sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
0d846a3ec740c85ae94380fc72c2e89c00a822d95659423b31770ca96c65f641 | Shell | 1,313 | 33 | #!/bin/bash -x
#SBATCH --account=training2410
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=128
#SBATCH --time=03:00:00
#SBATCH --partition=dc-cpu
#SBATCH --job-name=$ARG1_$ARG2
# Handle dynamic log paths inside the script
out_log="logs/outputs/${ARG2}_${ARG1}.out"
err_log="logs/errors/${ARG2}_... |
40c508cfb35a3dcb8c2700020378563afaa3de7cca09a286869581d7dcf5a432 | Shell | 1,313 | 28 | #!/bin/bash
# set up environment
CONDA_BASE=$(conda info --base)
source $CONDA_BASE/etc/profile.d/conda.sh
conda env update -f environment.yml
conda activate diffbloch
# Run synthetic data thicknessNN experiment with 0.2A displacements
# Quartz 5 epochs
python scripts/main.py program=asu_refinement refinement.optimi... |
a5ac24a8a7845d65d62d3b4845fc095366b16055b63df2cf31728e62a0ac134a | Shell | 1,314 | 35 | #!/bin/bash
# Generate phantom 01
c3d phantom01_source.nii.gz -scale 60 -smooth 1vox -info -type uchar -o phantom01_fixed.nii.gz
# Create a mask
c3d phantom01_source.nii.gz -thresh 0.5 inf 1 0 -dilate 1 2x2x2 \
-type uchar -o phantom01_mask.nii.gz
# Generate the rigid transform
c3d_affine_tool \
-tran -64 -64 64... |
8bd07fc6adcbcaaaced8722af8dc126d0b6f59e7fb22e94545afee00f653a87c | Shell | 1,316 | 43 | #!/bin/bash
#SBATCH --partition=organ
#SBATCH --nodelist=gpu1
#SBATCH --cpus-per-task=12
#SBATCH --gpus-per-task=1
#SBATCH --time=72:00:00
#SBATCH --signal=USR2
#SBATCH --job-name=Seg_Calc
#SBATCH --output=/home/%u/slurm_log/%j.%x.out
var_list="${HOME}/script/batch_list.csv"
donor=$(awk -F',' -v x=${SLURM_ARRAY_TASK... |
3cf9f81ad6ecc241856902e9d648f43649c2b7f413255e1149892a42609e3b6a | Shell | 1,319 | 37 | #!/bin/bash
###############################################################################
# A quick and dirty gene coordinate fetcher #
# ARGS: <GENE FILE> <FLANK> <REST> #
####################################################################... |
8815c7af651777e90372701e2939f8b6343f097fd04ae26a777828af1a7a2e16 | Shell | 1,323 | 41 | #!/bin/bash
#
# Copyright 2021 DeepMind Technologies Limited
#
# 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 applica... |
98d02775783ec0f46e54c104970b5084f6fd72da8cb72c78e247255e9f091cbc | Shell | 1,323 | 40 | #!/bin/bash
# This script reads D, Dstar and F files from each algorithm and transform them to T1w space.
# Define input arguments
csv_file=$1
reference_image=$2
xfm_file=$3
interpolation_method=$4
output_path=$5
output_csv=$6
echo "Algorithm,Metric" >> "$output_csv"
# Read the CSV file column by column
column_count... |
82983a71a24927b6de38dc810cb62ab8552d1be6ad64a37c7072af9098e76a11 | Shell | 1,325 | 75 | #!/bin/sh
names=`sed -n '
/extern /s/extern [a-z*]* \(nrnmpi_[a-zA-Z0-9_]*\)(.*);/\1/p
/BGPDMA/s/.*/BGPDMA/p
$s/.*/ENDIF/p
' nrnmpidec.h`
#generate nrnmpi_dynam_wrappers.inc
sed -n '
/extern void/s/extern \(void\) \(nrnmpi_[a-zA-Z0-9_]*\)\(.*\);/\1 \2\3 {@ (*p_\2)\3;@}/p
/extern [^v]/s/extern \([a-z*]*\) \(nrnmpi_[a... |
b5409dfc1728b41f3ddabc221608b8af83cdeae69e1185da9bf422f12577c616 | Shell | 1,327 | 46 | #!/bin/bash
# package the build artifacts
set -ex
. "$(dirname $0)/utils.sh"
# Generate artifacts for release
mk_artifacts() {
cargo build --target "$TARGET" --release
}
mk_tarball() {
# When cross-compiling, use the right `strip` tool on the binary.
local gcc_prefix="$(gcc_prefix)"
# Create a temp... |
5a551b18f38ad6dc5123d63e05fb7521402d2627c5dfc9acdcffcf0c8d88a399 | Shell | 1,330 | 32 | #!/bin/bash -x
#SBATCH --account=training2410
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=128
#SBATCH --time=03:00:00
#SBATCH --partition=dc-cpu
# Handle dynamic log paths inside the script
out_log="logs/SHIP_Liege/outputs/${ARG2}_${ARG1}.out"
err_log="logs/SHIP_Liege/errors/${ARG2}_${ARG1}.e... |
ddeda46601f69f8e68c59774e8ff8500c9ab64049a01f1cf6afdd3aa711956d0 | Shell | 1,331 | 41 | #!/usr/bin/env bash
#
# Copyright 2021 DeepMind Technologies Limited
#
# 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... |
09e3c68944407381c93f4bdea2eeff6bd78a74e97b81f7993238e4d1d2c7c8a4 | Shell | 1,332 | 48 | #!/bin/bash
codedir="/home/antonio/Codes/bronchinet/"
basedata="./DLCST_Testing/"
#basedata="./LUVAR_Testing/"
ln -s $basedata "./BaseData"
# 1: DISTRIBUTE DATA
modelbasedir="./Models_TestDLCST/"
#modelbasedir="./Models_TestLUVAR/"
list_files_order_train=$(find "${modelbasedir}/CVfoldsInfo/" -name "train[0-9].txt... |
8aa6c8d6d918dd28e44de24cd05ec1b65f780ad465c836b03190e92455611193 | Shell | 1,333 | 52 | #!/bin/bash
#reading trait1
trait1f=./traitFolder/trait1/
trait1n=$(ls $trait1f)
for t1 in $trait1n
do
trait1nb=$(basename "$t1")
IFS='_' read -r -a trait1_array <<< "$trait1nb"
trait1name=${trait1_array[1]}
# reading trait2
trait2f=./traitFolder/trait2/
trait2n=$(ls $trait2f)
# loop starts here
for t2 in $trait2n... |
11482a2d46e53a5e5626a04d529b1e04a6e770b598f6e9b654b0a6f15ed2326e | Shell | 1,336 | 56 | #!/bin/bash
usage() {
cat << EOF
Usage: direct SUBJECT_ID OUTPUT_DIR
Continue DL+DiReCT starting from an existing segmentation in OUTPUT_DIR
EOF
exit 0
}
die() {
echo "ERROR: $1"
exit 1
}
# defaults
if [ -z "${ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS}" ] ; then
# number of threads for DiReCT
export ITK_GLOBAL_DEF... |
d3d907319c90d63760fc3bd4074c6f56c518cc6a1e2905d9695ecd1071f9f7eb | Shell | 1,336 | 59 | #!/bin/bash
SERIES=$1 ## GSE123456
if (( $# != 1 ))
then
>&2 echo "USAGE: ./convert_to_fastq.sh <series_id>"
>&2 echo
>&2 echo "(requires bsub_bam2fastq.sh/bsub_sra2fastq.sh, bam_to_10x_fastq_gz.sh/sra_to_10x_fastq_gz.sh,"
>&2 echo "and non-empty <series_id>.parsed.tsv)"
exit 1
fi
## all BAM/SRA -> fast... |
0da1bb140ceb63d71133e65657ddc416f12f55b3cfe70afc84de7e915c6ba135 | Shell | 1,337 | 33 | #!/bin/bash -x
#SBATCH --account=training2410
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=128
#SBATCH --time=02:00:00
#SBATCH --partition=dc-cpu
#SBATCH --job-name=$ARG1_$ARG2
# Handle dynamic log paths inside the script
out_log="logs/SHIP/outputs/${ARG2}_${ARG1}.out"
err_log="logs/SHIP/error... |
ee99b7f7511880825f31bd736e6746d5563c8e54566d3a9a08c10e2433cd4f14 | Shell | 1,338 | 40 | #!/bin/bash
set -e
set -x
set -u
TESTPATH=${1:-/src/nipype/nipype}
WORKDIR=${WORK:-/work}
PYTHON_VERSION=$( python -c "import sys; print('{}{}'.format(sys.version_info[0], sys.version_info[1]))" )
# Create necessary directories
mkdir -p ${WORKDIR}/tests ${WORKDIR}/crashfiles ${WORKDIR}/logs/py${PYTHON_VERSION}
# Cr... |
2f29409fca0d2c14a563182412d8156495708d0a73886484f2a4d227988fa254 | Shell | 1,339 | 62 | #!/bin/bash
SCRIPTS_PATH="$(dirname "$(realpath "$0")")"
SOURCE_PATH=$SCRIPTS_PATH/../..
BUILD_PATH=$SOURCE_PATH/build
BUILD_OPTION=""
INSTALL_PATH=$SOURCE_PATH/pymeshlab
INSTALL_OPTION=""
WHEELS_PATH=$SOURCE_PATH/wheels
NIGHTLY_OPTION=""
QT_OPTION=""
CCACHE_OPTION=""
#check parameters
for i in "$@"
do
case $i in... |
5bf7f094d37d2c291b8dc02774a08e69f39ae94700374a2d1135477523b72224 | Shell | 1,339 | 33 | #!/bin/sh
# Written by Pansheng Chen and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
# This script is specific to CBIG HPC cluster.
prefix=$1
base_dir=$CBIG_CODE_DIR"/stable_projects/predict_phenotypes/Chen2024_MMM"
rep_dir=$base_dir"/replication"
log_dir=$rep_dir"/log"
# submi... |
3c3d70e61c629cff367f9606c544413586015916a672a3abaaf3b11b00c3a202 | Shell | 1,340 | 40 | #!/bin/bash
#
# Train Chemprop model with SMILES + solvent features
#
echo "====================================================================================================
GENERATING SOLVENT FEATURES
====================================================================================================
"
python gener... |
8a40b161a77db17fc615c231da36ec83f2d396de4d2071013a1dc69a1b6215b0 | Shell | 1,341 | 26 | basedir="/mnt/y/PROJECTS/GMmicrostructure/DATA"
#basedir="/mnt/y/PROJECTS/GMmicrostructure/DATA/Longitudinal_VIPD/SESSION2"
mapfile -t allsubs < ../DATA/Batch.txt
cd ${basedir}
#allsubs=("VIPD_007")
for sub in "${allsubs[@]}"; do
subdir=$basedir/$sub
cd $subdir
echo $sub
# Create T1 segmentations and m... |
ee53a12a822c8bcd2994a492d8fc61ae6eea3f50f34d4e3e0d93e73bb78a0689 | Shell | 1,344 | 58 | #!/bin/bash
CONDA_EV=~/miniconda3
SCRIPT_DIR="$(
cd -- "$(dirname -- "${BASH_SOURCE[0]}")" >/dev/null 2>&1 && pwd
)"
WORK_ROT="$(
cd -- "$SCRIPT_DIR/../../.." >/dev/null 2>&1 && pwd
)"
cd ${WORK_ROT} || exit
RUN_NAME=mecap_ref_mca_layer_0
SRCP_DIR=src
BASE_DIR=${WORK_ROT}/data/references
RESL_DIR=${WORK_ROT}/... |
0529156fa8ff6ed101c2d547412a27348d35d4108100cb226e0d5a4d744b71fe | Shell | 1,347 | 38 | #! /bin/bash
step=2
## Check whether recon-all is finished
if [[ $step -eq 1 ]]
then
sour_dir=/Data/sharehome/huyang/HuYang/HY_20250709/PROCDATA/NIIDATA/T1
targ_dir=/Data/sharehome/huyang/HuYang/HY_20250709/PROCDATA/LIST
sublist=/Data/sharehome/huyang/HuYang/HY_20250709/PROCDATA/LIST/sublist.txt
for cur... |
857bb28a152940c484aa56abc3f01e4b1dfe293f6ea384585fdca0e5eb8d5efa | Shell | 1,347 | 29 | #!/usr/bin/env bash
#
# Licensed to the Apache Software Foundation (ASF) under one or more
# contributor license agreements. See the NOTICE file distributed with
# this work for additional information regarding copyright ownership.
# The ASF licenses this file to You under the Apache License, Version 2.0
# (the "Lice... |
b44479d077e01d40d7ecc6e886de49bc589cb604da397f6ac4e7c9babf349898 | Shell | 1,347 | 58 | #!/bin/bash
CONDA_EV=~/miniconda3
SCRIPT_DIR="$(
cd -- "$(dirname -- "${BASH_SOURCE[0]}")" >/dev/null 2>&1 && pwd
)"
WORK_ROT="$(
cd -- "$SCRIPT_DIR/../../.." >/dev/null 2>&1 && pwd
)"
cd ${WORK_ROT} || exit
RUN_NAME=mecap_ref_mca_v2_layer_0
SRCP_DIR=src
BASE_DIR=${WORK_ROT}/data/references
RESL_DIR=${WORK_RO... |
071c02011b90896d07cdf73c2a228959c15079654aa206458dd2ce5ab6ca5eef | Shell | 1,348 | 58 | #!/bin/bash
CONDA_EV=~/miniconda3
SCRIPT_DIR="$(
cd -- "$(dirname -- "${BASH_SOURCE[0]}")" >/dev/null 2>&1 && pwd
)"
WORK_ROT="$(
cd -- "$SCRIPT_DIR/../../.." >/dev/null 2>&1 && pwd
)"
cd ${WORK_ROT} || exit
RUN_NAME=mecap_ref_maa_layer_0
SRCP_DIR=src
BASE_DIR=${WORK_ROT}/data/references
RESL_DIR=${WORK_ROT}/... |
41e69cf430b267b3697f20c3c76f0c9e0f3e7ab53d22bdfccee832eae21d237b | Shell | 1,350 | 57 | #!/bin/bash
CONDA_EV=~/miniconda3
SCRIPT_DIR="$(
cd -- "$(dirname -- "${BASH_SOURCE[0]}")" >/dev/null 2>&1 && pwd
)"
WORK_ROT="$(
cd -- "$SCRIPT_DIR/../../.." >/dev/null 2>&1 && pwd
)"
cd ${WORK_ROT} || exit
RUN_NAME=mecap_scaf_mca_v2_layer_0
SRCP_DIR=src
RUN_MODE=train
BASE_DIR=${WORK_ROT}/data/references
RE... |
d33fe20118c5fbf069912e1787f6c1fedefa0232686c89c4358d42f63a4ed3ac | Shell | 1,350 | 38 | #!/usr/bin/env bash
#
# Script to update OpenTelemetry proto files in the MLflow repository.
#
# Usage:
# ./mlflow/protos/opentelemetry/update.sh
#
set -eo pipefail
# Commit SHA from opentelemetry-proto repository
# v1.7.0: https://github.com/open-telemetry/opentelemetry-proto/commit/8654ab7a5a43ca25fe8046e59dcd693... |
974b8f281fde3f9cdb71a11afae8b3da93a870f8ec81fae51a577681751bc2dc | Shell | 1,352 | 58 | #!/bin/bash
CONDA_EV=~/miniconda3
SCRIPT_DIR="$(
cd -- "$(dirname -- "${BASH_SOURCE[0]}")" >/dev/null 2>&1 && pwd
)"
WORK_ROT="$(
cd -- "$SCRIPT_DIR/../../.." >/dev/null 2>&1 && pwd
)"
cd ${WORK_ROT} || exit
RUN_NAME=mecap_scaf_maa_layer_0
SRCP_DIR=src
BASE_DIR=${WORK_ROT}/data/references
RESL_DIR=${WORK_ROT}... |
af3fb64dd63e4bd1c6c6de41df523e17d1277ea7f4c2d6188fa786c5b81c3c97 | Shell | 1,352 | 59 | #!/bin/bash
CONDA_EV=~/miniconda3
SCRIPT_DIR="$(
cd -- "$(dirname -- "${BASH_SOURCE[0]}")" >/dev/null 2>&1 && pwd
)"
WORK_ROT="$(
cd -- "$SCRIPT_DIR/../../.." >/dev/null 2>&1 && pwd
)"
cd ${WORK_ROT} || exit
RUN_NAME=mecap_ref_maa_v2_layer_0
SRCP_DIR=src
BASE_DIR=${WORK_ROT}/data/references
RESL_DIR=${WORK_RO... |
d9fda35c0570a8c2baec0c450a4362a9accf5648fdb2936274c00e657e8da57d | Shell | 1,352 | 43 | #!/usr/bin/env bash
echo "Checking docs/environment-variables.md for completeness..."
# Directories to check. For cmd/, only check Controller, Executor, and Server. The CLI has generated docs
dirs=(./workflow ./persist ./util ./server ./cmd/argo/commands/server.go ./cmd/argoexec ./cmd/workflow-controller)
not_found="... |
2dc031ba594e86ee72ee326793cda854c9d207b0a0405a39729717eea89dbab2 | Shell | 1,354 | 41 | #!/bin/bash
#
# Copyright 2021 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... |
b4a30628bc45efe3d233848b6efd2b72ec3da5b6e4038480bb7f22a30a98a31b | Shell | 1,355 | 58 | #!/bin/bash
CONDA_EV=~/miniconda3
SCRIPT_DIR="$(
cd -- "$(dirname -- "${BASH_SOURCE[0]}")" >/dev/null 2>&1 && pwd
)"
WORK_ROT="$(
cd -- "$SCRIPT_DIR/../../.." >/dev/null 2>&1 && pwd
)"
cd ${WORK_ROT} || exit
RUN_NAME=mecap_scaf_maa_v2_layer_0
SRCP_DIR=src
BASE_DIR=${WORK_ROT}/data/references
RESL_DIR=${WORK_R... |
32ff7bcfd2b4ed971988222d4f0585dc03c9d0d166d2d38a29bd350a1273654a | Shell | 1,357 | 30 | #!/usr/bin/env bash
set -euo pipefail
echo "[before] running in: ${PWD}"
echo "CI_COMMIT_BRANCH: ${CI_COMMIT_BRANCH:-}"
echo "CI_DEFAULT_BRANCH: ${CI_DEFAULT_BRANCH:-}"
python --version
# The runner's helper clones the repository as root, but merit-ci-3.13 runs
# the job as the ordinary user `ci`. Git refuses a reposi... |
b0560eea6e737182780671574b6c773926d20c7940f52f2d6674ed002784a1d2 | Shell | 1,359 | 18 | # =============================================================================
# 1d linear interpolation for VGG-9
# =============================================================================
mpirun -n 3 python plot_surface.py --x=-0.5:1.5:401 --model vgg9 --dir_type states --mpi --cuda \
--model_file cifar10/train... |
9dea22c1c8d42547fdcbb8eb6fac313467a488dbc755213261489351c83e5aeb | Shell | 1,362 | 41 | #!/usr/bin/env bash
#
# Copyright 2021 DeepMind Technologies Limited
#
# 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... |
b0f1e88e616efa7d3feea8ca38a62b2035da2896bc7fa2eab54fbc4b3c341cf5 | Shell | 1,362 | 56 | #!/usr/bin/env bash
### in this directory should be only VCF files
GENOTYPE_DIR=$1
SAVE_DIR=$2
HASEDIR=$3
STUDYNAME=$4
SUBJECT_ID_FILE='SUB_ID.txt'
SNPs_INFO='SNPs_info.txt'
CWD=`pwd`
cd $GENOTYPE_DIR
rm -f ${SAVE_DIR}/${SUBJECT_ID_FILE}
rm -f ${SAVE_DIR}/${SNPs_INFO}
count=1
for file in *; do
files_order[${c... |
775560047b2cc43c720d7383d2dd21537ee4266f4e1032e2e7898360be84188f | Shell | 1,364 | 48 | #!/bin/bash
# Build all .md files to PDF using pandoc
# Check if pandoc is available, if not tell the user and stop
if ! command -v pandoc &> /dev/null; then
echo "Error: pandoc is not installed or not in PATH"
exit 1
fi
SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
# Define the folders to proce... |
f3eca4d7ff88b81edea19180ad7ef30c67b7cfa1a28232dec4edd3004530096f | Shell | 1,364 | 63 | #!/bin/bash
set -e
function usage ()
{
echo "Usage: $0 [-s <server name>] [-u <user name>] [-p <password>] [-d <directory>] [-t <target dir>]" 1>&2
exit 1
}
directory="$(pwd)"
target="$(date -Id)"
while getopts ":s:u:p:d:t:" key; do
case "${key}" in
s)
server_name="${OPTARG}"
... |
01c0370a9fe90cd6d14d3af017cd3056ab23dd29f8e9a6c150f675de30f6a623 | Shell | 1,367 | 18 | # ===========================================================
# 1d linear interpolation for ResNet-56
# ===========================================================
mpirun -n 4 python plot_surface.py --cuda --mpi --x=-0.5:1.5:401 --model resnet56 --dir_type states \
--model_file cifar10/trained_nets/resnet56_sgd_lr=0.1_... |
f664657f08cf7592a235a3966a6035e2fb1eb4f7b4f0fb7d7e5f00ef6167fcaf | Shell | 1,367 | 65 | #!/bin/bash
SCRIPTS_PATH="$(dirname "$(realpath "$0")")"
SOURCE_PATH=$SCRIPTS_PATH/../..
BUILD_PATH=$SOURCE_PATH/build
INSTALL_PATH=$SOURCE_PATH/pymeshlab
NIGHTLY_OPTION=""
QT_DIR=""
CCACHE=""
#check parameters
for i in "$@"
do
case $i in
-b=*|--build_path=*)
BUILD_PATH="${i#*=}"
shift # past argu... |
7bc19808c9b4f0a08d39bae6fdfa96bd864f615529450db3c40157dd6ecfed1e | Shell | 1,368 | 42 | MODEL_NAME_S="resunet_combined_scaled_1000"
# Each dataset is defined as: "<image_dir>::<avg_radius>"
DATASETS=(
"data/raw/1_c_elegans_nuclei/test/images::6.0"
"data/raw/2_livernuclei/test/images::12.0"
"data/raw/3_mesoSPIM_dataset/test/images::3.5"
"data/raw/4_Mouse_NucMM-M/test/images::6.5"
"data... |
e4d92b4a67509a924268b43d3009889c0f0cc56709791ff2bd880d2bd0772652 | Shell | 1,368 | 35 | ##Directory
CCS_DIR=/your_project_path/CCS
SUBJECTS_DIR=/your_project_path/FreeSurfer60/
##PARAMETERS
rest_dir_name=rest
rest_name=rest
TR=2
numDropping=5 ## 10 seconds
sliceOrder=alt+z
FWHM=6
##SUBJECT
subject=CCSsubjectname
echo ${subject}
CCS_APP=/brain/zuoxinian/LCBT_app/CCS_SCRIPTS
##PREPROCESSING
${CCS_APP}/Bas... |
27479c2221566960638bb1bb1e079306da12e032074345005f3e29be5c47c9e8 | Shell | 1,373 | 59 | #!/bin/bash
CONDA_EV=~/miniconda3
SCRIPT_DIR="$(
cd -- "$(dirname -- "${BASH_SOURCE[0]}")" >/dev/null 2>&1 && pwd
)"
WORK_ROT="$(
cd -- "$SCRIPT_DIR/../.." >/dev/null 2>&1 && pwd
)"
cd ${WORK_ROT} || exit
RUN_NAME=mecap_ref_mca_layer_0_wo_pretrain
SRCP_DIR=src
BASE_DIR=${WORK_ROT}/data/references
RESL_DIR=${W... |
7f31456ee41ddb4113c8e25fbfa175384ded2f3ac71234452764733c10451edf | Shell | 1,375 | 59 | #!/bin/bash
CONDA_EV=~/miniconda3
SCRIPT_DIR="$(
cd -- "$(dirname -- "${BASH_SOURCE[0]}")" >/dev/null 2>&1 && pwd
)"
WORK_ROT="$(
cd -- "$SCRIPT_DIR/../../.." >/dev/null 2>&1 && pwd
)"
cd ${WORK_ROT} || exit
RUN_NAME=mecap_ref_mca_layer_1
SRCP_DIR=src
BASE_DIR=${WORK_ROT}/data/references
RESL_DIR=${WORK_ROT}/... |
e1d1c8923d6b1fc3602e7c61d1c5817b04350cdb687558bb4d206cbc3782af4a | Shell | 1,375 | 43 | #!/usr/bin/env bash
# Quick smoke test for IRAF + PyRAF on the login node (same venv logic as PBS + run_ngc1566_full_pipeline_gadi.sh).
#
# Usage (Gadi):
# export IRAF=/g/data/jh2/jt4478/iraf-2.17 # or your IRAF root
# bash scripts/test_photometry_login_node.sh
#
# Optional env (match your PBS job):
# PROJECT_R... |
39ea5251b8fa0b9a1b8d7c063d184e9b0ded384bb2f50e571303b68fc87a4625 | Shell | 1,376 | 59 | #!/bin/bash
CONDA_EV=~/miniconda3
SCRIPT_DIR="$(
cd -- "$(dirname -- "${BASH_SOURCE[0]}")" >/dev/null 2>&1 && pwd
)"
WORK_ROT="$(
cd -- "$SCRIPT_DIR/../.." >/dev/null 2>&1 && pwd
)"
cd ${WORK_ROT} || exit
RUN_NAME=mecap_ref_mca_v2_layer_0_wo_pretrain
SRCP_DIR=src
BASE_DIR=${WORK_ROT}/data/references
RESL_DIR=... |
5ac1c4ede9cf15c3ac96d3ac1800fb448e1591fc67f03287b5f4dd17ce8b7444 | Shell | 1,376 | 65 | #!/bin/bash
SCRIPTS_PATH="$(dirname "$(realpath "$0")")"
SOURCE_PATH=$SCRIPTS_PATH/../..
BUILD_PATH=$SOURCE_PATH/build
INSTALL_PATH=$SOURCE_PATH/pymeshlab
NIGHTLY_OPTION=""
QT_DIR=""
CCACHE=""
#check parameters
for i in "$@"
do
case $i in
-b=*|--build_path=*)
BUILD_PATH="${i#*=}"
shift # past argu... |
6c1fdbd611635b08f6bf3d0ce38bdcc930ce5902fe9cfb204604dce975d88306 | Shell | 1,376 | 41 | #!/bin/bash
#PBS -q batch
#PBS -l walltime=72:00:00 -l nodes=1:ppn=8
#PBS -N AppendCB
#PBS -j oe
#PBS -o /home/whe/qsub_opt/${PBS_JOBID}.${PBS_JOBNAME}.log
# activate env
conda_env="bulk-seq"
_CONDA_ROOT="${HOME}/Programs/miniconda3"
source ${_CONDA_ROOT}/bin/activate ${conda_env}
export OMP_NUM_THREADS=${PBS_NP}
ex... |
c9f041fd8fcddd29696e08b8cd5ad0d7ee751206ec7bb4fd509a19c1981f423c | Shell | 1,376 | 39 | #!/bin/bash
#SBATCH --account=girirajan # TODO: set account name
#SBATCH --partition=girirajan # TODO: set slurm partition
#SBATCH --job-name=gangstr
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --time=400:0:0
#SBATCH --mem-per-cpu=50G
#SBATCH --chdir /data7/ipsc/16p12_1_del/str_calls # TODO: set dir to projec... |
033dc77b97c77851f473f6a63ca909c91d57a0b1134dbeaf4207b8e48c2d6516 | Shell | 1,377 | 38 | #!/bin/bash
train_iteration=1 # could be 1, 2, ...
path_to_dataset_train=/path/to/your/training/dataset.csv
path_to_dataset_val=/path/to/your/validation/dataset.csv
val_interval=4000
mask_time_prob=0.33 # optimal masking ratio found empirically (see supplementary material)
batch_size=448
alpha=1.0
kmeans_path=/path/to... |
6bbd0192728bae730848c69c49302c268c6ebaa9d0fc92742a88c3f970627f16 | Shell | 1,377 | 27 | #!/bin/bash
# this function runs all the kernel regressions in Chen & Tam 2021 paper
#
# Written by Jianzhong Chen and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
pred_results_dir=$1
perm_out_dir=$2
################################################################################... |
aa52c52ca3b941bd06944860d2e86fcd7480f8bd9f372a89cdab1c06abbbee81 | Shell | 1,377 | 58 | #!/bin/bash
CONDA_EV=~/miniconda3
SCRIPT_DIR="$(
cd -- "$(dirname -- "${BASH_SOURCE[0]}")" >/dev/null 2>&1 && pwd
)"
WORK_ROT="$(
cd -- "$SCRIPT_DIR/../../.." >/dev/null 2>&1 && pwd
)"
cd ${WORK_ROT} || exit
RUN_NAME=mecap_ref_mca_v2_layer_1
SRCP_DIR=src
RUN_MODE=train
BASE_DIR=${WORK_ROT}/data/references
RES... |
d991b7dabed29b7e0ba54b8432d87956c85f43f83defd9d910eb15a9dd1b9bbe | Shell | 1,377 | 59 | #!/bin/bash
CONDA_EV=~/miniconda3
SCRIPT_DIR="$(
cd -- "$(dirname -- "${BASH_SOURCE[0]}")" >/dev/null 2>&1 && pwd
)"
WORK_ROT="$(
cd -- "$SCRIPT_DIR/../.." >/dev/null 2>&1 && pwd
)"
cd ${WORK_ROT} || exit
RUN_NAME=mecap_ref_maa_layer_0_wo_pretrain
SRCP_DIR=src
BASE_DIR=${WORK_ROT}/data/references
RESL_DIR=${W... |
8141829c30d53f60f6cb6151aba6979a2c457614d586d1d9abc3c2062b9531cc | Shell | 1,379 | 40 | #!/bin/bash
#SBATCH --account=girirajan # TODO: set account name
#SBATCH --partition=girirajan # TODO: set slurm partition
#SBATCH --job-name=mergestr
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --time=400:0:0
#SBATCH --mem-per-cpu=50G
#SBATCH --chdir /data7/ipsc/16p12_1_del/str_calls # TODO: set dir to proje... |
88228747b3f448ea1b2b2d5026d28bb439f67d75c2b1fef8381366165c98263a | Shell | 1,379 | 59 | #!/bin/bash
CONDA_EV=~/miniconda3
SCRIPT_DIR="$(
cd -- "$(dirname -- "${BASH_SOURCE[0]}")" >/dev/null 2>&1 && pwd
)"
WORK_ROT="$(
cd -- "$SCRIPT_DIR/../../.." >/dev/null 2>&1 && pwd
)"
cd ${WORK_ROT} || exit
RUN_NAME=mecap_ref_maa_layer_1
SRCP_DIR=src
BASE_DIR=${WORK_ROT}/data/references
RESL_DIR=${WORK_ROT}/... |
3514ddb236c55407ddfdbc6db8439bc9b6b96d83a86af85b0954f5c79a5474db | Shell | 1,380 | 59 | #!/bin/bash
CONDA_EV=~/miniconda3
SCRIPT_DIR="$(
cd -- "$(dirname -- "${BASH_SOURCE[0]}")" >/dev/null 2>&1 && pwd
)"
WORK_ROT="$(
cd -- "$SCRIPT_DIR/../.." >/dev/null 2>&1 && pwd
)"
cd ${WORK_ROT} || exit
RUN_NAME=mecap_ref_maa_v2_layer_0_wo_pretrain
SRCP_DIR=src
BASE_DIR=${WORK_ROT}/data/references
RESL_DIR=... |
d23a10a7c399a302bbebd7a9d85306e238700ab2925bed8056fcdcab13f5f399 | Shell | 1,380 | 60 | #!/bin/bash
CONDA_EV=~/miniconda3
SCRIPT_DIR="$(
cd -- "$(dirname -- "${BASH_SOURCE[0]}")" >/dev/null 2>&1 && pwd
)"
WORK_ROT="$(
cd -- "$SCRIPT_DIR/../../.." >/dev/null 2>&1 && pwd
)"
cd ${WORK_ROT} || exit
RUN_NAME=mecap_ref_mca_layer_2
SRCP_DIR=src
BASE_DIR=${WORK_ROT}/data/references
RESL_DIR=${WORK_ROT}/... |
6b1e3f4f82fe0cb11217f2f92a3b3626ecb983266a4bb22073b23c798ead20f3 | Shell | 1,382 | 59 | #!/bin/bash
CONDA_EV=~/miniconda3
SCRIPT_DIR="$(
cd -- "$(dirname -- "${BASH_SOURCE[0]}")" >/dev/null 2>&1 && pwd
)"
WORK_ROT="$(
cd -- "$SCRIPT_DIR/../../.." >/dev/null 2>&1 && pwd
)"
cd ${WORK_ROT} || exit
RUN_NAME=mecap_ref_maa_v2_layer_1
SRCP_DIR=src
BASE_DIR=${WORK_ROT}/data/references
RESL_DIR=${WORK_RO... |
87cfd0b3488fb56dc14a9aface007abb94a7d25fce3ba9a03943f75ff8b18b40 | Shell | 1,382 | 59 | #!/bin/bash
CONDA_EV=~/miniconda3
SCRIPT_DIR="$(
cd -- "$(dirname -- "${BASH_SOURCE[0]}")" >/dev/null 2>&1 && pwd
)"
WORK_ROT="$(
cd -- "$SCRIPT_DIR/../../.." >/dev/null 2>&1 && pwd
)"
cd ${WORK_ROT} || exit
RUN_NAME=mecap_ref_mca_v2_layer_2
SRCP_DIR=src
BASE_DIR=${WORK_ROT}/data/references
RESL_DIR=${WORK_RO... |
1c0ee39eea31f378b13bcba4afea0451d29499888fd4eac0c45e67e365e85632 | Shell | 1,383 | 37 | #!/bin/bash
#SBATCH -J banc_nblast_compile_chain
#SBATCH -c 4
#SBATCH -t 0-23:00
#SBATCH -p medium
#SBATCH --mem=128G
#SBATCH -o jobs/banc_nblast_compile_chain_%j.out
#SBATCH -e jobs/banc_nblast_compile_chain_%j.err
# Post-fleet finalisation: dedupe wrong matches → compile feathers → push to
# CAVE → push to GCS. Subm... |
994d490db1bf3ce3858ec7a979a8c7de926ffead858057cb74005f0705f557a6 | Shell | 1,383 | 59 | #!/bin/bash
CONDA_EV=~/miniconda3
SCRIPT_DIR="$(
cd -- "$(dirname -- "${BASH_SOURCE[0]}")" >/dev/null 2>&1 && pwd
)"
WORK_ROT="$(
cd -- "$SCRIPT_DIR/../../.." >/dev/null 2>&1 && pwd
)"
cd ${WORK_ROT} || exit
RUN_NAME=mecap_ref_maa_layer_2
SRCP_DIR=src
BASE_DIR=${WORK_ROT}/data/references
RESL_DIR=${WORK_ROT}/... |
7bdef8a0463a3cf6fe291d99d0bf522389de3e5439c886e9a8a39cc285889c2f | Shell | 1,385 | 44 | #!/bin/bash
set -e # Exit on error
# Prepare weights for release by removing subject ids and unneeded files and zipping
#
# Usage: ./prepare_weights_for_release.sh DATASET_ID [DATASET_ID2 ...]
#
# Example: ./prepare_weights_for_release.sh 527 528 529 ...
# todo: select as needed
# cd /mnt/nvme/data/multiseg/weights_... |
9e54aaf27a9d355c2f18a186c9592271fcf3f44db7ab4efa3ba21dd6d2f8844d | Shell | 1,386 | 59 | #!/bin/bash
CONDA_EV=~/miniconda3
SCRIPT_DIR="$(
cd -- "$(dirname -- "${BASH_SOURCE[0]}")" >/dev/null 2>&1 && pwd
)"
WORK_ROT="$(
cd -- "$SCRIPT_DIR/../../.." >/dev/null 2>&1 && pwd
)"
cd ${WORK_ROT} || exit
RUN_NAME=mecap_ref_maa_v2_layer_2
SRCP_DIR=src
BASE_DIR=${WORK_ROT}/data/references
RESL_DIR=${WORK_RO... |
0813b57f2758c51e1ec7227c5628e873a415c8d71f48994cba2183505b9f58ff | Shell | 1,390 | 52 | #!/bin/bash
default_wrkbase=multiallelics/istrs/custom_filter/ # or whatever the working directory is
usage() {
echo "Usage: $0 [-c chr] [-w working dir] [-h]"
exit 1
}
wrk_base=""
chr=""
while getopts ":c:w:h" opt; do
case $opt in
c) chr="$OPTARG" ;;
w) wrk_base="$OPTARG" ;;
h) ... |
c506bc345e452e5306e7880e2e1a2ecdf5b173e96059e0d29547171c93cc8abc | Shell | 1,390 | 46 | #!/bin/bash
rm random_walk/*.{mp4,db} 2>/dev/null
rm random_walk/*_wire.pdf 2>/dev/null
rm random_walk/*_radii* 2>/dev/null
rm random_walk/*swc* 2>/dev/null
rm demo_attraction/*.{mp4,db} 2>/dev/null
rm demo_attraction/*_wire.pdf 2>/dev/null
rm demo_attraction/*_radii* 2>/dev/null
rm demo_attraction/*swc 2>/dev/null
... |
db6bbefc82065bc1351115dd38ee8507c0fc20f4d6beb74757150b67b0c0298e | Shell | 1,393 | 59 | #!/bin/bash
set -euo pipefail
err() {
echo "ERROR: $*" >&2
exit 1
}
usage() {
cat <<EOF
Usage: $(basename "$0") <subject> <hemi> <label1> <label2>
Print Overall Dice from mris_compute_parc_overlap.
Arguments:
subject FreeSurfer subject ID or subject directory
hemi lh or rh
label1 first labe... |
4f50afd146e9415cce585bc6c3c125ee1602f4ba40f8199bc03caf329a9b9bc7 | Shell | 1,394 | 41 | #!/bin/bash
#
# Copyright 2021 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... |
7b9fb59ee341a243ab3417d10fbc5493a88aa3b09c9483c0c7d31a60350ea55a | Shell | 1,395 | 30 | #!/usr/bin/env bash
# Creates a set of files that map records between GENCODE and HGNC.
# Pulled directly from the ensemble database.
# Currently not used by Funcotator.
outFileBaseName="gencode_xhgnc"
outExt=".tsv"
hg19db="homo_sapiens_core_75_37"
hg38db="homo_sapiens_core_110_38"
hg19FileName=${outFileBaseName}_v... |
52201fc91dcb02ebb090c5c104fbb40f17f1c82325d3ee436eff064dca4cdabe | Shell | 1,397 | 52 | #!/bin/sh
# extract commit version info from src/nrnoc/nrnversion.h
# and PACKAGE_VERSION from configure.ac
if test "$NSRC" = "" ; then
NSRC=$HOME/neuron/nrn
fi
if test -f $NSRC/src/nrnoc/nrnversion.h ; then
VERHFILE=`cat $NSRC/src/nrnoc/nrnversion.h`
elif test -d $NSRC/.git ; then
VERHFILE=`sh $NSRC/git2nrnversio... |
abc82cb861ed954a258c9bbcbd605b607a5b60fe867243fb5de78b5de8ac8b62 | Shell | 1,397 | 46 | #!/bin/bash
#
# Collects the pull-requests since the latest release and
# aranges them in the CHANGES.txt file.
#
# This is a script to be run before releasing a new version.
#
# Usage /bin/bash update_changes.sh 1.0.1
#
# Setting # $ help set
set -u # Treat unset variables as an error when substituting.
... |
9d5d6352ed390f677c4c540e5f7f258f11c62928aebf01bc45108cca3e046819 | Shell | 1,399 | 36 | #!/bin/bash -e
#
# SVRTK : SVR reconstruction based on MIRTK
#
# Copyright 2018-2021 King's College London
#
# 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/licens... |
307918fef9669bbb167a27a7a80a4b92e92e24ede6df6767f13eac934e0c1150 | Shell | 1,401 | 46 | #!/usr/bin/env bash
# Copyright (c) Meta Platforms, Inc. and its affiliates.
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
# Propagate failures properly
set -e
if [[ $# -eq 1 ]]; then
export mcss_path=$1
elif [[ $# -ne 0 ]]; then
echo ... |
6fa578bc2ff57ce171080cc64d2b0e1992eae0dc113b0d3d0d1743bff67b844f | Shell | 1,402 | 41 | #!/usr/bin/env bash
#
# Copyright 2021 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by... |
a893ecc5821759b8c45d97799e5cb2e1c4a258d82fe8ffad6d6cbcbff291b2e3 | Shell | 1,403 | 38 | #!/usr/bin/env bash
# Download UCI Gas Sensor Array Drift Dataset (Vergara 2012) and the
# Wörner et al. 2025 12-month MOS-sensor dataset.
#
# Total ~150 MB. Requires curl, unzip.
#
# Usage:
# bash scripts/download_data.sh
set -euo pipefail
cd "$(dirname "$0")/.."
mkdir -p data/raw data/worner_2025
# ---- UCI Ver... |
43151d5b727a3080315510c7567606cc1d7945c9a44e41dbea6d14519d2e5f11 | Shell | 1,404 | 50 | #!/bin/bash
# Zizhuang Miao
# This script runs fmriprep on the high-performance computing cluster at Dartmouth College
# The raw data following the BIDS format is located at ${BIDSDIR}
# See below or the paper for the details of the preprocessing pipeline
# Slurm parameters ___________________________________________... |
42cb4885c06f1ffc273b069f86aa4378574a76b6f52d11b2c60063e739bb98d5 | Shell | 1,405 | 28 | #!/usr/bin/env bash
# Creates a set of files that map records between many known databases of genes.
# Pulled directly from the ensemble database.
# Currently not used by Funcotator.
outFileBaseName="all_TX_mappings"
outExt=".tsv"
hg19db="homo_sapiens_core_75_37"
hg38db="homo_sapiens_core_90_38"
hg19FileName=${outF... |
abb4735a70fbf66663c2626acf908ebd19753460c9945d8ab8c1dfe55d6f51f2 | Shell | 1,405 | 35 | #!/bin/bash
#SBATCH --job-name=fmriprep # Name of the job
#SBATCH --cpus-per-task=8 # Number of CPU cores
#SBATCH --mem=32G # Maximum system memory (RAM)
#SBATCH --time=0-24:00 # Time limit (DD-HH:MM)
#SBATCH --nice=1 # Lower priority to allow higher-priority jobs to... |
2f65a88055e3b1745b4df4b5de1f2ab8be28f7a671f9e210be56ce4b9a907b8c | Shell | 1,406 | 41 | #!/bin/bash
#
# Copyright 2021 DeepMind Technologies Limited
#
# 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 applica... |
c2d8477b271de491b81bb1e251c324af4f5719774697cc2cab379b082bf0f862 | Shell | 1,406 | 36 | #!/bin/bash
# Written by Jianzhong Chen and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
bold_file=$1
outdir=$2
tmp_dir=$3
low_f=$4
high_f=$5
root_dir=`dirname "$(readlink -f "$0")"`
if [ -z "$bold_file" ] || [ -z "$outdir" ] || [ -z "$outdir" ]; then
echo "bold_file, outdir... |
8a6953ec7fb06c240e59eef8855c186dc04c53f4ae2aa47c9905ad7315a1ac86 | Shell | 1,407 | 44 | #!/bin/bash
# This wrapper function performs KRR using a publicly-available air quality dataset.
# The aim of this example to let the users familiarize our KRR workflow, please
# refrain from making any conclusion regarding this air quality dataset per se.
# This script will firstly generate a setup file, then pass th... |
ac8c2c9b68f8a304540f191dc91b7651b40a43634be3868525ec5e27a92e2548 | Shell | 1,413 | 41 | #!/bin/bash
# Written by Jianzhong Chen and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
###########################################
# Usage and Reading in Parameters
###########################################
# Usage
usage() { echo "
Usage: $0 -p <paramfile> -n <N_test_folds>... |
367582de736e3c9b6a6125400dfa35b04149824116ae2e2dc41353f3b2d391eb | Shell | 1,414 | 41 | #!/usr/bin/env bash
#
# Copyright 2021 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by... |
9a3c70a6b9d1846628bc3293b5c6513b894ff1baed9ced70eec661ae8631b434 | Shell | 1,414 | 78 | #!sh
set -e
NEURONHOME=$N
M=$N/lib
# get the last argument
for last; do true; done
OUTPUTDIR=.
# if the last argument begins with --NEURON_HOME=
if [[ $last == "--OUTPUTDIR="* ]] ; then
OUTPUTDIR=${last#"--OUTPUTDIR="}
# remove the last argument
set -- "${@:1:$(($#-1))}"
fi
if test $# -gt 0
then
files=$*
else
fi... |
0f8fefc3bb0bbb28a954d56ab16037c3937675bb67c676823a9eba5717856e3f | Shell | 1,417 | 53 | #!/bin/bash
# local directories
export parameters_dir="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
export code_dir=$parameters_dir/..
# setup path from installation
[ ! -f $parameters_dir/path.sh ] || . $parameters_dir/path.sh
# cortical structures of labels file
export cortical_structures=`cat $DRAWEMDIR/par... |
548607ff8642b4f2341a5aa8f685437530db12c52c42311fbd6ba318c3249888 | Shell | 1,420 | 24 | #!/bin/sh
#
# Written by Pansheng Chen and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
cd ~/storage
rsync -a --exclude .git $CBIG_CODE_DIR/* Standalone_Chen2024_MMM
# remove useless stable projects
rm -r Standalone_Chen2024_MMM/stable_projects/brain_parcellation
rm -r Standalon... |
17cc46cc294101663be97c7a8ce54ea34e185dbfc894828d41854198d1926b97 | Shell | 1,424 | 68 | #!/bin/bash
unameOut="$(uname -s)"
case "${unameOut}" in
Linux*) machine=Linux; folder=Other;;
Darwin*) machine=Mac; folder=macOS;;
CYGWIN*) machine=Windows; folder=Windows;;
MINGW*) machine=Windows; folder=Windows;;
*) machine="UNKNOWN"
esac
if [ ${machine} == "UNKNOWN" ];... |
321b4b4d1128a35ab82654e06ea6cf460a3d083af0f87c7da9bbbeaccbef34f6 | Shell | 1,424 | 35 | #!/bin/bash
# Germline small and structural variant analysis of NA24385 against Genome in a Bottle references
# Uses 50x HiSeq x10 dataset from 10x genomics:
# https://support.10xgenomics.com/de-novo-assembly/datasets
# http://biorxiv.org/content/early/2016/08/19/070425
set -eu -o pipefail
CORES=4
mkdir -p input
cd ... |
e663b843a0684c74d0624e52f77840c787efd02636d65c9dcc13652b7fea0b4d | Shell | 1,426 | 42 | #!/usr/bin/env bash
# Copyright (c) Meta Platforms, Inc. and affiliates.
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
# Propagate failures properly
set -e
if [[ $# -eq 1 ]]; then
export mcss_path=$1
elif [[ $# -ne 0 ]]; then
echo "usa... |
0b791dd275832e4471c9dbd5a256ccf7cb153bef07cdef720e427dac9c3b5483 | Shell | 1,429 | 54 | #!/bin/bash
#PBS -P jh2
#PBS -q gpuvolta
#PBS -l walltime=04:00:00
#PBS -l ncpus=12
#PBS -l ngpus=1
#PBS -l mem=64GB
#PBS -l jobfs=200GB
#PBS -l wd
#PBS -N comp_nn_train
#PBS -j oe
#PBS -m bea
#PBS -l storage=scratch/jh2+gdata/jh2+scratch/mk27
set -euo pipefail
# ========= Fill paths =========
PROJECT_ROOT="${PROJECT... |
a017644b5d5c92940bd87e8389dd3db1b563fae4999ffff4dd62b360e7314b66 | Shell | 1,432 | 42 | #!/bin/bash
# =======================================================
# Bash config for make_data.R
# =======================================================
# ---- CONFIG VARIABLES ----
cd TSProm/src/0_generate_data
export benchmark="make_data.R"
export modelA="make_modelA_negSet.sh"
export modelB="make_modelB_null... |
b0ff698c6e2fef058c90f20cc8e61cfadfb802587c03d06ab8fb1a4c8f63a4a3 | Shell | 1,433 | 25 | #!/bin/bash
# define project directory and working directory
pd=/your/project/directory
wd=$pd/data/validations/sequence_divergence
mkdir -p $wd
cd $wd
# download human-gorilla protein alignments
mkdir gorGor6_protein_alignments
wget --no-check-certificate https://genome.senckenberg.de/download/TOGA/human_hg38_refere... |
2908132d00299e75780b34b30ac059df2580c64319df67ed5081970075e5ca99 | Shell | 1,438 | 43 | #!/usr/bin/env bash
#
# Copyright 2021 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by... |
0e712b1437d2ecd9505f06845129bedd666bcf09e3e748028100cb2514188c80 | Shell | 1,439 | 43 | #!/bin/bash
#
# Copyright 2021 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... |
fd530f494d040901d292e71d979e7f1a973bb4072572b20cfbd20d2bcdf13c91 | Shell | 1,441 | 38 | #!/bin/bash
# define project directory and working directory
pd=/your/project/directory/
input_dir=$pd/data/validations/nanopore_BAM
output_dir=$pd/data/validations/nanopore_BAM_merged
mkdir -p $output_dir
# index BAMs
for i in `ls $input_dir`
do
sbatch --cpus-per-task=10 --wrap="samtools index -@ 10 ${input_dir... |
f033307a75f5df2c8f3e6663b991c4eaba44982f0900f4be775a543c2010d312 | Shell | 1,447 | 36 | #!/usr/bin/env bash
#
# Licensed to the Apache Software Foundation (ASF) under one or more
# contributor license agreements. See the NOTICE file distributed with
# this work for additional information regarding copyright ownership.
# The ASF licenses this file to You under the Apache License, Version 2.0
# (the "Lice... |
d22ddfd780546696e779d8fab0c8578985321a6983071349512c7c262ff3ac78 | Shell | 1,448 | 57 | #!/bin/sh
git --version > /dev/null
if [ $? -ne 0 ]
then
echo "Could not find git executable"
exit 1
fi
top_level=$(git rev-parse --show-toplevel)
if [ -z "$top_level" ]
then
echo "This is not a git repository"
exit 1
fi
if [ -z "$(git tag)" ]
then
echo "Could not find any tags!"
echo "This looks like a... |
849b6bed93ebc8e28b4cebbae71c8a06463035cf580b1450c3d502d080a892ac | Shell | 1,449 | 21 | #!/bin/bash
diff ../../atac-seq-pipeline/src/encode_task_bam2ta.py encode_task_bam2ta.py
diff ../../atac-seq-pipeline/src/encode_lib_blacklist_filter.py encode_lib_blacklist_filter.py
diff ../../atac-seq-pipeline/src/encode_lib_genomic.py encode_lib_genomic.py
diff ../../atac-seq-pipeline/src/encode_lib_log_parser.... |
519268cf5789ee1d125e201854709cb18409b189b4b5250f5925a2ccf70dfebf | Shell | 1,450 | 45 | # conda activate scrna-seq
# bash /data/private/psurana/TSpDNA2/src/3_attention/2B_meme.sh
res_pdir="/data/projects/dna/pallavi/DNABERT_runs/DATA_RUN/dnabert2_FineTune_Zhihan_attention_extracted/july_2025_mmseq/RESULT/lr3e-5_ep10/"
dirs=(
"TSp_vs_nonProm_3k_tspAll_nonPromHu"
"TSp_vs_nonProm_3k_tspliver_nonPromHu"
... |
e30950e50d77ffa63926a81b82f30cf58e5cffe430e85e2f74bf19a85728c76d | Shell | 1,450 | 62 | #!/bin/bash
CONDA_EV=~/miniconda3
SCRIPT_DIR="$(
cd -- "$(dirname -- "${BASH_SOURCE[0]}")" >/dev/null 2>&1 && pwd
)"
WORK_ROT="$(
cd -- "$SCRIPT_DIR/../.." >/dev/null 2>&1 && pwd
)"
cd ${WORK_ROT} || exit
LAYER=0
RUN_NAME=mecap_mca_mmff_layer_${LAYER}
SRCP_DIR=src
RUN_MODE=train
BASE_DIR=${WORK_ROT}/data/refe... |
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