sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
a53054fe9bdebb376109f4cc00dc343f842fc6efb1e04aa9e7cd76afc568776f | Shell | 608 | 24 | # SLURM Script to allocate gpus and run trainings
#!/bin/bash
#SBATCH --partition=npl-2024
#SBATCH --job-name=train1
#SBATCH --nodes=4
#SBATCH --ntasks-per-node=8
#SBATCH --gres=gpu:8
#SBATCH --cpus-per-task=8
#SBATCH --time=06:00:00
#SBATCH --output=__train_%j.out
#SBATCH --error=__error_%j.err
source ~/scratch/... |
d0d87644708e22788e17d61b53f2effd7907ec621ca5ba12a2f7860af2cb1e2f | Shell | 609 | 16 | #!/bin/bash
for contrast in "motor" "ffa" "vwfa" "shape1" "shape3" "all_shapes" "house" "tool"; do
python 03d_output_cluster_table.py --task=category --contrast=$contrast &
python 03d_output_cluster_table.py --task=category --contrast=$contrast --kids &
done
for contrast in "geom_theory" "geom_behavior_online" "g... |
0a5a6bb5b87aedb9dfc3cc9e286a6f95256c4509881bf18a9fa798f70c1074dd | Shell | 610 | 27 | #!/bin/bash
#SBATCH --time=05:00:00
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --gpus-per-node=1
#SBATCH --job-name=gnn_pbd_pars_est_val_diffpool
#SBATCH --output=logs/gnn_pbd_pars_est_val_diffpool-%j.log
#SBATCH --mem=64GB
#SBATCH --partition=gpu
ml Python/3.8.16-GCCcore-11.2.0
source $HOME/venvs/eve/bin/activate
... |
ac7a93ac22d68369aa80bf546a6942069354dd34c15f2f0a96d1d2f7ca3c5405 | Shell | 610 | 27 | #!/bin/bash
# Script to run all steps of com in a single job using multi-gpu prediction.
#
# Inputs: com_config - path to com config.
#
# Example: sbatch com_multi_gpu.sh /path/to/com_config.yaml
#SBATCH --job-name=com_multi_gpu
#SBATCH --mem=10000
#SBATCH -t 5-00:00
#SBATCH -N 1
#SBATCH -c 1
#SBATCH -p olveczky... |
c298cb8d1b2abfacd6f47f3b1bbd88b1384cb8ff38d95ceb9d269d727b452ece | Shell | 612 | 24 | #!/bin/bash
input_file="/cmd_heart_brain.txt"
output_dir="/cmd_heart_brain"
ldsc_script="/ldsc.py"
ref_ld_chr="/eur_w_ld_chr"
w_ld_chr="/eur_w_ld_chr"
# Initialize the row counter
i=1
# Loop through each line in the input file
tail -n +2 "$input_file" | while IFS=' ' read -r file1 file2; do
# Execute the ldsc.py... |
55d86b64bfbf0517a4a267c1c81b0cab90532ce90977c4fb01fc147cd6e4c6d9 | Shell | 613 | 20 | # This sample has an edit at the very end of the read. But we want to make sure it is not included if dist from end filter
# is active.
mypython=$1
$mypython $MARINE/marine.py \
--bam_filepath \
$MARINE/tests/singlecell_tests/bams/10_C-1_orig.bam \
--annotation_bedfile_path \
$MARINE/annotations/cellranger-GRCh38-3.0... |
9ddf125415702f8b512f464d4762d27627fca79cc0e3dbb8964cc778978a9486 | Shell | 616 | 26 | #!/bin/bash
#SBATCH --mem=16G
#SBATCH -c 8
#SBATCH -t 02:00:00
#SBATCH --error=/logs/err_%j.err
#SBATCH --output=/logs/out_%j.out
#SBATCH -p gpuq
#SBATCH --gres=gpu:a100:1
module load cuda11.8/toolkit/11.8.0
nvidia-smi
date
# Activate the Miniconda base environment.
source {your_conda_directory}/miniconda3/bin/activa... |
aaf33ad5909f14d020ce9a9017361dc3607cc339032eb7f4cfdc1de8eee4546f | Shell | 616 | 9 | #GM12878 hotspots:
wget https://www.encodeproject.org/files/ENCFF828AUX/@@download/ENCFF828AUX.bed.gz -O hotspots_ENCFF828AUX.bed.gz
wget https://www.encodeproject.org/files/ENCFF452DZE/@@download/ENCFF452DZE.bed.gz -O hotspots_ENCFF452DZE.bed.gz
#GM12878 peaks:
wget https://www.encodeproject.org/files/ENCFF598KWZ/@@do... |
8333f982cf84920b8ebbb9f44f16c032bf955adf2c83758757cf1e2771acde4d | Shell | 617 | 13 | eval "$(/pollard/home/sdrusinsky/miniforge3/bin/conda shell.bash hook)"
source /pollard/home/sdrusinsky/miniforge3/bin/activate test_pt231
cd "$(dirname "${BASH_SOURCE[0]}")" #cd into the directory containing this script
cd .. #cd into `code` directory
script_path=./select_drivers_enformer.py
select_drivers=true
eval... |
a5c1c68ca82947006829b24baf0b0ceb0f255aa67670e9482e17300f26022302 | Shell | 618 | 14 | fold=0
seed=0
model_type=MultiGene
# config_path=configs/blood_train_RefAvg_config.yaml
# for monitor in mean_loss_train_genes_across_valid_donors mean_loss_valid_genes_across_valid_donors; do
# sbatch slurm_train_gtex_ref_avg.sh $config_path $fold $model_type $seed $monitor
# done
#train with infinite epochs, ba... |
d830d273982f59cc3471b8ad7a1a77724b046024f273a7a3560bbce2ec173846 | Shell | 618 | 27 | #!/bin/bash
# Exit on error
set -e
# Container name/ID to stop
CONTAINER_NAME="surface_morphometrics_container"
# Timeout in seconds
TIMEOUT=5
# Handle Ctrl+C
trap 'echo "Received interrupt signal..."; exit 1' INT
echo "Stopping container $CONTAINER_NAME..."
# Check if container is running and stop it
if docker ... |
087b3589b0d4833d749d4eab3daab9516e0bfe44538cdc6127e177b3cbd1514b | Shell | 619 | 11 | python3 generate_ogbn_dataset_hard_inputs.py --dataset BALBc_no1 &
python3 generate_ogbn_dataset_hard_inputs.py --dataset BALBc_no2 &
python3 generate_ogbn_dataset_hard_inputs.py --dataset BALBc_no3 &
wait
python3 generate_ogbn_dataset_hard_inputs.py --dataset C57BL_6_no1 &
python3 generate_ogbn_dataset_hard_inputs.py ... |
48ef291053e62959085350b447e86b9b457f483026c274d72487e41324171d6a | Shell | 619 | 28 | #!/bin/bash
#SBATCH --time=6:00:00
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --job-name=gnn_training
#SBATCH --output=logs/gnn_training-%j.log
#SBATCH --mem=32GB
#SBATCH --partition=regular
ml Python/3.8.16-GCCcore-11.2.0
source $HOME/venvs/eve/bin/activate
# Check if at least two arguments are provided (name and ... |
1b72fbe853769c6ba5c17921ed4530f41a554c6bfce6b6aca8d6532e3502f885 | Shell | 620 | 7 | #!/bin/bash
mkdir -p deps
wget https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/releases/fslinstaller.py -O deps/fslinstaller.py
wget https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.4.1/freesurfer_ubuntu22-7.4.1_amd64.deb -O deps/freesurfer_ubuntu22-7.4.1_amd64.deb
wget https://github.com/conda-forge/miniforge... |
a3e34ebb7b11c4be0c329164e87940196de479f0cb0c2e37e969ccefa01a2285 | Shell | 620 | 19 | #!/bin/bash
if [ ! -e Trinity.fasta ]; then
gunzip -c Trinity.fasta.gz > Trinity.fasta
gunzip -c genome_alignments.gmap.gff3.gz > genome_alignments.gmap.gff3
fi
../../TransDecoder -t Trinity.fasta $*
# gmap was used to align the Trinity.fasta transcripts to the genome,
# using the gmap '-f 3' output formatti... |
64e3d2e0bb2eea992f851c3d899809017a2f3b46d50b763875432924cf64679a | Shell | 621 | 19 | #!/bin/bash
# Set the partition and other SBATCH specifications for individual subject jobs
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --time=12:00:00
#SBATCH --job-name=recon_all_subject
#SBATCH --output=/imaging/hauk/rl05/fake_diamond/scripts/preprocessing/mri/job_log/%j_subject_output.log
#SBATCH --error... |
ce0afb706e636a42a3bc272dc94e2888f70250e3ab502043c1ce4818a7bd2ce5 | Shell | 622 | 27 | #!/bin/bash
set -e -E -u -o pipefail
rm -f ./_FIRST_RUN.flag
export PATH="${CONDA}/bin:${PATH}"
curl \
-sL \
-o "${HOME}/miniforge.sh" \
"https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-$(arch).sh"
/bin/bash "${HOME}/miniforge.sh" -b -p "${CONDA}"
conda config --set ... |
2fbf37e21a05aac26935dac8c890fbd169e94b09f1742da9fa1c9b833f574359 | Shell | 624 | 27 | #!/bin/bash
#SBATCH --time=22:59:00
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --gpus-per-node=1
#SBATCH --job-name=gnn_eve_pars_est_diffpool_cls
#SBATCH --output=logs/gnn_eve_pars_est_diffpool_cls-%j.log
#SBATCH --mem=64GB
#SBATCH --partition=gpu
ml Python/3.8.16-GCCcore-11.2.0
source $HOME/venvs/eve/bin/activate
... |
948bee3fbf64e03ad8a4c71774a79fcb6d33fa46fb672dc7df121ffa986905da | Shell | 625 | 27 | #!/bin/bash
#SBATCH --time=2-01:00:00
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --gpus-per-node=1
#SBATCH --job-name=gnn_ddd_pars_est_opt_diffpool
#SBATCH --output=logs/gnn_ddd_pars_est_opt_diffpool-%j.log
#SBATCH --mem=64GB
#SBATCH --partition=gpu
ml Python/3.8.16-GCCcore-11.2.0
source $HOME/venvs/eve/bin/activate... |
874f6f4eb30bcb74018cb5d4c531a5b62df52c14425e20f735be8e424c7b4c76 | Shell | 628 | 8 | #!/bin/bash
read -p "Enter your csic.som.emory.edu username: " CSIC_USERNAME
# This script is currently set up to FULLY SYNC THE CSIC AND ARCHIVAL VERSIONS OF THE FOLDER
# so if there is any data in the CSIC folder you don't want to download... DEAL WITH IT!
# it may take a while to index the files at the beginning b... |
12876fb86613d403f7ff6114df4dd44551af5813781bf9e3c588befe03557d98 | Shell | 631 | 25 | #!/bin/bash
# Script to run all steps of dannce in a single job using multi-gpu prediction.
#
# Inputs: dannce_config - path to com config.
# Example: sbatch dannce_multi_gpu.sh /path/to/dannce_config.yaml
#SBATCH --job-name=dannce_multi_gpu
#SBATCH --mem=10000
#SBATCH -t 5-00:00
#SBATCH -N 1
#SBATCH -c 1
#SBATCH -p o... |
b917a72bc249a08bf38b78261a8da4b1e7937a3d71ba302b307e920d49be105f | Shell | 631 | 17 | # k in (10, 20, 30)
# h in (512, 768, 1280)
# use single model for inference (default)
DATASET=proteingym-benchmark
CUDA_VISIBLE_DEVICES=0 python compute_fitness.py \
--gnn_model_name k10_h512 \
--mutant_dataset_dir data/mutant_example/$DATASET \
--result_dir result/$DATASET
# select the models for ensemb... |
56d406209d12ebe0c49c6bf73bb5dc08ab9bd2f12359d5e6b030da37aa78cd75 | Shell | 633 | 19 | #!/bin/bash
# Set the partition and other SBATCH specifications for individual subject jobs
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --time=01:00:00
#SBATCH --job-name=watershed_subject
#SBATCH --output=/imaging/hauk/rl05/fake_diamond/scripts/preprocessing/mri/job_log/%j_subject_output.log
#SBATCH --error... |
170a70ddf576745327aa15d22ad4e46b335266c2a3a3dd75a81959a5b5abdd83 | Shell | 635 | 23 | #!/bin/bash
#
# upsample.sh <filename> <factor> <method>
#
# -upsamples in all 3 dimensions using AFNI 3dresample
mapfile=$1
factor=$2
method=$3
scaled_mapfile=$(dirname ${mapfile})/scaled_$(basename ${mapfile})
delta_x=$(3dinfo -di ${mapfile})
delta_y=$(3dinfo -dj ${mapfile})
delta_z=$(3dinfo -dk ${mapfile})
sdelta... |
5727b76d43d81f7a454f1f24a767a276758ccfee357c4c659bc532fc8ce17101 | Shell | 635 | 20 | #!/bin/bash
# Author: Abhishek Choudhary
set -euo pipefail
IFS=$'\n\t'
input_bam=$1
prefix=$2
output_bam=${prefix}.Aligned.toTranscriptome_noIDS.out.bam
samtools view ${input_bam} | awk '{print $1}' | sort | uniq > readids_all
samtools view ${input_bam} | awk '$6 ~ "I|D|S"' | awk '{print $1}' | sort | uniq > readid... |
d2f9221e00881e9f61493f8a2c5ffcdd8191f7055559a2e696e5d98edd6297b6 | Shell | 640 | 18 | #!/bin/bash
#$ -M jnajera2@nd.edu # Email address for job notification
#$ -m abe # Send mail when job begins, ends and aborts
#$ -pe mpi-24 48 # Specify parallel environment and legal core size
#$ -q debug # Specify queue
#$ -N genomeGenerate # Specify job name
module load bio/star/2.7.2
GENOMEDIR="/afs/crc/gro... |
d9f574cb07b636b2e0acd80aaea3dd6856b781f10c8a994fe6f9d3b0b429798d | Shell | 641 | 24 | #!/bin/bash
set -euo pipefail
fs_dir="/mnt/f/BIDS/demo_BIDS/derivatives/freesurfer"
fs4fmriprep_dir="/mnt/f/BIDS/demo_BIDS/derivatives/freesurfer4fmriprep"
mkdir -p "$fs4fmriprep_dir"
shopt -s nullglob
for sub_dir in "$fs_dir"/sub-*; do
sub=$(basename "$sub_dir")
for ses_dir in "$sub_dir"/ses-*; do
ses=$(bas... |
aee3354357a774b28db85a7f2148223102b69130748c1325d6251b7ea7a690bf | Shell | 643 | 16 | #!/usr/bin/bash
export ROSETTA=/path_to_rosetta/rosetta_src_2018.33.60351_bundle/main
export ROSETTA_BIN=$ROSETTA/source/bin
export ROSETTA_DB=$ROSETTA/database
# Do the mutation and get the energetics
echo "Mutation in progress..."
$ROSETTA_BIN/rosetta_scripts.linuxgccrelease @flags_mutate -out:level 200
echo "Ener... |
bcf5ef373e35ad48e6bae542cee245a5ff876ba350a749b3e4903768810ef07a | Shell | 643 | 18 | #!/bin/bash
echo $LSB_JOBINDEX
echo $1
data=$(head -n $LSB_JOBINDEX $1 | tail -n1)
echo $data
INPUTBAM=$(echo $data | awk {'print $1'} )
poolnum=$(echo $data | awk {'print $2'})
INPUTVCF=genotypes/MLOallgenotypes.vcf.bgz
DEMUXLET=/software/demuxlet/demuxlet
rootfolder=$(echo $INPUTBAM | sed 's/possorted_genome_bam.b... |
72931327beed37bfa69f74f2629f99a7f7e5db9588f9abc368954b1279c98653 | Shell | 645 | 15 | #!/bin/bash
set -e
# -------
# Run this bash script while inside demo/markerless_mouse_1/
# Note: this script will only work with --start-sample=0 (default) because the prediction
# output file is named `save_data_AVG{start-batch}`. To operate with a different start-sample,
# adjust the first argument to makeStructure... |
bb5baf880889157739f6868cb0fce780110baf73d9f4eb65d8da435524b2e477 | Shell | 645 | 17 | #!/bin/bash
echo $LSB_JOBINDEX
echo $1
data=$(head -n $LSB_JOBINDEX $1 | tail -n1)
echo $data
INPUTBAM=$(echo $data | awk {'print $1'} )
poolnum=$(echo $data | awk {'print $2'})
INPUTVCF=genotypes/inVitroLines_hg38LO.vcf
DEMUXLET=/software/demuxlet/demuxlet
rootfolder=$(echo $INPUTBAM | sed 's/possorted_genome_bam.ba... |
95b91e0cae278979da60b54679a81d162054eb5dc0464e7221890f32c911ff64 | Shell | 646 | 28 | #!/bin/bash
if (($# < 2)); then
echo "Usage: $0 compilerlist.txt benchfile.cpp"
else
compilerlist=$1
benchfile=$2
g=0
source $compilerlist
# for each compiler, compile benchfile and run the benchmark
for (( i=0 ; i<g ; ++i )) ; do
# check the compiler exists
compiler=`echo ${CLIST[$i]} | cut ... |
f068896364a9b91cf877fdd5983a82b523adbfa13f8e6dd7eb6f573176adafc8 | Shell | 646 | 28 | #!/bin/bash
#SBATCH --time=6:59:00
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --gpus-per-node=1
#SBATCH --job-name=gnn_bd_pars_est_diffpool
#SBATCH --output=logs/gnn_bd_pars_est_diffpool-%j.log
#SBATCH --mem=64GB
#SBATCH --partition=gpu
ml Python/3.8.16-GCCcore-11.2.0
source $HOME/venvs/eve/bin/activate
# Check if ... |
0ce4b3ec717a3fbb88189466dc722fb4687028ba298a47298372b380f80c90e2 | Shell | 648 | 13 | #!/usr/bin/env bash
set -euo pipefail
cd ..
device=0
for ed in 0.9 0.91 0.92 0.93 0.94 0.95 0.96 0.97 0.98 0.99
do
python online_main.py --model_type RLIF --nb_epochs 100 --method esd-rtrl --nb_hiddens 1024 --devices "$device" --normalization none --lr 0.01 --lr_step_size 5 --etrace_decay $ed --nb_layers 3 --state_i... |
63a5c8c9fb1c706c8a4b5c2bb4c301255bd431419fbd753bcbddf91bda680f9a | Shell | 649 | 4 | # sh code we used to derive the brain maps associated with state anxiety. Please refer to code derive4Dmaps.m to see how we made our arousal_map_543_subj.nii file.
#For information on how to make a contrast matrix or design matrix go here : https://web.mit.edu/fsl_v5.0.10/fsl/doc/wiki/GLM(2f)CreatingDesignMatricesByHan... |
03fb9ca1799b0c2b0ce1fad7c783e66522be63377cecf3786277ec081e73f1d5 | Shell | 650 | 28 | #!/bin/bash
#SBATCH --time=23:59:00
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --gpus-per-node=1
#SBATCH --job-name=gnn_ddd_pars_est_diffpool
#SBATCH --output=logs/gnn_ddd_pars_est_diffpool-%j.log
#SBATCH --mem=64GB
#SBATCH --partition=gpu
ml Python/3.8.16-GCCcore-11.2.0
source $HOME/venvs/eve/bin/activate
# Check ... |
aa645097f84e2abb1d1eb4eb9f242e1481f4d680f3de57dacf5dfc3a019f2edf | Shell | 650 | 18 | #!/bin/bash
# Ultralytics 🚀 AGPL-3.0 License - https://ultralytics.com/license
# Download COCO128 dataset https://www.kaggle.com/ultralytics/coco128 (first 128 images from COCO train2017)
# Example usage: bash data/scripts/get_coco128.sh
# parent
# ├── ultralytics
# └── datasets
# └── coco128 ← downloads here
#... |
cd5c7b7e6e01c9db6a92437472f8cd4457edd663e447114022c22176990945be | Shell | 650 | 28 | #!/bin/bash
#SBATCH --time=23:59:00
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --gpus-per-node=1
#SBATCH --job-name=gnn_eve_pars_est_diffpool
#SBATCH --output=logs/gnn_eve_pars_est_diffpool-%j.log
#SBATCH --mem=64GB
#SBATCH --partition=gpu
ml Python/3.8.16-GCCcore-11.2.0
source $HOME/venvs/eve/bin/activate
# Check ... |
d7e589531638425b3711b90975e54b54c1de52fb278fec66926293909e4e1a38 | Shell | 650 | 28 | #!/bin/bash
#SBATCH --time=6:00:00
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --job-name=gnn_training
#SBATCH --output=logs/gnn_training-%j.log
#SBATCH --mem=32GB
#SBATCH --partition=regular
ml Python/3.8.16-GCCcore-11.2.0
source $HOME/venvs/eve/bin/activate
# Check if at least two arguments are provided (name and ... |
ef52dc08b1b30c7565d9ee788107f6eea9cbcff451ad12718d0d1715ffbb5f67 | Shell | 650 | 28 | #!/bin/bash
#SBATCH --time=11:59:00
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --gpus-per-node=1
#SBATCH --job-name=gnn_pbd_pars_est_diffpool
#SBATCH --output=logs/gnn_pbd_pars_est_diffpool-%j.log
#SBATCH --mem=64GB
#SBATCH --partition=gpu
ml Python/3.8.16-GCCcore-11.2.0
source $HOME/venvs/eve/bin/activate
# Check ... |
5ace9354238be6d64c9dd39072fc2c3784efc6c95c7a10fb1e27370c586bd3c3 | Shell | 651 | 35 |
# BABS installation notes
## 1. make python env
cd /cbica/projects/luo_wm_dev/two_axes/software/
conda create -n babs python=3.9.16
conda activate babs
### Install DataLad, Git, and git-annex:
conda install -c conda-forge datalad git git-annex
### Install datalad-container:
pip install datalad_container
## 2. ... |
5c2f996d2f1cfe12bc24075da7c19ca587c81492612da6b25b5da710f93d3ff8 | Shell | 651 | 17 | #!/bin/bash
echo "=== TWOM Voxel Plotting Example ==="
echo "Plotting individual subject effects at example coordinates..."
echo ""
# Plot effects at an example voxel
echo "Command: python ../twom.py nifti_files.txt --input_dir data/ --plotvoxel 45 54 18"
echo ""
python ../twom.py nifti_files.txt --input_dir data/ --... |
f4fa818069cea1c76e3772253ce22da77410e37a3b4e11e0dd631fd3165fa1e7 | Shell | 653 | 28 | #!/bin/bash
#SBATCH --time=12:59:00
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --gpus-per-node=1
#SBATCH --job-name=gnn_eve_pars_est_diffpool_reg
#SBATCH --output=logs/gnn_eve_pars_est_diffpool_reg-%j.log
#SBATCH --mem=64GB
#SBATCH --partition=gpu
ml Python/3.8.16-GCCcore-11.2.0
source $HOME/venvs/eve/bin/activate
... |
08d662fe5dd038a5b9fef255517bed3e1417ff2a50f18e4b40aa461e69163243 | Shell | 654 | 7 | rm -f tensor_contract_sycl_bench
: "${COMPUTECPP_PACKAGE_ROOT_DIR:?Need to set COMPUTECPP_PACKAGE_ROOT_DIR}"
echo "COMPUTECPP_PACKAGE_ROOT_DIR is set to: "$COMPUTECPP_PACKAGE_ROOT_DIR
${COMPUTECPP_PACKAGE_ROOT_DIR}/bin/compute++ tensor_contract_sycl_bench.cc -I ../../ -I ${COMPUTECPP_PACKAGE_ROOT_DIR}/include/ -std... |
2703ec37fa8e378210ff2cba89586ebbf3afb6454b527be57a5b4573052b4491 | Shell | 656 | 20 | mypython=$1
$mypython $MARINE/marine.py \
--bam_filepath \
$MARINE/tests/singlecell_tests/bams/9_3000526_only_5_cells.bam \
--annotation_bedfile_path \
$MARINE/annotations/cellranger-mm10-3.0.0.annotation.genes.bed \
--output_folder \
$MARINE/tests/singlecell_tests/only_4_cells_all_cells_coverage_test \
--min_dist_fro... |
1e7d97d33c25c90c8e86dd7989aef338a3026b65c0ca839865e7c8b0f45ac8f2 | Shell | 659 | 19 | #!/bin/bash
set -e
# Check out and prepare the source
# Multibuild doesn't have releases, so --depth would break eventually (see
# https://superuser.com/questions/1240216/server-does-not-allow-request-for-unadvertised)
git submodule update --init --recursive
source multibuild/common_utils.sh
# https://github.com/matth... |
06c699bcfcbcbc7601671469bc5022d635ecc44a5fcef4f31470f1417a73ca72 | Shell | 661 | 28 | #!/bin/bash
#SBATCH --time=6:59:00
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --gpus-per-node=1
#SBATCH --job-name=gnn_bd_pars_est_diffpool_full
#SBATCH --output=logs/gnn_bd_pars_est_diffpool_full-%j.log
#SBATCH --mem=64GB
#SBATCH --partition=gpu
ml Python/3.8.16-GCCcore-11.2.0
source $HOME/venvs/eve/bin/activate
#... |
084478684639c8c32cc20c19974f4aa02de7cc3017d6d64266ae837608147091 | Shell | 661 | 18 | #!/bin/bash
set -e
# Check out and prepare the source
# Multibuild doesn't have releases, so --depth would break eventually (see
# https://superuser.com/questions/1240216/server-does-not-allow-request-for-unadvertised)
git submodule update --init multibuild
source multibuild/common_utils.sh
# https://github.com/matthe... |
01eee08fe14090c42c45cc353571ce772cd7707e13c09211df7a4a991fab4b89 | Shell | 664 | 28 | #!/bin/bash
#SBATCH --time=9:59:00
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --gpus-per-node=1
#SBATCH --job-name=gnn_pbd_pars_est_diffpool_full
#SBATCH --output=logs/gnn_pbd_pars_est_diffpool_full-%j.log
#SBATCH --mem=64GB
#SBATCH --partition=gpu
ml Python/3.8.16-GCCcore-11.2.0
source $HOME/venvs/eve/bin/activate
... |
03438616cf6a89f316aff94e80ef6293ebf10127e2960483536f568eff30cb70 | Shell | 664 | 28 | #!/bin/bash
#SBATCH --time=9:59:00
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --gpus-per-node=1
#SBATCH --job-name=gnn_ddd_pars_est_diffpool_full
#SBATCH --output=logs/gnn_ddd_pars_est_diffpool_full-%j.log
#SBATCH --mem=64GB
#SBATCH --partition=gpu
ml Python/3.8.16-GCCcore-11.2.0
source $HOME/venvs/eve/bin/activate
... |
2adc2e1898897bc8e6160acbb93c31d3aa0701a6ce37647cddc7e9014635c490 | Shell | 664 | 28 | #!/bin/bash
#SBATCH --time=05:00:00
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --gpus-per-node=1
#SBATCH --job-name=gnn_ddd_pars_est_val_diffpool
#SBATCH --output=logs/gnn_ddd_pars_est_val_diffpool-%j.log
#SBATCH --mem=64GB
#SBATCH --partition=gpu
#SBATCH --exclude=v100gpu24
module --ignore_cache load "Python/3.8.16... |
9da812bfa1b2779aaaba64a0290c0a55a8b76bf8c9b893559aa5306662e79eb7 | Shell | 664 | 16 | #!/bin/bash
#
# register_fs-to-vasoT1_prepare.sh <vaso_T1_file> <fs_dir> [<itksnap_binary>]
#
# - converts FS T1 to nifti
# - starts ITK-SNAP in order to perform semi-automatic rigid-body registration in ITK-SNAP and save transformation matrix as initial_matrix.txt
# - after running this, register_fs-to-vasoT1.sh will ... |
a97de0874152344e6ed45980a49375256312e9865f89ccbc6015966385c6ad63 | Shell | 665 | 20 | #!/bin/bash
# Check R version
R_VERSION=$(R --version 2>/dev/null | head -n1 | grep -o "R version [0-9.]*" | cut -d' ' -f3)
if [[ "$R_VERSION" != "4.0.5" ]]; then
echo "R version 4.0.5 not found (found: ${R_VERSION:-'none'})"
echo "Please check if R 4.0.5 is added to your .bashrc"
exit 1
fi
# Check Python... |
eb4a12caee6f6212d709361dacac3d3dff2e87577937781b1a96642af2e713bc | Shell | 665 | 25 | #!/bin/bash
# Module author: Aditya Lahiri
# Shell script author: Jo Lynne Rokita
# 2022
# This script runs the steps for generating manuscript tables.
set -e
set -o pipefail
# run the notebook to create manuscript tables
Rscript -e "rmarkdown::render('01-output_tables.Rmd')"
# run the R script to create molecular ... |
353e884c6483298a2b6c86c1f914663ac261b486a94e997ec9dffb563b7951a1 | Shell | 667 | 21 | #!/bin/bash
#Make Filepaths
BFILE="/path/to/1000G_EUR_Phase3_plink/1000G.EUR.QC.@.bim"
LD_FILE="/path/to/1000G_EUR_Phase3_plink/1000G.EUR.QC.@.run4.ld"
OUT_DIR="/path/to/output_dir/fit1/"
TRAIT_FILE="/path/to/trait.txt"
EXTRACT_DIR="/path/to/snp_output"
REP="${SLURM_ARRAY_TASK_ID}"
#Run mixer
apptainer exec /path/to... |
d01a831de3b08b890715b069cdabe02be0610a441cb4ba8089297d58b1bd0d29 | Shell | 667 | 9 | #!/usr/bin/bash
filename="/home/jurici/MAPS/PLAC-Seq_datasets/test_dataset2/feather_output/test_current/test.all.bedpe"
cat $filename | awk '{
if($9=="+" && $10=="+") printf "%s\t%d\t%s\t%d\t%d\t%d\t%s\t%d\t%d\t%d\t%d\n", $7, 0, $1, $2, 0, 0, $4, $5, 1, 60, 60
if($9=="+" && $10=="-") printf "%s\t%d\t%s\t%d\t%d\t%d\t%s... |
0e8211b789950051f5def0436d734d2a0f2cab6f5f0e71350e210060c9462aa6 | Shell | 669 | 19 | #! /bin/sh
cd tests/
. ./compat.sh
sort -k2,2 > ${pref}.md5sum <<EOF
bd7a5f6ba000b282cd79cb9f342e7ede ${pref}_m35_s2M_if.histo
8eb6d4a50aeba178e4847c2da71dbb70 ${pref}_m10_s2M_if.histo
EOF
# Partial count (in _0 and _2) with 35-mers
$JF count -t $nCPUs -o ${pref}_m35_s2M_if.jf -s 2M -C -m 35 --if seq1m_0.fa --if seq... |
e648b2c9a5d09fff9df99c2f94563d59c03e5221317b4a1bced781e723fbb42b | Shell | 669 | 31 | #!/bin/bash
set -euxo pipefail
V=$(grep "^version" Cargo.toml | sed 's/.*= //g' | sed 's/"//g' | xargs)
echo $V
cargo clippy
cargo test
cargo run --bin rb -- --help
# broken for some reason
# target=aarch64-unknown-linux-musl
# target=x86_64-unknown-linux-gnu
# aarch64-apple-darwin
mkdir -p dists
for target in x86_... |
1a8455bc5951f967d355ee2efeb7cf5c3f65185e5661ed5cb62fc9d4ae50571c | Shell | 670 | 27 | #!/bin/bash
#SBATCH --time=00:10:00
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --job-name=gnn_eve_pars_start
#SBATCH --output=logs/gnn_eve_pars_start-%j.log
#SBATCH --mem=500MB
#SBATCH --partition=regular
# Ensure the script is called with the necessary argument for 'name'
if [ "$#" -ne 1 ]; then
echo "Usage: $0... |
20b28abd4503278a520937310c5eadf1dd04a5a89cb6fbe3e95dea7d25b47597 | Shell | 671 | 16 | #!/bin/bash
#SBATCH --job-name=basecalling-benchmarks
#SBATCH --output=slurm_logs/%x-%j.out
#SBATCH --error=slurm_logs/%x-%j.err
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1 # Adjust this to the desired number of threads
#SBATCH --mem=16G # Adjust this to the desired memory allocation
#SBA... |
5515d1648594ddb246308c9ab04dd41f3803a3a6826e063589090dfb373f1dbb | Shell | 673 | 18 | #!/bin/sh
# Copyright (C) CVAT.ai Corporation
#
# SPDX-License-Identifier: MIT
# This is a wrapper script for running backend services. It waits for services
# the backend depends on to start before executing the backend itself.
# Ideally, the check that all DB migrations have completed should also be here,
# but it... |
e27c3e039e91d50df538a3cf9af720302eaea9483032efcda205544238e4a530 | Shell | 673 | 35 | #!/usr/bin/env bash
# Usage: ./populate-gsheets_sequencing-summary.sh
# Load the required executables
source ~/.bash_profile
module load miniconda/4.12.0
for s in {clinical,pop,nhp}:{nanopore,PacBio_HiFi}
do
c=$(echo $s | cut -f1 -d':')
t=$(echo $s | cut -f2 -d':')
if [ $t == "PacBio_HiFi" ]
then
nt="hifi... |
e563823280f2e59826f6fd8a58d3d65d07390730b2968bb3970a206f97e5900d | Shell | 673 | 28 | #!/bin/bash
set -e
set -o pipefail
# set up running directory
cd "$(dirname "${BASH_SOURCE[0]}")"
# Run script to select pathology diagnoses
Rscript --vanilla 00-select-diagnoses.R
# Run script to subset CNV and TPM files for MYCN calls
Rscript -e "rmarkdown::render('01-subset-for-NBL.Rmd')"
# Match DNA and RNA b... |
169586f641bb6b8dc4f7efd7f0ec918e2f625a3005d903c179d892668e041791 | Shell | 674 | 18 | LIB_STATIC_DEPS="utils alg config_helpers tinyexpr sds"
CHECK_CUSTOM_FILE
#if [ -n "$CUDA_FOUND" ]; then
# LIB_STATIC_DEPS="$LIB_STATIC_DEPS"
#fi
COMPILE_SHARED_LIB "default_matrix_assembly" "matrix_assembly.c ${CUSTOM_FILE}" "assembly_common.c" "${LIB_STATIC_DEPS}"
if [ -n "$COMPILE_WITH_DDM" ]; then
COMPILE... |
fd5667e5115c3dcfb63f067e0ee188a74eae472065286ba24d0016c329ea8b18 | Shell | 675 | 20 | #!/bin/bash
set -e -u -x
# Adapted from the F big workflow:
# https://github.com/psychoinformatics-de/fairly-big-processing-workflow/blob/main/bootstrap_forrest_fmriprep.sh
SUB_ID=$1
TASK_ID=$2
OUTPUT_SPACES=$3
# execute fmriprep. Its runscript is available as /singularity within the
# container. Custom fmriprep par... |
29ce846711ae1e8b09786a90f3f357f3241c1560a68cffd79532ad7a6475b6fa | Shell | 677 | 25 | #!/bin/bash -l
export DATE=$(date +%Y%m%d_%H%M%S)
export LABEL="$2"
export JOB_NAME=optimize_EIANN_"$LABEL"_"$DATE"
export CONFIG_FILE_PATH="$1"
sbatch <<EOT
#!/bin/bash -l
#SBATCH -J $JOB_NAME
#SBATCH -o /scratch1/06441/aaronmil/logs/EIANN/$JOB_NAME.%j.o
#SBATCH -e /scratch1/06441/aaronmil/logs/EIANN/$JOB_NAME.%j.e
#S... |
3a327ab1c63ba4d8f09afba6a41a219071c9d8bb2d325b99ae54a854bba4ba4a | Shell | 678 | 28 | #!/bin/bash
#SBATCH --mem=32G
#SBATCH -c 16
#SBATCH -t 16:00:00
#SBATCH --error=/logs/err_%j.err
#SBATCH --output=/logs/out_%j.out
#SBATCH -p gpuq
#SBATCH --gres=gpu:a100:1
#SBATCH --job-name=drp_p0
module load cuda11.8/toolkit/11.8.0
nvidia-smi
date
# Activate the Miniconda base environment
source {your_conda_direct... |
45c5ddda84285d343dd4dc0d7f62ca33674c14f415c2e5c3fa1b2a5fb7262813 | Shell | 678 | 17 | METHOD=shap
ATTR_FILES_DIR=../results/DeepSTARR_lr-decay/distilled_with_std
REF_FILE=../results/DeepSTARR_lr-decay/average_top500_shap.npy
python analyze_attr_scores.py --files_dir $ATTR_FILES_DIR --reference $REF_FILE --method $METHOD --rmse
# message the user on slack if possible
exit_code="$?"
if command -v 'sla... |
0caed870f4ed25a188060ca00c286ccb5715e899c45f753a67fe6a6dc98f60f3 | Shell | 680 | 28 | #!/bin/bash
#SBATCH --mem=32G
#SBATCH -c 16
#SBATCH -t 16:00:00
#SBATCH --error=/logs/err_%j.err
#SBATCH --output=/logs/out_%j.out
#SBATCH -p gpuq
#SBATCH --gres=gpu:a100:1
#SBATCH --job-name=drp_p10
module load cuda11.8/toolkit/11.8.0
nvidia-smi
date
# Activate the Miniconda base environment
source {your_conda_direc... |
402f919a87aa47b6019fe62da5bfe56d2354619c76470087d6a6a8fdb2bd76b0 | Shell | 680 | 28 | #!/bin/bash
#SBATCH --mem=32G
#SBATCH -c 16
#SBATCH -t 16:00:00
#SBATCH --error=/logs/err_%j.err
#SBATCH --output=/logs/out_%j.out
#SBATCH -p gpuq
#SBATCH --gres=gpu:a100:1
#SBATCH --job-name=drp_p40
module load cuda11.8/toolkit/11.8.0
nvidia-smi
date
# Activate the Miniconda base environment
source {your_conda_direc... |
526bc560ddf64e217669a808980d2e5d4cc15efe91cfe9d8f3383e37f29753a7 | Shell | 680 | 28 | #!/bin/bash
#SBATCH --mem=32G
#SBATCH -c 16
#SBATCH -t 16:00:00
#SBATCH --error=/logs/err_%j.err
#SBATCH --output=/logs/out_%j.out
#SBATCH -p gpuq
#SBATCH --gres=gpu:a100:1
#SBATCH --job-name=drp_p50
module load cuda11.8/toolkit/11.8.0
nvidia-smi
date
# Activate the Miniconda base environment
source {your_conda_direc... |
782446d87acd2fea565e85bb298633d4118c243f37ac8f9c4af7d45a9f2df018 | Shell | 680 | 28 | #!/bin/bash
#SBATCH --mem=32G
#SBATCH -c 16
#SBATCH -t 16:00:00
#SBATCH --error=/logs/err_%j.err
#SBATCH --output=/logs/out_%j.out
#SBATCH -p gpuq
#SBATCH --gres=gpu:a100:1
#SBATCH --job-name=drp_p60
module load cuda11.8/toolkit/11.8.0
nvidia-smi
date
# Activate the Miniconda base environment
source {your_conda_direc... |
7c85539bcdd2d03ee9bb0c3aa66472bf424111c8cfa205b429f2b525edd5967f | Shell | 680 | 28 | #!/bin/bash
#SBATCH --mem=32G
#SBATCH -c 16
#SBATCH -t 16:00:00
#SBATCH --error=/logs/err_%j.err
#SBATCH --output=/logs/out_%j.out
#SBATCH -p gpuq
#SBATCH --gres=gpu:a100:1
#SBATCH --job-name=drp_p30
module load cuda11.8/toolkit/11.8.0
nvidia-smi
date
# Activate the Miniconda base environment
source {your_conda_direc... |
855afcf577d4ef816a40b2a8ad5e8761701059d0eb6f179e1372c15b3508e1e2 | Shell | 680 | 28 | #!/bin/bash
#SBATCH --mem=32G
#SBATCH -c 16
#SBATCH -t 16:00:00
#SBATCH --error=/logs/err_%j.err
#SBATCH --output=/logs/out_%j.out
#SBATCH -p gpuq
#SBATCH --gres=gpu:a100:1
#SBATCH --job-name=drp_p70
module load cuda11.8/toolkit/11.8.0
nvidia-smi
date
# Activate the Miniconda base environment
source {your_conda_direc... |
a111b4ccf2ceb6903aa0994f32aa71b63c6606b0f4dff71c4eb3134f818a7d42 | Shell | 680 | 28 | #!/bin/bash
#SBATCH --mem=32G
#SBATCH -c 16
#SBATCH -t 16:00:00
#SBATCH --error=/logs/err_%j.err
#SBATCH --output=/logs/out_%j.out
#SBATCH -p gpuq
#SBATCH --gres=gpu:a100:1
#SBATCH --job-name=drp_p80
module load cuda11.8/toolkit/11.8.0
nvidia-smi
date
# Activate the Miniconda base environment
source {your_conda_direc... |
a12a509fb51940da654901212f21001f7154aa28ead93150f69af13cb11e927e | Shell | 680 | 25 | #!/bin/bash -l
export DATE=$(date +%Y%m%d_%H%M%S)
export LABEL="$2"
export JOB_NAME=optimize_EIANN_"$LABEL"_"$DATE"
export CONFIG_FILE_PATH="$1"
sbatch <<EOT
#!/bin/bash -l
#SBATCH -J $JOB_NAME
#SBATCH -o /scratch1/06441/aaronmil/logs/EIANN/$JOB_NAME.%j.o
#SBATCH -e /scratch1/06441/aaronmil/logs/EIANN/$JOB_NAME.%j.e
#S... |
bdc204f435231a714f2d95a704df51fb3ea1f8cb2de55fbd6ac3336b2fe5a9a7 | Shell | 680 | 28 | #!/bin/bash
#SBATCH --mem=32G
#SBATCH -c 16
#SBATCH -t 16:00:00
#SBATCH --error=/logs/err_%j.err
#SBATCH --output=/logs/out_%j.out
#SBATCH -p gpuq
#SBATCH --gres=gpu:a100:1
#SBATCH --job-name=drp_p20
module load cuda11.8/toolkit/11.8.0
nvidia-smi
date
# Activate the Miniconda base environment
source {your_conda_direc... |
d0445b12b0195370df0626f791c9799036a2b11afeee3064b97621bf35b5d172 | Shell | 680 | 28 | #!/bin/bash
#SBATCH --mem=32G
#SBATCH -c 16
#SBATCH -t 16:00:00
#SBATCH --error=/logs/err_%j.err
#SBATCH --output=/logs/out_%j.out
#SBATCH -p gpuq
#SBATCH --gres=gpu:a100:1
#SBATCH --job-name=drp_p90
module load cuda11.8/toolkit/11.8.0
nvidia-smi
date
# Activate the Miniconda base environment
source {your_conda_direc... |
090471a531c3176de2de7fc201197d825557c988d2a58fb8f62f449bd97ddc45 | Shell | 681 | 23 | #! /bin/sh
cd tests
. ./compat.sh
# sort -k2,2 > ${pref}.md5sum <<EOF
# EOF
$JF count --bf-size 10M --bf-fp 0.001 -t $nCPUs -o ${pref}_10m.jf -s 1M -m 40 seq10m.fa
$JF histo ${pref}_10m.jf > ${pref}_10m.histo
COLLISIONS=$(cut -d\ -f2 ${pref}_10m.histo | paste -sd+ - | bc)
[ $((COLLISIONS > 10000)) = 0 ] || {
ec... |
6b1d6bde440a45b9d0609dbe60a9b6d877cc7b9a91e340337cd882be1bbae0af | Shell | 682 | 25 | #!/bin/bash
while getopts p:f:t: option
do
case "${option}"
in
p) PYTHON_VERSION=${OPTARG};;
f) ENV_NAME="jamies${OPTARG}";;
t) MACOS_TARGET=${OPTARG};;
esac
done
echo "PYTHON_VERSION=${PYTHON_VERSION}"
echo "ENV_NAME=${ENV_NAME}"
echo "MACOS_TARGET=${MACOS_TARGET}"
source ~/.bashrc
source ... |
7909cc63521b9feca765cd2eccb54264ea7e30d827027d2c7fca318ea0c2d769 | Shell | 682 | 28 | #!/bin/bash
#SBATCH --mem=32G
#SBATCH -c 16
#SBATCH -t 16:00:00
#SBATCH --error=/logs/err_%j.err
#SBATCH --output=/logs/out_%j.out
#SBATCH -p gpuq
#SBATCH --gres=gpu:a100:1
#SBATCH --job-name=drp_p100
module load cuda11.8/toolkit/11.8.0
nvidia-smi
date
# Activate the Miniconda base environment
source {your_conda_dire... |
a4b4e5b3bea56159beaf16a7f6f1c32da1f769903a574eae885df31d40f14d9c | Shell | 684 | 17 | #!/usr/bin/bash
# Script to run inference on a single subject
# PLEASE TEST IF IT WORKS BY SETTING THE PATHS
# TO A TRAINING DATA SAMPLE AND RUNNING THIS SCRIPT
# BY UNCOMMENTING THE LINES BELOW
# t2w_image=/path/to/t2w_image.nii.gz
# participants=/path/to/participants.tsv
# output_seg=/path/to/output_seg.nii.gz
# ou... |
2d056d5ff3b70761f98953e605795e027d2c7e4491b6122ef86f645ad21ba044 | Shell | 686 | 17 | # run annotator on tsv files, convert to jsonl and gzip
# pan-cancer cancer-group level
Rscript --vanilla 02-chunkwise-annotate-and-zip.R \
--input_file results/pan_cancer_plots_cancer_group_level.tsv
# pan-cancer cohort-cancer-group level
Rscript --vanilla 02-chunkwise-annotate-and-zip.R \
--input_file results/pan_c... |
26816b24950d4b62e85c06eb1732dec41032d610b745a546ee6f4621d5993bd7 | Shell | 687 | 20 | #!/bin/bash
# Set the partition and other SBATCH specifications for individual subject jobs
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --time=04:00:00
#SBATCH --job-name=maxfilter_job
#SBATCH --output=/imaging/hauk/rl05/fake_diamond/scripts/preprocessing/meg/job_log/%j_maxfilter_subject_run_output.log
#SBAT... |
4c78021f431113b27b92c4e6fc6fe2c82f9f664e618a5048abe420f8f327a670 | Shell | 690 | 25 | #!/bin/bash
set -e -u -x
sub_id=$1
#load variables from config
source fmriprepConfig.sh
# Execute fmriprep.
# Custom fmriprep parametrization can be done here.
# See:https://fmriprep.org/en/stable/usage.html
docker run -it --rm \
--user "$(id -u):$(id -g)" \
-v "${CODE_DIR}":/code \
-v "${INPUT_DIR}":/d... |
9baddb4557ae145e58b592dca5e87ad89c5c25c2eb8203e3d04864c90535bbcf | Shell | 691 | 50 | #! /bin/bash
set -e
cd ../..
if [ $# -eq 0 ]; then
echo "$0 animal_id?"
exit 1
else
ANIMAL=$1
fi
OUTPUT="e:/data/user/yu-ting/histology"
OUTPUT_FILE="$OUTPUT/${ANIMAL}/cli.log"
export NO_COLOR=1
exec > >(tee -a "$OUTPUT_FILE") 2>&1
##
run_query() {
local a=$1
shift 1
echo "*** now run ${ANIMAL} $a $*... |
98ea097f9db0fa61b4165f462b146aa2d4221c7438ddb4883f239825287b07cb | Shell | 693 | 12 | #!/usr/bin/env bash
set -euo pipefail
cd ..
device=0
for surrogate in boxcar relu gaussian multi_gaussian sigmoid; do
python online_main.py --model_type RLIF --nb_epochs 100 --method esd-rtrl --nb_hiddens 1024 --devices "$device" --normalization none --lr 0.01 --surrogate $surrogate --lr_step_size 5 --etrace_decay 0... |
a8419ac51e1b5aa19189d8950e4cd33c97ffe3b720f7e4022889542efc1d2c29 | Shell | 693 | 23 | #!/bin/tcsh -xef
#Set the paths for input and output volumes and for the mask
set inpath = /path/to/input/list
set outpath = /path/to/output/folder
set maskpath = /path/to/mask
#Set current directory to inpath
cd $inpath
#Run tICA for the human sample
#Set TR to 1.5s, use a mask of the same resolution of the functio... |
1052e2110a26d6eaa32e99a7b986ffe46b4eb5a0082cf76c25e1c656c5055336 | Shell | 695 | 17 | #!/bin/bash
#
#SBATCH --account=default
#SBATCH --time=24:00:00
#SBATCH --mem=32G
#SBATCH --partition day-long
# Outputs ----------------------------------
#SBATCH -o /home/%u/log/%x-%j.out
#SBATCH -e /home/%u/log/%x-%j.err
# ------------------------------------------
# takes the TAR_PROJECT as a positional arg now!
c... |
382cb72e42119bfc7a4d2da993fc43fabfd0dc91daf189da338be83fb3947320 | Shell | 699 | 23 | #!/usr/bin/env bash
set -e
# === Argument parsing ===
DWI_NIFTI=$1
DWI_BVEC=$2
DWI_BVAL=$3
OUTPUT_DIR=$4
if [[ $# -ne 4 ]]; then
echo "Usage: $0 <DWI.nii.gz> <DWI.bvec> <DWI.bval> <output_dir>"
exit 1
fi
mkdir -p "$OUTPUT_DIR"
mrconvert "$DWI_NIFTI" "$OUTPUT_DIR/dwi4degibbs.mif" -fslgrad "$DWI_BVEC" "$DWI_BVAL" ... |
74a238a49bec29279f6ac792d6026aced6b4ba4be7e83f39b3defbcc79d3a4d8 | Shell | 700 | 35 | #!/bin/bash
#Create Debian package for all versions of MRIcron
# Fail if anything not planed to go wrong, goes wrong
set -eu
sw=mricron-data
source ../vers.inc
ver=$kVers
pkg=${sw}_${ver}_all
#deb=${pkg}.deb
resourcePath=${pkg}/usr/share/mricron/
SCRIPT_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" &> /dev/null && p... |
d5a6d8deef3da012cb2015d5f941f18138d036e800dc710d1a830db909b611af | Shell | 700 | 26 | #!/bin/bash
# HCPD
cd /cbica/projects/luo_wm_dev/input/HCPD/derivatives/babs_noddi/analysis/code
datalad save -m "add custom recon"
datalad push --to input
datalad push --to output
cd /cbica/projects/luo_wm_dev/input/HCPD/derivatives/babs_mapmri/analysis/code
datalad save -m "add custom recon"
datalad push -... |
bc8729cb7e2785b7029d6c03510a783ee0b2ecb084b76ab130cf2446739a367e | Shell | 703 | 21 | #!/bin/bash
# JN Taroni for ALSF CCDL 2022
# Create tables of git contributions to the current branch
set -euo pipefail
# Set the working directory to the directory of this file
cd "$(dirname "${BASH_SOURCE[0]}")"
# Shell script wrapped around git shortlog and git log
bash 01-count-contributions.sh
# Run notebook w... |
7344778058bde8af34967c634355b27598c33f8206e7ef7d858f2b82f058e1ab | Shell | 704 | 24 | #!/bin/bash
set -o nounset
#py__FIM_PSF_PSR_ASSEMBLY_DETECTION ACTIVITY_FIM_RASTER_file
#
#
# === Jan Moelter, The University of Queensland, 2018 ===================
#
SCRIPT=$( readlink --canonicalize $0 )
ROOT=$( dirname $SCRIPT )
ACTIVITY_FIM_RASTER_DAT=$1
FIM_PSF_PSR_ASSEMBLIES_DAT=${ACTIVITY_FIM_RASTER_DAT/_... |
c88bf9704d4e28076efaaac4dfe4ffb6b3758fbf27e6fb30b36d930025a8295d | Shell | 704 | 16 | #!/bin/bash
#################################################
# stand2fun roi maker
# flirt -ref -in -out -init .mat -applyxfm
#################################################
for ith_sub in {21..35}; do
fieldmap_phase_ima="/Users/bo/Documents/data_liujia_lab/analysis_liuP1_greeble/MRI_fieldmap_pha/sub"$ith_... |
c336429a5062ece34fb0db68d8cf846fc58cadcbc61b517dc1433f6057a58051 | Shell | 705 | 26 | #!/usr/bin/env bash
function abspath() {
echo `readlink -f "$1"`
}
function adddir() {
if [ -d "$2" ] && [[ ":${!1}:" != *":$2:"* ]]; then
export $1="${!1}:$2"
fi
}
# $SLURM_ROOTDIR is the absolute path of the nn-intrinsic project
SLURM_ROOTDIR=`dirname "${BASH_SOURCE[0]}"`
export SLURM_ROOTDIR=`abspath ... |
ad7accc18e4f3cad1369cb74d9294ca7fa002f34fb599c6bb2d37ae803bec292 | Shell | 706 | 22 | # Bethell and Taroni for CCDL 2019
# This generates multipanel dimension reduction plots for RSEM and kallisto
# data, with points colored either by RNA library or broad histology
#
# Usage: bash 03-multipanel-plots.sh
# This script should always run as if it were being called from
# the directory it lives in.
script_... |
a57be78dd370e781df09b63f2d0f91f7f1cc10968c3c68211890725844e6ff92 | Shell | 707 | 28 | #!/usr/bin/env bash
# get absolute path of a directory or file
function abspath() {
echo `readlink -f "$1"`
}
# add a directory ($2) to a list of directories ($1)
function adddir() {
if [ -d "$2" ] && [[ ":${!1}:" != *":$2:"* ]]; then
export $1="${!1}:$2"
fi
}
# $SLURM_ROOTDIR is the absolute path of par... |
e9010f95c291d70becc962bd051fe632ca5d79a3f1d47857179ac1c299c2613c | Shell | 707 | 23 | #!/bin/bash
#Make Filepaths
BFILE="/path/to/1000G_EUR_Phase3_plink/1000G.EUR.QC.@.bim"
LD_FILE="/path/to/1000G_EUR_Phase3_plink/1000G.EUR.QC.@.run4.ld"
OUT_DIR="/path/to/test"
TRAIT1_FILE="/path/to/trait1.txt"
TRAIT2_FILE="/path/to/trait2.txt"
PARAMS="/path/to/params/"
REP="${SLURM_ARRAY_TASK_ID}"
#Run mixer
apptain... |
efead447feb8918b2ae84a5cb492d0c5822cd2c9da00544f203af9ff01e79741 | Shell | 710 | 26 | #!/usr/bin/env bash
## Basically a script to create the data to make the exercise yourself
# Destroy any previous data (id there was any)
rm -rf ./scan
# Make the folder where all the simulation folders will be
mkdir scan
# Use preconfig.py to make a bunch of config files, you can change the number to the desired... |
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