c30fecdd8311b95ee2b867224672c0b4e22f9e1032f0239 | Shell | 1,684 | 44 | #! /bin/bash
root=/gpfs51/dors2/gpc/JamesBooth/JBooth-Lab/BDL/jinwang/PlausGram_9-10
subjects_file_path=${root}
subjects_file=scripts/5mvpa/data_info.txt #This should be a txt file with only a list of subject numbers
contrastsname=('Gram_vs_PC_run1' 'Gram_vs_PC_run2' 'SCon_vs_PC_run1' 'SCon_vs_PC_run2')
contrasts=('spm... |
847cbd50e56fc5fb96ed696a46c2ca15926413e950eb82819e683d7923ac4def | Shell | 1,685 | 36 | #!/bin/bash
set -e
# Makes programs, downloads sample data, trains a GloVe model, and then evaluates it.
# One optional argument can specify the language used for eval script: matlab, octave or [default] python
make
CORPUS=text8
VOCAB_FILE=vocab.txt
COOCCURRENCE_FILE=cooccurrence.bin
COOCCURRENCE_SHUF_FILE=cooccurre... |
97d5099aebbda1e13fcbd3287653835023d41721ed67b9fb8067f2660907ce85 | Shell | 1,688 | 37 | #!/usr/bin/env bash
# Copyright 2017 Google Inc.
# All Rights Reserved.
#
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# * Redistributions of source code must retain the above copyright
# notice, this list of... |
0eda39b18bd69bd8a9195d4ec47350e58944abda9771c44ad8c76597b4bed51b | Shell | 1,691 | 59 | #!/usr/bin/env bash
set -x
export MASTER_PORT=$((12000 + $RANDOM % 20000))
export OMP_NUM_THREADS=1
OUTPUT_DIR='YOUR_PATH/work_dir/vit_g_hybrid_pt_1200e_ssv2_ft'
DATA_PATH='YOUR_PATH/data/sthv2'
MODEL_PATH='YOUR_PATH/model_zoo/vit_g_hybrid_pt_1200e.pth'
JOB_NAME=$1
PARTITION=${PARTITION:-"video"}
# 8 for 1 node, 16 ... |
730b3d499b8d7bc71d73bb160faf6129095e6702ed4b973908e0f924e9586b9d | Shell | 1,691 | 59 | #!/usr/bin/env bash
set -x
export MASTER_PORT=$((12000 + $RANDOM % 20000))
export OMP_NUM_THREADS=1
OUTPUT_DIR='YOUR_PATH/work_dir/vit_h_hybrid_pt_1200e_k400_ft'
DATA_PATH='YOUR_PATH/data/k400'
MODEL_PATH='YOUR_PATH/model_zoo/vit_h_hybrid_pt_1200e.pth'
JOB_NAME=$1
PARTITION=${PARTITION:-"video"}
# 8 for 1 node, 16 f... |
ccb44b35fea47e5cd0f7a66079aeeff164dda8977ef34cdeec975975f270da32 | Shell | 1,694 | 36 | #!/bin/bash
# Written by Jianzhong Chen and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
########## Get input and environment variables
id=$1
path_file=$2
config_folder=$3
root_dir="$(dirname "$(dirname "$(readlink -fm "$0")")")"
source $path_file
source ${config_folder}/qc_thr... |
421ca6cf3cdc0bd53dabe27b7c993647bca7de5909107d00dbe62a601fa83a30 | Shell | 1,697 | 40 | #! /bin/sh
# Last successfully run on Jan 12nd, 2018
# Written by CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
# DO NOT CHANGE: This clears old freesurfer variables if they previously exists
if [ -n "$FREESURFER_HOME" ]; then
$FREESURFER_HOME/bin/clear_fs_env.csh
fi
# PLEASE C... |
27bc02a16a3b99aa7c163600259852c666d31c9212081ddce62639626a8dc507 | Shell | 1,699 | 52 | #!/bin/bash
if [ $# -ne 4 ]
then
echo "Please, give 4 input files:"
echo "1) sorted bam file (map with star)"
echo "2) intron bed file"
echo "3) exon bed file"
echo "4) output root files"
exit
fi
p2b=/hpc/hub_oudenaarden/aalemany/bin/bedtools2/bin
p2s=/hpc/hub_oudenaarden/bdebarbanson/bin/samt... |
6e6d408cd715c4aa8292ac2b9c6ab272b62251d374d87cf318b5ccae43ba5ccd | Shell | 1,699 | 52 | #!/bin/bash
# Written by Jianzhong Chen and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
id_list=`readlink -f $1`
timepoint=$2
job_limit=$3
path_file=$4
root_dir="$(dirname "$(dirname "$(readlink -fm "$0")")")"
if [ -z $path_file ];then
path_file=$root_dir/config/CBIG_ABCD_... |
1bec5106639e111c08775dc9b0c90eb1bf38ead31ee84817fa76f607d80fc210 | Shell | 1,704 | 47 | #!/bin/bash
curr_dir=`pwd`
sample=AHRB # abcd, AHRB, MLS
task=mid # mid = AHRB, reward = MLS
run=1 # 1, 2 or None (no need for leading 0, added in code
ses=1 # 1 or 2
type=run # run or session
subj_list=$1
outfold=/oak/stanford/groups/russpold/data/${sample}/derivatives/analyses/proj_reliability/group
# if using run... |
5353bdc40563f7074323661c03c8190d7d0598d06a00b1eb6811f8928e8f46d4 | Shell | 1,705 | 44 | #! /bin/bash
root=/gpfs51/dors2/gpc/JamesBooth/JBooth-Lab/BDL/jinwang/PlausGram_9-10
subjects_file_path=${root}
subjects_file=scripts/5mvpa/data_info.txt #This should be a txt file with only a list of subject numbers
contrastsname=('Finite_vs_PC_run1' 'Finite_vs_PC_run2' 'InCon_vs_PC_run1' 'InCon_vs_PC_run2')
contrasts... |
39d5eada4be2cfb537bb287e7c6b53bdacabce20ac086328addd8de2d9d708e4 | Shell | 1,708 | 40 | #!/usr/bin/env bash
# Copyright 2017 Google Inc.
# All Rights Reserved.
#
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# * Redistributions of source code must retain the above copyright
# notice, this list of... |
9ded6164e64b536615e9bfb8e9108f45d3a827a0e7fe01e3f21f03b45093f247 | Shell | 1,708 | 58 | #!/bin/bash
# Run feature selection experiments for prediction of mutation status, with
# stratified train/test sets
RESULTS_DIR=./08_cell_line_prediction/results/drug_response_stratified
RESULTS_ALL_CANCERS_DIR=./08_cell_line_prediction/results/drug_response_stratified_all_cancers
ERRORS_DIR=./drug_response_stratifi... |
ea6f7ef25273c19210e6b37e341f8f85b59dc9d98a32a07d9c0982aa0906f10e | Shell | 1,709 | 65 | #!/bin/bash
#==========================================
# basic QC
#==========================================
pfile=tmp/adc_rsid
prefix=adc
#--------------------------------
# identify duplicates
#--------------------------------
plink2 --pfile "$pfile" --maf 0.05 --make-bed --out tmp/"$prefix"_maf05
king -b tmp/... |
4506116d8d44c53c025036533eb95d9875117dc60e7f2f0e01946cbb97e30ebf | Shell | 1,711 | 58 | #!/bin/bash
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable ... |
7219428b754ad6ac6e57b28d82504fe5025c6102581fc2ec51090dec740a65e5 | Shell | 1,715 | 38 | #!/bin/bash
# Written by Jianzhong Chen and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
########## Get input and environment variables
id=$1
path_file=$2
config_folder=$3
root_dir="$(dirname "$(dirname "$(readlink -fm "$0")")")"
source $path_file
source ${config_folder}/qc_thr... |
8e297f264b8be92035ff7fc3ce1a2a947c603210f392e118869c1cae8292f8a6 | Shell | 1,717 | 53 | #!/bin/bash
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable ... |
fcb556990640262b2144c04a1f95ea7689981d682ac0fe8e77ddf6f700c02181 | Shell | 1,721 | 55 | #!/bin/bash
#########################################################################
# Copyright (c) 2018-~ Beisi Xu && St Jude
# This source code is released for free distribution under the terms of the
# CreativeCommons BY-NC-SA 4.0 International License
#*Author: Beisi Xu < xubeisi [at] gmail DOT com >
# File... |
7638bcfe01ba9aff38f45b8dfdc61b957d32ba8a1e2defcab77a971db38b45a3 | Shell | 1,724 | 51 | #!/bin/bash
curr_dir=`pwd`
sample=abcd # abcd, ahrb or mls
task=MID
run=2 # 1, 2 or None (no need for leading 0, added in code
ses=2YearFollowUpYArm1 # baselineYear1Arm1 or 2YearFollowUpYArm1 for ABCD
type=run # run or session
subj_list=${1}
outfold=/scratch.global/${USER}/analyses_reliability/group_lowmotion
counter_... |
bb8285e9ee868477f76386314d4aa32513497a469fc6001fa31d72a3868a4f6f | Shell | 1,724 | 60 | #!/usr/bin/env bash
set -x
export MASTER_PORT=$((12000 + $RANDOM % 20000))
export OMP_NUM_THREADS=1
OUTPUT_DIR='YOUR_PATH/work_dir/vit_h_hybrid_pt_1200e_k710_ft'
DATA_PATH='YOUR_PATH/data/k710'
MODEL_PATH='YOUR_PATH/model_zoo/vit_h_hybrid_pt_1200e.pth'
JOB_NAME=$1
PARTITION=${PARTITION:-"video"}
# 8 for 1 node, 16 f... |
1016236caa1d9fa998f22649ac12f43dd1ca246a1befe945333d5db67a9a1f57 | Shell | 1,728 | 58 | #!/bin/bash
rm -r collapsed_bam_KO_20230801
mkdir collapsed_bam_KO_20230801
mkdir -p KO_tmp2
mkdir dedupped_bam_KO_20230801
mkdir edit_output_KO_v7
for FILE in cb_listsKO/v7/*.txt
do
ter_id="$(echo $FILE | cut -d'_' -f2)"
ter_id="$(echo $ter_id | cut -d'/' -f3)"
file_name="$(echo $FILE | cut -d'/' -f3)"
file_nam... |
a58894cc14987fcd4258c9408d53b6e4dc11365e0c20fc14d25191793ce94dc3 | Shell | 1,733 | 56 | #!/bin/bash
# seed=1
cmd="python 02_cancer_type_classification/run_cancer_type_classification.py "
cmd+="--custom_genes CDKN2A "
cmd+="--gene_set custom "
cmd+="--holdout_cancer_types LGG "
cmd+="--pancancer_only "
cmd+="--results_dir results/coral_cancer_type/coral_control "
cmd+="--subset_mad_genes 5000 "
cmd+="2>co... |
799766d43fab8e1d476c7025d2172b629a1b0a66f077052a8872319d52c712cc | Shell | 1,740 | 60 | #!/bin/bash
# Load necessary modules
module purge
module load gcc/8.2.0
module load python/anaconda3.10-2022.10
source activate deeptools
# Define constants
BLACKLIST="/ix1/ialdiri/Genomes/mm10-blacklist.v2.bed.gz"
CHROM_SIZE="2650000000"
WINDOW_SIZE=10
BIGWIG_FILES=("$SOX2_BIGWIG_DIR/SOX2_S3_R1.bigWig" "$ATAC... |
826124b2a6d300d4127a2d5ad2fc2126a2b81d18dfa5771d07ef2bf39413b7eb | Shell | 1,743 | 60 | #!/usr/bin/env bash
set -x
export MASTER_PORT=$((12000 + $RANDOM % 20000))
export OMP_NUM_THREADS=1
# official train/test splits. valid numbers: 1, 2, 3
SPLIT=${SPLIT:-1}
OUTPUT_DIR='YOUR_PATH/work_dir/vit_g_hybrid_pt_1200e_k710_it_hmdb51_'${SPLIT}'_ft'
DATA_PATH='YOUR_PATH/data/hmdb51_'${SPLIT}
MODEL_PATH='YOUR_PAT... |
5685fb6c5148102e08430cf0af10294f58e0f3017361bac17cab8adbb447fea6 | Shell | 1,744 | 60 | #!/usr/bin/env bash
set -x
export MASTER_PORT=$((12000 + $RANDOM % 20000))
export OMP_NUM_THREADS=1
# official train/test splits. valid numbers: 1, 2, 3
SPLIT=${SPLIT:-1}
OUTPUT_DIR='YOUR_PATH/work_dir/vit_g_hybrid_pt_1200e_k710_it_ucf101_'${SPLIT}'_ft'
DATA_PATH='YOUR_PATH/data/ucf101_'${SPLIT}
MODEL_PATH='YOUR_PAT... |
aed79c0d5312569dc486e85ba61b2ab75fd00e1713dab27368b6ff296369de85 | Shell | 1,753 | 52 | #!/bin/bash
# Load necessary modules
module purge
module load gcc/8.2.0
module load python/anaconda3.10-2022.10
module load rgt/0.12.3
# Define Paths
ATAC_DIR="/bgfs/ialdiri/ATAC-Seq/Sox2_Stages/ATAC/outDir/bowtie2/merged_library"
OUTPUT_DIR="/bgfs/ialdiri/ATAC-Seq/Sox2_Stages/Motif_Footprinting_P7"
SOX2_PEAKS="/bg... |
515f70ed14cbd1628ed4235170812131fd5c1600162dd51ad87aae050537b305 | Shell | 1,756 | 48 | #!/bin/bash
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable ... |
de2759a7ffd50c12b6a462a55fc29574558a0c867392db908a0f143d8d1cd95b | Shell | 1,758 | 37 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../data"
# the most simplistic test on four atoms:
echo -e "./str_calc -calc::crmsd -in:pdb=test_inputs/four_atoms-1.pdb -in:pdb:native=test_inputs/four_atoms-2.pdb -out::pdb"
./str_calc -calc::crmsd -in:pdb=test_inputs/four_atoms-1.pdb -in:pdb:native=test_inputs/four_at... |
3703ec4e38c09e309d0f031fee075e5db1c9ed54a9e0efb746c57c4349d019e3 | Shell | 1,763 | 66 | #!/bin/bash
# Copyright 2020 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to ... |
74bae0c590eeb8c7f4430dc514b76f96898feb0cf685d608d6caf7fcc6d98ea2 | Shell | 1,773 | 52 | #!/bin/bash
sample=AHRB # abcd, AHRB, MLS
task=mid # mid = AHRB, reward = MLS
ses=1 # 1 or 2
mask_label=None # None, or wilson-sub, wilson-supra
type=run # run or session
outfold=/oak/stanford/groups/russpold/data/${sample}/derivatives/analyses/proj_reliability/icc_mods
scratch=/scratch/groups/russpold/${USER}/${sampl... |
4750ef0b2de46350c45c4f19d7e713a856f4ab28d290c50930497c71f0e8da8f | Shell | 1,776 | 86 |
SDIR=.../MRIQC
BDIR=$SDIR/data
ODIR=$SDIR/out
WDIR=$SDIR/work
######
# copy data
IDIR=.../subjects-5.3.0-STORAGE-freesurfer
doit=1
# find all input files
cd $IDIR
for file in `find ./*/???_TP? -name "orig.mgz"` ; do
ID=`echo $file | cut -f3 -d"/"`
OID=sub-`echo $ID | sed s/_//g`_T1w
echo $ID $OID
TODIR=$BD... |
46aeb19e7394ee1b33583b2bc94bd0443121396aad0df6d09b8e5ca4176ce2ec | Shell | 1,778 | 32 | #!/bin/sh
# Canonical-name `bismark` version-probe wrapper for the Rust-suite container
# (nf-core/methylseq drop-in).
#
# methylseq's 7 Bismark modules ALL capture the suite version from the `bismark`
# binary (verified against methylseq master), via two parser shapes:
# Parser-1 (align, topic: versions): `bismark -... |
b1ea04824b10a69d6f9b54a6778c0f4b2082b7c219419598bba2f944d53e17e5 | Shell | 1,786 | 43 | #! /bin/sh
#
# DO NOT CHANGE: This clears old freesurfer variables if they previously exists
if [ -n "$FREESURFER_HOME" ]; then
$FREESURFER_HOME/bin/clear_fs_env.csh
fi
# PLEASE CHANGE: Please specify location of CBIG repository
export CBIG_CODE_DIR=$HOME/storage/CBIG_private
# PLEASE CHANGE: define locations for ... |
0dd9c1fb722970b833a51a4dc2a4726f555e2e9637e7de67bdf04db66f53c2dc | Shell | 1,794 | 72 | #!/bin/bash
# author : sjn
# date : Dec.2022
set -euox pipefail
# For a 1kb bin along the genome, calculate the proportion of MSPs>150bp
# Numerator: Number of MSPs overlapping that bin by at least 1 bp that are >=150bp in length
# Denominator: Number of MSPs overlapping that bin by at least 1 bp
# Shift the bin ... |
13cb2f99f0daf5c2698012f22917a58aa577fd5417b866aa37ea7e4d1c0abf1b | Shell | 1,794 | 40 | #! /bin/sh
# Last successfully run on Apr 23th, 2019
# Written by CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
# DO NOT CHANGE: This clears old freesurfer variables if they previously exists
if [ -n "$FREESURFER_HOME" ]; then
$FREESURFER_HOME/bin/clear_fs_env.csh
fi
# PLEASE C... |
59fa764bb5a0bfe215755b47d8081a616993259f25a807e751f27e91abe1329b | Shell | 1,796 | 69 | #!/bin/bash
# Some quick shortcuts to ease running Syncopy's testing pipeline
# First and foremost, check if `srun` is available
_useSLURM=$(command -v srun)
# Stuff only relevant in here
_self=$(basename "$BASH_SOURCE")
_selfie="${_self%.*}"
_ppname="<$_selfie>"
# Brief help message explaining script usage
usage()
... |
00cff212e42c6377cdb6064598cb2505da466e0f46b0e6610387ec59c0827f03 | Shell | 1,800 | 47 | #!/bin/bash
# Description:
# This script makes copies of files generated from pipelines with opt3 and 4 for
# subjects that have a mean framewise-displacement <0.9. The subject list that is included should contain sub-IDs with mFD<.9
# This is done to avoid rerunning high resource modeling.
# Set meaningful variab... |
978351f1c73f1394834eff930d64b5f0cafe1e3fd581d5661cf93bf49152750a | Shell | 1,803 | 38 | #Purpose: Calculate SA per network using fsaverage6 resolution surfaces
#Inputs: Kong2019 parc parc2annot and annot2gii output. Midthickness Conte69 in fsaverage6 space.
#Output: Surface area for LH and RH for 17 networks
#Software: wb_command (HCP), freesurfer
#Written by M. Peterson, Nielsen Brain and Behavior Lab u... |
0c4d198d5e8b5fe9d6bfa1766586bb205f7cad1dc55006d7702c9d746c61f68e | Shell | 1,804 | 49 | #!/bin/bash
#SBATCH --time=20:00:00 # walltime
#SBATCH --ntasks=1 # number of processor cores (i.e. tasks)
#SBATCH --nodes=1 # number of nodes
#SBATCH --mem-per-cpu=51250M # memory per CPU core
#SBATCH -J "HCPprep" # job name
# Set the max number of threads to use for programs using OpenMP. Should be <= pp... |
c19215b67ded9b2914fbbb9dc85c10db09e9adac329c4e527466f341578985ee | Shell | 1,810 | 60 | #!/bin/bash
# File: run_example.sh
# Author: Kelly Chang
# Date: Oct 2017
# Version: 1.0
#
# Description: Bash script to demonstrate the use of hERG bootstrap fitting
# code. This code is provided for example only.
#
mkdir logfiles
#--- create bootstrap samples
DRUG="beprid... |
8ff17c1e7f1f8a85dde4e5eaf09c3cc421c2cda8834bf77812d813eed0856edb | Shell | 1,816 | 32 | #!/bin/bash
#
# train and evaluate Polarbear model
#conda activate polarbear
## download data in https://noble.gs.washington.edu/~ranz0/Polarbear/data/ to ./data/
data_dir=./data
cur_dir=.
train_test_split=$1 # train/val/test split: "babel" or "random"
semi_version=$2 # only use co-assay to train "coassay" or also inc... |
a457afb2eaa4d6aaf02fb166ae40a4137591320d06594be262c32ee9c27fdafc | Shell | 1,821 | 51 | #!/bin/bash
# =============================================================================
# Author: Gerard Martí
# Description: Runs a few commands to do quality control of the tracking,
# generating relevant images that show the tracking generated
# =================================================================... |
62b7fd4add806f5f52b14f316c583f35c6a606c6314b58e24aa1608ab720f568 | Shell | 1,823 | 56 | # command interpreter to be used
#$ -S /bin/bash
#
# name
#$ -N ref_rln_mbf
#
# merge stdout and stderr stream of job
#$ -j y
#
# output file
#$ -o ../../../../data/tutorials/synth_sumb/rln/mbf_align_post/out_run2.log
#
# use current working directory
#$ -cwd
#
# define mail notification events
#$ -m n
#
# request the ... |
7921dd8e5d5adde01ef6ef6a902b14a3effe0cd70be279ffbcc37f102bfa4937 | Shell | 1,829 | 24 | #!/usr/bin/env bash
# Reproduce the "Infinite Nekrasov" continuous-generation experiments (RTX 3070 Ti: ~1 h).
# Every run: seed "Однажды в студёную зимнюю пору", 128-token window, greedy decoding,
# EOS suppressed identically in all conditions (each suppression is recorded).
set -euo pipefail
project_root="$(cd -- "$(... |
8055aa71abd05a789490a8e86a38bae786fb236b030dcba06736ee7882c86473 | Shell | 1,830 | 60 | #! /bin/sh
#
# Copyright 2000 Free Software Foundation, Inc.
#
# This file is part of the GNU MP Library.
#
# The GNU MP Library is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as published
# by the Free Software Foundation; either version 3 of the L... |
d16cf92a23605bfad2a89ba4cd6adc36c3f0606f82a93afb5213a11b882e5e65 | Shell | 1,835 | 61 | #!/bin/bash
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable ... |
a43fab9b20f67cca5d571edeb464654425a4eeafe9a7957c6b11219320892599 | Shell | 1,837 | 25 | ### Ran from datasets/ directory on GPU
mkdir subsampled_10fold
for x in `seq 2000 2000 16000`; do { echo $x; python subsample.py $x pM10Kb_1KTest subsampled_10fold/$x; } done
for z in `seq 2000 2000 16000`; do { for y in {0..9}; do { for x in {0..9}; do { python Xpresso.py --fold $y --trial $x train tpe_1K_10epochs... |
c01bfbc1c789d97ed3cff6b3dc648728c5186a54c3e4558e2b749a728c5677dc | Shell | 1,843 | 36 | export CARLA_ROOT=${1:-/home/kchitta/Documents/CARLA_0.9.10.1}
export WORK_DIR=${2:-/home/kchitta/Documents/misc/transfuser}
export CARLA_SERVER=${CARLA_ROOT}/CarlaUE4.sh
export PYTHONPATH=$PYTHONPATH:${CARLA_ROOT}/PythonAPI
export PYTHONPATH=$PYTHONPATH:${CARLA_ROOT}/PythonAPI/carla
export PYTHONPATH=$PYTHONPATH:$CAR... |
1c4ed9915db3f02b5d1e0021a20149094a1a62bc415aec1918c8febdaaede2dd | Shell | 1,847 | 44 | #!/bin/bash
# Written by Ruby Kong and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
orig_mesh=${1} # original data mesh
resample_mesh=${2} # target mesh of resampling
project_dir=${3} # output directory
data_type=${4} # data_type = metric/label.
version=${5} # version = 201... |
ebd790298f528c27d848032503ecf9a0619ec0c3878bbd1cf41c80a416726f6b | Shell | 1,847 | 39 | #!/bin/bash
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable ... |
6d19700019001bcd6cb75ab0d79cbd7eaa98217d39d4981886f37f8ae46b5164 | Shell | 1,848 | 54 | #!/bin/bash
# Written by Xiuming Zhang and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
###########################################
# Usage and Reading in Parameters
###########################################
# Usage
usage() { echo "
Usage: $0 -d <docs> -k <noTopics> -r <noIni... |
cbb799c46e41c4d068c4aa5782012ab3e8acf7d7266d6f3fee551f90f90e2361 | Shell | 1,849 | 45 | #! /bin/sh
# Last successfully run on April 1st, 2018
# Written by CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
# DO NOT CHANGE: This clears old freesurfer variables if they previously exists
if [ -n "$FREESURFER_HOME" ]; then
$FREESURFER_HOME/bin/clear_fs_env.csh
fi
# PLEASE ... |
9d0577cecfffcc3833cd989c88a4191d79e5b00219ddd9d0a91c847ad60f6ab8 | Shell | 1,851 | 62 | #!/bin/bash
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable ... |
d6002bafd2258f8d112aff72bf8f0c178881390bef883393d31e348a04432956 | Shell | 1,857 | 58 | #!/bin/bash
# Written by Xiuming Zhang and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
###########################################
# Usage and Reading in Parameters
###########################################
# Usage
usage() { echo "
Usage: $0 -g <GMList> -o <outDir> [-q <queu... |
1e795604bd60e8ce5693e5ec06a8d640b21ea7a6c92a0081bddaf93cb2b89d39 | Shell | 1,868 | 78 | #!/usr/bin/env bash
set -euo pipefail
MOCHI_ROOT="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
MOCHI_REPO="${MOCHI_REPO:-${MOCHI_ROOT}}"
MOCHI_VENV="${MOCHI_VENV:-${MOCHI_REPO}/.venv}"
PYTHON_SPEC="${PYTHON_SPEC:-3.11}"
UV_INSTALL_DIR="${UV_INSTALL_DIR:-${HOME}/.local/bin}"
ensure_uv() {
if command -v uv >/dev/... |
26fc98a198b5ca38ba0f41d2350ed116426a3e43b8d2d003e8ec62c7e4aefd25 | Shell | 1,871 | 49 | #!/bin/bash
#SBATCH -D /well/woolrich/users/olt015/Cho2024_MEEG_RSN/results/dynamic_no_struct/camcan
#SBATCH -p gpu_short
#SBATCH --gres gpu:1
#SBATCH --mem-per-gpu 80G
#SBATCH --constraint "a100|v100"
# Check the number of arguments
if [ $# -lt 6 ]; then
echo "Too few arguments. Usage: $0 [lemon|camcan] [hmm|dyn... |
d96f89c51fc722bcfc011813e4fd1c3ec3b638d14d1d2bf27c96507fbf7633a6 | Shell | 1,873 | 89 | #!/bin/bash -efx
# author : sjn
# date : Aug 22, 2022
set -euo pipefail
if [[ $# != 4 ]]; then
printf "Expect $0 <sample-name> <input-file> <output-pdf> <output-stat.txt>\n"
exit 1
fi
samplenm=$1
inp=$2 # fiber-all-table.tbl.gz
outpdf=$3
outstat=$4
ftype=rq
tmpd=/tmp/$(whoami)/$$
if [ -s $tmpd ]; then
... |
b0b4cc7c1e8432b0cc96deb62aac98c76feeaa04e1c484b927575743a1f7774c | Shell | 1,895 | 33 | #!/bin/bash
#Purpose: Create Conte69 midthickness surface file in fsaverage6 space using Workbench.
#Inputs: Conte69 midthickness fs_LR 32k (download: https://raw.githubusercontent.com/MidnightScanClub/MSCcodebase/master/Utilities/Conte69_atlas-v2.LR.32k_fs_LR.wb/Conte69.L.midthickness.32k_fs_LR.surf.gii)
#Outputs: Co... |
372f9d13127fe61e1c1bc745d23953609ee3b1a6b50798f3660d54d8aa5e0a80 | Shell | 1,897 | 51 | #!/usr/bin/env bash
# Written by Wu Jianxiao and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
#This functions creates a temporary pbs file in the work_dir to submit, according to the input parametres, so that the outputs of the job reside in the work_dir
#Note that input cmd shoul... |
52e4a4a68f26130f14f6877a9fd9573609231c180011b586506ada4dc140af31 | Shell | 1,915 | 73 | #!/usr/bin/env bash
set -e
# Change to the script directory
cd "$(dirname "$0")"
# Get root directory
REPO_ROOT_DIR=$(git rev-parse --show-toplevel)
# Check if emscripten is installed
if ! command -v emcmake &> /dev/null; then
echo "Emscripten is not installed. Please install it and make sure it is in your PATH... |
57f553d05dd86e30bdbdc28e2b5e18a2b40e0cbb5e5be22c9897b41f652e5824 | Shell | 1,917 | 44 | #! /bin/sh
# Last successfully run on July 8th, 2019
# Written by Valeria Kebets and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
# DO NOT CHANGE: This clears old freesurfer variables if they previously exists
if [ -n "$FREESURFER_HOME" ]; then
$FREESURFER_HOME/bin/clear_fs_env.... |
5fb93666ce37823d0a334337ea4c8cdb7ebf7f7c923adc5f465e673db4c50a56 | Shell | 1,919 | 61 | #!/bin/bash
n_components=500
for kernel_type in linear rbf; do
for mu in 0.1 1 10 100; do
cmd="python 02_cancer_type_classification/run_cancer_type_classification.py "
cmd+="--tca "
cmd+="--tca_mu $mu "
cmd+="--tca_kernel_type $kernel_type "
cmd+="--tca_n_components $n_comp... |
55694af525f2cc3061d5b346cd130e9c2ef1d3c238b8f5ed1c003859a0ad05dd | Shell | 1,922 | 41 | #!/usr/bin/env bash
# Copyright 2017 Google Inc.
# All Rights Reserved.
#
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# * Redistributions of source code must retain the above copyright
# notice, this list of... |
64dfa5cab4b987a03df90250812014c9381f2061ab0d601a2d613c5451edf93f | Shell | 1,922 | 44 | #! /bin/sh
# Last successfully run on Dec 2nd, 2019
# Written by CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
# DO NOT CHANGE: This clears old freesurfer variables if they previously exists
if [ -n "$FREESURFER_HOME" ]; then
$FREESURFER_HOME/bin/clear_fs_env.csh
fi
# PLEASE CH... |
05b78b460f12f162c579e6e0500450dae4972b5c433d12271e5497241fe6fbb8 | Shell | 1,923 | 45 | #! /bin/sh
# Last successfully run on Jan 12nd, 2018
# Written by CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
# DO NOT CHANGE: This clears old freesurfer variables if they previously exists
if [ -n "$FREESURFER_HOME" ]; then
$FREESURFER_HOME/bin/clear_fs_env.csh
fi
# PLEASE C... |
40a4be64abee7a3d738a5f57efc5f642346543fee361d76c6c8a6915a5471423 | Shell | 1,923 | 68 | #!/bin/bash
## 1. receive arguments from 06mpileup.sub
outdir_staging=$1
indir_staging=$2
conda_pack_squid=$3
genome_seq_squid=$4
job=$5
## 2. configure the conda enviroment
set -e
workdir_pac=$(basename $conda_pack_squid)
ENVNAME=$(basename $conda_pack_squid .tar.gz)
ENVDIR=$ENVNAME
# these lines handle setting up... |
5f6f8553bb75ec1199638c9050efe93291aaf6f02ede03a3dd1e1a7930aaa459 | Shell | 1,923 | 44 | #! /bin/sh
# Last successfully run on Nov 18th, 2019
# Written by CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
# DO NOT CHANGE: This clears old freesurfer variables if they previously exists
if [ -n "$FREESURFER_HOME" ]; then
$FREESURFER_HOME/bin/clear_fs_env.csh
fi
# PLEASE C... |
1df57de8d17da15042fae38403a65de9e2e4d77a7752256c267ca6db314fa52a | Shell | 1,928 | 24 | #$ -N partherit
#$ -cwd
#$ -q multi15.q
#$ -S /bin/bash
# Dyslexia
/data/workspaces/lag/workspaces/lg-genlang/Working/SCRIPTS/23andMe/clap-beat_dyslexia/pleiotropyevo/ldsc/partherit_baseline.sh /data/clusterfs/lag/users/gokala/beat-dyslexiaevol/data/munged/dyslexia.sumstats.gz HAQER.sorted /data/clusterfs/lag/users/g... |
5e01371537d5342619b9299034d52257af246ee3f91d25912aac2e0a6e27f39c | Shell | 1,934 | 40 | #Purpose: Calculate SA per network using fsaverage6 resolution surfaces
#Inputs: Kong2019 parc parc2annot and annot2gii output. Midthickness Conte69 in fsaverage6 space.
#Output: Surface area for LH and RH for 17 networks
#Software: wb_command (HCP), freesurfer
#Written by M. Peterson, Nielsen Brain and Behavior Lab u... |
0939ef62ad793ec4dcc57d12581affb2425ebf12141dea11f978e4541e6ff6c0 | Shell | 1,937 | 41 | #!/bin/bash
# Copyright 2020 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to ... |
4e816616662e05fc15777d60b6a258f95a0ea8aa14ae0d34a7543f5d6b6d1f57 | Shell | 1,938 | 40 | #Purpose: Calculate SA per network using fsaverage6 resolution surfaces
#Inputs: Kong2019 parc parc2annot and annot2gii output. Midthickness Conte69 in fsaverage6 space.
#Output: Surface area for LH and RH for 17 networks
#Software: wb_command (HCP), freesurfer
#Written by M. Peterson, Nielsen Brain and Behavior Lab u... |
7aa1f5f9645059ec450b0e819b6b36ce685456eca0fb35a82578553436c967ca | Shell | 1,938 | 40 | #Purpose: Calculate SA per network using fsaverage6 resolution surfaces
#Inputs: Kong2019 parc parc2annot and annot2gii output. Midthickness Conte69 in fsaverage6 space.
#Output: Surface area for LH and RH for 17 networks
#Software: wb_command (HCP), freesurfer
#Written by M. Peterson, Nielsen Brain and Behavior Lab u... |
06681a68b5a4621fe4cc2ee24c0b276a3090183f6c733d01e737f9ec5a696a09 | Shell | 1,944 | 79 | #!/bin/bash
## sanitizing - final check removing gaps and Ns
remove_gaps_check_fun(){
## $1 is the file argument
conda activate seqkit
mv $1 tempX.fasta
seqkit seq -g -G "- N n " -o $1 tempX.fasta
rm tempX.fasta
conda deactivate
}
## to run if formatting problem - windows endings
## se... |
203da102662bc47aedc687b006d99cc20f318b775f3e3101f6eb0d37b950f02f | Shell | 1,948 | 58 | #!/bin/bash
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable ... |
ceda912ae2ae39970c5c06ff030e442ca7a0f4dbaa9e64dee9cf7dea601982fa | Shell | 1,959 | 38 | #!/usr/bin/env bash
RESULT_PATH="./arch_results"
FIGURE_PATH="./arch_results/Figures"
QUPATH_PROJECT_PATH=../data/ProjectQuPath_for_test.qpproj
TRAINING_PATH=../data/ml-training
PREDICTION_PATH=../data/ml-pred
rm -rf $RESULT_PATH
printf "\nPIPELINE INFO: Convert cells features and annotation to pandas dataframes\n"
... |
04459f9648c3d4e6c4b4cc988a6cd01932f5f2d7705b2466880085059c30f2d8 | Shell | 1,960 | 53 | #!/bin/bash
h2oLog="/opt/h2oai/logs/init.log"
if [ ! -f $h2oLog ]; then
#Put here your initialization sentences
mkdir -p /opt/h2oai/logs
cd /opt/h2oai
echo "Installing latest version of h2o" >>$h2oLog
# Adjust based on the build of H2O you want to download.
h2oBranch=rel-va... |
abb62b691b9c038ed4214fca2f151f5b7edcdfffd8044a313dc1400f274a1605 | Shell | 1,970 | 41 | #Purpose: Calculate SA per network using fsaverage6 resolution surfaces
#Inputs: Kong2019 parc parc2annot and annot2gii output. Midthickness Conte69 in fsaverage6 space.
#Output: Surface area for LH and RH for 17 networks
#Software: wb_command (HCP), freesurfer
#Written by M. Peterson, Nielsen Brain and Behavior Lab u... |
564471da6a8008a3c1ab9fb27412c169605565127673f9364a55e58ace663c00 | Shell | 1,972 | 40 | #!/usr/bin/env bash
# Phase C real-data byte-identity gate: Perl NOMe_filtering vs Rust
# NOMe_filtering_rs on a common real `--yacht` input + genome. The DECOMPRESSED
# outputs must be byte-identical (the gzip container is impl-dependent — Perl
# `gzip -c` vs Rust `flate2` — so we compare post-decompression; SPEC §6 /... |
8c56ec07598dba47436b17af85b6a6bf5fc6c1ea6efff1a020865128fba34a62 | Shell | 1,975 | 72 | #!/bin/bash
set -ex
if [ -z "$TRINOTATE_HOME" ]; then
TRINOTATE_HOME=`pwd`/..
fi
for file in input_data/*.gz
do
if [ ! -e ${file%.gz} ]; then
gunzip -c $file > ${file%.gz}
fi
done
if [ ! -d DESeq2_trans ]; then
tar xvf input_data/DESeq2_trans.tar
fi
if [ ! -d DESeq2_gene ]; then
tar xvf input... |
e0757ea31bde447d50474a7ce152c73b3e22b81a03694ae89a32a9fee28b86c0 | Shell | 1,976 | 45 | #! /bin/sh
# Last successfully run on Mar 19th, 2018
# Written by Wu Jianxiao and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
# DO NOT CHANGE: This clears old freesurfer variables if they previously exists
if [ -n "$FREESURFER_HOME" ]; then
$FREESURFER_HOME/bin/clear_fs_env.csh... |
f5bf9126c23f8e7a1f803a16b8ebc3be595b8015be53621f207a8c9023d8c0e8 | Shell | 1,976 | 63 | #!/bin/bash
#==============================================================
# basic QC
#==============================================================
#--------------------------------------------------------------
# make plink fileset of only those with autopsy data
#-------------------------------------------------... |
2218f5a5765c45b3da9e87056c954288249a65734dece43e415bd61c006bebe3 | Shell | 1,977 | 45 | #! /bin/sh
# Last successfully run on Jan 12nd, 2018
# Written by CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
# DO NOT CHANGE: This clears old freesurfer variables if they previously exist
if [ -n "$FREESURFER_HOME" ]; then
$FREESURFER_HOME/bin/clear_fs_env.csh
fi
# PLEASE CH... |
0a882f799a4c9f36e4d2f030f7057b383d177620309c8a672fe453bf4fa43839 | Shell | 1,978 | 45 | #! /bin/sh
# Last successfully run on Jan 12nd, 2018
# Written by CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
# DO NOT CHANGE: This clears old freesurfer variables if they previously exist
if [ -n "$FREESURFER_HOME" ]; then
$FREESURFER_HOME/bin/clear_fs_env.csh
fi
# PLEASE CH... |
d87e22c3f59f260bcf8392e98ecc599a28c07ed21406148b970e26c9af453fcd | Shell | 1,980 | 91 | #!/bin/bash
trap 'kill 0' EXIT
if [ $# -ge 1 ]; then
CMD="$@"
else
CMD=
fi
INTERVAL=5
COUNT=12
LOGDIR=logs
if [ ! -d $LOGDIR ]; then
mkdir $LOGDIR
else
echo "WARNING: logs dir exists. OK? (y/n)"
read -sn1 ANSW
if [ "$ANSW" = "n" -o "$ANSW" = "N" ]; then
echo "Canceled."
exit 1
fi
fi
echo "... |
7c2faacb817167223da68d0dec79697b742591e62deba8c8d2cd5e658f7494d1 | Shell | 1,985 | 23 | python3 -W ignore scperb.py --model_name CD4T --exclude_celltype CD4T --data pbmc --supervise True
python3 -W ignore scperb.py --model_name CD14+Mono --exclude_celltype CD14+Mono --data pbmc --supervise True
python3 -W ignore scperb.py --model_name B --exclude_celltype B --data pbmc --supervise True
python3 -W ignore s... |
9730bba0be5f5d0f4a268bd712332233a0ff16e5f5e917541e0a8109540ac0bd | Shell | 1,987 | 69 | #!/bin/bash
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable ... |
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