sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
e4c0826dbb49de15d5eecd7368c674fa77ffc8c1a3a806031ebe757c6ca3460e | Shell | 2,419 | 100 | #!/bin/bash
# 3D object clean-up with MeshLab
# Author: David Young 2018, 2019
HELP="
Clean up 3D object surfaces using MeshLab scripting.
Will attempt to identify the MeshLab path based on the current
platform to run the meshlabserver command-line executable.
Arguments:
-h: Show help and exit.
-m [path[: Path ... |
90bb90334cfdf3791b4e46a5d47ef135c24e4d0b7efa033bae4a546b216fc818 | Shell | 2,427 | 79 | #!/bin/bash
BAM_DIR="/cluster/projects/epigenomics/Aminnn/CNR/EpigenomeLab/EPI_P003_CNR_MM10_07172022/Four_DN/batch_2/sorted_bams/filese_renamed_adjusted"
OUTPUT_DIR="/cluster/projects/epigenomics/Aminnn/CNR/EpigenomeLab/EPI_P003_CNR_MM10_07172022/Four_DN/batch_2/sorted_bams/filese_renamed_adjusted/results_2/GOPEAKS"... |
accc73d1e7ce0f0eb674fd144891dde3971e51ae3e9f39de183e788e0c164dbc | Shell | 2,433 | 103 | MODEL_NAME="IDEA-CCNL/Erlangshen-MegatronBert-1.3B"
TEXTA_NAME=sentence1
TEXTB_NAME=sentence2
LABEL_NAME=label
ID_NAME=id
BATCH_SIZE=1
VAL_BATCH_SIZE=1
ZERO_STAGE=3
config_json="./ds_config.json"
cat <<EOT > $config_json
{
"train_micro_batch_size_per_gpu": $BATCH_SIZE,
"steps_per_print": 1000,
"gradient_clippi... |
cd2de6553a5c31483c2db3734ad424297009e29ba4000ba955e8b55c77c40b72 | Shell | 2,437 | 71 | #!/usr/bin/env bash
# CI testing script
# Installs SCT from scratch and runs all the tests we've ever written for it.
# stricter shell mode
# https://sipb.mit.edu/doc/safe-shell/
set -eo pipefail # exit if non-zero error is encountered (even in a pipeline)
set -u # exit if unset variables used
shopt -s fa... |
d8ee59db439df98bfc7f27639a9123332ee89fdbc024e5b7431d6aa605cf4b70 | Shell | 2,448 | 78 | #!/usr/bin/env bash
ENVDIR=${ENVDIR:-~/pkgenv}
SRCDIR=${SRCDIR:-~/pkgsrc}
mkdir -p $ENVDIR
mkdir -p $ENVDIR/include
mkdir -p $ENVDIR/lib
mkdir -p $ENVDIR/lib/cmake
mkdir -p $SRCDIR
# If CentOS server, set C++ compiler manually
if [ -f /etc/redhat-release ]; then
export CC=/opt/ohpc/pub/compiler/gcc/8.3.0/bin/gc... |
43f660e1f12132c67fd6f63f094c5a83972736b3f1fa5b62f99eeb2c23ad937b | Shell | 2,459 | 87 | #!/bin/bash
#SBATCH --job-name=pretrain_bart # create a short name for your job
#SBATCH --nodes=1 # node count
#SBATCH --ntasks-per-node=8 # number of tasks to run per node
#SBATCH --cpus-per-task=30 # cpu-cores per task (>1 if multi-threaded tasks)
#SBATCH --gres=gpu:8 # number of gpus per node
#SBATCH -o %x-%j.log # ... |
b8001b962f50483cc314e7bbfe356fb3bf6cc9c52257bd458700eed9c34e83a8 | Shell | 2,462 | 84 | #!/bin/bash
#SBATCH --partition=imgcomputeq
#SBATCH --qos=img
# This specifies type of node job will use
#SBATCH --nodes=1
# This specifies job uses 1 node
#SBATCH --ntasks-per-node=1
# This specifies job only use 1 core on the node
#SBATCH --mem=1g
# This specifies maximum memory use will be 10 gigabytes
#SB... |
c36ec630686d99e4ffa291da125a5b4d35124c53b58dd808580cbffca8a88578 | Shell | 2,463 | 79 | #!/bin/sh -e
# Sequence search workflow script
fail() {
echo "Error: $1"
exit 1
}
notExists() {
[ ! -f "$1" ]
}
#pre processing
[ -z "$MMSEQS" ] && echo "Please set the environment variable \$MMSEQS to your MMSEQS binary." && exit 1;
# check number of input variables
[ "$#" -ne 4 ] && echo "Please provide <q... |
1bd3bedf3aa57c78ffd045c103924d4d1a8290f6204d13f14223f3d62d693dc7 | Shell | 2,464 | 67 | #!/bin/bash -l
logit(){
echo ">>>> $(date '+%d.%m.%Y %H.%M.%S') : $@"
}
env_name=${1:-"mlenv"};
mode=${2:-"cpu"};
if [ ${#env_name} -eq 0 ]; then
logit "Please define a environment name: bash ${0} <environment name>";
exit -1
else
logit "Installing the environment named: ${env_name}";
fi
# Check the install... |
92883b100eb14c5a1b45684a73ee0fb6417e641165cd9b73dc152b5327d98037 | Shell | 2,465 | 83 | #!/bin/sh
#
# Downloads sequence for the GRCh38 release 84 version of H. sapiens (human) from
# Ensembl.
#
# Note that Ensembl's GRCh38 build has three categories of compressed fasta
# files:
#
# The base files, named ??.fa.gz
#
# By default, this script builds and index for just the base files,
# since alignments to ... |
b1518eb48fd8de383522b8e3d69b2a660de91c8fe50a22273c2a195177eecc57 | Shell | 2,480 | 85 | #!/bin/sh
#
# Downloads sequence for the GRCm38 release 81 version of M. musculus (mouse) from
# Ensembl.
#
# By default, this script builds and index for just the base files,
# since alignments to those sequences are the most useful. To change
# which categories are built by this script, edit the CHRS_TO_INDEX
# va... |
8d05390df6981e8464dbd5471aa1c171c9287187bc32246990c1b6f9eafd72e9 | Shell | 2,484 | 83 | #!/bin/sh
#
# Downloads sequence for the GRCh37 release 75 version of H. sapiens (human) from
# Ensembl.
#
# Note that Ensembl's GRCh37 build has three categories of compressed fasta
# files:
#
# The base files, named ??.fa.gz
#
# By default, this script builds and index for just the base files,
# since alignments to ... |
34762e25a7bd6a2654dfd8241ae9fbd21b09cf23674451f7f7cb182f5b0837fd | Shell | 2,486 | 110 | #!/bin/bash
# Read arguments
while [ "${1:-}" != "" ]; do
case "$1" in
"--ca_config"*)
ca_config="${1#*=}"
;;
"--pki_assets"*)
pki_assets="${1#*=}"
;;
*)
task=$1
;;
esac
shift
done
# validate arguments
if [ -z "$ca_config" ]; then
ca_config="... |
6860dbdc7d11dc8738fb5ba7a8d71cf87ac3c73b551a66e4ff6bc016d82f5305 | Shell | 2,515 | 79 | #!/bin/bash -l
#env_name=${1}
tstamp(){
echo ">>>> $(date '+%d.%m.%Y %H.%M.%S') : "
}
logit(){
echo ">>>> $(date '+%d.%m.%Y %H.%M.%S') : $@"
}
env_name="mlenv";
if [ ${#env_name} -eq 0 ]; then
logit "Please define a environment name: bash ${0} <environment name>";
exit -1
else
logit "Installing the envir... |
8b78f9d274a09bc4bcaf84a2d8ad868813055365fe3c13b92f62b61907606c5c | Shell | 2,524 | 55 | #! /bin/bash
dis_range=5
model=ScaleDense
loss=mse
batch_size=32
lbd=10
beta=1
first_stage_net=./pretrained_model/ScaleDense/ScaleDense_best_model.pth.tar
save_path=./pretrained_model/second_stage_test/
label=./data/dataset.xls
train_data=./data/train
valid_data=./data/val
test_data=./data/test
sorter_path=./TSAN/Sod... |
8f35aacd355f922c13284b54584a85385fce5ca4de5c7055ba7d13b500e79522 | Shell | 2,525 | 87 | #!/bin/bash
#SBATCH --job-name=pretrain_bart # create a short name for your job
#SBATCH --nodes=1 # node count
#SBATCH --ntasks-per-node=8 # number of tasks to run per node
#SBATCH --cpus-per-task=30 # cpu-cores per task (>1 if multi-threaded tasks)
#SBATCH --gres=gpu:8 # number of gpus per node
#SBATCH -o %x-%j.log # ... |
44393abd3506a6fe862aff65798ca9fd5804b1ce071926c6fcc53463da7b9e14 | Shell | 2,531 | 84 | #!/bin/bash
BAM_DIR="/cluster/projects/epigenomics/Aminnn/CNR/EpigenomeLab/EPI_P003_CNR_MM10_07172022/Four_DN/batch_2/sorted_bams/filese_renamed_adjusted/HFFc6"
OUTPUT_DIR="/cluster/projects/epigenomics/Aminnn/CNR/EpigenomeLab/EPI_P003_CNR_MM10_07172022/Four_DN/batch_2/sorted_bams/filese_renamed_adjusted/results_2/M... |
19f6d6ecf12ea7baa6d6a518dfc821752d190a9e93396d6d6df06f142686d560 | Shell | 2,539 | 71 | #!/bin/bash -l
#SBATCH --job-name=spctp_fmriprp
#SBATCH --nodes=1
#SBATCH --ntasks=16
#SBATCH --mem-per-cpu=8gb
#SBATCH --time=2-00:00:00
#SBATCH -o ./log/preproc_%A_%a.o
#SBATCH -e ./log/preproc_%A_%a.e
#SBATCH --account=DBIC
#SBATCH --partition=standard
#SBATCH --array=6
## --array=1-17%5
#source /optnfs/common/min... |
1999ad8dbbb8c3d93c862d26619408e8a9e9ebb89db9c2d9406294d397265bc7 | Shell | 2,554 | 97 | #!/bin/bash
#SBATCH --job-name=bart_qg # create a short name for your job
#SBATCH --nodes=1 # node count
#SBATCH --ntasks-per-node=8 # number of tasks to run per node
#SBATCH --cpus-per-task=10 # cpu-cores per task (>1 if multi-threaded tasks)
#SBATCH --gres=gpu:1 # number of gpus per node
#SBATCH -o %x-%j.log # output... |
437a6a69d9062ffda2590bb5180085111400313849ba41bfff3e7b8014eaa6c5 | Shell | 2,563 | 96 | #!/bin/bash
## Build XGBoost with CUDA
set -euo pipefail
if [[ -z "${GITHUB_SHA:-}" ]]
then
echo "Make sure to set environment variable GITHUB_SHA"
exit 1
fi
if [[ "$#" -lt 2 ]]
then
echo "Usage: $0 [image_repo] {enable-rmm,disable-rmm}"
exit 2
fi
image_repo="$1"
rmm_flag="$2"
# Validate RMM flag
case "${rm... |
61d03d20b5da2b96878db4b45a025567f13ccd213633f261b92afb3769e8e7de | Shell | 2,567 | 86 | #!/bin/bash
cd resultados_clusters_sdf
# In the cycle the format of the sdf files is changed to mae, they are prepared with ligprep from schrodinger and the files are separated into folders according to the corresponding extension
echo ::::: Preparate LigPrep :::::
echo
for dir in $(ls)
do
cd $dir
echo Running ligp... |
925919c52abeb50733c9b174a0e6ac334eaba44583a42d9eb498c3054299b826 | Shell | 2,586 | 112 | #!/bin/bash
#
# Library for logging functions
# Constants
RESET='\033[0m'
RED='\033[38;5;1m'
GREEN='\033[38;5;2m'
YELLOW='\033[38;5;3m'
MAGENTA='\033[38;5;5m'
CYAN='\033[38;5;6m'
# Functions
########################
# Print to STDERR
# Arguments:
# Message to print
# Returns:
# None
#########################
std... |
becb495c81a89619d429156df3fe4098e3ad528f22105c34972a25e0c5ed797c | Shell | 2,592 | 88 | #!/bin/bash
#SBATCH --job-name=pretrain_bart # create a short name for your job
#SBATCH --nodes=1 # node count
#SBATCH --ntasks-per-node=8 # number of tasks to run per node
#SBATCH --cpus-per-task=30 # cpu-cores per task (>1 if multi-threaded tasks)
#SBATCH --gres=gpu:8 # number of gpus per node
#SBATCH -o %x-%j.log # ... |
db927088dfd1a815c6a98ce1f0682a9a93defc584a41749628b7cec04f5cf682 | Shell | 2,599 | 88 | #!/bin/bash
#SBATCH --job-name=finetune_taiyi # create a short name for your job
#SBATCH --nodes=1 # node count
#SBATCH --ntasks-per-node=8 # number of tasks to run per node
#SBATCH --cpus-per-task=30 # cpu-cores per task (>1 if multi-threaded tasks)
#SBATCH --gres=gpu:8 # number of gpus per node
#SBATCH -o %x-%j.log #... |
a33e1fa900e71b6ec38cf9837822c6456a13b1b0f64fbfb6c90dd58d9f14e862 | Shell | 2,600 | 89 | #!/bin/sh
#
# Downloads sequence for the GRCh38 release 84 version of H. sapiens (human) from
# Ensembl.
#
# Note that Ensembl's GRCh38 build has three categories of compressed fasta
# files:
#
# The base files, named ??.fa.gz
#
# By default, this script builds and index for just the base files,
# since alignments to ... |
ad322b53c5fab7b168b944ade5150d328696ff06b2eb562db6e6e0431bc7b0a0 | Shell | 2,602 | 95 | #!/usr/bin/env bash
# Build script to compile a wheel for Python-Bioformats
HELP="
Compile a build a wheel for Python-Bioformats.
The repository will be cleaned to its original state, removing all untracked
files, to ensure that the build does not have stale artifacts.
By default, a forked Python-Bioformats reposito... |
82d05b71d1ddefc15a2544022d1e78f8007e13c023920a12f5de2732ae91fcee | Shell | 2,608 | 72 | #!/bin/bash
BASE_DIR="/Aminnn/CNR/EpigenomeLab/Four_DN/results"
SNR_DIR="${BASE_DIR}/snr_analysis"
OUTPUT_DIR="${BASE_DIR}/idr_analysis"
mkdir -p $OUTPUT_DIR
process_peaks() {
local mark=$1
local celltype=$2
local caller=$3
echo "Processing $mark $celltype $caller"
mapfile -t files < <(find $... |
4d052fd2118dafd5e5fc298f62e8af06b3e60cd3ea78fb75f2afd430326233c0 | Shell | 2,609 | 89 | #!/bin/sh
#
# Downloads sequence for the BDGP6 release 84 version of drosophila melanogaster (fly) from
# Ensembl.
#
# Note that Ensembl's build has three categories of compressed fasta
# files:
#
# The base files, named ??.fa.gz
#
# By default, this script builds and index for just the base files,
# since alignments ... |
8a1a2d1eb01c85afa16f9cb969ec8c14c75fd3345f2462c4dbac92f5fabfc519 | Shell | 2,612 | 89 | #!/bin/sh
#
# Downloads sequence for the RNor_6.0 release 84 version of rattus_norvegicus (rat) from
# Ensembl.
#
# Note that Ensembl's build has three categories of compressed fasta
# files:
#
# The base files, named ??.fa.gz
#
# By default, this script builds and index for just the base files,
# since alignments to ... |
93b80d42a6f2418ef6f1aaf8eb4ef8e2e589a6ce47a7290af656a2924b4035e6 | Shell | 2,614 | 89 | #!/bin/sh
#
# Downloads sequence for the WBcel235 release 84 version of caenorhabditis elegans (worm) from
# Ensembl.
#
# Note that Ensembl's build has three categories of compressed fasta
# files:
#
# The base files, named ??.fa.gz
#
# By default, this script builds and index for just the base files,
# since alignmen... |
9ab21179a560b15996199b8b6e8981fa2e1bedfdca8c451c739b2cbb7be8d3b8 | Shell | 2,619 | 89 | #!/bin/sh
#
# Downloads sequence for the GRCh37 release 75 version of H. sapiens (human) from
# Ensembl.
#
# Note that Ensembl's GRCh37 build has three categories of compressed fasta
# files:
#
# The base files, named ??.fa.gz
#
# By default, this script builds and index for just the base files,
# since alignments to ... |
bdadf9cf6034a40cdbc6ceeb340ec82d75b1a77c3200f22a1bd4392e4b42db94 | Shell | 2,622 | 89 | #!/bin/sh
#
# Downloads sequence for the R64-1-1 release 84 version of saccharomyces cerevisiae (yeast) from
# Ensembl.
#
# Note that Ensembl's build has three categories of compressed fasta
# files:
#
# The base files, named ??.fa.gz
#
# By default, this script builds and index for just the base files,
# since alignm... |
ff68587e7a0856c256f4a8954f3b7628c53f9ef6ed4ff7015d86f871d9e77c6e | Shell | 2,634 | 47 | #!/bin/bash
#SBATCH --job-name=pred0429
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=6
#SBATCH --nodes=1
#SBATCH --gres=gpu:1
#SBATCH --time=800
#SBATCH --mem=1600G
#SBATCH --partition=gpu
#SBATCH --error=/private/groups/brookslab/gabai/projects/Add-seq/scripts/sbatch/log/lsf_%j_%x.err # error file
#SBATCH --output=... |
a46e2e637be98b8c6c0c10d845eb51693c782fa3a70c91306e718ed7541fb80a | Shell | 2,639 | 109 | #!/bin/bash
#SBATCH --job-name=finetune-cmrc
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --gres=gpu:1 # number of gpus
#SBATCH --cpus-per-task=4 # cpu-cores per task (>1 if multi-threaded tasks)
#SBATCH -o $YOUR_PROJECT_DIR/%x-%j.log
#SBATCH -e $YOUR_PROJECT_DIR/%x-%j.err
set -x -e
echo "START... |
4d41aa25b83ffacba2c18310d8ca23f57d5b423bbfdb054fd4ba3b18748cc0ac | Shell | 2,640 | 104 | # !/bin/sh
set -e
# Benchmarks run on a Ubuntu 14.04 VM with 2 cores and 4 GiB of RAM.
# The VM is running on a Macbook Pro with a 3.1 GHz Intel Core i7 processor and
# 16 GB of RAM and an SSD.
# silesia is a directory that can be downloaded from
# http://mattmahoney.net/dc/silesia.html
# ls -l silesia/
# total 203M
... |
08ec3eceff7988a93c1b8df600fa721b98be3daa90eabb3ad8f793ed7543faae | Shell | 2,659 | 100 | #!/bin/bash
# ============================================================================
# Rica - Test Runner Script
# ============================================================================
#
# Purpose:
# Runs the test suite for rica using Jest (via react-scripts).
# Currently the project has minimal test c... |
22b892c275428dd170293e3878ab6e35baf46de9bbae20e66c5b0580b9c56328 | Shell | 2,666 | 107 | #!/usr/bin/env bash
# Build script to compile Javabridge
HELP="
Compile Python-Javabridge and build wheels.
The repository will be cleaned to its original state, removing all untracked
files, to ensure that the build does not have stale artifacts.
Assumes that the Venv environments have been set up by
\"bin/setup_mu... |
d24ee708c7e98561bf4591dab8a9560d26760b6dba3e682bf2ae55c1ac40a83d | Shell | 2,672 | 47 | #!/bin/bash
#SBATCH --job-name=predsphenucleimodel
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=6
#SBATCH --nodes=1
#SBATCH --gres=gpu:1
#SBATCH --time=1440
#SBATCH --mem=1500G
#SBATCH --partition=gpu
#SBATCH --error=/private/groups/brookslab/gabai/projects/Add-seq/scripts/sbatch/log/lsf_%j_%x.err # error file
#SBAT... |
b31acfa255e24f6b7cdb04948fd5345d0fbc0069c053eea966581e739e865e76 | Shell | 2,705 | 82 | #!/bin/sh -e
fail() {
echo "Error: $1"
exit 1
}
notExists() {
[ ! -f "$1" ]
}
[ -z "$MMSEQS" ] && echo "Please set the environment variable \$MMSEQS to your MMSEQS binary." && exit 1;
[ "$#" -ne 4 ] && echo "Please provide <seqDB> <clusterDB> <outClusterDB> <tmp>" && exit 1;
[ ! -f "$1.dbtype" ] && echo ... |
91ae257c1fa0a3bc3108bc18e1d081f0be56d873cc573cfd9b75840adf57163c | Shell | 2,711 | 110 | #!/bin/bash
#SBATCH --job-name=predict-cmrc
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --gres=gpu:1 # number of gpus
#SBATCH --cpus-per-task=4 # cpu-cores per task (>1 if multi-threaded tasks)
#SBATCH -o $YOUR_SLURM_LOG_PATH/%x-%j.log
#SBATCH -e $YOUR_SLURM_LOG_PATH/%x-%j.err
#
set -x -e
echo... |
437c23cf8805ed5a904ec9cd57ee9a769105cefd695034ef24c78efa5c98f302 | Shell | 2,725 | 105 | #!/bin/bash
# Process via nohup while tracking output
# Author: David Young 2018
HELP="
Run command in nohup, storing output in unique file and
automatically printing output to screen.
Arguments given after \"--\" (or not recognized by this script)
will be passed to nohup to run without hanging up if the
current s... |
eae657843d7019d284a7d5c1617ff83533ecd881b3801e251f7d239f5d8f03e6 | Shell | 2,740 | 110 | #!/bin/sh
set -e
# Constants
SED_COMMANDS="commands.tmp"
CLANG_FORMAT="clang-format-3.9"
INCLUDE='include/linux/'
LIB='lib/zstd/'
SPACES=' '
TAB=$'\t'
TMP="replacements.tmp"
function prompt() {
while true; do
read -p "$1 [Y/n]" yn
case $yn in
'' ) yes='yes'; break;;
[Yy]* ) yes='yes'; bre... |
00256130324e74ade0bc3fa099c6d5bae7b7fbaa1d9da704a86c179daa9404b8 | Shell | 2,749 | 113 | #!/bin/bash
# e $dt $num_msg $num_elements
function e {
dt=$1 # sec
num_msg=$2
num_elements_per_msg=$(($3 / $2))
output_file=./dt${dt}_num_msg${num_msg}_num_el${num_elements}.data
echo "Sending " $3 " data elements distributed in " $2 " with " $num_elements_per_msg "ele... |
468ab0eaa67ba9cce0ac4f19dc02ad850ffcdd1966af416df1894ea03c8c4e56 | Shell | 2,753 | 97 | #!/bin/bash
export CUDA_VISIBLE_DEVICES=0
# activate you conda env if not
# conda activate your_env_name
# run the training
## single gpu start
python main.py \
--task iterative_optical \
--num_gpu 1 \
--data_path ./data/your_dataset_path \
--output_dir ./logs/exp \
--sample_size 32 \
--in_ch... |
c87036636675f2b9be4859bb39ae17e8f082dbd7913d36e31294aaf55a398f95 | Shell | 2,769 | 112 | #!/bin/bash
# install dependencies
# (this script must be run as root)
BASEDIR=$(dirname $0)
source $BASEDIR/defaults.sh
apt-get -y update
apt-get install -y --no-install-recommends \
build-essential \
graphviz \
libboost-filesystem-dev \
libboost-python-dev \
libboost-system-dev \
libboost-thread-dev \
... |
5c457f9b098e8e3d908f872245c363ee26d7f935c75a563a1e4551993cee88ed | Shell | 2,788 | 91 | #!/bin/bash
#SBATCH --job-name=zen2_large_weibo # create a short name for your job
#SBATCH --nodes=1 # node count
#SBATCH --ntasks=1 # total number of tasks across all nodes
#SBATCH --cpus-per-task=30 # cpu-cores per task (>1 if multi-threaded tasks)
#SBATCH --gres=gpu:1 # number of gpus per node
#SBATCH --mail-type=AL... |
689bf28c32f5254e2d0538aebde6dc438d5b99a8e2c7a9523c4cf320267e8b30 | Shell | 2,809 | 109 | #!/bin/bash
# ============================================================================
# Rica - Development Server Script
# ============================================================================
#
# Purpose:
# Starts the React development server with hot reload for rapid iteration.
# Optionally starts Tai... |
f68e3a9fafa5d82c6325b0931af3f33a2ebd6c54aa55bff07e7fb803b1527617 | Shell | 2,809 | 101 | #!/bin/bash
export CUDA_VISIBLE_DEVICES=0
# activate you conda env if not
# conda activate your_env_name
# run the training
## single gpu start
python main.py \
--task snapshot_optical \
--num_gpu 1 \
--data_path ./data/your_data_path \
--output_dir ./logs/exp \
--sample_size 32 \
--in_channe... |
4f9c3e3308bf2d6b7c39046753b4c5645f407f8d32d2412c0c5f6a6c55685500 | Shell | 2,848 | 93 | #!/bin/bash
#SBATCH --job-name=zen2_large_tnews # create a short name for your job
#SBATCH --nodes=1 # node count
#SBATCH --ntasks=1 # total number of tasks across all nodes
#SBATCH --cpus-per-task=30 # cpu-cores per task (>1 if multi-threaded tasks)
#SBATCH --gres=gpu:1 # number of gpus per node
#SBATCH --mail-type=AL... |
0142276e15872384dbd9fee876bb1e66a26efac3889dc8eb91b2f6b2855ebaec | Shell | 2,849 | 92 | #!/bin/bash
#SBATCH --job-name=zen2_base_cmeee # create a short name for your job
#SBATCH --nodes=1 # node count
#SBATCH --ntasks=2 # total number of tasks across all nodes
#SBATCH --cpus-per-task=30 # cpu-cores per task (>1 if multi-threaded tasks)
#SBATCH --gres=gpu:2 # number of gpus per node
#SBATCH --mail-type=ALL... |
19127b2a76ac85eaf04285e0c7ee7ad65d564728b131bd4446af2aadecb2453b | Shell | 2,850 | 91 | #!/bin/bash
#SBATCH --job-name=zen2_base_weibo # create a short name for your job
#SBATCH --nodes=1 # node count
#SBATCH --ntasks=1 # total number of tasks across all nodes
#SBATCH --cpus-per-task=30 # cpu-cores per task (>1 if multi-threaded tasks)
#SBATCH --gres=gpu:1 # number of gpus per node
#SBATCH --mail-type=ALL... |
bb51c78f374482d556f27c628313773c6f468825d1ae8d0189d0bc0db43c189c | Shell | 2,851 | 91 | #!/bin/bash
#SBATCH --job-name=zen2_large_cmeee # create a short name for your job
#SBATCH --nodes=1 # node count
#SBATCH --ntasks=1 # total number of tasks across all nodes
#SBATCH --cpus-per-task=30 # cpu-cores per task (>1 if multi-threaded tasks)
#SBATCH --gres=gpu:1 # number of gpus per node
#SBATCH --mail-type=AL... |
6fb307df833bc6f11453503603bd804ccd36ef2930bff4ddf8482639e6081dd2 | Shell | 2,853 | 91 | #!/bin/bash
#SBATCH --job-name=zen2_base_msra # create a short name for your job
#SBATCH --nodes=1 # node count
#SBATCH --ntasks=1 # total number of tasks across all nodes
#SBATCH --cpus-per-task=30 # cpu-cores per task (>1 if multi-threaded tasks)
#SBATCH --gres=gpu:1 # number of gpus per node
#SBATCH --mail-type=ALL ... |
3970d69b314cef3c35ff1f863fdb5cc52f618c0d5d5a7a3d404a3da6631a500e | Shell | 2,854 | 93 | #!/bin/bash
#SBATCH --job-name=zen2_base_ocnli # create a short name for your job
#SBATCH --nodes=1 # node count
#SBATCH --ntasks=1 # total number of tasks across all nodes
#SBATCH --cpus-per-task=30 # cpu-cores per task (>1 if multi-threaded tasks)
#SBATCH --gres=gpu:1 # number of gpus per node
#SBATCH --mail-type=ALL... |
3409f7dd5996ace28259a28724fe7c6a978fa3d9cb08663ac4f54e88f2dae15f | Shell | 2,857 | 93 | #!/bin/bash
#SBATCH --job-name=zen2_large_afqmc # create a short name for your job
#SBATCH --nodes=1 # node count
#SBATCH --ntasks=1 # total number of tasks across all nodes
#SBATCH --cpus-per-task=30 # cpu-cores per task (>1 if multi-threaded tasks)
#SBATCH --gres=gpu:1 # number of gpus per node
#SBATCH --mail-type=AL... |
6701ce2af633cd12267913e55df07169a8d471bf4ec778edd591b066958b1737 | Shell | 2,857 | 91 | #!/bin/bash
#SBATCH --job-name=zen2_base_cluener # create a short name for your job
#SBATCH --nodes=1 # node count
#SBATCH --ntasks=1 # total number of tasks across all nodes
#SBATCH --cpus-per-task=30 # cpu-cores per task (>1 if multi-threaded tasks)
#SBATCH --gres=gpu:1 # number of gpus per node
#SBATCH --mail-type=A... |
6f218e75864e425260f7ee36fec2a86ee1e5a7a123f654ed1e03cb4c517d6226 | Shell | 2,857 | 93 | #!/bin/bash
#SBATCH --job-name=zen2_large_ocnli # create a short name for your job
#SBATCH --nodes=1 # node count
#SBATCH --ntasks=1 # total number of tasks across all nodes
#SBATCH --cpus-per-task=30 # cpu-cores per task (>1 if multi-threaded tasks)
#SBATCH --gres=gpu:1 # number of gpus per node
#SBATCH --mail-type=AL... |
78c6f925e936ae6ae80e131ae2dfdc3d504d0df78d930b3e2d1ac79fc1f0bba7 | Shell | 2,857 | 91 | #!/bin/bash
#SBATCH --job-name=zen2_large_msra # create a short name for your job
#SBATCH --nodes=1 # node count
#SBATCH --ntasks=1 # total number of tasks across all nodes
#SBATCH --cpus-per-task=30 # cpu-cores per task (>1 if multi-threaded tasks)
#SBATCH --gres=gpu:1 # number of gpus per node
#SBATCH --mail-type=ALL... |
2fa2ac72a8c250c97d87029ef9e47617a5105e0d0553c1311f4f050013802a0a | Shell | 2,859 | 83 | #!/bin/sh -e
# Clustering workflow script
fail() {
echo "Error: $1"
exit 1
}
notExists() {
[ ! -f "$1" ]
}
# check number of input variables
[ "$#" -ne 3 ] && echo "Please provide <sequenceDB> <outDB> <tmp>" && exit 1;
# check if files exist
[ ! -f "$1.dbtype" ] && echo "$1.dbtype not found!" && exit 1;
[ ... |
d320954c9063a7d90445be40b7110fc746b521b3856a31cc24ccab5e617515ab | Shell | 2,859 | 91 | #!/bin/bash
#SBATCH --job-name=zen2_base_resume # create a short name for your job
#SBATCH --nodes=1 # node count
#SBATCH --ntasks=1 # total number of tasks across all nodes
#SBATCH --cpus-per-task=30 # cpu-cores per task (>1 if multi-threaded tasks)
#SBATCH --gres=gpu:1 # number of gpus per node
#SBATCH --mail-type=AL... |
2531ada9be8de682fc29bb44be47b5aa275b617fc5529e1a2ec54e7fc440adfd | Shell | 2,861 | 91 | #!/bin/bash
#SBATCH --job-name=zen2_large_cluener # create a short name for your job
#SBATCH --nodes=1 # node count
#SBATCH --ntasks=1 # total number of tasks across all nodes
#SBATCH --cpus-per-task=30 # cpu-cores per task (>1 if multi-threaded tasks)
#SBATCH --gres=gpu:1 # number of gpus per node
#SBATCH --mail-type=... |
58c7257ed823ba4058c13aa201df3ab256c0c190c581acea4564dae5a940437a | Shell | 2,861 | 93 | #!/bin/bash
#SBATCH --job-name=zen2_base_iflytek # create a short name for your job
#SBATCH --nodes=1 # node count
#SBATCH --ntasks=1 # total number of tasks across all nodes
#SBATCH --cpus-per-task=30 # cpu-cores per task (>1 if multi-threaded tasks)
#SBATCH --gres=gpu:1 # number of gpus per node
#SBATCH --mail-type=A... |
b3daf7c74658358138f770d1dc91cbbe8d101e4bbb6bb2446ffc9ed3d114d809 | Shell | 2,862 | 66 | #!/usr/bin/env bash
# Verify a commit->bucket mapping covers every commit in BASE..RELEASE exactly
# once, and emit an audit TSV (hash, date, bucket, subject) for review.
#
# This is step 1 of the release-branch split workflow documented in
# docs/RunningBabel.md ("Releasing a new Babel version"): it proves the
# class... |
6a7fe20611e470b675d74b741f74a0513646a5522305e1ab702016b0cde830ac | Shell | 2,863 | 67 | #!/bin/sh -e
# Fast profile-guided representative selection.
# Reuses the representative-to-member alignments produced by clustering (run with
# --include-align-files) instead of realigning a profile against every member, then
# rewrites the cluster DB with the best-scoring observed member as the new rep.
# Output is 1... |
fc738f127dff59454292e349a3a61381bfa1acb48375b1769df5ce62925e0043 | Shell | 2,863 | 91 | #!/bin/bash
#SBATCH --job-name=zen2_large_resume # create a short name for your job
#SBATCH --nodes=1 # node count
#SBATCH --ntasks=1 # total number of tasks across all nodes
#SBATCH --cpus-per-task=30 # cpu-cores per task (>1 if multi-threaded tasks)
#SBATCH --gres=gpu:1 # number of gpus per node
#SBATCH --mail-type=A... |
68c93cd3e09c916cceb6451a8f66d5eb3f11ba01138f7364a5c538a30e89ed30 | Shell | 2,864 | 93 | #!/bin/bash
#SBATCH --job-name=zen2_large_iflytek # create a short name for your job
#SBATCH --nodes=1 # node count
#SBATCH --ntasks=1 # total number of tasks across all nodes
#SBATCH --cpus-per-task=30 # cpu-cores per task (>1 if multi-threaded tasks)
#SBATCH --gres=gpu:1 # number of gpus per node
#SBATCH --mail-type=... |
431bff2852055c455c8e3ae323926659db935f9b35c04736d6eb149fc7f41093 | Shell | 2,867 | 93 | #!/bin/bash
#SBATCH --job-name=zen2_base_cmnli # create a short name for your job
#SBATCH --nodes=1 # node count
#SBATCH --ntasks=1 # total number of tasks across all nodes
#SBATCH --cpus-per-task=30 # cpu-cores per task (>1 if multi-threaded tasks)
#SBATCH --gres=gpu:1 # number of gpus per node
#SBATCH --mail-type=ALL... |
784c4533f43c3d64ec28cb9b318b833e54e223856120565936ac2ae24f94b204 | Shell | 2,867 | 91 | #!/bin/bash
#SBATCH --job-name=zen2_large_ontonotes4 # create a short name for your job
#SBATCH --nodes=1 # node count
#SBATCH --ntasks=1 # total number of tasks across all nodes
#SBATCH --cpus-per-task=30 # cpu-cores per task (>1 if multi-threaded tasks)
#SBATCH --gres=gpu:1 # number of gpus per node
#SBATCH --mail-ty... |
79c4f5ac045c96000934894c3e469c27549c5a3f18e943e9b393e5a92b53cb33 | Shell | 2,869 | 90 | # As advised by https://twitter.com/plexus/status/499194992632811520?lang=en
# Based on https://github.com/travis-ci/travis-build/blob/20903aad38a9db0717827275b70c8a2c53820f85/lib/travis/build/templates/header.sh
# MIT LICENSE
#
# Copyright (c) 2016 Travis CI GmbH <contact@travis-ci.org>
#
# Permission is hereby grant... |
4c98ad062639fb7aed92df806dd6e23c6ab60d40d8f1df7f8a4be4ff62972ee1 | Shell | 2,870 | 93 | #!/bin/bash
#SBATCH --job-name=zen2_large_cmnli # create a short name for your job
#SBATCH --nodes=1 # node count
#SBATCH --ntasks=1 # total number of tasks across all nodes
#SBATCH --cpus-per-task=30 # cpu-cores per task (>1 if multi-threaded tasks)
#SBATCH --gres=gpu:1 # number of gpus per node
#SBATCH --mail-type=AL... |
678881c68027afa6621417cdf5123f65c2cee385460d8945331e87f4a65a2b57 | Shell | 2,877 | 89 | #!/bin/sh -e
DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
ECHO=echo
RM="rm -f"
GREP="grep"
INTOVOID="/dev/null"
die() {
$ECHO "$@" 1>&2
exit 1
}
isPresent() {
$GREP $@ tmplog || die "$@" "should be present"
}
mustBeAbsent() {
$GREP $@ tmplog && die "$@ should not be there !!"
$ECHO "... |
83f72eb80414054195b7c3b02efd26aaaaddfd2365a0e1c4e832c5fa9f7fcfa4 | Shell | 2,881 | 101 | #!/bin/bash
export CUDA_VISIBLE_DEVICES=0
# activate you conda env if not
# conda activate your_env_name
# run the training
## single gpu start
python main.py \
--task multicolor_optical \
--num_gpu 1 \
--data_path ./data/your_dataset_path \
--output_dir ./logs/exp \
--sample_size 32 \
--in_c... |
96f99a57e3d26fc7cc765eeebad1c064a9e7632dfe2e0b5b09f2c0856b4cd4a4 | Shell | 2,886 | 86 | #!/bin/sh -e
fail() {
echo "Error: $1"
exit 1
}
notExists() {
[ ! -f "$1" ]
}
if notExists "${TMP_PATH}/query.dbtype"; then
# shellcheck disable=SC2086
"$MMSEQS" createdb "${QUERY}" "${TMP_PATH}/query" ${CREATEDB_QUERY_PAR} \
|| fail "query createdb died"
QUERY="${TMP_PATH}/query"
fi
if ... |
c4a9ada50e967d3d477c76b7b4aa5820f21d4d981e9ce772892de7a56f40c457 | Shell | 2,886 | 91 | #!/bin/bash
#SBATCH --job-name=zen1_base_ontonotes4 # create a short name for your job
#SBATCH --nodes=1 # node count
#SBATCH --ntasks=1 # total number of tasks across all nodes
#SBATCH --cpus-per-task=30 # cpu-cores per task (>1 if multi-threaded tasks)
#SBATCH --gres=gpu:1 # number of gpus per node
#SBATCH --mail-typ... |
05a0610a7200db806a9702bfaf65f511c51c3b6ce4b8ab2c73e30fe5493a508e | Shell | 2,922 | 94 | #!/bin/bash
#SBATCH --job-name=zen2_base_tnews # create a short name for your job
#SBATCH --nodes=1 # node count
#SBATCH --ntasks=1 # total number of tasks across all nodes
#SBATCH --cpus-per-task=30 # cpu-cores per task (>1 if multi-threaded tasks)
#SBATCH --gres=gpu:1 # number of gpus per node
#SBATCH --mail-type=ALL... |
44a9342e9c2b6c144d3ee1df5195377f6f2552259592c977f93ea6dd2bf01d9a | Shell | 2,926 | 99 | # !/bin/sh
set -e
# Benchmarks run on a Ubuntu 14.04 VM with 2 cores and 4 GiB of RAM.
# The VM is running on a Macbook Pro with a 3.1 GHz Intel Core i7 processor and
# 16 GB of RAM and an SSD.
# silesia is a directory that can be downloaded from
# http://mattmahoney.net/dc/silesia.html
# ls -l silesia/
# total 203M
... |
ccf31efba4d3f0652dc0835bbe452787fa3a20edc90acd38c64e305154be1174 | Shell | 2,931 | 46 | #create all position vcf file
mkdir -p ModernVCF/
cat Papuan_1kg_gvcfs.txt |awk -F "/" -v q="'" '{print "bcftools convert --gvcf2vcf --fasta-ref broadinstitute/Homo_sapiens_assembly38.fasta "$0" | bcftools view -i "q"MIN(FMT/DP)>0"q" -V indels | bcftools annotate -x ^FORMAT/GT,^FORMAT/DP,INFO |sed "q"s/<NON_REF>,//"q"... |
ac7e7b1eebfa031a84379f4341469c69be1feeef4f46f320cb1b5c503066aec1 | Shell | 2,932 | 94 | #!/bin/bash
#SBATCH --job-name=zen2_base_afqmc # create a short name for your job
#SBATCH --nodes=1 # node count
#SBATCH --ntasks=1 # total number of tasks across all nodes
#SBATCH --cpus-per-task=30 # cpu-cores per task (>1 if multi-threaded tasks)
#SBATCH --gres=gpu:1 # number of gpus per node
#SBATCH --mail-type=ALL... |
5b0324245a3d5f367b7a5f1eff0454d99bc5bc964586b2fb210eeb2a92d8b9bb | Shell | 2,940 | 92 | #!/bin/bash
#SBATCH --job-name=zen2_base_ontonotes4 # create a short name for your job
#SBATCH --nodes=1 # node count
#SBATCH --ntasks=1 # total number of tasks across all nodes
#SBATCH --cpus-per-task=30 # cpu-cores per task (>1 if multi-threaded tasks)
#SBATCH --gres=gpu:1 # number of gpus per node
#SBATCH --mail-typ... |
b109f96bd084ac141cb60ec696b08a4867918e9fd57d8b53bdd1f675f4b18c77 | Shell | 2,943 | 89 | #!/bin/sh -e
fail() {
echo "Error: $1"
exit 1
}
notExists() {
[ ! -f "$1" ]
}
if notExists "${TMP_PATH}/query.dbtype"; then
# shellcheck disable=SC2086
"$MMSEQS" createdb "$@" "${TMP_PATH}/query" ${CREATEDB_QUERY_PAR} \
|| fail "query createdb died"
fi
if notExists "${TARGET}.dbtype"; then
... |
5ce2f07f492fffa716db0669c89c655babea5f2d3be89126740933c74f0849e5 | Shell | 2,946 | 63 | # Demo for generating pseudo matched-normal sample
: ex: set ft=markdown ;:<<'```shell' #
The following CHISEL demo represents a guided example of the CHISEL command for generating a pseudo matched-normal sample starting from an exemplary barcoded [BAM file](https://doi.org/10.5281/zenodo.3952985) publicly available. ... |
50cbfa932c95c3580b0aa80951ee46c1ff6b9b75fbbd7dca1ba8b52f938240e4 | Shell | 2,949 | 95 | #!/bin/bash
#SBATCH --job-name=zen1_tnews # create a short name for your job
#SBATCH --nodes=1 # node count
#SBATCH --ntasks=1 # total number of tasks across all nodes
#SBATCH --cpus-per-task=30 # cpu-cores per task (>1 if multi-threaded tasks)
#SBATCH --gres=gpu:1 # number of gpus per node
#SBATCH --mail-type=ALL # se... |
bb789de74de8c02afa614a7c63b05ee5b9165723b9b3765956d8661f62277697 | Shell | 2,962 | 100 | #!/bin/bash
#SBATCH --job-name=taiyi-sd-dreambooth # create a short name for your job
#SBATCH --nodes=1 # node count
#SBATCH --ntasks-per-node=2 # number of tasks to run per node
#SBATCH --cpus-per-task=30 # cpu-cores per task (>1 if multi-threaded tasks)
#SBATCH --gres=gpu:2 # number of gpus per node
#SBATCH -o %x-%j.... |
46fd6a8e055f8363016d32917d09bd270969d0b4f9db06d68b9c0455b0697df2 | Shell | 2,978 | 71 | #!/bin/bash
set -e
set -x
export DEBIAN_FRONTEND=noninteractive
CODENAME="$(lsb_release -cs)"
# We seem to indirectly hit a virtualbox issue with Ubuntu 18.04, or more
# specifically with The VirtualBox Guest Additions v6.x, which is installed
# there: https://www.virtualbox.org/ticket/18776. A workaround is to down... |
7684036dbcdaeda2d2082c52f0941528847d523842a33803820f7bd53640bd46 | Shell | 2,981 | 74 | #!/bin/bash
# ==============================================================================
# SCRIPT INFORMATION:
# ==============================================================================
# SCRIPT: DE-IDENTIFICATION OF MRI DATA IN A BIDS DATASET
# PROJECT: ZOO
# WRITTEN BY LENNART WITTKUHN, 2020
# CONTACT: WIT... |
d01c5b1cfbec15229bfc0563a17cfaee7daa174b3c887cb28d0a5e58ca4f26e4 | Shell | 3,008 | 79 | #!/bin/bash
BAM_DIR="/cluster/projects/epigenomics/Aminnn/CNR/EpigenomeLab/EPI_P003_CNR_MM10_07172022/Four_DN/batch_2/sorted_bams/filese_renamed_adjusted"
OUTPUT_DIR="/cluster/projects/epigenomics/Aminnn/CNR/EpigenomeLab/EPI_P003_CNR_MM10_07172022/Four_DN/batch_2/sorted_bams/filese_renamed_adjusted/results_2/SEACR"
B... |
b67916cbe8022640c1cff12f7e3309ff38e026bd2db746bcca820b694ea372cc | Shell | 3,010 | 84 | while getopts t flag; do
case "${flag}" in
t) TWO_COL_SAME_CERT="true" ;;
esac
done
TWO_COL_SAME_CERT="${TWO_COL_SAME_CERT:-false}"
COL1_CN="col1@example.com"
COL2_CN="col2@example.com"
COL3_CN="col3@example.com"
COL1_LABEL="col1@example.com"
COL2_LABEL="col2@example.com"
COL3_LABEL="col3@example.com"
if ... |
16c5cae0d103f9481e6a8d008a3c05b438dab33fe58ce5940929c55acacba5c1 | Shell | 3,013 | 80 | #!/bin/bash
#
# Backup all Postgres databases, exclude some CATMAID tables that can be
# regenerated from other tables to reduce size of backups. Different environment
# variables can be used to configure the behavior:
#
# BASE_DIR: The backup target directory can be configured using the BASE_DIR
# environmen... |
88982dd9d8faba4b5ccc82f725f62bf6bae2fe8666114f3a52eb01fddaa5633e | Shell | 3,020 | 57 | #!/bin/bash
### Benchmarks for DCIC
### To run, get juicebox_tools.jar and the test data files:
### wget http://hicfiles.s3.amazonaws.com/internal/juicebox_tools/8.5.16/juicebox_tools.jar
### wget ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1551nnn/GSM1551552/suppl/GSM1551552_HIC003_merged_nodups.txt.gz
### wget h... |
39ca6010cb5e8df3118b2ce63c5f85df4eabf878ffee63a7e462dcc37968b2d8 | Shell | 3,022 | 99 | #!/bin/sh
#
# Downloads sequence for the GRCh38 release 84 version of H. sapiens (human) from
# Ensembl.
#
# Note that Ensembl's GRCh38 build has three categories of compressed fasta
# files:
#
# The base files, named ??.fa.gz
#
# By default, this script builds and index for just the base files,
# since alignments to ... |
7fd796e30ed4bf6feec25944ea77d0db6ce5715aeea8f777ed8aea63483afda8 | Shell | 3,040 | 118 | #!/bin/bash
#SBATCH --job-name=mt5_large_summary
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=4
#SBATCH --gres=gpu:4 # number of gpus
#SBATCH -o /cognitive_comp/ganruyi/fengshen/mt5_large_summary/%x-%j.log
#SBATCH -e /cognitive_comp/ganruyi/fengshen/mt5_large_summary/%x-%j.err
set -x -e
echo "START TIME:... |
e628610a1bdef65d395dc3f43cc4ddbffc12ddcf3bff4b21a56200c71a00c63d | Shell | 3,043 | 74 | # generate plan and copy it to each node
source ./.env
AGG_PATH=/home/hasan/work/medperf_ws/medperf/examples/flower/fl/workspace_agg
arg1="aggregator_config_path=$AGG_PATH/aggregator_config.yaml"
arg2="training_config_path=$AGG_PATH/training_config.yaml"
arg3="plan_path=$AGG_PATH/plan.yaml"
medperf container run_test ... |
34c9b0028268acda67cf857119c8255f738cfa6a3cc51559ae83f0852f78465f | Shell | 3,071 | 74 | #!/bin/bash
# ==============================================================================
# SCRIPT INFORMATION:
# ==============================================================================
# SCRIPT: DEFACING ANATOMICAL MRI DATA IN A BIDS DATASET
# PROJECT: ZOO
# WRITTEN BY LENNART WITTKUHN, 2020
# CONTACT: WITTK... |
8b32c58675b54491b4e0318b193f1d96f2db556bcc43306c0c5fede0d839ee5d | Shell | 3,093 | 101 | #!/usr/bin/env bash
#SBATCH --job-name=finetune_no_tp # create a short name for your job
#SBATCH --nodes=1 # node count
#SBATCH --ntasks-per-node=8 # total number of tasks across all nodes
#SBATCH --cpus-per-task=4 # cpu-cores per task (>1 if multi-threaded tasks)
#SBATCH --mem-per-cpu=20G # memory per cpu-core (4G is ... |
44a1c167f373227b69f6687b1c4e59bfa6a62f0c7eebb39ed0c62ee6515d3130 | Shell | 3,094 | 84 | #!/bin/bash
# Written by Tim Lawn 16/12/2024
# =============================================================================
# Summary for eventual methods section
# =============================================================================
# This script performs spatial processing and masking of PET atlas images... |
bed1cb0cf58849ebd3d951f58128fa7ccf92991e58b70f7db97bfd57a431f33e | Shell | 3,099 | 74 | #!/bin/bash -e
# Installs pytraj (github.com/Amber-MD/pytraj) from source into the active
# Python environment. PyPI's pytraj==2.0.5 (2020) doesn't build against
# modern Python/numpy/cython; pytraj's git master tracks cpptraj's current
# API instead (the two commits below are a pair tested together).
#
# This script i... |
7ca0603b062537b3760b756187d503fc455784dde739d5a4cf3bcda010bd0092 | Shell | 3,100 | 102 | #!/usr/bin/env bash
#SBATCH --job-name=finetune_with_tp # create a short name for your job
#SBATCH --nodes=3 # node count
#SBATCH --ntasks-per-node=8 # total number of tasks across all nodes
#SBATCH --cpus-per-task=4 # cpu-cores per task (>1 if multi-threaded tasks)
#SBATCH --mem-per-cpu=5G # memory per cpu-core (4G is... |
04b655b15b1b45c85d9db63974f3b552e19cfe2e9beb6532d0e1381278562a92 | Shell | 3,108 | 124 | #!/bin/bash
#SBATCH --job-name=bart_summary
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=4
#SBATCH --gres=gpu:4 # number of gpus
#SBATCH -o %x-%j.log
set -x -e
echo "START TIME: $(date)"
MODEL_NAME=bart-base
MICRO_BATCH_SIZE=16
ROOT_DIR=/cognitive_comp/dongxiaoqun/finetune/${MODEL_NAME}
ZERO_STAGE=1
exp... |
2ae284073cfadb72fdaa7dd8f7ccfe6ed1643fabb7ec492f85592aa8bfa576bc | Shell | 3,108 | 121 | #!/bin/bash
# ============================================================================
# Rica - Linting Script
# ============================================================================
#
# Purpose:
# Runs ESLint on the codebase to check for code quality issues.
# Uses the eslint configuration from react-ap... |
4d469c3d07aa76c5fad7278ac932ee8b48af3c85e1201860e17af03ebdd0dda4 | Shell | 3,108 | 85 | #!/bin/sh -e
fail() {
echo "Error: $1"
exit 1
}
notExists() {
[ ! -f "$1" ]
}
if notExists "${TMP_PATH}/query.dbtype"; then
# shellcheck disable=SC2086
"$MMSEQS" createdb "$@" "${TMP_PATH}/query" ${CREATEDB_QUERY_PAR} \
|| fail "query createdb died"
fi
if notExists "${TMP_PATH}/result.dbtype... |
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