sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 17k | content stringlengths 1 200k |
|---|---|---|---|---|
919771c2281dd8d2a90fa1d78c6c7b564a9165ad8aafa7b35bdba7028d4f9eea | Shell | 2,176 | 48 | #! /bin/sh
# Last successfully run on Dec 2, 2019 with git repository version v0.15.4-Update_KRR
# Written by Nanbo Sun and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
# DO NOT CHANGE: This clears old freesurfer variables if they previously exists
if [ -n "$FREESURFER_HOME" ]; t... |
a74a56e6023a297a437eba8d954885beb467cb68430f8fcbf018b6d0b99f8c65 | Shell | 2,184 | 75 | #!/bin/bash
# Usage: ./build-wheels.sh <workdir> <pyminorversion1> <pyminorversion2> ...
set -e -x
export MANYLINUX=1
export MEDAKA_DIST=1
export WITHDEFLATE=1
arch=$(uname -m)
workdir=$1
shift
echo "Changing cwd to ${workdir}"
cd ${workdir}
if [[ -z "${PACKAGE_NAME}" ]]; then
PACKAGE_NAME='medaka'
fi
PACKAGE_F... |
ffae2ad8c6fa8f66d0ddeb7c37db8d3f9095890ea72a8f6ce4bc296dfbd5ea66 | Shell | 2,202 | 78 | #!/bin/bash
# Written by Nanbo Sun and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
###########################################
# Usage and Reading in Parameters
###########################################
# Usage
usage() { echo "
Usage: $0 -i <inDir> -s <scriptDir> -p <spmDir>... |
79a943e771d7c583356eb39009242d3c1612e915bf4efe2f5abedeefd2c2904f | Shell | 2,203 | 56 | #!/bin/bash
# Example:
# sh CBIG_hMRF_replicate_400level_parcellation_wrapper.sh ~/storage/temporary/CBIG_hMRF_replication_output
#
# Written by Xiaoxuan Yan and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
out_dir=`realpath $1` # to be handled in CBIG_hMRF_generate_parcellat... |
3515647a9dcebaa58880cfebc56a3f0e667b06151937a8dc33f773d7acaa6256 | Shell | 2,218 | 48 | #! /bin/sh
# Last successfully run on Nov 18th, 2019 with git repository version v0.15.4-Update_KRR
# Written by CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
# DO NOT CHANGE: This clears old freesurfer variables if they previously exists
if [ -n "$FREESURFER_HOME" ]; then
$F... |
8264598a73392da432ce9f095b0866ffa0ba91d4902c45dd025f9a8457fcc552 | Shell | 2,226 | 64 | #!/bin/bash
# Download and prepare all reference resources and dockers required for variant annotation
set -e # Exit immediately if a command exits with a non-zero status
set -o pipefail # Properly propagate errors through pipelines
# ============================
# Check argument
# ============================
if ... |
81e8752881da7eecb8db4a66edcebe71c9c63381bfccf08697e9cb2f354e36c5 | Shell | 2,230 | 78 | #!/bin/bash
# Written by Nanbo Sun and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
###########################################
# Usage and Reading in Parameters
###########################################
# Usage
usage() { echo "
Usage: $0 -i <inDir> -d <idList> -s <scriptDir>... |
9a1a7c1c3db65a25c86b8320a63d6262b106f08dbe3885fce18e8e5d73092179 | Shell | 2,237 | 78 | #!/usr/bin/env zsh
# Copyright (c) Facebook, 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.
source_dir=$1
tgt_dir=$2
model=$3
if [ -z "$4" ]
then
dim=512
else
dim=$4
fi
echo "using $dim dim for PCA"
i... |
ddae96adb9688e39b21d3f7f2b710807fa831b2009b8e270cb9f8d4262736c13 | Shell | 2,249 | 63 | #!/bin/bash
# This function submits the job for generation of the final parcellation.
#
# Written by Xiaoxuan Yan and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
###########################
# Set up output folder
###########################
out_dir=`realpath $1`
log_dir="${out_d... |
d81c0f5cea898565ca74777e3fe9cdcc80fc635a0e7135155937cb525e81584e | Shell | 2,253 | 58 | #! /bin/sh
#
# DO NOT CHANGE: This clears old freesurfer variables if they previously exists
if [ -n "$FREESURFER_HOME" ]; then
# Save LD_LIBRARY_PATH to restore it later. This variable defines shared libraries used
# by matlab to open GUI/compute/etc.
# clear_fs_env.csh removes it when clearing old freesu... |
2b22f84c33a628acbbd5ad2137ea45a12765195ffba753caaa6a397c4faa05ac | Shell | 2,256 | 77 | #!/bin/bash
# Written by Nanbo Sun and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
###########################################
# Usage and Reading in Parameters
###########################################
# Usage
usage() { echo "
Usage: $0 -i <inDir> -d <idList> -s <scriptDir>... |
395d2d379e73758e00099263fa6b54d06516967f71c129cd257f42939da60732 | Shell | 2,259 | 77 | #!/bin/bash
# Written by Nanbo Sun and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
###########################################
# Usage and Reading in Parameters
###########################################
# Usage
usage() { echo "
Usage: $0 -i <inDir> -s <scriptDir> -p <spmDir>... |
3d5ec8925eab7f0e7337e7b8205a0478b68fc31d3232c2c1ed3ae97b09d5e330 | Shell | 2,268 | 82 | #!/bin/bash
# run_expC_markov_nomask.sh
#
# Exp C 补充：Markov 任务真正无约束基线
# KNET_uncons_nomask = 无 groups + 无 band mask（完全无约束）
#
# 在 192.168.3.17 上运行：
# cd /rd1/liut/K-attention/K-attention/Kattn-sim-dev/src/simulation
# bash run_expC_markov_nomask.sh
set -e
SCRIPT_DIR="$(cd "$(dirname "$0")" && pwd)"
cd "$SCRIPT_DIR"... |
b360c39d6bec7d5a81e3076eebd68d7973173fb5eadb59d0496c4be7b7dce6c4 | Shell | 2,275 | 64 | #!/bin/bash
# Written by Xiuming Zhang and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
###########################################
# Usage and Reading in Parameters
###########################################
# Usage
usage() { echo "
Usage: $0 -g <GMList> -t <affineTmp> -o <ou... |
25cefa715d13e463a16d48ff45d0be8d95e9b1fc9eaf4bf9b3d9c4b9eff4defb | Shell | 2,278 | 62 | #!/bin/bash
# do not touch these settings
# number of tasks and nodes are fixed at 1
#SBATCH -n 1
#SBATCH --ntasks-per-node=1
# job name for pipeline
# this name will appear when you monitor jobs with "squeue -u $USER"
#SBATCH --job-name=ENCSR356KRQ_subsampled
# walltime for your job
# give long time enough to fi... |
58a1d4e90a8c854b4519d3b27105eb1b36e3f472b7bde5adbcd9c64e82dccfb7 | Shell | 2,278 | 62 | #!/bin/bash
# do not touch these settings
# number of tasks and nodes are fixed at 1
#SBATCH -n 1
#SBATCH --ntasks-per-node=1
# job name for pipeline
# this name will appear when you monitor jobs with "squeue -u $USER"
#SBATCH --job-name=ENCSR356KRQ_subsampled
# walltime for your job
# give long time enough to fi... |
61aba0da1fd68a27438a5648e5be68eccd18516bdf26d7b2c46f2c39fcd9a00b | Shell | 2,281 | 80 | #!/bin/sh
#
# Estimate factors in two random splits independently
#
# Written by Siyi Tang and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
output_dir=$1
data_dir=${CBIG_REPDATA_DIR}/stable_projects/disorder_subtypes/Tang2020_ASDFactors/results/splitHalf
corpus_set1=${data_dir}/... |
9e0e7ed26241ccb2312eaf3e24762cdb005014175fda0777b88800993d0e451a | Shell | 2,290 | 79 | #!/usr/bin/env bash
set -euo pipefail
DATASETS=(
"a1data_remove_undef"
"allen_scope_neuropixel_area_subset"
"cellexplorer_cell_type"
"dandi_000041_cell_type"
"dandi_000473_cell_type"
"dandi_000955_cell_type"
"hausser_cell_type"
"hull_cell_type"
"juxtacellular_mouse_s1_area"
"lisberger_labeled_cell_... |
1f2974a19200036f660b5b76d9c4bde9038a083e6e99f405ae2565809c360930 | Shell | 2,292 | 62 | #!/bin/bash
# do not touch these settings
# number of tasks and nodes are fixed at 1
#SBATCH -n 1
#SBATCH --ntasks-per-node=1
# job name for pipeline
# this name will appear when you monitor jobs with "squeue -u $USER"
#SBATCH --job-name=ENCSR356KRQ_subsampled
# walltime for your job
# give long time enough to fi... |
632ba16f1ce78981b68c9d36dc0305f7e77610c55644bc25a32cd48bfc9efe5f | Shell | 2,292 | 62 | #!/bin/bash
# do not touch these settings
# number of tasks and nodes are fixed at 1
#SBATCH -n 1
#SBATCH --ntasks-per-node=1
# job name for pipeline
# this name will appear when you monitor jobs with "squeue -u $USER"
#SBATCH --job-name=ENCSR356KRQ_subsampled
# walltime for your job
# give long time enough to fi... |
14d25e3e11a7c03923f0447e60d46d0e5ad373beea32f1d8534c30c36a6f8f48 | Shell | 2,293 | 62 | #!/bin/bash
# do not touch these settings
# number of tasks and nodes are fixed at 1
#SBATCH -n 1
#SBATCH --ntasks-per-node=1
# job name for pipeline
# this name will appear when you monitor jobs with "squeue -u $USER"
#SBATCH --job-name=ENCSR356KRQ_subsampled
# walltime for your job
# give long time enough to fi... |
379b06c2ddaa53e42e6beaa5eb63cbac98724a733eb54059a1d1926e2ada01df | Shell | 2,293 | 62 | #!/bin/bash
# do not touch these settings
# number of tasks and nodes are fixed at 1
#SBATCH -n 1
#SBATCH --ntasks-per-node=1
# job name for pipeline
# this name will appear when you monitor jobs with "squeue -u $USER"
#SBATCH --job-name=ENCSR356KRQ_subsampled
# walltime for your job
# give long time enough to fi... |
3403daae6335e057e348f8179abc2c386901fb3341b4f131e49d569540340906 | Shell | 2,295 | 65 | #!/bin/bash
# Written by Xiuming Zhang and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
###########################################
# Usage and Reading in Parameters
###########################################
# Usage
usage() { echo "
Usage: $0 -b <brainList> -o <outDir> -t <br... |
3be53e062cca73233b5a2be64c60c1c64a0d8408f79f90ef078fca9015e49127 | Shell | 2,297 | 79 | #!/bin/bash
## BWA mapping statistics
## Note that the statistics are in number of reads (not pairs)
function usage {
echo -e "usage : getBWAstats.sh -i INPUT [-p PROC] [-h]"
echo -e "Use option -h|--help for more information"
}
function help {
usage;
echo
echo "getBWAstats.sh"
echo "------... |
d906493d3804935dcf77eb6544ffe3436a1f6026b0dba8b9511dd1ebf335b980 | Shell | 2,302 | 70 | #!/bin/sh
# CBIG_IndCBM_generate_example_list.sh <output_dir>
# This function generate 6 file lists as input for the example. Each list contains the directories of the fmri files
# either on the surface or in the volume.
# Input:
# output_dir: Path of output folder.
# Output:
# 6 list files will be saved under ... |
454ba3ef36ab7bfe433c2e702a724d6c4e6b8abbeb3cd01b36eb56b125b03e3a | Shell | 2,318 | 65 | #!/bin/bash
# do not touch these settings
# number of tasks and nodes are fixed at 1
#SBATCH -n 1
#SBATCH --ntasks-per-node=1
# job name for pipeline
# this name will appear when you monitor jobs with "squeue -u $USER"
#SBATCH --job-name=ENCSR356KRQ_subsampled
# walltime for your job
# give long time enough to fi... |
414619501f8c597c6045a3d6768f8bfd70f05c54d44255ad965f89c0e05a685c | Shell | 2,319 | 81 | #!/bin/bash
# Written by Nanbo Sun and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
###########################################
# Usage and Reading in Parameters
###########################################
# Usage
usage() { echo "
Usage: $0 -i <id_list> -o <out_dir> [-q <queue>... |
56a732055367d3a10928c00ce686e734163b576d6a0d1355a7135037e8f47f07 | Shell | 2,324 | 65 | #!/bin/bash
# do not touch these settings
# number of tasks and nodes are fixed at 1
#SBATCH -n 1
#SBATCH --ntasks-per-node=1
# job name for pipeline
# this name will appear when you monitor jobs with "squeue -u $USER"
#SBATCH --job-name=ENCSR356KRQ_subsampled
# walltime for your job
# give long time enough to fi... |
678b6e583d21a28eb39d4da91f717dbb6dbdb5402bce3e40117b77edaac3f5d2 | Shell | 2,324 | 65 | #!/bin/bash
# do not touch these settings
# number of tasks and nodes are fixed at 1
#SBATCH -n 1
#SBATCH --ntasks-per-node=1
# job name for pipeline
# this name will appear when you monitor jobs with "squeue -u $USER"
#SBATCH --job-name=ENCSR356KRQ_subsampled
# walltime for your job
# give long time enough to fi... |
13da9840eee5115a861ffd53b7e25ac47c0bdb58ffc7e0e8fb5ad56ec7fdf9cd | Shell | 2,328 | 65 | #!/bin/bash
# do not touch these settings
# number of tasks and nodes are fixed at 1
#SBATCH -n 1
#SBATCH --ntasks-per-node=1
# job name for pipeline
# this name will appear when you monitor jobs with "squeue -u $USER"
#SBATCH --job-name=ENCSR356KRQ_subsampled
# walltime for your job
# give long time enough to fi... |
1830104347ac7c23299e99e813252ce0df358c61e751655ffb64566efca92b2f | Shell | 2,328 | 65 | #!/bin/bash
# do not touch these settings
# number of tasks and nodes are fixed at 1
#SBATCH -n 1
#SBATCH --ntasks-per-node=1
# job name for pipeline
# this name will appear when you monitor jobs with "squeue -u $USER"
#SBATCH --job-name=ENCSR356KRQ_subsampled
# walltime for your job
# give long time enough to fi... |
e1b448a7e53a61ff6b020f9f37112f35910fd63cd5a392a3fabf24d933f4d1e0 | Shell | 2,329 | 85 | #!/bin/bash
# Download and prepare all reference resources and dockers required for variant annotation
set -e # Exit immediately if a command exits with a non-zero status
set -o pipefail # Properly propagate errors through pipelines
# ============================
# Check argument
# ============================
if ... |
b93438360d5f823f24d26248c9fd78f29ca9260edff34d3b34cfb42c2cbbb5bb | Shell | 2,331 | 92 | #!/bin/bash
set -e
sizes="base large xlarge"
declare -A ckpt_urls
ckpt_urls[base]="https://dl.fbaipublicfiles.com/hubert/hubert_base_ls960.pt"
ckpt_urls[large]="https://dl.fbaipublicfiles.com/hubert/hubert_large_ll60k.pt"
ckpt_urls[xlarge]="https://dl.fbaipublicfiles.com/hubert/hubert_xtralarge_ll60k.pt"
declare -A... |
b6d3252974e61a44e0818042f8db02f1354d6ff690e689d21d0b6c24101991db | Shell | 2,340 | 67 | export CUDA_VISIBLE_DEVICES=6
NPROC_PER_NODE=1
TRAINING_DATA_DIR=./dataset/de_occluding_broadband_metalens_training_data
TEST_DATA_DIR=./dataset/de_occluding_broadband_metalens_test_data
NETWORK_DIR=None # if exist, load pretrained network weights from this path
BATCH_SIZE=2 # For patch training, use 14. For full ima... |
a5908eef0ff1f82af5c505a07598ea15fe2935c218b08c78c8a2e0abca388f67 | Shell | 2,341 | 83 | #!/bin/bash
# Written by Nanbo Sun and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
###########################################
# Usage and Reading in Parameters
###########################################
# Usage
usage() { echo "
Usage: $0 -i <imgList> -d <idList> -o <outDir> ... |
d11c4bb75512a0b938e1b83917a64fb4c7739ad7d378cc3c411d0248c7570583 | Shell | 2,342 | 66 | #!/bin/bash
# do not touch these settings
# number of tasks and nodes are fixed at 1
#SBATCH -n 1
#SBATCH --ntasks-per-node=1
# job name for pipeline
# this name will appear when you monitor jobs with "squeue -u $USER"
#SBATCH --job-name=ENCSR356KRQ_subsampled
# walltime for your job
# give long time enough to fi... |
030e63e7b304a45a6ceb8ec419d24ecbd62f1a88fcde710a759cbc6d56eed644 | Shell | 2,343 | 65 | #!/bin/bash
# Written by Xiuming Zhang and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
###########################################
# Usage and Reading in Parameters
###########################################
# Usage
usage() { echo "
Usage: $0 -g <GMList> -t <nonlinTmp> -o <ou... |
7b00defd706e1c30e995fa3d78fbee11ea798530436f2b8f53e9c6e4eeaab158 | Shell | 2,354 | 81 | #!/bin/bash
# Experiment C: Ablation - constrained vs unconstrained KNET
# RC: KNET_rc vs KNET_uncons_rc; Markov: KNET vs KNET_uncons
# Runs 2 jobs in parallel
# Run from: Kattn-sim-dev/src/simulation/
source env_setup.sh
RC_DSTS=("abs-ran_fix2" "random_rand")
MARKOV_DSTS=("markov_1_0_50000")
SEEDS=(0 1 2)
MAX_EPOCHS... |
a587e5b00a8353dee0aca5a4c59b28301ccf7648dee8c79b62a9223f9fc3c8cf | Shell | 2,354 | 62 | #!/bin/bash
#
# Copyright 2008, Google Inc.
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# * Redistributions of source code must retain the above copyright
# notice, this list of condit... |
b47c3798fe566dca90d79a8efbb561abd3f0f18b81a503b681e8d21a78199987 | Shell | 2,380 | 78 | #!/usr/bin/env bash
# Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
CWD=`pwd`
INSTALL_PATH=$CWD/tokenizers/thirdparty
MOSES=$INSTALL_PATH/mosesdecoder
if [ ! -d $MOSES ]; then
echo 'Cl... |
97726337566e8c03658483804af2447bdb3d72eededc1c01f33da52ad82dd7c3 | Shell | 2,391 | 83 | #!/usr/bin/env bash
# Copyright (c) 2019-present, Facebook, Inc.
# All rights reserved.
#
# This source code is licensed under the license found in the
# LICENSE file in the root directory of this source tree.
#
set -e
TOKENIZERS_SCRIPTS=tokenizers
INSTALL_PATH=$TOKENIZERS_SCRIPTS/thirdparty
N_THREADS=8
lg=$1
MOSE... |
aa72e62f90604286fa9ebee43f5c0de9543704a03b85c0cb50b636d6f69e7758 | Shell | 2,394 | 66 | #!/bin/bash
# do not touch these settings
# number of tasks and nodes are fixed at 1
#$ -S /bin/sh
#$ -terse
#$ -V
# job name for pipeline
# this name will appear when you monitor jobs with "squeue -u $USER"
#$ -N ENCSR356KRQ_subsampled
# walltime for your job
# give long time enough to finish your pipeline
# <1... |
e45cfa0bb4e646e672238808e54860fe77af66f51ec59464b300dee038c0a6ea | Shell | 2,394 | 66 | #!/bin/bash
# do not touch these settings
# number of tasks and nodes are fixed at 1
#$ -S /bin/sh
#$ -terse
#$ -V
# job name for pipeline
# this name will appear when you monitor jobs with "squeue -u $USER"
#$ -N ENCSR356KRQ_subsampled
# walltime for your job
# give long time enough to finish your pipeline
# <1... |
d8cd35c8d9b58819f278eb4438ed72304b58fb19649426a864fec4b94b95e922 | Shell | 2,398 | 60 | # Run LDSC
### =========================================================================
### SGE variables
### -------------------------------------------------------------------------
###
#$ -l mem_free=6G
#$ -l h_vmem=8G
#$ -l h_fsize=500G
#$ -l bluejay
#$ -pe local 2
#$ -o ./logs/
#$ -e ./logs/
#$ -cwd
#$ -t 1-43... |
14a4f5606fe2c8f2cf9dce67ac9741a08477aa6c81cb03c2ceafa53755572be5 | Shell | 2,401 | 81 | #!/bin/bash
# Written by Nanbo Sun and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
###########################################
# Usage and Reading in Parameters
###########################################
# Usage
usage() { echo "
Usage: $0 -i <id_list> -o <out_dir> [-q <queue>... |
6a2aedb77ed073db6863cadb9b5176da1ebb02f0d098a2a7e5c946f8bcc98019 | Shell | 2,406 | 68 | #!/bin/bash
ARGS=`getopt -o "t:d:e:m:o:b:g:s:w:a:f:" -l "task_name:,data_cat:,epoch:,mean_output:,optimizer:,per_device_batch_size:,gradient_accumulation_steps:,eval_step:,warmup_ratio:,eval_batchsize:,frozen_bert:,model:,do_train:,learning_rate:,seed:,metric_for_best_model:,load_best_model_at_end:,evaluation_strategy... |
98d179329981191e457cf03cfde88ff182f94bc62797b779c4ebeb91b862808c | Shell | 2,407 | 59 | #!/usr/bin/env bash
# Build small synthetic uBAMs in three orderings to test samtools sort -n vs collate.
# Output: input.bam (interleaved), sorted_n.bam, collate.bam in same dir.
set -euo pipefail
cd "$(dirname "$0")"
# Generate a SAM with R1/R2 records for 5 read pairs, interleaved R1,R2,R1,R2,...
# Flag 77 = 0x4D ... |
4d71a1ddcc89559d6e9bd6ce180a58879cd9a9ffee77f4323fb75820f9ddfc67 | Shell | 2,410 | 80 | #!/bin/bash
# Written by Nanbo Sun and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
###########################################
# Usage and Reading in Parameters
###########################################
# Usage
usage() { echo "
Usage: $0 -i <inDir> -d <idList> -s <scriptDir>... |
0926c71074b8c798b5f2cda9f5265fa7030686164dabccfd73197dd9db1020b4 | Shell | 2,426 | 69 | #!/bin/bash
# do not touch these settings
# number of tasks and nodes are fixed at 1
#$ -S /bin/sh
#$ -terse
#$ -V
# job name for pipeline
# this name will appear when you monitor jobs with "squeue -u $USER"
#$ -N ENCSR356KRQ_subsampled
# walltime for your job
# give long time enough to finish your pipeline
# <1... |
2228badc42c8ef9314517d8235228d60aa076459cbc85da3c81275e3f94ebec1 | Shell | 2,426 | 69 | #!/bin/bash
# do not touch these settings
# number of tasks and nodes are fixed at 1
#$ -S /bin/sh
#$ -terse
#$ -V
# job name for pipeline
# this name will appear when you monitor jobs with "squeue -u $USER"
#$ -N ENCSR356KRQ_subsampled
# walltime for your job
# give long time enough to finish your pipeline
# <1... |
63b7b83533662aea8f07754c7dff14758aa6eb6304440c8a14e1721e1b3ab701 | Shell | 2,431 | 83 | #!/bin/bash
# Written by Nanbo Sun and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
###########################################
# Usage and Reading in Parameters
###########################################
# Usage
usage() { echo "
Usage: $0 -i <inDir> -d <idList> -s <scriptDir>... |
bcbaf4cd17262b73bc61bb9857996c2c4e6f5c464ba325dcf13681cdbfb1f3ef | Shell | 2,437 | 79 | #!/bin/bash
# Written by Nanbo Sun and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
###########################################
# Usage and Reading in Parameters
###########################################
# Usage
usage() { echo "
Usage: $0 -i <inDir> -d <idList> -s <scriptDir>... |
3132cdd61867eacabcf656d01b56b407e7cb8cc9d1710cd6ac4274c204b1cfb3 | Shell | 2,439 | 69 | # Florian Bénitière - 21/03/2025
# This script processes unique UKBB gVCF files to filter SNPs, INDELs, and non-homozygous ref sites.
#!/bin/bash
# Exit immediately if a command exits with a non-zero status, if an undefined variable is used, or if a command in a pipeline fails
# set -euo pipefail
# Define input arg... |
51646fc28d4778d2518879363fc975f490972c24e88fb258d29c06ce9c5e3125 | Shell | 2,446 | 69 | # Florian Bénitière - 21/03/2025
# This script processes unique UKBB gVCF files to filter SNPs, INDELs, and non-homozygous ref sites.
#!/bin/bash
# Exit immediately if a command exits with a non-zero status, if an undefined variable is used, or if a command in a pipeline fails
set -euo pipefail
# Define input argum... |
e6a4911c367d1710f90b0a6ee9e8e75484901ed3afbb27e2563e64279be862f4 | Shell | 2,447 | 90 | #!/bin/tcsh
# Usage: tcsh batch_qcc_recon-all.sh QianCC | tee QianCC.log
# Example 1) Averaged, high resolution (0.7 iso), T1_div_PD_fused/MP2RAGE_ns volume:
# 2017-05-09: Created by Chencan Qian
# We would like to thank Associate Researcher Qian Chencan from the Institute of Biophysics, Chinese Academy of Sciences
... |
f09a0b3a2423de324de9d0f6fc813d188bea02bca3694718e860fe4e1c790250 | Shell | 2,456 | 69 | #!/usr/bin/env bash
#
# Copyright (c) 2017-present, Facebook, Inc.
# All rights reserved.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
#
set -e
DATADIR=data/
if [ ! -d "$DATADIR" ]; then
mkdir $DATADIR
fi
cd $DATADIR
echo "preparing WN... |
0e3809905bba69f476eef54589aee6096119aa827964007daf73ff1e43eae5fd | Shell | 2,458 | 73 | #!/usr/bin/env bash
# MIT License
#
# Copyright 2025 Broad Institute
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, c... |
0f36a274bf055c68eac77aa01bfe00e19cd6182c7bf28f521bea5bdd00222b39 | Shell | 2,465 | 68 | #!/bin/bash
#
# CBIG_replace_old_with_new_function_name.sh $old_function_name $new_function_name $folder
# Search for all instances of old function name inside a given folder
# and replace them by the new function name ,if prompted
old_function_name=$1
new_function_name=$2
folder=$3
# function to join array into str... |
c0b713858484c2c77dd43f5e5b7a62c0de6789e4480d7130275473a1e196ec10 | Shell | 2,468 | 83 | #!/bin/bash
# Written by Nanbo Sun and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
###########################################
# Usage and Reading in Parameters
###########################################
# Usage
usage() { echo "
Usage: $0 -i <inDir> -d <idList> -s <scriptDir>... |
330685c6c5a63a0eca42cf5366e5088cc14b9959b12dba08ff6560e7106a40d6 | Shell | 2,473 | 44 | #!/usr/bin/env bash
set -euxo pipefail
# Import AppleID certificates on macOS
# This script is used to import the AppleID certificates into the keychain
# It expects the following environment variables to be set:
# - APPLE_INSTALLER_CERTIFICATE_BASE64: base64 encoded certificate
# - APPLE_INSTALLER_CERTIFICATE_PASSWO... |
bd8a39120dd0d28f6d6eb38b9ebabdc5eb80d43bd0711b90be37066f0e9865d1 | Shell | 2,474 | 81 | #!/bin/bash
# Written by Nanbo Sun and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
###########################################
# Usage and Reading in Parameters
###########################################
# Usage
usage() { echo "
Usage: $0 -i <inDir> -d <idList> -s <scriptDir>... |
586b4622a8181ae3828093ad2006f495512cd06e4e9caddcc6e3916313ae2b31 | Shell | 2,507 | 21 | #!/bin/bash
#SBATCH --job-name=CCVAE
#SBATCH --output=amnist_output3.txt
#SBATCH --error=amnist_error3.txt
#SBATCH --ntasks=1
#SBATCH --gres=gpu:1
#SBATCH --mem=16GB
#SBATCH --time=03:00:00
source $HOME/test/bin/activate
module load libffi
# python $HOME/ambiguous-dataset/ambiguous/train/train_MNIST_final_ccvae.py ... |
1a8bdaf0cd280c8038308d3ebbd9627d7fcc1d741d9d6701f8d62deb5b75acdd | Shell | 2,525 | 85 | #!/bin/bash
# ================================================
# Script: get_spliceai_resources.sh
# Author: Florian Bénitière
# Date: 11/05/2026
#
# Description:
# Downloads and sets up the necessary SpliceAI resources for VEP pipelines.
# Supports genome versions GRCh37 (hg19) and GRCh38 (hg38).
# Requires Base... |
47c04fd4ecec172a05e6041e257e839cda874497979ae4c235e57aa7c03af218 | Shell | 2,537 | 84 | #!/bin/bash
# Quick validation: verify KNET achieves AUROC~1.0 with lr=1e-2
# Uses 20000 samples for fast testing
# Run from: Kattn-sim-dev/src/simulation/
source env_setup.sh
KS=12
NK=128
MAX_EPOCHS=500
PATIENCE=30
MAX_LR=1e-2
BATCH_SIZE=512
AUROC_THRESHOLD=0.99
N=20000 # fast test size
MARKOV_... |
1fcfba9e93bde2b4424e8b560df31c4afd4777cec93b72997d99dbcf752c1f7b | Shell | 2,573 | 61 | #! /bin/sh
# Written by Mervyn Lim Jun Rui and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
# DO NOT CHANGE: This clears old freesurfer variables if they previously exists
if [ -n "$FREESURFER_HOME" ]; then
# Save LD_LIBRARY_PATH to restore it later. This variable defines sha... |
05fb2912fa9533944d5b431e87d7ad36dd54daa870c1528859e0b380035a818a | Shell | 2,576 | 89 | #!/usr/bin/env bash
# This script takes a macOS installer package (.pkg) and notarizes + staples it.
# It expects the following environment variables to be set:
# APPLE_NOTARIZATION_ISSUER_ID: Apple App Store Connect team identifier
# APPLE_NOTARIZATION_KEY_ID: Apple App Store Connect API key identifier
# APPLE_NOTARI... |
023fd4c014955e68991321840caf51bebca8d8fbdae069cbe0caedaa601a6c3b | Shell | 2,578 | 70 | #!/bin/bash
# Written by Xiuming Zhang and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
###########################################
# Usage and Reading in Parameters
###########################################
# Usage
usage() { echo "
Usage: $0 -b <brainList> -t <tmp> -s <sigma... |
f0d8995e9e617358fff4978bb17269b1ec476e298898ea9fdb86b4c725d5ea05 | Shell | 2,579 | 87 | #!/usr/bin/env bash
# MIT License
#
# Copyright 2023 Broad Institute
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, ... |
1a0672a4151b16f3c797478ba26c534e82b2faa603f90b9aa14e785805f7683a | Shell | 2,587 | 65 | #!/bin/bash
#
# Copyright 2008, Google Inc.
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# * Redistributions of source code must retain the above copyright
# notice, this list of condit... |
f666d47963e6eda73b3720a07205201bb72397b828d97542873e56c76a9428b4 | Shell | 2,605 | 86 | #!/bin/bash
# Git pre-commit hook to check staged Python files for formatting issues with
# yapf.
#
# INSTALLING: Copy this script into `.git/hooks/pre-commit`, and mark it as
# executable.
#
# This requires that yapf is installed and runnable in the environment running
# the pre-commit hook.
#
# When running, this fi... |
76b5f1d266d9216a08bd5c6154d94f8aa58da859ba85c8f13b878afae3cfafd8 | Shell | 2,606 | 90 | #!/bin/bash
CONDA_PATH=$(which conda)
# Activate the fastsam Conda environment
source "$(conda info --base)/etc/profile.d/conda.sh"
conda activate fastsam
# Define paths
proj_dir="/home/matt/HDD_exp/C2.1 gloid live imaging"
# REP 1 ----------------
data_dir="${proj_dir}/gastruloids c2.1 20220804__2022-08-04T15_46_1... |
02efa4496fac2ec0660c638a9a00d23cd57629aaa76727ef51f8ac18e826cdf3 | Shell | 2,632 | 88 | #!/bin/bash
# CRISPR CNN-Transformer baseline — 5-fold CV
# 11 datasets × 2 models (cnn_transformer, cnn_transformer_pm) × 5 sets × version=0
# = 110 runs total (~15-20 GPU-hours on RTX 4090)
# 已完成的 run 自动跳过（基于 test_metrics.csv 存在判断）
set -e
# ---- 环境变量 ----
BASE=/rd1/liut/K-attention/K-attention
export KATTN_SRC_DIR=... |
f5ae90f2fa6941bd593e2d9c48b27c42f91824bf9a93372ecbcec97b79a6fc54 | Shell | 2,632 | 59 | #!/bin/bash
# Download and prepare all reference resources and dockers required for variant annotation
set -e # Exit immediately if a command exits with a non-zero status
set -o pipefail # Properly propagate errors through pipelines
# ============================
# Check argument
# ============================
if [... |
42c97e69b789beab00bc6c0b67e4bd4bb8503e905be29969e055d5d1e8e5716f | Shell | 2,634 | 86 | #!/bin/bash
# Paths and Parameters
data_dir="/egor2/egor/MovieProject2/bids_data/derivatives"
output_dir="$data_dir/group_analysis/backtothefuture/isc"
isc_dir="$output_dir/ISC_maps"
# Create necessary directories
mkdir -p "$isc_dir"
# Detect subjects automatically (skip 01, 02, 03, 10, 24 and 36 since potential ali... |
58b40597a27ab593cba9c0cc1b0d8899c13e64ccb0002727b0cc6bdc6908c941 | Shell | 2,642 | 71 | #!/bin/bash
# Base path to derivatives
export deriv_root=/egor2/egor/MovieProject2/bids_data/derivatives
# Find all subjects with a backtothefuture results folder
subjects=$(find $deriv_root -maxdepth 3 -type d -name "sub-*.results.*" -path "*/backtothefuture/*" | sed -E 's|.*/sub-([0-9]+)\.results.*|\1|' | sort -u)
... |
27d6a481901ece7b3e174bc164fd96418078b7f11a373d8f2a5f5b7341cb42d4 | Shell | 2,659 | 77 | #!/bin/bash
# Written by Xiuming Zhang and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
###########################################
# Usage and Reading in Parameters
###########################################
# Usage
usage() { echo "
Usage: $0 -i <imgList> [-n <nameList>] -p <... |
a8d9bac6e4c16aada417291b12775afa2b641bd2e0cbbdc9cf3e505ea357131d | Shell | 2,676 | 81 | #!/bin/bash
# MIT License
#
# Copyright 2025 Broad Institute
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, mo... |
39c55ffe9a6a214dd136704e5343874af3747adde4ba504ff193749ea9e9affb | Shell | 2,687 | 100 | #!/bin/bash
# Example:
# sh CBIG_MSHBM_unit_test.sh ~/storage/Temporary/CBIG_MSHBM_replication_wrapper
#
# Written by Ru(by) Kong and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
###########################
# Specify output directory
###########################
out_dir=`real... |
1d5750ef79f90dae37c73ff8593d5890ac0e97d4da98576ee83622ae17544e15 | Shell | 2,730 | 90 | #!/bin/bash
# Written by Nanbo Sun and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
###########################################
# Usage and Reading in Parameters
###########################################
# Usage
usage() { echo "
Usage: $0 -i <id_list> -o <out_dir> [-q <queue>... |
eea6dcb19a9ff9e10c837bf4b43fc59f1235bc46052bc1042fe953c08f475546 | Shell | 2,742 | 86 | #!/usr/bin/env bash
set -euo pipefail
# ----------------------- Defaults (overridable) -----------------------
: "${TRAIN_DATASET:=hull_cell_type}"
: "${PREDICT_DATASET:=lisberger_labeled_cell_type}"
SCRIPT_DIR="$(cd "$(dirname "$0")" && pwd)"
PROJECT_ROOT="$(cd "$SCRIPT_DIR/../.." && pwd)"
: "${DEFAULT_DATASET_ROOT:... |
a54d9823f1a871ebe26da688f72ea7866de32585ce7f35156f5f092357e743e3 | Shell | 2,753 | 90 | #!/bin/bash
# Written by Nanbo Sun and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
###########################################
# Usage and Reading in Parameters
###########################################
# Usage
usage() { echo "
Usage: $0 -i <inDir> -d <idList> -t <newTemp> -... |
568409f09ae4056190519f29d06dd16d11774ddfa125d6e33675720ca2509892 | Shell | 2,766 | 83 | # Paths
dir="/root/dir"
csv_file="${dir}/derivatives/reliability/icc/mean_t/mean_master.csv"
txt_dir="${dir}/derivatives/reliability/icc/mean_t"
# Define order for sessions and ROIs
sessions=("run-1-avg" "run-2-avg" "ses-A-avg" "ses-B-avg")
roi_order=("cord" "network" "spinal_level_c5" "spinal_level_c6" "spinal_level_... |
2dcab9d92bf58084778993a04b271cbf693be1643ce64abb2cc8a2f3ae822074 | Shell | 2,817 | 69 | #!/usr/bin/env bash
# MIT License
#
# Copyright 2025 Broad Institute
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, c... |
1e3849ac8ddf1e9f6a69d431d0db66d0f87c175406a28a20548ab01149526714 | Shell | 2,820 | 101 | #!/bin/bash
# ----------------------------------------
# Predefined settings
# ----------------------------------------
INPUT_FASTQ="live_demo/data/input_fastq/input.fastq.gz"
NEXTFLOW_INPUT_DIR="live_demo/data/fastq_pass"
NEXTFLOW_OUTPUT_DIR="live_demo/output"
NUM_BARCODES=2
# ---------------------------------------... |
6f1a235ebb6670cd4575431710263dc0f1f5254f7bf2a92bf1919aa410b5f0b9 | Shell | 2,828 | 77 | # Path of the folder containing all data
dir="/root/dir"
# Define conditions and mask types
declare -A analyses=(
["standard"]="randomise_first_trial_censored"
["paramod"]="randomise_first_trial_censored_paramod"
)
declare -A avgs=(
["run-1-avg"]="run-13-avg"
["run-2-avg"]="run-24-avg"
["ses-A-avg"... |
fc98b4fa116df6cf6c1e66ab4a6acc1cc8220106f9295c95a12ec0542ab55e3b | Shell | 2,838 | 89 | #!/bin/bash
# Written by Nanbo Sun and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
###########################################
# Usage and Reading in Parameters
###########################################
# Usage
usage() { echo "
Usage: $0 -i <inDir> -d <idList> -r <reorientSa... |
ee58a8474fc92dfd90e78601d5a0f307bcd9d31709449703401f861d59edaa37 | Shell | 2,844 | 89 | #!/bin/bash
# Written by Nanbo Sun and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
###########################################
# Usage and Reading in Parameters
###########################################
# Usage
usage() { echo "
Usage: $0 -i <inDir> -d <idList> -s <scriptDir>... |
b8afd535e5d08e569c43d43c3b29564ac81f54e22c5aff9c5c3fb1094b1be27d | Shell | 2,849 | 106 | #!/bin/bash
#SBATCH -N 1
#SBATCH -n 20
#SBATCH -M priv
#SBATCH -p priv_para
#SBATCH --gres=gpu:4
#SBATCH --no-requeue
OUTPUT_DIR="output/pretrained/KeAP20"
PRETRAIN_DATA_DIR="data/ProteinKG25"
# protein sequence setting
IN_MEMORY=true
MAX_PROTEIN_SEQ_LENGTH=1024
# Go setting
USE_DESC=true
MAX_TEXT_SEQ_LENGTH=128
... |
3760382fbf42a78aac1bcaf735d90fa167fb6173fcb6f4efa89945654671b6a3 | Shell | 2,872 | 28 | #!/bin/bash
items=(123631 20635522 10341154 11640390 6253 9956222 82146 46931012 637858 24825971 1401 57339144 44462760 10451420 25167777 24889392 11667893 160355 3463933 42642645 5328940 10127622 9813758 5746 5459322 11485656 3218 10184653 10200390 44819241 5311510 159324 5289247 6710780 9952773 3005532 44632017 9967... |
1481a2cb9d6773a14e5e88fc721d549afa16bab6b7ccda6c2c44470c0822486d | Shell | 2,902 | 81 | #!/bin/bash
# Exit immediately if a command exits with a non-zero status.
set -e
ENV_NAME="BINND" # Name of your Conda environment
YML_FILE="BINND.yml"
REQUIREMENTS_FILE="requirements.txt"
# SET_ENV_SCRIPT="set_env.sh" # Name of your environment setup script
echo "--- Starting Environment Setup for $ENV_NAME ---"
#... |
934a56c7bb20d51547bf8ad1fda7c3455a347d801fc9e68a49bdcb155a932246 | Shell | 2,909 | 66 | #!/bin/bash
# TReNDs 112523
# Cyrus Eierud
# Helen Petropoulos 082024
# Prerequisits: FSL 7.4.1, Ubuntu 20.04
SUBJSESID=${1}
echo $SUBJSESID
SUBJID=$(echo $SUBJSESID | cut -d '_' -f 1 )
SESID=$(echo $SUBJSESID | cut -d '_' -f 2 )
DIR_BIDS_ROOT=${2}
DIR_BIDS_ROOT_GIFT=${2}"/derivatives/GIFT-BIDS/"
# Initiate all Inp... |
43e9c30b19a8c8e64066ce576478888625866573fcdada81dbcb36674a767b22 | Shell | 2,915 | 102 | #!/bin/bash
source ../scripts/config.py
test -d ./output || mkdir ./output
ss_bed="../data/hg19.ss-motif.for_umap.bed.gz"
sse_bed="../data/K562.SSE.hg38.for_visualization.bed.gz"
if [ ! -e $ss_bed ] || [ ! -e $sse_bed ]; then
test -e $ss_bed || echo "Missing file $ss_bed"
test -e $sse_bed || echo "Missing f... |
4a7c7134057cbeffd0e4ecff51cad2c0dc448f5656d63c84b69f36c306c683e0 | Shell | 2,939 | 66 | #!/bin/sh
#1. copy template into directoyr "peer"
rm -Rf ./peer
cp -R ./peer_template ./peer
#2. create symlinks
ln -s $(pwd)/../External/alglib/src/dataanalysis.cpp ./peer/src/
ln -s $(pwd)/../External/alglib/src/dataanalysis.h ./peer/src/
ln -s $(pwd)/../External/alglib/src/diffequations.cpp ./peer/src/
ln -s $(pwd... |
ea5f313d82b97a0f8346415f7fe73cae1b2117ad442f5cac45c3f462570b5bfd | Shell | 2,939 | 74 | #!/bin/bash
# Stop on error
set -e
CONDA_ENV=encode-atac-seq-pipeline
CONDA_ENV_PY3=encode-atac-seq-pipeline-python3
SH_SCRIPT_DIR=$(cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd)
REQ_TXT=${SH_SCRIPT_DIR}/requirements.txt
REQ_TXT_PY3=${SH_SCRIPT_DIR}/requirements_py3.txt
if which conda; then
echo "=== Found Conda ... |
799e51cf264013f7b0c5c6b90d8592f05c0688a5c2dfee453f64cc7a9313add6 | Shell | 2,948 | 83 | #!/bin/bash
# This script will generate the subject fullpaths for the two fake subjects: "Sub0734_Ses1" "Sub0207_Ses1"
# It checks through all possible runs (002, 003) of each subject if the corresponding fMRI file exists.
# A fullpath is then generated and tabulated into a csv file.
# The censor file paths will also ... |
3b0ef0406bf4c9ff13c9b477e7839c603c18620e5412dfff3ee61aa2b3692e4e | Shell | 2,958 | 99 | #!/bin/bash
# Experiment B: Learning curves (data size vs AUROC) for all models
# RC: subsample abs-ran_fix2 at multiple sizes × seeds
# Markov: use pre-split markov_1_0_{5000,10000,20000,50000,100000}
# Runs 2 jobs in parallel (GPU: ~19GB / 24.5GB)
# Run from: Kattn-sim-dev/src/simulation/
source env_setup.sh
RC_MOD... |
9ed4bd6b4b10b269970731cebee73ea53b36d41878dc96d322805f71a3a40e1d | Shell | 2,981 | 115 | #!/usr/bin/env bash
#
# Adapted from https://github.com/facebookresearch/MIXER/blob/master/prepareData.sh
echo 'Cloning Moses github repository (for tokenization scripts)...'
git clone https://github.com/moses-smt/mosesdecoder.git
echo 'Cloning Subword NMT repository (for BPE pre-processing)...'
git clone https://git... |
1208ff7118bea890679faca246322a4cfe36d12840b1c9d96c540f1ff106213d | Shell | 3,009 | 83 | #!/bin/bash
#
# CBIG_prepend_prefix_to_function_name.sh $input_function_name $folder
# Search for all instances of a function name (without prefix) inside a given folder
# and replace them by the new function name with the prefix prepended, if prompted
input_function_name=$1
folder=$2
# function to join array into s... |
b1e1a802b64cc5b59736b16d639e34bb075e15da09b472c5d2cb57b6b3a80baf | Shell | 3,010 | 77 | #!/bin/bash
# ==============================================================================
# Author: Florian Bénitière
# Date: 21/03/2025
# Description: Normalizes and filters unique gVCF files.
# - Targets: Autosomes (1-22) and Sex Chromosomes (X, Y)
# - Filters: SNPs/INDE... |
ac45bbff41a3e30fe08906ccb26430499d101b9b4b8f40e22fe3b41300bbb4cc | Shell | 3,024 | 71 | #!/bin/bash
# Does torch.compile pay for this model? Two arms, interleaved, in one command.
#
# bash scripts/compile_benchmark/run.sh
#
# Requires a Triton-capable GPU — compute capability 7.0 or newer. The runner
# refuses to start on anything else, and that refusal is the point: below 7.0
# `compile_model` returns ... |
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