sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
9d7962b328145dae00efcc901fb968326ecf11deef19d2ddd100a200aa799909 | Shell | 2,126 | 73 | #!/usr/bin/env bash
# the next line restart using vmd \
exec vmd "-dispdev text -e $0"
################################################################################
# #
# Generate the index file for calculating the Phi/Psi angles of the r... |
9c2527f16ce9a4cd22df816660e1d479585bb76127239d8783beab3821fd444f | Shell | 2,128 | 58 | #!/usr/bin/env bash
set -euo pipefail # Will fail on error
# ==============
# How to run this script
# 1) Load the input data
# https://scilpy.readthedocs.io/en/latest/documentation/getting_started.html
# 2) Call this script with
# ---> bash btensor_scripts.sh path/to/your/data path/to/save/outputs... |
6b40280aa2faae8b4192b282c052a1c530ce8e4e514e27b55e678dd44f541946 | Shell | 2,137 | 84 | #!/usr/bin/env bash
set -e
input_t1w=$1
output_dir=$2
if [[ $# -ne 2 ]]; then
echo "Usage: $0 <T1w.nii.gz> <chpseg_output_dir>"
exit 1
fi
mkdir -p "$output_dir"
input_temp_dir="${output_dir}/INPUTS"
mkdir -p "$input_temp_dir"
# make a copy of T1w in input_temp_dir -> T1w.nii.gz
cp "$input_t1w" "${input_temp_di... |
7cd34ef4b8992f206be81080fc2bcb8959c7e7064548636c898051ca79042796 | Shell | 2,138 | 49 |
rm cg.pdb
rm pace.pdb
rm pacem.pdb
rm cg.itp
rm pace.itp
pdbname='3gb1.pdb' #### input pdb name
######################################
### generating PACE pdb and topology files
### For guidance on the parameters and usage of the PACE force field, please refer to 'PACE for Gromacs' section found at https://github.... |
0142e45efb78614ceda102ffd894d876c3ea1a8dc99c25a2bdeca0a146fd6cd2 | Shell | 2,146 | 48 | #!/usr/bin/env bash
AP_DIR=$1
AP_PREFIX=$2
AP_LINE=$3
TOTAL_NUMBER_CELLS=$4
PRINT_RATE=$5
SIMULATION_NUMBER=$6
if [[ "$#" -ne 6 ]]; then
echo "---------------------------------------------------------------------------------"
echo "Usage:> $0 <AP_DIR> <AP_PREFIX> <AP_LINE> <TOTAL_NUMBER_CELLS> <PRINT_RATE> <SI... |
5c8317571f7200289a67a145c3c6da40c232c0629d9d30f7b2e7d70db18166d6 | Shell | 2,147 | 50 | #!/bin/bash -l
#SBATCH --job-name=mtrx_crunch
#SBATCH --account=proj134
#SBATCH --partition=prod
#SBATCH --constraint=uc2
#SBATCH --mem=0
#SBATCH --time=24:00:00
#SBATCH --output=outputs/%A_%a.log
#SBATCH --error=error/stderr-%A_%a.log
#SBATCH --array=0-4%5
echo "Copying files now.."
###
# cp files to be read by th... |
b59c41b6fc6600043cf4ec512d963deef8d9559dbcd69ebd49e130d390b4126e | Shell | 2,149 | 64 | # train distilled DeepSTARR models w/ mean+std using dynamic augmentations
AUG='random' # evoaug/mutagenesis/random
APPEND=false # if true, augmented seqs are appended to each mini batch
ENSEMBLE_DIR=../results/DeepSTARR_ensemble_NEW/ # path to pre-trained ensemble of models
DATA_DIR=../data/DeepSTARR_ensemble_NEW #... |
d34c702bf6480ac5b803d6db6713459e0e90b3a660b2698237e776eaf132d9b0 | Shell | 2,153 | 35 | #!/bin/bash
# This script captures the steps to generate the "blacklist" regions where CNV calls are not likely to be reliable,
# and will be excluded from downstream analysis.
#
# 1) The Immunogobulin (IG) regions, centromeric and telomeric regions are generated from
# the practice described by Kai Wang at his PennC... |
9410590b681c8b78b5c15725f01886774678ef1530d8a8a318145fb935c61953 | Shell | 2,159 | 54 | [ -z "${MASTER_PORT}" ] && MASTER_PORT=10087
[ -z "${MASTER_IP}" ] && MASTER_IP=127.0.0.1
[ -z "${n_gpu}" ] && n_gpu=$(nvidia-smi -L | wc -l)
[ -z "${OMPI_COMM_WORLD_SIZE}" ] && OMPI_COMM_WORLD_SIZE=1
[ -z "${OMPI_COMM_WORLD_RANK}" ] && OMPI_COMM_WORLD_RANK=0
[ -z "${arch}" ] && arch=uniprop_small
[ -z "${task}" ] && ... |
bdba6dce3685ade988eaa685a15fbdf489b484653a1c17379c9052026144ceb9 | Shell | 2,159 | 69 | #!/bin/bash
# Module author: Komal S. Rathi
# 2020
# This script runs the steps for molecular subtyping of Medulloblastoma samples
set -e
set -o pipefail
# This script should always run as if it were being called from
# the directory it lives in.
script_directory="$(perl -e 'use File::Basename;
use Cwd "abs_path";... |
7eb23f701762781880bbaaee0e0ece68df041b3ed037f9fd30ba4f8978881e04 | Shell | 2,168 | 66 | #!/bin/bash
set -e
set -x
# Run from project root (directory containing run_tests.sh)
SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
cd "$SCRIPT_DIR"
# Parse command line arguments
MODE="default"
if [[ "$1" == "--all" ]]; then
MODE="all"
elif [[ "$1" == "--distributed-only" ]]; then
MODE="distribu... |
daf86413f255fd10c0cef991cbce36b5e24d44d1e0da087e2839eb6311103fb5 | Shell | 2,183 | 69 | #!/bin/bash
# [description]
# Collect and download artifacts from all workflow runs for a commit.
#
# [usage]
# ./download-artifacts.sh <COMMIT_ID>
#
set -e -u -E -o pipefail
COMMIT_ID="${1}"
OUTPUT_DIR="./release-artifacts"
get-latest-run-id() {
gh run list \
--repo "light... |
84d09fda3df5961901c69ff90aea28ad1d07f8da650db4f1c0dd889899465336 | Shell | 2,185 | 59 | #!/bin/bash
# ============================================================================
# Developing brain Region Annotation With Expectation-Maximization (Draw-EM)
#
# Copyright 2013-2020 Imperial College London
# Copyright 2013-2020 Andreas Schuh
# Copyright 2013-2020 Antonios Makropoulos
#
# Licensed under the Ap... |
f5dcdd43fbe2c13d6a7de96b6266fdac094d0adb2030e81677dff7042e76c2da | Shell | 2,188 | 120 | #!/bin/sh
#
# Downloads sequence for the hg18 version of H. spiens (human) from
# UCSC.
#
# Note that UCSC's hg18 build has three categories of compressed fasta
# files:
#
# 1. The base files, named chr??.fa.gz
# 2. The unplaced-sequence files, named chr??_random.fa.gz
# 3. The alternative-haplotype files, named chr??... |
6ff003ada54af5e10b11c2b1644aac3a8a4946362d4db8402d1e7065be3d5b26 | Shell | 2,194 | 59 | #!/bin/bash
set -e
set -o pipefail
# This script should always run as if it were being called from
# the directory it lives in.
script_directory="$(perl -e 'use File::Basename;
use Cwd "abs_path";
print dirname(abs_path(@ARGV[0]));' -- "$0")"
cd "$script_directory" || exit
SCRATCHDIR=../../scratch/copy_consensu... |
3ae925b62aa163f01041b2ba8888cf304b07771590d5dad82fdb38ce84a25d18 | Shell | 2,195 | 85 | #!/bin/bash
# Exit on any error
set -e
echo "=== Creating twom environment ==="
# Remove existing environment if it exists
if conda env list | grep -q "twom"; then
echo "Removing existing 'twom' environment..."
conda env remove --name twom -y
fi
# Create environment
echo "Creating new environment..."
conda ... |
9185e4030e7594287500c65c93d666b06d0fb446e43199bea7a3d56338bc31de | Shell | 2,198 | 74 | #!/bin/bash
# 1. SAFETY CHECK: Ensure we are on the 'main' branch
CURRENT_BRANCH=$(git rev-parse --abbrev-ref HEAD)
if [ "$CURRENT_BRANCH" != "main" ]; then
echo "Error: Releases must be performed from the 'main' branch."
echo "Current branch: $CURRENT_BRANCH"
exit 1
fi
# 2. SAFETY CHECK: Ensure the working dir... |
36b7f2ec004afd8febda27d7e1ce8002eefd1d379d387469a7aa3830ce7e9fec | Shell | 2,200 | 60 | #!/bin/bash
# Eric Wafula
# Pediatric OpenTargets 2021
# Purpose: Run a CNV consensus gene-level frequecies anaysis for PediatricOpenTargets
# Set this so the whole loop stops if there is an error
set -e
set -o pipefail
# This script should always run as if it were being called from
# the directory it lives in.
scri... |
22b41edccb0305e206fcc21b5c9528d6180da8b31c71d3d0f0a63682593fb653 | Shell | 2,210 | 60 | #!bin/bash
### This is an example of running a single pair of swc file + annotation polygons (pia,wm,soma,layers) through
### feature calculation pipeline. This involves:
### 1. Uprighting the swc so that pia is up and white-matter is down
### 2. Layer aligning the cell so that laminar profiles are standardized to an a... |
8e6c4ee2fa689bd72f96496b61bd0aa8778ea7a747462b224650f97ec091495c | Shell | 2,212 | 77 | # ===== SET UP =====
set -ueo pipefail
if [ $# -ne 1 ]; then
echo -e "Usage: $0 <input_data_and_params>"
exit 1
fi
echo -e "#=====================\n#"
echo -e "# $(basename "$0") \n#"
echo -e "#=====================\n#"
# Read input config
neda=$(dirname $(dirname "$0"))
source $neda/scripts/process_input.sh... |
a0feec4b6bc63e817a91a59d7a119ccb045c4f930c3a26356a6b1d7f9ad76034 | Shell | 2,230 | 77 | #!/bin/bash
#SBATCH --time=120:00:00
#SBATCH --partition=sussexneuro
#SBATCH --mem=2G
#SBATCH --cpus-per-task=1
#SBATCH --job-name=batch_controller
# ======= USER SETTINGS =======
total_batches=10 # total number of batches you want to run
max_active=4 # how many batches to keep active at once
declare -A active_job... |
c2bb8700c62f43e1c49f13f8edb5a3b8db6856dcac520b39cb92acce7f6159b9 | Shell | 2,230 | 77 | #!/bin/bash
#SBATCH --time=120:00:00
#SBATCH --partition=sussexneuro
#SBATCH --mem=2G
#SBATCH --cpus-per-task=1
#SBATCH --job-name=batch_controller
# ======= USER SETTINGS =======
total_batches=10 # total number of batches you want to run
max_active=4 # how many batches to keep active at once
declare -A active_job... |
f0972577269cae927f3b2e58cc9fdc14a0335002b7b5fa168b59059919fb3b74 | Shell | 2,230 | 77 | #!/bin/bash
#SBATCH --time=120:00:00
#SBATCH --partition=sussexneuro
#SBATCH --mem=2G
#SBATCH --cpus-per-task=1
#SBATCH --job-name=batch_controller
# ======= USER SETTINGS =======
total_batches=10 # total number of batches you want to run
max_active=4 # how many batches to keep active at once
declare -A active_job... |
f6fd906bc16dfbbc086e6bde4d5e8ff90f68ccc2c88e91e2bed5db59b866426b | Shell | 2,230 | 77 | #!/bin/bash
#SBATCH --time=120:00:00
#SBATCH --partition=sussexneuro
#SBATCH --mem=2G
#SBATCH --cpus-per-task=1
#SBATCH --job-name=batch_controller
# ======= USER SETTINGS =======
total_batches=10 # total number of batches you want to run
max_active=4 # how many batches to keep active at once
declare -A active_job... |
53470286a15e30504bbfac621394fbd18750cb5a0282c705c445d26a4671ac0f | Shell | 2,231 | 88 | #!/usr/bin/env bash
set -u
if [ $# -lt 1 ]; then
echo "Usage: bash qsirecon_batch.sh <bids_dir>"
exit 1
fi
bids_dir="$1"
single_script="$bids_dir/code/qsirecon_single.sh"
qsiprep_root="$bids_dir/derivatives/qsiprep"
qsirecon_root="$bids_dir/derivatives/qsirecon-DSIStudio"
if [ ! -d "$bids_dir" ]; then
echo "... |
1ddee9f6c95c6b69e8024ec3fde5a80e8138219589f5e2d0d1caab42377ffaad | Shell | 2,232 | 52 | #!/bin/bash
# ============================================================================
# Developing brain Region Annotation With Expectation-Maximization (Draw-EM)
#
# Copyright 2013-2020 Imperial College London
# Copyright 2013-2020 Antonios Makropoulos
#
# Licensed under the Apache License, Version 2.0 (the "Lice... |
95b83a153510b0261728caa544af5737129684ac0b46b75c3d0edf20236ff129 | Shell | 2,232 | 74 | #!/bin/bash -l
#SBATCH -J eiann_multi_gpu_mnist_ray
#SBATCH -o /ocean/projects/bio250022p/chennawa/logs/EIANN/eiann_multi_gpu_mnist_ray.%j.o
#SBATCH -e /ocean/projects/bio250022p/chennawa/logs/EIANN/eiann_multi_gpu_mnist_ray.%j.e
#SBATCH --nodes=2
#SBATCH --ntasks-per-node=1
#SBATCH --partition=GPU
#SBATCH --gres=gpu:v... |
1bd1b97ab6164e3c2a9c6a0d207f36aa3ab50bc257dc6cbaec78e0b6c2d13e0b | Shell | 2,234 | 74 | #!/bin/bash
# fsf_list=(/Users/boo/Desktop/fmri_script/fc_analysis/rois/roi_1*)
#
# for i in "${fsf_list[@]}"; do
#
# #################################################
# # stand2fun roi maker
# # flirt -ref -in -out -init .mat -applyxfm
# #################################################
#
#
# root_path="/Users/b... |
69677fa7bf1737f079a340f5443437e26de3bfe7e3539edeee132150156ad0c7 | Shell | 2,234 | 77 | #!/bin/bash
#
# Usage: sh_ACMGfilter.sh </path/to/.csv/containing/folder> [/path/to/destination/folder]
#
##############################################################
## Description ##
##############################################################
#
# This script will look... |
ee61f6146ef0a00d93d68fababd62f2d67d2976f8971efb05c535f9e09cd1141 | Shell | 2,237 | 84 | #!/bin/bash
#Lucas Sancéré -
## As hovernet is a submodule of the repo, it is better to use sh files and not python script
## as we need activate corresponding env and the inference was also originally performed
## thourgh as sh file (see src/models/hover_net/run_wsi.sh)
################ PARSE CONFIG ARGS
# Extract... |
44472307eafc00668918c7d319282f6d10172cf256dc084d97382a874c6dc62d | Shell | 2,239 | 65 | #!/bin/bash
#fix grep argument after pattern
unset POSIXLY_CORRECT
if [ "$3" == "" ] ; then
echo "Usage: <original bvecs> <affine matrix> <rotated (output) bvecs>"
echo ""
echo "<affine matrix> is a FLIRT affine"
echo ""
exit 1;
fi
input=$1
matrix=$2
output=$3
if [ ! -e ${input} ] ; then
echo "Source bvecs $... |
dc9dec73ebb8039d07ba6caf1e7d319f2acc7276c982d2a1554c452eaff747f6 | Shell | 2,241 | 49 | #!/bin/bash
#SBATCH -p gidbkb
#SBATCH --nodes=1
#SBATCH --gpus-per-node=1
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-gpu=8
#SBATCH --mem=100G
#SBATCH -o /pollard/data/projects/sdrusinsky/enformer_fine_tuning/logs/eval/slurm_stdout/%j.out
#SBATCH -e /pollard/data/projects/sdrusinsky/enformer_fine_tuning/logs/eval/sl... |
2637078c6db9227a5480a8e14717a765df0923d488aed08986f39cba3c877c83 | Shell | 2,243 | 66 | #!/bin/bash
# Jaclyn Taroni for ALSF CCDL 2020
# Configure environmental variables for MCR
ORIG_LD_LIBRARY_PATH=$LD_LIBRARY_PATH
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/mcr/v83/runtime/glnxa64:/opt/mcr/v83/bin/glnxa64:/opt/mcr/v83/sys/os/glnxa64
export XAPPLRESDIR=/opt/mcr/v83/X11/app-defaults
# This script sho... |
09c3b8a7eb627a801325e04d8ec1c314ec5a4be3342b3a728abd1a54fcc46ffa | Shell | 2,246 | 61 | #!/bin/bash
export DATE=$(date +%Y%m%d_%H%M%S)
export LABEL="$2"
export JOB_NAME=optimize_EIANN_"$LABEL"_"$DATE"
export CONFIG_FILE_PATH="$1"
export OMP_NUM_THREADS=1
export MKL_NUM_THREADS=1
export NUMEXPR_NUM_THREADS=1
export OPENBLAS_NUM_THREADS=1
mkdir -p /scratch/${USER}/data/EIANN
sbatch <<EOT
#!/bin/bash
... |
a7a86922cb6e1d67acf032376c610ce292df50c6910acc4138d51b814f8d5397 | Shell | 2,246 | 87 |
<<comment
cd /home/aleksandr/Desktop/WORK/OLINK_suicide_PSY_project/
chmod +x Prepare_supplementary_figures.sh
./Prepare_supplementary_figures.sh prepared_supplementary_figures
comment
#!/bin/bash
# Usage: ./Prepare_supplementary_figures.sh /path/to/input_dir
if [ $# -lt 1 ]; then
echo "Usage: $0 <input_dir>"
... |
0213cef962a355cae3a436cdf45cf0713df3a90c1d5dea4e4ef133ea99cbad53 | Shell | 2,249 | 44 | python -u generate_dataset.py --num-train 5000 --seed 43 --n_isolated 5 --n_stick 0 --n_hinge 0 --n_workers 50
python -u generate_dataset.py --num-train 5000 --seed 43 --n_isolated 1 --n_stick 2 --n_hinge 0 --n_workers 50
python -u generate_dataset.py --num-train 5000 --seed 43 --n_isolated 2 --n_stick 0 --n_hinge 1 ... |
018ac835a5fc38cd7505ee7a265b3e203bd25c55dae2ed6bff6f11347db10fb1 | Shell | 2,250 | 82 | #!/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=decoding_job
#SBATCH --output=/imaging/hauk/rl05/fake_diamond/scripts/analysis/neural/decoding/job_log/%j_decod_output.log
#SBATCH --error... |
31571064a4c4f33a0353f9c0217510d15919b0c3c5dfd9716651bfb7e6019393 | Shell | 2,251 | 67 | #!/bin/bash
# Drive baseline_sweep.py one cell per python invocation. Each cell writes to
# the same CSV; the per-cell mode auto-skips already-done cells via
# _resume_state(). Intentionally no `set -e` so a SIGKILL on one cell doesn't
# stop the loop.
#
# Why one-process-per-cell: heavy 5-fold cluster_k5 cells on bigg... |
bdbe99b7ff280cca158e3dc090ec717839ced82e902da7ea903be00c1cffc883 | Shell | 2,260 | 26 | #!bin/bash
labdir=$1
frontal=(superiorfrontal rostralmiddlefrontal caudalmiddlefrontal parsopercularis parsorbitalis parstriangularis lateralorbitofrontal medialorbitofrontal precentral paracentral insula frontalpole rostralanteriorcingulate caudalanteriorcingulate)
patietal=(superiorparietal inferiorparietal suprama... |
01e6be1fb29665bd9d67daaf3c2086f46e7e438162ab6b0db9b709ab309f1531 | Shell | 2,262 | 57 | #!/bin/bash
# ============================================================================
# Developing brain Region Annotation With Expectation-Maximization (Draw-EM)
#
# Copyright 2013-2020 Imperial College London
# Copyright 2013-2020 Andreas Schuh
# Copyright 2013-2020 Antonios Makropoulos
#
# Licensed under the Ap... |
41286c6d3de24c893cf08bbc750ead607f706e0601c0999e9939922e269f86e0 | Shell | 2,267 | 14 | #!/usr/bin/env bash
set -euo pipefail
cd ..
device=0
python offline_main.py --model_type RLIF --nb_epochs 100 --nb_hiddens 1024 --normalization none --lr 0.005 --devices $device --new_exp_folder bptt-augm-shift-blend --nb_layers 3 --surrogate sigmoid --use_augm 1 --lr_step_size 5 --aug_random_shift 40 --aug_random_di... |
86fcd1829eecef66bff0d28978e25c4ce6a647ae30c228f9eb13d90193241541 | Shell | 2,268 | 81 | #!/bin/bash
#SBATCH --nodes=5
#SBATCH --ntasks=5
#SBATCH --cpus-per-task=24
#SBATCH --job-name=n-5nodes
#SBATCH --mem=200GB
#SBATCH --gres=gpu:4
#SBATCH --partition=a100
#SBATCH --output=logs/mgpus_%x-%j.out
#SBATCH --error=logs/mgpus_%x-%j.err
#SBATCH --time=20-00:00:00
#SBATCH --exclude=gpu101,gpu113
set -x -e
# lo... |
dc20861b129c6740076957f03f8e80de04566134f17b860e2a59f48347aaffd8 | Shell | 2,275 | 58 | # calculates stdev of DeepSTARR ensemble predictions on train/test/val
# MODELS_DIR=../results/DeepSTARR_lr-decay
MODELS_DIR=../results/DeepSTARR_ensemble_NEW # path to ensemble of teacher models
N_MODS=10 # nr. of models in ensemble
DATA=../data/DeepSTARR/Sequences_activity_all.h5 # path to STARR-seq data
OUTDIR=..... |
cf8071727734d8686ee7b9b336ab3e9173a00e9c3422c994c9948a0efbcecba6 | Shell | 2,279 | 71 | #!/bin/bash
# --------------------------------------------------------------------------------
# Usage Description Function
# --------------------------------------------------------------------------------
script_name=$(basename "${0}")
show_usage() {
cat <<EOF
${script_name}: Sub-script of GenericfMRISurfacePr... |
8cfad73f80e566110534123327179a1736db889636f8fb64efca9a9832acdaea | Shell | 2,290 | 71 | #!/bin/bash
# helper file for RVC snakemake rule changeHeader
# 1 {input.bam}
# 2 {input.bai}
# 3 {params.ref}
# 4 {params.known_sites}
# 5 {params.ucsc2ncbi}
# 6 {params.ncbi2ucsc}
# 7 {log}
# 8 {resources.tmpdir}
# 9 {output.bqsr_table}
input_bam=$1
input_bai=$2
ref=$3
tmp_known_sites=$4
IFS=';' read -r -a known_s... |
c14fc0102d5ad8b1c0d9b21a0867d7bfce64c6653bf187a0138c58e6dffdf07b | Shell | 2,299 | 68 | #!/bin/bash
#SBATCH --job-name=babs_mergeds_tractprofiles
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=5
#SBATCH --array=1-3
#SBATCH --time=3:00:00
#SBATCH --output=/dev/null # suppress default output file
#SBATCH --error=/dev/nul... |
5a34fd7dc0fb8f8d62ae24257b7a3de8c0d58a9158c099642c6d1bc6c65cfc54 | Shell | 2,309 | 44 |
source /share/scripts/gromacs-XXX.env
# Based on the geometric shape of the PIEZO2 dome (PDB: 6kg7, from OPM database), we created a hemisphere structure comprising 2129 dummy particles (dome shape), and a torus structure with a minor radius of 2 nm and a major radius of 16 nm, made up of 1800 particles (doughnut sh... |
be23f048fadf7922f9d11c5b383490480976a06e3ebff3da42c56c02303db9e9 | Shell | 2,316 | 59 | # calculates stdev of MPRAnn model (activity+aleatoric) ensemble predictions on train/test/val sets
CELLTYPE=HepG2
MODELS_DIR=../results/MPRAnn_aleatoric/${CELLTYPE}
OUTDIR=../data/MPRAnn_aleatoric
N_MODS=10
CONFIG=../config/MPRAnn.yaml
DATA=../data/lentiMPRA/${CELLTYPE}_data_with_aleatoric.h5
# boolean flags
EVOAUG=... |
550fbd8339c86f4edf91914650cef80cc005c52f9acd5d2d7272a3db9bc9aa6f | Shell | 2,319 | 53 | # runs ensemble_predict_DeepSTARR.py in distill mode
# for DeepSTARR ensemble trained on full training data
# toggle DOWNSAMPLED to control whether distilled training data is obtained for downsampled models
DOWNSAMPLED=true # toggle true/false
MODEL_DIR=../results/DeepSTARR_lr-decay
N_MODS=10
DATA=../data/DeepSTARR/Se... |
8b4359d8d48caba75d2cd7879af0fd7edd6acec2ad63d77d69b0319ef0a6aae9 | Shell | 2,319 | 61 | #!/bin/bash
declare -a volume_num_pool
declare -a voxel_num_pool
volume_num_pool[21]=1965
volume_num_pool[22]=2116
volume_num_pool[23]=1994
volume_num_pool[24]=1988
volume_num_pool[25]=2003
volume_num_pool[26]=2056
volume_num_pool[27]=2043
volume_num_pool[28]=2075
volume_num_pool[29]=1949
volume_num_pool[30]=1940
volum... |
99dbcecba20f96c475baf2980ef81d92f60136d950ba3e9cbe1962082e31a608 | Shell | 2,319 | 61 | #!/bin/bash
declare -a volume_num_pool
declare -a voxel_num_pool
volume_num_pool[21]=1965
volume_num_pool[22]=2116
volume_num_pool[23]=1994
volume_num_pool[24]=1988
volume_num_pool[25]=2003
volume_num_pool[26]=2056
volume_num_pool[27]=2043
volume_num_pool[28]=2075
volume_num_pool[29]=1949
volume_num_pool[30]=1940
volum... |
d5b7dc1af134e79b829bef78010f014a77d0fe78dabf1970928b2ce58e71079a | Shell | 2,319 | 76 | #!/bin/csh -f
# MODIFY FOLLOWING DIRECTORIES
# FSL_PATH IS THE MAIN FSL PATH AND SHOULD CONTAIN BIN/, CONFIG/, LIB/... SUBDIRECTORIES)
# PYTHON_EXEC IS THE PATH FOR THE PYTHON EXECUTABLE
# set for MRN Arvind
set FWMRN_PATH = /mnt/e/codes/cvdproc/cvdproc/pipelines/external/MarkVCID2/scripts_FW_CONSORTIUM
set PYTHON_... |
266c840a49f14d1c9fc554bfe628dc7af2e226abf65207f44394a5e16be1a636 | Shell | 2,324 | 59 | # Created by May Ho on 18.09.19.
# Notes for script
## The steps to preprocess FASTQ files of barcodes are as follows:
# 1. Trim and select reads
# 2. Remove short reeads and re-pair
# 3. Identify cell barcodes from R1 sequencing file/Seurat
# 4. Add the cell barcodes from step 3 to R2 reads
# I use different versi... |
3aa21038bf4f7de0f8e30f40d27ce3ec411ce24dbc39d8cd6af55bf29d617bfa | Shell | 2,336 | 55 | # run ensemble_predict_lentiMPRA.py with both --distill and --eval flags set
# evaluates performance of ensemble average and returns ensemble average on training seqs
MODELS_DIR=../results/lentiMPRA # path to directory containing teacher models
N_MODS=10 # number of teacher models in ensemble
DATA_DIR=../data/lenti... |
9ed84de9e083cc5cb864f2ee3c9ed79e59321d0f1fb8997945ed8c5ad38024b1 | Shell | 2,341 | 52 | #!/bin/bash
#$ -o /pollard/data/projects/sdrusinsky/enformer_fine_tuning/logs/gen_fasta_consensus/stdout/$JOB_ID.o
#$ -e /pollard/data/projects/sdrusinsky/enformer_fine_tuning/logs/gen_fasta_consensus/stderr/$JOB_ID.e
#$ -r y
#$ -l mem_free=50G
#$ ... |
2ffb74cfc9dd1f7fa84e13f98ebd4940f447ac87590459898bd3bfc1e16e9c96 | Shell | 2,344 | 161 | #!/bin/bash
set -e
set -x # Enable shell tracing
cd ../..
if [ $# -eq 0 ]; then
echo "$0 experimental_date animal_id ?"
exit 1
else
ED=$1
ID=$2
nP=$3
fi
OUTPUT="e:/data/user/yu-ting/analysis/phys"
OUTPUT_FILE="$OUTPUT/${ED}_${ID}__2P_YW/plane${nP}/cli.log"
mkdir -p "$OUTPUT/${ED}_${ID}__2P_YW/plane${nP}"... |
d71fe39adf60d7bfe679a37a5b3dbcf0b311c1b38badb1e2a10b45833e2ca52c | Shell | 2,345 | 84 | #!/bin/bash -l
#SBATCH -J eiann_gpu_mnist_ray_multi
#SBATCH -o /scratch2/11358/yashchennawar5555/logs/EIANN/eiann_gpu_mnist_ray_multi.%j.o
#SBATCH -e /scratch2/11358/yashchennawar5555/logs/EIANN/eiann_gpu_mnist_ray_multi.%j.e
#SBATCH --nodes=2
#SBATCH --ntasks-per-node=1
#SBATCH --partition=rtx
#SBATCH --mem=80G
#SBATC... |
e9c753616f4d94b995456183499470e6453eb1f9db8a053f15198d0191496f9f | Shell | 2,347 | 53 | #!/bin/bash
#
# calc1t.sh <basename>
#
# - calculate t1 contrast from VASO data (nulled and notnulled according to basename)
# - also calculates mask from notnulled data and generated an additional brain only T1 image
fBaseName=$1
NumVol=$(3dinfo -nv ${fBaseName}_nulled.nii)
# combine nulled and notnulled
3dTcat -pre... |
f3e643a25a254e0ca60adf004bbfe0a3ca8b21451addead969de23431e2bc723 | Shell | 2,354 | 79 | outdir=$1
dataset_name=$2
shift 2
dirs=$@
printf "${dirs[@]}"
all_chrs=()
long_suffix=".long.intra.bedpe"
short_suffix=".shrt.vip.bed"
function extract_chrs (){
dir_arg=$1
#echo "looking for: " $dir_arg
long_pattern=$dir_arg"/*"$long_suffix
short_pattern=$dir_arg"/*"$short_suffix
... |
fe6b735861acd66760d7f11b84a8197767c4b2a7b37f6031220645c88cd14a42 | Shell | 2,357 | 96 | #!/bin/bash
#
# Usage: sh_mergeFastQ.sh <.fastq(.gz) folder>
#
##############################################################
## Description ##
##############################################################
#
# Simple script to consolidate fragmented .fastq files from differ... |
822ff0d156a4282907a3aee2bb10f064cfa6d8f73f749f564e16e663a004c1a2 | Shell | 2,358 | 65 | #!/bin/bash
# OPenPedCan 2022
# Eric Wafula
set -e
set -o pipefail
printf "Start methylation pre-processing...\n\n"
# This script should always run as if it were being called from
# the directory it lives in.
script_directory="$(perl -e 'use File::Basename;
use Cwd "abs_path";
print dirname(abs_path(@ARGV[0]));' --... |
319297b3f57b9ccdff8fcf2f5bc2f36769c75e4591f54fc685a683cdf9832733 | Shell | 2,361 | 93 | #!/bin/bash
indv=$1
binnum=$2
target_gene=$3
echo $target_gene
rm -rf ${indv}"_bin"${binnum}
mkdir -p ${indv}"_bin"${binnum}
cd ${indv}"_bin"${binnum}
#pwd
#target_gene='gene_name_xu230330_gen_data.txt'
pos_file="cell_pos_db_filter_singlecell/${indv}.txt"
awk -v binnum=$binnum 'BEGIN{
yxmin=100;
... |
8c857d937ac52e9d5fa5741a2363daa2b0892001dda2e67cba2fab79255fa722 | Shell | 2,365 | 59 | # calculates stdev of MPRAnn model (activity+aleatoric) ensemble predictions on train/test/val sets
CELLTYPE=HepG2
MODELS_DIR=../results/MPRAnn_heteroscedastic/${CELLTYPE}
OUTDIR=../data/MPRAnn_heteroscedastic
N_MODS=10
DATA=../data/lentiMPRA/${CELLTYPE}_data_with_aleatoric.h5
CONFIG=${MODELS_DIR}/config.yaml
# boole... |
458a89356b79c4ce2dfc13ccae4096ed895adfeae7f1a308d564f9eaa6655f08 | Shell | 2,377 | 72 | #!/bin/bash
# Eric Wafula, OPenPedCan 2022
# Run OpenPedCan modules to generate MTP tables
set -e
set -o pipefail
printf "Start generating mtp tables...\n\n"
# Use the bucket that contains mtp files
URL="s3://d3b-openaccess-us-east-1-prd-pbta/open-targets"
RELEASE="v12"
MTP_DIR="mtp-tables/commit"
# This script ... |
65fe8b92d1dba14022ba21cca1e7bf0e8d9a204c56072a8495af6da91f00bdad | Shell | 2,388 | 74 | #!/bin/bash
# PediatricOpenTargets 2023
# Eric Wafula
set -e
set -o pipefail
# This script should always run as if it were being called from
# the directory it lives in.
script_directory="$(perl -e 'use File::Basename;
use Cwd "abs_path";
print dirname(abs_path(@ARGV[0]));' -- "$0")"
cd "$script_directory" || exit
... |
1201eaec497c22699d628469aea3c0cb1fc494c294724a8aa1de4bae2124fb63 | Shell | 2,392 | 71 | #! /bin/bash
#
# This is a shell script to register T1w image to MNI 2009c
#
# Dependencies: (1)ANTs
#
# Creator: Kwok-shing Chan @DCCN
# kwokshing.chan@donders.ru.nl
# Date created: 6 October 2022
# Date edit:
############################################################
# # get SEPIA_HOME and atlas dir
# script_dir=`r... |
e326db87303d75cd06d6766588f9937fa0eccef67fcba2431e29519b202d87d4 | Shell | 2,393 | 53 | #!/bin/bash -l
#SBATCH -J simulate_EIANN_mnist
#SBATCH -o /scratch1/06441/aaronmil/logs/EIANN/simulate_EIANN_mnist.%j.o
#SBATCH -e /scratch1/06441/aaronmil/logs/EIANN/simulate_EIANN_mnist.%j.e
#SBATCH -p normal
#SBATCH -N 2
#SBATCH -n 102
#SBATCH -t 2:00:00
#SBATCH --mail-user=milstein@cabm.rutgers.edu
#SBATCH --mail-t... |
ae209a193c653196837087e04aefee76afd86c52f8213531e0f1f994248de6a2 | Shell | 2,403 | 113 | #!/bin/bash
# Job name:
#SBATCH --job-name=Matrix5
#
# Project:
#SBATCH --account=ec-huah
#SBATCH --nodes=10 --mem=512G --cpus-per-task=2048
#SBATCH --qos=devel
#SBATCH --partition=accel
#SBATCH --gpus=1
# Wall time limit:
#SBATCH --time=10-00:00:01
## Set up job environment:
module --quiet purge # Reset the modu... |
5b2527825f2bf9aba0f9ad3baac30f76a63630e49c65374012603956de14b95a | Shell | 2,412 | 50 | # run DeepSTARR_ensemble_attr_analysis.py
# set DISTILLED to perform attribution analysis for distilled models (on activity output heads)
# set METHOD as saliency or shap to define method of attribution analysis
# set HEAD as mean/std/logvar (must be mean if distilled is false)
# set EPISTEMIC_METRIC as std/logvar (use... |
bdadfd5e74b525088a271803cbda907ee22376dec4ee4d2cebb176dc30a1971b | Shell | 2,419 | 59 | # calculates stdev of ResidualBind model (activity+aleatoric) ensemble predictions on train/test/val sets
CELLTYPE=HepG2
MODELS_DIR=../results/ResidualBind_heteroscedastic/${CELLTYPE}
OUTDIR=../data/ResidualBind_heteroscedastic
N_MODS=10
DATA=../data/lentiMPRA/${CELLTYPE}_data_with_aleatoric.h5
CONFIG=${MODELS_DIR}/co... |
c9afb98dde0db14a5c2b53a3fcf587172cd0dcb1ab8b76f0335e707035ae5910 | Shell | 2,422 | 77 | #!/bin/sh
# You do not want to run this. It was used to create the initial repo by
# extracting the relevant bits from Canu and renaming things.
if [ `pwd` != "/scratch/git/canu-filtered" ] ; then
echo Wrong directory.
exit
fi
echo DELETE
rm -rf .git *
echo SYNC
rsync -a ../canu-orig/ .
echo REWRITE
../git-... |
d9e6ba5b47e88ed3f9f904797a71066208860456371d155909b46c14dc637ef3 | Shell | 2,422 | 89 | #!/bin/bash
################################################################################
# This script will
# 1) split your PLINK data into training and testing (with proportions
# $PROP and 1 - $PROP)
# 2) Run SCCA on the training data
# 3) Project the test SNPs data onto the eigenvectors, producing "principa... |
35740e92bc200029c1da95a6a71bedf8d5a6f8bf58b5e90e2af5538e380e81a6 | Shell | 2,428 | 61 | #!/bin/bash
set -eu
## Guess HCPPIPEDIR if not set
pipedirguessed=0
if [[ "${HCPPIPEDIR:-}" == "" ]]
then
pipedirguessed=1
#fix this if the script is more than one level below HCPPIPEDIR
export HCPPIPEDIR="$(dirname -- "$0")/.."
fi
## Source libraries
source "$HCPPIPEDIR/global/scripts/newopts.shlib" "$@"... |
e21424665ed51d90858467103e952dc630bb92a0dc46a71dcc571a86606c4a25 | Shell | 2,435 | 67 | #!/bin/bash
# helper file for RVC snakemake rule changeHeader
# 1 {input.bam}
# 2 {input.bai}
# 3 {params.sample}
# 4 {log}
# 5 {output.bam}
# 6 {output.bai}
# 7 {output.newHeader}
input_bam=$1
input_bai=$2
sample=$3
log=$4
output_bam=$5
output_bai=$6
output_newHeader=$7
SM_internalHeader=""
PL_internalHeader=""
sa... |
74185014a16cadc6008895b805f55cb5caa4d9b71ed7ca0e31709be08026d19a | Shell | 2,437 | 76 | # train distilled ResidualBInd models w/ mean+aleatoric+epistemic using dynamic augmentations
AUG=mutagenesis # evoaug/mutagenesis/random
APPEND=false
CELLTYPE=K562
ENSEMBLE_DIR=../results/lentiMPRA_aleatoric/${CELLTYPE}
DATA_DIR=../data/lentiMPRA
DATA=${DATA_DIR}/${CELLTYPE}_distillation_data_with_epistemic.h5
CONFI... |
393a7f3b8415c2d65de61ded8a480195f313e783d1ff125930319285939c9a69 | Shell | 2,458 | 80 | #!/bin/sh
#
# Downloads sequence for H. sapiens (human) from NCBI. This script was
# used to build the Bowtie index for H. sapiens.
#
# From README_CURRENT_BUILD:
# Organism: Homo sapiens (human)
# NCBI Build Number: 36
# Version: 3
# Release date: 24 March 2008
#
GENOMES_MIRROR=ftp://ftp.ncbi.nih.gov/genomes
FI... |
09ec52e96de935a9011d6ffedb81ee0db4d131adebe8e7c22ed0a5d5092d0835 | Shell | 2,464 | 80 | #!/usr/bin/env bash
# Run Parsl + EnsembleLauncher smoke tests on a Crux compute node (MACE on CPU).
#
# Must be executed INSIDE an interactive PBS allocation on Crux:
# qsub -I -A <proj> -l select=1 -l walltime=00:30:00 -q debug
# cd /lus/eagle/projects/ChemGraph/thang/ChemGraph
# bash scripts/smoke/run_crux_smo... |
36cd07226406f6442766ecc826e3e13c12883c7d24696a23d5ebe211637310c5 | Shell | 2,470 | 95 | #!/bin/bash
set -e
echo "=========================================="
echo "Heart Organoids Single-Cell Analysis"
echo "=========================================="
# Default values
STEPS="all"
SAMPLES="VEGF,PDGFBB"
# Parse arguments
while [[ $# -gt 0 ]]; do
case $1 in
--steps)
STEPS="$2"
... |
5abea7e5f94d5baab8e87c02f5a2e5ce79dc45c216f5acca49b4a6a4ed6d3f90 | Shell | 2,477 | 96 | # ===== SET UP =====
set -ueo pipefail
if [ $# -ne 1 ]; then
echo -e "Usage: $0 <input_data_and_params>"
exit 1
fi
echo -e "#=====================\n#"
echo -e "# $(basename "$0") \n#"
echo -e "#=====================\n#"
# Read input config
neda=$(dirname $(dirname "$0"))
source $neda/scripts/process_input.sh... |
86bf8e52dddfa71c88c6ddcbf2b7f7a4f53e910a58f8410b43b2bd1a1f625976 | Shell | 2,496 | 82 | #!/bin/bash
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --time=00:30:00
#SBATCH --output=/dev/null # suppress default output file
#SBATCH --error=/dev/null # suppress default error file
# datalad get t1w, dwiref, GM_pr... |
0faaf38cd25779a688d3ae98aea76f02aef49306fde2ae0a4e8c494e8b83250f | Shell | 2,503 | 59 | #!/bin/bash
#
#SBATCH --account=default
#SBATCH --time=7-00:00:00
#SBATCH --mem=48G
#SBATCH --partition week-long # Queue names you can submit to
# Outputs ----------------------------------
#SBATCH -o /home/%u/log/%x-%A-%a.out
#SBATCH -e /home/%u/log/%x-%A-%a.err
#SBATCH --mail-user=laberma@emory.edu
#SBATCH --mail-t... |
b5a29fe88970d829c3d865425fdc18867060131475871dd9c49767af5b4143a5 | Shell | 2,510 | 59 | #!/bin/bash
script_name=$(basename "${0}")
# ------------------------------------------------------------------------------
# Check that HCPPIPEDIR is defined and Load Function Libraries
# ------------------------------------------------------------------------------
if [ -z "${HCPPIPEDIR}" ]; then
echo "${script... |
b890071fef778b9149c37a4f458572f5df834141396c5403c1453f485fc03eab | Shell | 2,511 | 168 | #! /bin/bash
set -e
set -x
cd ../..
if [ $# -eq 0 ]; then
echo "$0 experimental_date animal_id ?"
exit 1
else
ED=$1
ID=$2
fi
OUTPUT="e:/data/user/yu-ting/analysis/phys"
OUTPUT_FILE="$OUTPUT/${ED}_${ID}__2P_YW/concat_etl.log"
export NO_COLOR=1
# Redirect all script output (stdout and stderr) to the log fil... |
272019727fc715fbee8bfb6ef7125eaf9289ecc510799ba788ab9ac4f09a2f23 | Shell | 2,517 | 80 | #!/usr/bin/env bash
set -euo pipefail
# Minimal GWAS pipeline (PLINK) for producing a SNP matrix for downstream ML.
#
# Usage:
# bash gwas_pipeline.sh --bfile <plink_prefix> --pheno <pheno.tsv> --pheno-col <colname> --out <out_dir>
#
# Notes:
# - Expects PLINK 1.9+ available on PATH as `plink`
# - Phenotype file sho... |
38707c46c41678b8afab43267b945304b648086e4b86c759702b99e17f2173bc | Shell | 2,517 | 64 | #!/bin/bash
###############################################
# Shell script for RRBS data analysis
###############################################
## Prerequisite
## Ensure the following software is available in the current environment:
## fastqc, multiqc, trim_galore, bismark, samtools, parallel
## Set directories
... |
59e1a60b25a997e8575dede7b911b023353401f3f63fa2c021a6f5722aaa9863 | Shell | 2,524 | 89 |
usage="$(basename "$0") [-h] <list_file_counts> <sample_names>
\n\n
Description:\n
Merge files generated by HTseq by combining read count columns.
This assumes that the different read count files contain the same \
number of rows and same genes at the same row across files. \
\n\n
Arguments:\n
<list_fi... |
6ce3c76d31ecff1262262ff24aac1f0b89c9fc004d3770049c146028810ef7d9 | Shell | 2,539 | 60 | #!/bin/bash
datasets=("PNC")
for dataset in "${datasets[@]}"; do
config_file="/cbica/projects/luo_wm_dev/two_axes/code/config/config_${dataset}.json"
# where to save output and error logs
logs_dir="/cbica/projects/luo_wm_dev/two_axes/code/logs/tract_to_cortex/supp_gyralhops/${dataset}"
if [ ! -d... |
79e2a8acd224127abb30797cd1b71a4e5535889c0fcde724c2cc50b2120ea45e | Shell | 2,544 | 58 | # calculates stdev of ResidualBind (mean+aleatoric) ensemble predictions on train/test/val sets
CELLTYPE=K562 # cell type
MODELS_DIR=../results/lentiMPRA_aleatoric/${CELLTYPE} # path to directory with ensemble of models
OUTDIR=../data/lentiMPRA # path to output directory
N_MODS=10 # nr. of models in ensemble
CONFIG=... |
46c539ae69d6ebf7d04f1771fbdfe96e5a563571dace966edc1547471deb3681 | Shell | 2,554 | 56 | #!/bin/bash
# ============================================================================
# Developing brain Region Annotation With Expectation-Maximization (Draw-EM)
#
# Copyright 2013-2020 Imperial College London
# Copyright 2013-2020 Andreas Schuh
# Copyright 2013-2020 Antonios Makropoulos
#
# Licensed under the Ap... |
1b19c629ab017b14b994110c34efc186a305b9af4854d442b9e8837ee46a4a9d | Shell | 2,563 | 51 | #!/bin/bash
# ============================================================================
# Developing brain Region Annotation With Expectation-Maximization (Draw-EM)
#
# Copyright 2013-2020 Imperial College London
# Copyright 2013-2020 Antonios Makropoulos
#
# Licensed under the Apache License, Version 2.0 (the "Lice... |
b5347f7118e4b8c48506526bfc63e4419a52ccec733f8cb7df2cca2deb721ccf | Shell | 2,591 | 88 | #!/bin/bash
# Sangeeta Shukla
# Purpose: Automate search for EFO, MONDO, NCIT codes for cancer_group found in current release version of histologies.txt
# Note: Relevant cancer_group list extracted from efo-mondo-map-prefill.tsv
# efo-mondo-map-prefill.tsv file is generated by molecular-subtype-integrate module in Ope... |
c8bfc5fa24432d9a407b3fbb20ed4b1705213c42ffd09dd03e662638416be9f0 | Shell | 2,596 | 134 | #!/bin/sh
#
# Downloads sequence for the mm10 version of M. musculus (mouse) from
# UCSC.
#
# Note that UCSC's mm10 build has two categories of compressed fasta
# files:
#
# 1. The base files, named chr??.fa.gz
# 2. The unplaced-sequence files, named chr??_random.fa.gz
#
# By default, this script indexes all these fil... |
f2899c3eaef2e62af8ffd6ddfd677ba3fc8342665fe51c114502448c689f45c6 | Shell | 2,598 | 86 | #! /bin/bash
#
# This is a shell script to register GRE image to T1w image
#
# Dependencies: (1)ANTs
#
# Creator: Kwok-shing Chan @DCCN
# kwokshing.chan@donders.ru.nl
# Date created: 6 October 2022
# Date edit: 15 June 2025
############################################################
# export ITK_GLOBAL_DEFAULT_NUMBER... |
137ee04f0c9fcb4e047e39443f910d9f5ff8442d7cfda9004aaa9bf7fea6ddf3 | Shell | 2,600 | 64 | #!/bin/bash
datasets=( "PNC" "HCPD" "HBN")
# submit this with ./a00_wrapper_make_tdi.sh
for dataset in "${datasets[@]}"; do
config_file="/cbica/projects/luo_wm_dev/two_axes/code/config/config_${dataset}.json"
# where to save output and error logs
logs_dir="/cbica/projects/luo_wm_dev/two_axes/cod... |
18f05fd10a0fc77ae56f315f5cdaf7dd2f7ae5cf669820e7c063b96fe9dd23e6 | Shell | 2,617 | 50 | #!/bin/bash -l
#SBATCH --job-name=mtrx_crunch
#SBATCH --account=proj134
#SBATCH --partition=prod
#SBATCH --constraint=cpu
#SBATCH --mem=0
#SBATCH --time=12:00:00
#SBATCH --output=outputs/%A_%a.log
#SBATCH --error=error/stderr-%A_%a.log
#SBATCH --array=0-399%400
echo "Copying files now.."
###
# cp files to be read b... |
31b9aefc8fa021b73b46f0f429edc7aa0bdc0990e1fd20ed9255b13a8e73e385 | Shell | 2,619 | 86 | #!/bin/bash
#$ -o /pollard/data/projects/sdrusinsky/enformer_fine_tuning/logs/gen_fasta_consensus/stdout/$JOB_ID.o
#$ -e /pollard/data/projects/sdrusinsky/enformer_fine_tuning/logs/gen_fasta_consensus/stderr/$JOB_ID.e
#$ -r y
#$ -l mem_free=50G
#$ ... |
fb65dec964025085236b68fbc58ebebf34fa9e82255967e83823e8d4289b19ff | Shell | 2,628 | 89 |
<<comment
cd /home/aleksandr/Desktop/WORK/OLINK_suicide_PSY_project/cell_type_imputation_performance/Merged_files_highres_performance/
chmod +x Combine_performance_to_pdf.sh
./Combine_performance_to_pdf.sh
comment
#!/usr/bin/env bash
set -euo pipefail
# Combine all PNGs in this folder into a single bookmarked PD... |
0767fb34845c82ffa0e8136f37b5890da1c3a48b3f01abf0ac031e80cfa8fb08 | Shell | 2,629 | 89 |
<<comment
cd /home/aleksandr/Desktop/WORK/OLINK_suicide_PSY_project/cell_type_imputation_performance/Merged_Highres_performance_harmon/
chmod +x Combine_performance_to_pdf.sh
./Combine_performance_to_pdf.sh
comment
#!/usr/bin/env bash
set -euo pipefail
# Combine all PNGs in this folder into a single bookmarked P... |
88904a0980a70f51cce8ef04315de84788564901d5702ce6d7e27b60c58163a5 | Shell | 2,630 | 116 | #!/usr/bin/env bash
SOLVER=$1
file=$2
SCRIPTPATH="$( cd "$(dirname "$0")" ; pwd -P )"
TEST=$SCRIPTPATH/checktest.sh # relative from testdir
#relative or absolute path?
if [[ ! $file = /* ]]; then
file=../$file
fi
if [[ ! $SOLVER = /* ]]; then
SOLVER=../$SOLVER
fi
#create tmp-dir and copy config file and config in... |
35dc32d72d9f491d8b85e47e1fde233c8e215e87bdcb6b0e05e7382a341481f5 | Shell | 2,631 | 69 | # run ensemble_predict_heteroscedastic_MPRAnn.py with both --distill and --eval flags set
# runs ensemble_predict_heteroscedastic_MPRAnn.py in distill mode
# for ensemble of MPRAnn models trained with heteroscedastic regression
# toggle DOWNSAMPLED to control whether distilled training data is obtained for downsampled... |
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