sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
69b661bf0a4fcc04923c0cae212190b423c907fc81d5b06de30577aa3c5a4e08 | Shell | 664 | 18 | bestnumtrimix=$(( `cat bestnumtrimix` - 2))
HTK=$1
PATH=$PATH:$HTK/HTKTools
cd work
cp dict dict2
echo -e "h#\th#" >> dict2
HVite -f -a -T 1 -C hvite.config -H tri-nmix${bestnumtrimix}-npass4/MMF -S train.scp -I trainMono.mlf -i trainFATri.mlf dict2 tiedlist
HVite -f -a -T 1 -C hvite.config -H tri-nmix${bestnumtrim... |
9ee7d76c7bc942b0f59369276c3bc047ddf2d57a32d92c02342dd5a1ae59341d | Shell | 664 | 27 | #!/usr/bin/env bash
set -e
INFO=$1
DST=$2
tmpdir=`mktemp -d`
wget https://salilab.org/modbase-download/projects/genomes/H_sapiens/2013/ModBase_H_sapiens_2013_refseq.tar.xz -P ${tmpdir}
tar -C ${tmpdir} -xf ${tmpdir}/ModBase_H_sapiens_2013_refseq.tar.xz ModBase_H_sapiens_2013_refseq/models/model
src=${tmpdir}/ModBas... |
ff5f8b6f11297e167d1fd51d571d68c944186d5fdc1883125bce087958b4aceb | Shell | 667 | 15 | #!/bin/sh
# ____________________________________________________________________________________
#
# Pyomo: Python Optimization Modeling Objects
# Copyright (c) 2008-2026 National Technology and Engineering Solutions of Sandia, LLC
# Under the terms of Contract DE-NA0003525 with National Technology and Engineering
# So... |
4288baf1b1665feeb69fdead7314e603ed39b62807e105ac9496335b3d8fbef2 | Shell | 669 | 26 | #!/bin/bash
set -e
source ../paths.sh
bash clean.sh
verificarlo-c test.c -o test
${GCC_PATH:-gcc} test_dlopen.c -o test_dlopen -ldl
export VFC_BACKENDS="libinterflop_ieee.so"
export VFC_BACKENDS_LOGGER=False
echo "Running test binary linked against libinterflop_vfcwrapper..."
./test > runtime.log 2>&1
grep -q "Resu... |
39caf4711139e670a2310663dc83bef1e5d10c32169b255e7ebeed335a0af94a | Shell | 672 | 31 | #!/bin/bash
# base name of this script (without extension)
scriptname=$(basename $0 .sh)
echo -e "\n*** Running batch script '"$scriptname"' ***\n"
# path to Matlab code directory
codedir=~/git/ssdi
# current directory (the directory this script is run in - log files will go here)
currdir=$(pwd -P)
# Parameters
N... |
86eff2746942518477a1167f9eb56d63abbeb2aee854335dc2eae17654f1bc11 | Shell | 672 | 34 | #!/bin/bash
set -e
REGIONS=$1
CADD_FILE=$2
CORES=$3
OUTPUT=$4
tmpdir=$(mktemp -d)
if [[ "${CORES}" -eq 1 ]]
then
zcat ${REGIONS} | tail -n +2 > ${tmpdir}/split.0
else
divisor=$((${CORES}-1))
zcat ${REGIONS} | tail -n +2 > ${tmpdir}/input
lines=`cat ${tmpdir}/input | wc -l`
split -l$((${lines}/${divisor})) ${tmp... |
b0c4ca83d2c4dad1c65777731408fb4ef8a45429ad8fad6157b797f790e2159a | Shell | 672 | 10 | #!/bin/bash -l
source inputs.sh && \
export LOG_LOC=${SIM_FOLDER}/prepare_axons_$(date "+%Y%m%d_%Hh%Mm%Ss").out; \
# $1 : path to folder containing bioname == sim_folder
# $2 : region to synth axons (eg "MOp")
# $3 : mtype to synth axons (eg "PC")
# $4 : path to axon-synth config file
# $5 : path to axonal-projection o... |
07929593a0a2bef313724d9113841bef6aa22b6cefd6564926ff51c66d91f31b | Shell | 673 | 14 | #!/bin/sh
# ____________________________________________________________________________________
#
# Pyomo: Python Optimization Modeling Objects
# Copyright (c) 2008-2026 National Technology and Engineering Solutions of Sandia, LLC
# Under the terms of Contract DE-NA0003525 with National Technology and Engineering
# So... |
8223a34a24ab74a4b6ef2522547fefd85fe350dff020f2fc0ce022c87b36eef7 | Shell | 673 | 23 | #!/bin/bash
set -e
# Create an indexed transcriptome for pseudoaligning sequences derived
# from human mRNA and ERCC spike-in controls.
# + Download transcript sequences (fasta format) for Human (hg38) and ERCC spike-in
# + Build index for pseudoaligning with kallisto
# First argument is output directory
OUT_DIR=$1
... |
8269c2f054def9a0bdee029a148e7ce461abaec2b988f70b96efdc6d2e3a9c3d | Shell | 673 | 36 | #!/bin/bash
set -e
SCRIPT=`realpath $0`
SCRIPTPATH=`dirname $SCRIPT`
PYPROF="$SCRIPTPATH/../.."
parse="python -m apex.pyprof.parse"
prof="python -m apex.pyprof.prof"
for net in "resnet50"
do
for optim in adam sgd
do
for batch in 32 64
do
base="torchvision".$net.$optim.$batch
sql=$base.sql
dict=$base.... |
c3036c8cc81af979c5e0b4cafc7256c93ad933a89cb83cd54187294f944b0edc | Shell | 673 | 14 | #!/bin/sh
# ____________________________________________________________________________________
#
# Pyomo: Python Optimization Modeling Objects
# Copyright (c) 2008-2026 National Technology and Engineering Solutions of Sandia, LLC
# Under the terms of Contract DE-NA0003525 with National Technology and Engineering
# So... |
d80cd53c9cce6149b31c0a0d7cb68f19b27b793239d27e873fddb8008f726c76 | Shell | 673 | 15 | #!/bin/sh
# ____________________________________________________________________________________
#
# Pyomo: Python Optimization Modeling Objects
# Copyright (c) 2008-2026 National Technology and Engineering Solutions of Sandia, LLC
# Under the terms of Contract DE-NA0003525 with National Technology and Engineering
# So... |
073843a004b8bcf3234bc55d29baae6fe1d69b6fd08189f3315c759a62fa5ff5 | Shell | 675 | 15 | #!/bin/sh
# ____________________________________________________________________________________
#
# Pyomo: Python Optimization Modeling Objects
# Copyright (c) 2008-2026 National Technology and Engineering Solutions of Sandia, LLC
# Under the terms of Contract DE-NA0003525 with National Technology and Engineering
# So... |
fcc27189b3daa1d7c6226aaee3929dfb1a8cb9611bcb0217bb229baf4406e436 | Shell | 675 | 14 | #!/bin/bash
#
# MICAPIPE function that renames multiple acquisitions log files
log_file_str="$1"
labelStr="$2"
randStr="$3"
if [ -f "${log_file_str}".txt ]; then
new_log_str="${log_file_str/-${randStr}/}"
tagMRI=$(grep "${labelStr}" "${log_file_str}".txt | awk -F ':' 'NR==1 {print $2}'| tr -d '[:space:]' | se... |
a52db19a7c80669fe84dfd00dfc32c81a5986c9b6cc30038e739e4f050d81e98 | Shell | 676 | 30 | #!/bin/bash
set -e
# Test for the --daz/--ftz options
export VFC_BACKENDS_LOGGER=False
export VFC_BACKENDS_SILENT_LOAD="TRUE"
parallel --header : "make --silent type={type}" ::: type float double
parallel -j $(nproc) --header : "./compute_error.sh {type} $PWD/test_{type} {backend}" ::: type float double ::: backend... |
baa688bcf8d33e8ca2a71d5caaaab428f0a982d1eda7f564263623387261c256 | Shell | 679 | 15 | #!/bin/sh
# ____________________________________________________________________________________
#
# Pyomo: Python Optimization Modeling Objects
# Copyright (c) 2008-2026 National Technology and Engineering Solutions of Sandia, LLC
# Under the terms of Contract DE-NA0003525 with National Technology and Engineering
# So... |
e7c48cc568eba32ea2beba6ad912c97604606ca957cd41330b6a92b8cce8787c | Shell | 679 | 15 | #!/bin/sh
# ____________________________________________________________________________________
#
# Pyomo: Python Optimization Modeling Objects
# Copyright (c) 2008-2026 National Technology and Engineering Solutions of Sandia, LLC
# Under the terms of Contract DE-NA0003525 with National Technology and Engineering
# So... |
1e402031b7d7af7980a8e0afd0e257af14fa03812d870f749db466626db62910 | Shell | 680 | 15 | #!/bin/sh
# ____________________________________________________________________________________
#
# Pyomo: Python Optimization Modeling Objects
# Copyright (c) 2008-2026 National Technology and Engineering Solutions of Sandia, LLC
# Under the terms of Contract DE-NA0003525 with National Technology and Engineering
# So... |
6ec59e97b27338eb0942f5ea8a300db1c49ed6bf26b86f83e5ad2472aeab5a1b | Shell | 680 | 14 | #!/bin/sh
# ____________________________________________________________________________________
#
# Pyomo: Python Optimization Modeling Objects
# Copyright (c) 2008-2026 National Technology and Engineering Solutions of Sandia, LLC
# Under the terms of Contract DE-NA0003525 with National Technology and Engineering
# So... |
e416132f9d3ad82a7c0ab6d0db0e73809376071f9cf2a046fe0d9437ba3b814c | Shell | 683 | 18 | #!/bin/bash
# This script clones the stylegan_xl repository and makes it accessible using the python path.
git_repo="git@github.com:autonomousvision/stylegan_xl.git"
repo_path="./stylegan_xl"
conda activate objdim
if [ ! -d "$repo_path" ]; then
echo "Cloning repository to ${repo_path}"
git clone $git_repo $re... |
48044bf99dae609aa8f001bfbf367218d6469e21675d46a6475f74480c9f09da | Shell | 684 | 15 | #!/bin/bash
# Generates BIDS structure for input to pyAFQ from mrtrix/freesurfer preprocessed DWI and tractography files
# Example: mrtrix2bids_sep.sh </path2/mrtrix-freesurfer_folder> </path2/pyAFQ_folder>
fun=`dirname $(which mrtrix2bids_sep.sh)`
cp -R ${fun}/temp ${2}
cp ${1}/reg_N4_pre_den_dwi.nii.gz ${2}/deri... |
94db352d56282a375da1d51086f7ddabfff929f6562d50325ba47325c017750f | Shell | 685 | 15 | #!/bin/sh
# ____________________________________________________________________________________
#
# Pyomo: Python Optimization Modeling Objects
# Copyright (c) 2008-2026 National Technology and Engineering Solutions of Sandia, LLC
# Under the terms of Contract DE-NA0003525 with National Technology and Engineering
# So... |
12df5626c594fefa3ce229c955125ecd2b10ba30bb1f3bb719f37c5de213aed4 | Shell | 686 | 12 | # train the prediction model
python -m train --dataset=syn1
python -m train --dataset=syn2
python -m train --dataset=syn4
python -m train --dataset=syn5
# train the explainer
python -m explainer_main --explain-node=300 --dataset=syn1 # change explain-node to 301, 302, etc. (basis graph is of size 300)
python -m expl... |
2661d2baac87ee4bc5f972bfdfe72ef29907b35ed1fe31e816b560db1cb4d256 | Shell | 686 | 38 | #!/bin/bash
set -e
ANALYSIS=$1
MEM=$2
FILES=${*:3}
NAME=`basename $ANALYSIS`
mkdir -p ~/log/$NAME
let numfiles=$#-2
echo $numfiles
echo "#! /bin/bash
files=( ${FILES[@]} )
let index=\$SGE_TASK_ID-1
F=\${files[\$index]}
$ANALYSIS \$F
EXIT_CODE=\$?
if [ \$EXIT_CODE == 0 ]
then
echo -e \"success\t\$F\"
elif [ \$... |
ef285a7abe8eeee2815359edebc4dec80375030d62dfaf3c86c28d1577f9ad09 | Shell | 686 | 18 | #!/bin/sh
# wget http://www.candidagenome.org/download/gff/C_albicans_SC5314/archive/C_albicans_SC5314_version_A21-s02-m09-r08_features_with_chromosome_sequences.gff.gz
zcat C_albicans_SC5314_version_A21-s02-m09-r08_features_with_chromosome_sequences.gff.gz \
| sed "s/Ca21chr1_C_albicans_SC5314/chr1/g" \
| sed "s/C... |
6dd11a79d2d0c5a693086a4113c3b9abae537c4da2d21ae20ae4182fe41ce509 | Shell | 690 | 15 | #!/bin/sh
# ____________________________________________________________________________________
#
# Pyomo: Python Optimization Modeling Objects
# Copyright (c) 2008-2026 National Technology and Engineering Solutions of Sandia, LLC
# Under the terms of Contract DE-NA0003525 with National Technology and Engineering
# So... |
887fc7b79b081b346138730e3a2820780db07ea467180748323db913cd3cb17c | Shell | 690 | 32 | #/bin/bash
source env.sh
BATCH=${1:?}
ENVCHECK=$(printenv | grep BDBC_TEMP_LOG_DIR | wc -w)
if test $ENVCHECK -eq 0; then
echo "specify BDBC_TEMP_LOG_DIR"
exit 1
fi
LOGDIR=$BDBC_TEMP_LOG_DIR
if test -d $LOGDIR; then
:
else
mkdir -p $LOGDIR
fi
LOGFILE="$LOGDIR/package_${BATCH}_$(date +'%Y%m%d-%H%M%S'... |
3e1479791805e2e06db822a1046a1c86ab13b97ec7ceb7fc3227a9a9acc0e09d | Shell | 691 | 20 | #!/bin/bash
FLOW_CELL="/rawdata/Illumina_Runs/141222_SN_0795_0412_AHB79JADXX/Unaligned2"
SUBREAD="/mnt/lustre/home/jdblischak/src/subread-1.4.4-Linux-x86_64/bin"
REF_GENOME="data/genome/combined"
SEQ="data/2014-12-22"
FASTQC="/mnt/lustre/data/tools/FastQC"
# Combine unaligned reads
zcat $FLOW_CELL/Undetermined_indice... |
01fcd2094c0c59212d2c7d9f8b6598c4facb7020f39f42bd58ac3b5cf6f1e4da | Shell | 692 | 30 | #!/bin/bash
#set -euo pipefail
input="$(pwd)/scripts/datasets_links_640.txt"
while getopts f:l: flag
do
case "${flag}" in
f) format=${OPTARG};;
l) location=${OPTARG};;
esac
done
# default values
format=${format:-coco}
location=${location:-$(pwd)/rf100}
echo "Starting downloading RF100..."
for... |
4a0ce0b0c8580fdb1fd3c12d355c1041c51bba41b6210906b6767b34a3beb025 | Shell | 692 | 15 | #!/bin/sh
# ____________________________________________________________________________________
#
# Pyomo: Python Optimization Modeling Objects
# Copyright (c) 2008-2026 National Technology and Engineering Solutions of Sandia, LLC
# Under the terms of Contract DE-NA0003525 with National Technology and Engineering
# So... |
3fd604a65a3b53d45c1f4df2c1408993364f601def8f56d873c0897b5f054a3b | Shell | 695 | 30 | #!/bin/bash
set -e
SEED=5929
export VFC_BACKENDS_SILENT_LOAD="True"
export VFC_BACKENDS_LOGGER="True"
parallel --header : "verificarlo-c test_{type}.c -o test_{type}" ::: type float double
rm -f output.txt
for i in $(seq 0 23); do
export VFC_BACKENDS="libinterflop_cancellation.so --tolerance $i --seed=$SEED --wa... |
1cecd2585243a50cedb602b85ac87521d8b1bf516ad41f5330dd044e79ec7c28 | Shell | 701 | 27 | #!/bin/bash
# Clones the HCP open access dataset
# Note: This script has "datalad" as a dependency, which is not installed as one of the package
# dependencies, but should instead be installed e.g. via miniforge.
cd $(dirname $0)
if [ -f ../../.env ]; then
source ../../.env
fi
if [ -z "$HCP_INPUT_DATASET_PATH" ]... |
932c6512d6bcdbb16a371cad9d36c1851f6e4ec831e6f447eb539eb9340ee900 | Shell | 704 | 22 | # 通过不同的lora ckpt来获得image的coarse grained embedding
python run_get_embeddings_coco.py
# ------------------------------------------------
# 运行单次imagebind推理 (baseline)
python run_infer_coco_lora.py
#得到每个图片对应的层数
python run_get_labels.py
#根据得到的label进行模型训练
python run_get_models_lora.py
# ----------------------------------... |
ea1430158403c19d66717fb0bb9c14f3baef4b5fa5d522199042fb28c610bc38 | Shell | 706 | 16 | #!/bin/sh
# ____________________________________________________________________________________
#
# Pyomo: Python Optimization Modeling Objects
# Copyright (c) 2008-2026 National Technology and Engineering Solutions of Sandia, LLC
# Under the terms of Contract DE-NA0003525 with National Technology and Engineering
# So... |
275ea234105ade653b6dd056f56736e96858ed194e3a80e2e293073a1f470105 | Shell | 708 | 33 | #!/bin/bash
# Inputs:
# 1 - full path to subject list file
# 2 - output directory
# Check inputs
if [[ ! -f "${1}" ]]; then
echo "Subject list file not specified or does not exist."
exit 1
fi
if [[ ! -d "${2}" ]]; then
echo "Output directory not specified. Saving to current directory"
out_dir=./
el... |
5e8cfd3b3beca87504ea524eebd34053f28b681133b59b5d860569de59a09e1a | Shell | 708 | 30 | #!/bin/bash
set -e
experiments=(FLOAT FLOAT_POW2 DOUBLE DOUBLE_POW2)
precisions=("--precision-binary32=24" "--precision-binary64=53")
parallel --header : "make --silent exp={exp}" ::: exp ${experiments[@]}
backends=libinterflop_mca.so
parallel -j $(nproc) --header : "./compute_error.sh ${backends} {exp} {prec} ${PWD... |
0d4e792bbf819cd98d249663348c6fd7415b91d503004d31e35637dd95cb4358 | Shell | 709 | 14 | #!/bin/tcsh -efx
mkdir -p out
encodePatchTdb in/add1.ra trackDb.ra -test=out/add1.ra
diff expected/add1.ra out/add1.ra
encodePatchTdb in/add3.ra trackDb.ra -test=out/add3.ra
diff expected/add3.ra out/add3.ra
encodePatchTdb mode=replace in/replace1.ra trackDb.ra -test=out/replace1.ra
diff expected/replace1.ra out/replac... |
3f56d29191abeea21dc209733c7137c3d40ecd41f6906960f9237e4e8a65f7f9 | Shell | 710 | 33 | #!/bin/bash
# Function to run the commands in parallel batches of 5
run_batch() {
local batch=()
for cmd in "$@"; do
batch+=("$cmd")
if [ ${#batch[@]} -eq 6 ]; then
for b in "${batch[@]}"; do
eval "$b" &
done
wait
batch=()
... |
99495c0b3b963c6537d9572b56f18f8c20b7758d0f04e5cd0270169386893d86 | Shell | 711 | 25 | export num_gpus=8
export CUBLAS_WORKSPACE_CONFIG=":16:8" # https://docs.nvidia.com/cuda/cublas/index.html#cublasApi_reproducibility
export PYTHONHASHSEED=0
export output_dir="./qqp"
python -m torch.distributed.launch --nproc_per_node=$num_gpus \
examples/text-classification/run_glue.py \
--model_name_or_path roberta-la... |
366238948c974977b30fcc8773ff72f6f90ad58ae5797bbd57b9bce1d661fcb9 | Shell | 713 | 16 | #!/bin/sh
# ____________________________________________________________________________________
#
# Pyomo: Python Optimization Modeling Objects
# Copyright (c) 2008-2026 National Technology and Engineering Solutions of Sandia, LLC
# Under the terms of Contract DE-NA0003525 with National Technology and Engineering
# So... |
372f5d90a35afc5f69d4a99b215e7b87670bbd7e0e2fbd2535dfd5093cf2c235 | Shell | 713 | 25 | export num_gpus=8
export CUBLAS_WORKSPACE_CONFIG=":16:8" # https://docs.nvidia.com/cuda/cublas/index.html#cublasApi_reproducibility
export PYTHONHASHSEED=0
export output_dir="./cola"
python -m torch.distributed.launch --nproc_per_node=$num_gpus \
examples/text-classification/run_glue.py \
--model_name_or_path roberta-l... |
78042caa6a624a54e9496179d9b12b7c2f4bf28a4552afb748edbe955c317279 | Shell | 713 | 25 | export num_gpus=8
export CUBLAS_WORKSPACE_CONFIG=":16:8" # https://docs.nvidia.com/cuda/cublas/index.html#cublasApi_reproducibility
export PYTHONHASHSEED=0
export output_dir="./sst2"
python -m torch.distributed.launch --nproc_per_node=$num_gpus \
examples/text-classification/run_glue.py \
--model_name_or_path roberta-l... |
9f3eb048dd9cee8ed4ec8f8d68e63e7f0e9bb151e1d8885ca076c79c56c26326 | Shell | 713 | 25 | export num_gpus=8
export CUBLAS_WORKSPACE_CONFIG=":16:8" # https://docs.nvidia.com/cuda/cublas/index.html#cublasApi_reproducibility
export PYTHONHASHSEED=0
export output_dir="./mnli"
python -m torch.distributed.launch --nproc_per_node=$num_gpus \
examples/text-classification/run_glue.py \
--model_name_or_path roberta-l... |
afdff05c02931d44da6e21396337f753ba741c2514baa8573359c3284006e724 | Shell | 713 | 25 | export num_gpus=8
export CUBLAS_WORKSPACE_CONFIG=":16:8" # https://docs.nvidia.com/cuda/cublas/index.html#cublasApi_reproducibility
export PYTHONHASHSEED=0
export output_dir="./qnli"
python -m torch.distributed.launch --nproc_per_node=$num_gpus \
examples/text-classification/run_glue.py \
--model_name_or_path roberta-l... |
d3d92e5c4a5132226c9f269de296d247094b3bdcd5b40cbfe6595014e6971ca2 | Shell | 713 | 17 | #!/bin/sh
# Run at FMNH server
conda activate varKoder
export CUDA_VISIBLE_DEVICES=2
#VARKODER_PATH=/n/home08/souzademedeiros/programs/varKoder/varKoder.py
VARKODER_PATH=/home/bdemedeiros/varKoder_test/varKoder/varKoder.py
#time python $VARKODER_PATH train --overwrite -b 300 -r 0.1 --single-label -e 30 -z 0 varkode... |
943df32a246a22cf13dbb345cf5f5ab7e228422e98bd951fff1c7315d823c543 | Shell | 714 | 33 | #!/bin/bash
# Function to run the commands in parallel batches of 5
run_batch() {
local batch=()
for cmd in "$@"; do
batch+=("$cmd")
if [ ${#batch[@]} -eq 6 ]; then
for b in "${batch[@]}"; do
eval "$b" &
done
wait
batch=()
... |
e25d4752601866c08992dd2ba757325a927880c859971d2c55c5322c3cce6e0c | Shell | 714 | 17 | #!/bin/bash
SIF_VERSION="${AIND_DATA_TRANSFER_VERSION//./_}"
echo "AIND_DATA_TRANSFER_VERSION=${AIND_DATA_TRANSFER_VERSION}"
echo "SIF_VERSION=${SIF_VERSION}"
if [[ -z "${SIF_VERSION}" ]]; then
echo "Using latest version"
singularity build build/aind_data_transfer_latest.sif aind_data_transfer.def
chmod 775 bui... |
0a0c5755156d43d07dcc27bdd84cbff2df1d14088eacff7b8f2b453a1fd2497b | Shell | 715 | 15 | #!/bin/sh
# ____________________________________________________________________________________
#
# Pyomo: Python Optimization Modeling Objects
# Copyright (c) 2008-2026 National Technology and Engineering Solutions of Sandia, LLC
# Under the terms of Contract DE-NA0003525 with National Technology and Engineering
# So... |
dd01e9ef452d7b7b21796ba208d4422f20516fbf114682bf313712cbdfa88dbc | Shell | 715 | 25 | #!/usr/bin/env bash
# This script is used to build and deploy the GCR docker image for Picard
# The dockerhub image is built using a dockerhub automated build: https://hub.docker.com/r/broadinstitute/picard/builds
if [[ "$1" == "" ]]
then
echo "Usage: build_push_docker.sh <git-tag>"
exit 1
fi
declare -r TAG=... |
e4ac4bcfbbdcf3b60636bbc845f9a2b51dba675696ea9168236fbcfac45e43a4 | Shell | 718 | 19 | #!/usr/bin/env bash
set -e
FOLDER=$1
IMAGE=$2
tmpdir=`mktemp -d`
## if you have root permission you can uncomment the following:
# (cd ${FOLDER} && sudo singularity build ${tmpdir}/$(basename ${IMAGE}) Singularity)
# mv ${tmpdir}/$(basename ${IMAGE}) ${IMAGE}
# sudo chown ${USER}: ${IMAGE}
## if you DO NOT have ro... |
4e1defddf9f3663bf0fc2840630a8c181eacdf7e997d729aa503f51603caddb4 | Shell | 719 | 16 | #!/bin/sh
# ____________________________________________________________________________________
#
# Pyomo: Python Optimization Modeling Objects
# Copyright (c) 2008-2026 National Technology and Engineering Solutions of Sandia, LLC
# Under the terms of Contract DE-NA0003525 with National Technology and Engineering
# So... |
750906072855c5371063631570bcafed07ee4627390025a72bdf500be7edb2f2 | Shell | 719 | 24 | #!/bin/bash
#
# Quick function to QC func masks
#
# Inputs:
# $1 : subject ID (01..30)
# $2 : Session number (1 or 2)
#
#
# 2023 Mark C Nelson, McConnell Brain Imaging Centre, MNI, McGill
#-------------------------------------------------------------------------------
# Settings & inputs
rootdir=/data_/tardiflab/... |
d26e58a2894cb66eafc3cbd2cce807e428a58f2e028a0cc346d44f73bf1f25f0 | Shell | 720 | 26 | #!/bin/bash
set -eu
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# DATA PATHS
# - DATA: Folder containing input data
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
DATA="3D-microglia-netoglitazone/data"
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# SAMPLES
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
samples=("340258_2LD_5" "84... |
15b4051a350a0b80964a34466ec7d46b84e305d4de4928caaa4be73be00baeb2 | Shell | 721 | 16 | #!/bin/sh
# ____________________________________________________________________________________
#
# Pyomo: Python Optimization Modeling Objects
# Copyright (c) 2008-2026 National Technology and Engineering Solutions of Sandia, LLC
# Under the terms of Contract DE-NA0003525 with National Technology and Engineering
# So... |
39add216120bdb651241e177205d19dafd2df9e82cb4b5296d42bc0e5c81bfb1 | Shell | 721 | 18 | #!/usr/bin/env bash
set -euo pipefail
cd "$SRC_DIR"
source scripts/linux-target.sh
conda list
./scripts/build-native-unix.sh -j "${CMAKE_BUILD_PARALLEL_LEVEL:-${CPU_COUNT:-2}}"
./scripts/publish-unix.sh
PUBLISH_DIR="$SRC_DIR/Release/$WARP_RUNTIME_ID/publish"
mkdir -p "$PREFIX/bin" "$PREFIX/lib"
# Executables, debug... |
aa4dcb3a27882dd3fccb62130000ce83e0b190c545ad07a7efef5aad3bc3084e | Shell | 721 | 22 | # 通过不同的lora ckpt来获得image的coarse grained embedding
python run_get_embeddings_harsmart.py # without head
# ------------------------------------------------
# 运行单次imagebind推理 (baseline)
python run_infer_harsmart_lora.py
#得到每个图片对应的层数
python run_get_labels_harsmart.py
python e2e_clotho_val_ground_truth.py
# # ---------... |
b04b14c2729d00bd9f409a665e7930620c8110f838fa69255f4d53afe8446405 | Shell | 721 | 16 | #!/bin/sh
# ____________________________________________________________________________________
#
# Pyomo: Python Optimization Modeling Objects
# Copyright (c) 2008-2026 National Technology and Engineering Solutions of Sandia, LLC
# Under the terms of Contract DE-NA0003525 with National Technology and Engineering
# So... |
31071fff188df3aaab32ac5dbeba7d1528adcff0cffe4c0f7d5e380bea826d55 | Shell | 723 | 33 | #!/bin/bash
# Function to run the commands in parallel batches of 5
run_batch() {
local batch=()
for cmd in "$@"; do
batch+=("$cmd")
if [ ${#batch[@]} -eq 6 ]; then
for b in "${batch[@]}"; do
eval "$b" &
done
wait
batch=()
... |
6b441b325847478715b74007810f0201d2cad2faf378fcc6a79a9fe64030c75f | Shell | 723 | 26 | CUDA_VISIBLE_DEVICES=0
NPROC=1
ANATOMY=brain
NATIVE_SNR=32dB
ROOT=/path/to/root/
MODEL_PATH=network-snapshot.pkl
MEAS_PATH=/path/to/meas/$NATIVE_SNR
STEPS=500
SAMPLE_START=0
SAMPLE_END=100
DATA=noisy32dB
INFERENCE_SNR=32dB
R=4
SEED=15
KSP_PATH=/path/to/ksp/$INFERENCE_SNR
torchrun --standalone --nproc_per_node=$NPROC ... |
97f76e49bf720fe36b399b27c286d4b55fbdb83af8781e4111081d104cc7e2b5 | Shell | 723 | 28 | #!/usr/bin/env bash
echo "Trim script called"
while getopts ':i:o:r:n:f:l:j:' flag; do
case "${flag}" in
i) Fastqs_Joined="${OPTARG}" ;;
o) Trim_Output_File="${OPTARG}" ;;
r) Read_Count="${OPTARG}" ;;
n) nThreads="${OPTARG}" ;;
l) Trim_Log="${OPTARG}" ;;
f) Trim_Fla... |
dac3ef332af4f50805fb55b4b98271e2581f6629cd9215504ea3ca56e510436e | Shell | 725 | 29 | #!/bin/bash
set -e
# Create an indexed genome for mapping sequences derived from human
# mRNA and ERCC spike-in controls.
# + Download sequences (fasta format) for Human (hg19) and ERCC spike-in
# + Build index for mapping with Subread
# First argument is output directory
OUT_DIR=$1
mkdir -p $OUT_DIR
cd $OUT_DIR
e... |
b76e49721ae32c58172d4559d3d7aff288e37c7b16b94c62b394cec913fddd1e | Shell | 726 | 26 | #!/bin/bash
set -eu
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# DATA PATHS
# - DATA: Folder containing input data
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
DATA="3D-microglia-netoglitazone/data"
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# SAMPLES
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
samples=("340258_2LD_5" "84... |
6db101937b1a46f06670ad40b777b73ca82f6a10f272556ef36a204fe61b6b7d | Shell | 728 | 16 | #!/bin/sh
# ____________________________________________________________________________________
#
# Pyomo: Python Optimization Modeling Objects
# Copyright (c) 2008-2026 National Technology and Engineering Solutions of Sandia, LLC
# Under the terms of Contract DE-NA0003525 with National Technology and Engineering
# So... |
4fe99d4ee240dff1d7da03792b3a1b24de29b4e14aa4d1ca63c8f6661070b060 | Shell | 729 | 19 | #!/bin/bash
picard=/nfs/software/helmod/apps/Core/picard-tools/2.4.1-gcb01/picard.jar
index_dir=/data/anderslab/MelBrM/Annotation/Human_GENCODE_STAR2.7.2b/STARINDEX/
refFlat=${index_dir}/gencode.v31.primary_assembly.annotation.refFlat
intervalList=${index_dir}/gencode.v31.primary_assembly.annotation.rRNA.intervalList
... |
247ef6d58a893251d31f309f34b3f5083ca9e9558fac4d684fe3763a2c77b4be | Shell | 731 | 33 | set -eu
# List of available graph convolution methods.
methods=(nfp ggnn schnet weavenet rsgcn relgcn relgat megnet)
prefix=eval_
# device identifier; set it to -1 to train on the CPU (default).
device=${1:--1}
# Number of training epochs (default: 1).
epoch=${2:-1}
label=${3:-all}
echo evaluating label ${label}
f... |
523064d7934a5e53d6ced33e338c3991944205671716a8ae21e00a7a67ee67b2 | Shell | 731 | 15 | #!/bin/sh
# ____________________________________________________________________________________
#
# Pyomo: Python Optimization Modeling Objects
# Copyright (c) 2008-2026 National Technology and Engineering Solutions of Sandia, LLC
# Under the terms of Contract DE-NA0003525 with National Technology and Engineering
# So... |
01b9ca75a3e4a219a0dbf8df0ef49aae7b6a9ce96c18d7a101bfb9bf6907906b | Shell | 733 | 28 | #!/bin/sh
# Run at FMNH server
set +e
source /home/bdemedeiros/software/miniconda3/etc/profile.d/conda.sh
conda activate base
#create folder with query images (i. e. those chosen as validation)
mkdir -p query_cgrs
cat validation_set.txt | tr ',' '\n' | xargs -L 100 -I {} bash -c '
chunk_index=$(printf "%03d" $((... |
890e3d974bccce40fea65ee07fe29916a4d91134e2961235beea6c9450a40628 | Shell | 734 | 17 | #!/bin/sh
# ____________________________________________________________________________________
#
# Pyomo: Python Optimization Modeling Objects
# Copyright (c) 2008-2026 National Technology and Engineering Solutions of Sandia, LLC
# Under the terms of Contract DE-NA0003525 with National Technology and Engineering
# So... |
048ec7e76f37d4efd8731ef6569fad76f4a6acbe4270ff22b6ef3fbdbb20a447 | Shell | 735 | 23 | #!/usr/bin/env bash
# Run GPU-marked tests on an Engaging GPU node via srun.
# Usage: bash tests/run_gpu.sh [extra pytest args]
#
# Defaults follow the lab convention (see ~/.cursor/skills/engaging-cluster/SKILL.md):
# request multiple partitions at once, modest memory for a sanity job.
# Override with env vars, e.g.
#... |
44b9afedce87bad335a3bf1e01f7114b4d98bb856e983fe1ea6611d1f0abb96a | Shell | 736 | 26 | export num_gpus=8
export CUBLAS_WORKSPACE_CONFIG=":16:8" # https://docs.nvidia.com/cuda/cublas/index.html#cublasApi_reproducibility
export PYTHONHASHSEED=0
export output_dir="./qqp"
python -m torch.distributed.launch --nproc_per_node=$num_gpus \
examples/text-classification/run_glue.py \
--model_name_or_path roberta-ba... |
0891221fbaf9e991b48035f2f2c523ce3b85f4a58e0accbba00e33b4f7f756b2 | Shell | 738 | 26 | export num_gpus=8
export CUBLAS_WORKSPACE_CONFIG=":16:8" # https://docs.nvidia.com/cuda/cublas/index.html#cublasApi_reproducibility
export PYTHONHASHSEED=0
export output_dir="./mnli"
python -m torch.distributed.launch --nproc_per_node=$num_gpus \
examples/text-classification/run_glue.py \
--model_name_or_path roberta-b... |
4e19559c957eb12f9938f02b3faf9d9d4419f1eefac57aa4b60c7d1639797a42 | Shell | 738 | 26 | export num_gpus=8
export CUBLAS_WORKSPACE_CONFIG=":16:8" # https://docs.nvidia.com/cuda/cublas/index.html#cublasApi_reproducibility
export PYTHONHASHSEED=0
export output_dir="./sst2"
python -m torch.distributed.launch --nproc_per_node=$num_gpus \
examples/text-classification/run_glue.py \
--model_name_or_path roberta-b... |
8b68dc425a012d890775dd8d8e6e7621a89f15f53a74e92baa1a65819a590a60 | Shell | 738 | 26 | export num_gpus=8
export CUBLAS_WORKSPACE_CONFIG=":16:8" # https://docs.nvidia.com/cuda/cublas/index.html#cublasApi_reproducibility
export PYTHONHASHSEED=0
export output_dir="./qnli"
python -m torch.distributed.launch --nproc_per_node=$num_gpus \
examples/text-classification/run_glue.py \
--model_name_or_path roberta-b... |
9c08e2316fb68c886f862c3daaaf508770424dd964d105d1157be513e9c20c37 | Shell | 738 | 26 | export num_gpus=2
export CUBLAS_WORKSPACE_CONFIG=":16:8" # https://docs.nvidia.com/cuda/cublas/index.html#cublasApi_reproducibility
export PYTHONHASHSEED=0
export output_dir="./cola"
python -m torch.distributed.launch --nproc_per_node=$num_gpus \
examples/text-classification/run_glue.py \
--model_name_or_path roberta-b... |
5a33b12239c62eff03ed3827a1f971fe78ff4095c2c937b012940d35fff1063d | Shell | 740 | 7 | #!/bin/bash -l
source inputs.sh && \
export LOG_LOC=${SIM_FOLDER}/synth_axons_$(date "+%Y%m%d_%Hh%Mm%Ss").out; \
source /gpfs/bbp.cscs.ch/project/proj135/home/petkantc/axon/axonal-projection/axon_projection/new_venv135/bin/activate && \
export FILTERED_COLLECTION_PATH=$(python /gpfs/bbp.cscs.ch/project/proj135/home/pet... |
e473caea99fa1e0913930446e0a4940436fcf3c5dddb27edb83dcf1ace7284cc | Shell | 740 | 24 | # Note: An intermediate model must first be trained, used to make predictions, and assignments must be labeled to utilize this model
CUDA_VISIBLE_DEVICES=1,2,3 python src/ms_pred/scarf_pred/inten_hyperopt.py \
--seed 5 \
--num-workers 10 \
--max-epochs 200 \
--dataset-name nist20 \
--dataset-labels labels.tsv \
--lo... |
d6c4f91610d74a436d28b61a2006b296742ef5e15b932315f79432dc5ce4ce16 | Shell | 744 | 21 | #!/bin/sh -e
#file=zzz.1660.txt.gz
file=$1
cat $file | ./filterAllZero.pl > circuits.non_zero.raw.txt
cut -f 1,2 circuits.non_zero.raw.txt | tr -d "-" | tr -s "_" > ids.txt
cut -f 3- circuits.non_zero.raw.txt > nums.txt
wc -l nums.txt ids.txt circuits.non_zero.raw.txt
# Create file
cat $file | head -n 1 | tr -d "-... |
2fdb490e35bfe515f19a9e7cd947033a820980b0dc0ed1c3ba75fb5c39b7c187 | Shell | 745 | 25 | CUDA_VISIBLE_DEVICES=0
NPROC=1
ANATOMY=brain
NATIVE_SNR=32dB
ROOT=/path/to/root/
MODEL_PATH=ckpt_9.pt
MEAS_PATH=/path/to/data/brain/val/$NATIVE_SNR
SAMPLE_START=0
SAMPLE_END=100
METHOD=modl
DATA=noisy32dB
INFERENCE_SNR=32dB
R=4
KSP_PATH=/path/to/data/brain/val/$INFERENCE_SNR
torchrun --standalone --nproc_... |
bce3210922c6b53ed5de09c45b79b47b5763274e91c4bd3d39338d1c37ed1d94 | Shell | 745 | 35 | #!/bin/sh -e
echo "Processing GFF file"
gunzip -c Gmax_109_gene.gff3.gz > genes.gff
# | sed "s/.five_prime_UTR.1//" \
# | sed "s/.three_prime_UTR.1//" \
# > genes.gff
echo "Adding FASTA sequence"
( echo "###" ; echo "##FASTA" ; gunzip -c Gmax_109.fa.gz ) >> genes.gff
ehco "Create CDS file"
gunzip -c Gmax_109_cds.fa.... |
a173666daca88fbe54756ad83ac237f063376524c1a15fac30e1739174429c30 | Shell | 746 | 39 | #!/bin/bash
#set -e
check_status() {
if [[ $? != 0 ]]; then
echo "Error"
exit 1
fi
}
export VFC_BACKENDS_SILENT_LOAD=True
export VFC_BACKENDS_LOGGER=False
status=0
parallel --header : "verificarlo-c -O0 -DREAL={type} test.c -o test_{type}" ::: type float double
check_status
parallel -k -j $(nproc) --hea... |
06124656fcecb94a801d2a746507c01dbcbf2acdf9be9b95260731a5bf10b26d | Shell | 747 | 27 | #!/bin/bash
# Parameters
expe_name="technical_validation"
main_script=/srv/tempdd/egermani/hcp_pipelines/results/run_technical_validation.py
echo "Create dir for log"
CURRENTDATE=`date +"%Y-%m-%d"`
echo "currentDate :"
echo $CURRENTDATE
PATHLOG="/srv/tempdd/egermani/Logs/${CURRENTDATE}_OARID_${OAR_JOB_ID}/"
echo "pa... |
67397661b9d1fb9c5e6e084374b99627427d1796b93c2f6fd4e37f8e8a152570 | Shell | 755 | 26 | export num_gpus=8
export CUBLAS_WORKSPACE_CONFIG=":16:8" # https://docs.nvidia.com/cuda/cublas/index.html#cublasApi_reproducibility
export PYTHONHASHSEED=0
export output_dir="./rte"
python -m torch.distributed.launch --nproc_per_node=$num_gpus \
examples/text-classification/run_glue.py \
--model_name_or_path roberta-la... |
e0127d65b49e96569b13d794ca1e9610984939fdece056edc3a806463c4e21e3 | Shell | 755 | 28 | #!/bin/bash
ENV_NAME="simopt"
YML_FILE="environment.yml"
echo "Checking for Conda installation..."
if ! command -v conda &> /dev/null; then
echo "Conda not found! Please install Miniconda or Anaconda first."
exit 1
fi
# Ensure Conda is initialized
source "$(conda info --base)/etc/profile.d/conda.sh"
# Check... |
4fba5cf8cf82380468f8d43e19e53770ff0aedafe0df54d463bb0e9a3bdcc588 | Shell | 756 | 28 | #!/bin/bash
cd "$(dirname "$0")"
cross="cross1"
cp config.yaml run_cross.yaml
task_name=`cat run_cross.yaml | head -n 1 | cut -d' ' -f2`
new_task_name="${task_name}_${cross}"
sed -i "s|^task_name: .*$|task_name: $new_task_name|" run_cross.yaml
sed -i "s|^split_mode: .*$|split_mode: $cross|" run_cross.yaml
export CU... |
022f10d868131f9baedd62053405ee7bbfc726d29802aca9c87b6db9d6e30313 | Shell | 757 | 36 | #!/bin/bash
#睡眠1小时
# sleep 1h
# Function to run the commands in parallel batches of 5
run_batch() {
local batch=()
for cmd in "$@"; do
batch+=("$cmd")
if [ ${#batch[@]} -eq 6 ]; then
for b in "${batch[@]}"; do
eval "$b" &
done
wait
... |
22776b4aa5acf0cb4e05977624b83de904759499a9676e0c4d198c1a0cbd5d54 | Shell | 757 | 26 | export num_gpus=8
export CUBLAS_WORKSPACE_CONFIG=":16:8" # https://docs.nvidia.com/cuda/cublas/index.html#cublasApi_reproducibility
export PYTHONHASHSEED=0
export output_dir="./mrpc"
python -m torch.distributed.launch --nproc_per_node=$num_gpus \
examples/text-classification/run_glue.py \
--model_name_or_path roberta-l... |
a0a4a01e283d91280d2e86caef5153ed35443296a1ada07abe626aebb5235cec | Shell | 757 | 29 | #/bin/bash
#
# Preps hand label files by adding leading line and moving to melodic dirs
#
# $1: subject dir
#
# 2023 Mark C Nelson, McConnell Brain Imaging Centre, MNI, McGill
#------------------------------------------------------------------------------------------------------------------------------------
# Setup
... |
e8f19902a3f0e9e90d9d08a480d4ded697b46fc5c521dda347648c9aafe244ed | Shell | 757 | 26 | export num_gpus=8
export CUBLAS_WORKSPACE_CONFIG=":16:8" # https://docs.nvidia.com/cuda/cublas/index.html#cublasApi_reproducibility
export PYTHONHASHSEED=0
export output_dir="./stsb"
python -m torch.distributed.launch --nproc_per_node=$num_gpus \
examples/text-classification/run_glue.py \
--model_name_or_path roberta-l... |
3f51f091137054b9e5ff807b8a95971faa1add49670348e9b0cb79db7668f752 | Shell | 758 | 19 | #!/bin/sh
# Run at FMNH server
set +e
source /home/bdemedeiros/software/miniconda3/etc/profile.d/conda.sh
conda activate varKoder
export CUDA_VISIBLE_DEVICES=0,1
#varKoder convert --overwrite -n 24 cgr varkoder_images_SRA vkfCGR_images_SRA
#varKoder convert --overwrite -n 24 cgr varkoder_query_images vkfCGR_query_ima... |
966c9a6bb91ec65cac4760564766f16f0c75b81fee4a03078de69636c1920fd4 | Shell | 758 | 20 | # Copyright 2020 The HuggingFace Team. All rights reserved.
#
# 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 applicabl... |
c2c2e250a650cd9a4b16e325867c5ae38ef3e82b42bd35438855b2a8282dcda0 | Shell | 758 | 16 | #!/bin/bash
#SBATCH --cpus-per-task=32
#SBATCH --time=24:00:00
module load bowtie2
module load samtools
module load bedtools
module load dimelo
awk -F"\t" '$11!="nan"&& $11>0' RRMS_FOXA2_2day_IgG_5mc.bed > RRMS_FOXA2_2day_IgG_5mc_remove_nan_zero.bed
awk -v OFS='\t' '{print $1,$2,$3,$11}' RRMS_FOXA2_2day_IgG_5mc_rem... |
9ba8917db593d2d956857048178ae68da864b6307e6cd22bf4fa8e78feb79a41 | Shell | 760 | 36 | #!/bin/bash
#睡眠1小时
# sleep 1h
# Function to run the commands in parallel batches of 5
run_batch() {
local batch=()
for cmd in "$@"; do
batch+=("$cmd")
if [ ${#batch[@]} -eq 6 ]; then
for b in "${batch[@]}"; do
eval "$b" &
done
wait
... |
f56acc54ad20cb8543121cdba6d2e33e0663f211c916fc28313185484044498d | Shell | 761 | 27 | #!/bin/bash
#: Title : test_logan
#: Date : 2019-03-25
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../logan_new
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"... |
a7ce4579ced468c5566829af20e1bbcbc679e5d49d115f670769fc75774edcb1 | Shell | 762 | 40 | #!/bin/bash
#SBATCH --account INSERT
#SBATCH --partition=INSERT
#SBATCH --job-name=xrai
#SBATCH --nodes=1
#SBATCH --gpus=INSERT
#SBATCH --mem=128G
#SBATCH -t 24:00:00
#SBATCH -n 32
#SBATCH --output=logs/%j.log
POSITIONAL=()
while [[ $# -gt 0 ]]; do
key="$1"
case $key in
-c|--config)
RELATVECONFIGPATH="$... |
c5230eb030f2f5ea56fc6e28713aa165192a4b98617fc91920d00a454ab7cfa7 | Shell | 762 | 36 | #!/bin/bash -eu
set -o pipefail
# SnpEff wrapper script
# Extracts -Xm* and -D* JVM args from the argument list.
jardir="$HOME/snpEff"
java=java
if [ -n "${JAVA_HOME:-}" ] && [ -e "$JAVA_HOME/bin/java" ]; then
java="$JAVA_HOME/bin/java"
fi
default_jvm_mem_opts="-Xms1g -Xmx8g"
jvm_mem_opts=""
jvm_prop_opts=""
pass_... |
306b4cf738bf6bdb980ede4c8dc6308122a576fbd317dac7e13f137c73fcfc3e | Shell | 763 | 29 | #!/bin/sh
# Delete old databases
rm -vf *.bin
# Create genes file
gunzip -c ../hg19/genes.refseq.gz \
| grep -w \
-e binNum \
-e NM_001269 -e NM_001048194 -e NM_001048195 -e NM_001048199 \
-e NM_001242466 -e NM_006218 -e NM_181504 -e NM_181523 -e NM_181524 \
-e NM_001048194 -e NM_001048195 -e NM_00104819... |
35388a31766e562e2492f993d8de8755a4967636d2ae230718d828a9ac84bd23 | Shell | 763 | 27 | #!/bin/bash
#: Title : test_patlak
#: Date : 2019-03-25
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../patlak_new
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\... |
9eeda7eaf64257bbf638ba38da79419c09a937053a0be91f5529696ddd7e31ee | Shell | 764 | 20 | #!/usr/bin/env bash
export PYTHONPATH="../":"${PYTHONPATH}"
export WANDB_PROJECT=dmar
# export MAX_LEN=128
python distillation.py \
--learning_rate=3e-4 \
--do_train \
--fp16 \
--val_check_interval 0.25 \
--teacher Helsinki-NLP/opus-mt-en-ro \
--max_source_length $MAX_LEN --max_target_length $MAX_LEN --val_... |
c664fedcf1e3f41dcaba1de922c4396cdf9e666183d7af1d1976472b0c6ab2ab | Shell | 764 | 36 | #!/bin/bash -eu
set -o pipefail
# SnpSift wrapper script
# Extracts -Xm* and -D* JVM args from the argument list.
jardir="$HOME/snpEff"
java=java
if [ -n "${JAVA_HOME:-}" ] && [ -e "$JAVA_HOME/bin/java" ]; then
java="$JAVA_HOME/bin/java"
fi
default_jvm_mem_opts="-Xms1g -Xmx4g"
jvm_mem_opts=""
jvm_prop_opts=""
pass... |
8232d2f17516c731e5bac901b8c41d10580a29bba45494491aefc3042725c04c | Shell | 766 | 29 | #!/usr/bin/env bash
set -e
INFO=$1
DST=$2
tmpdir=`mktemp -d`
wget https://salilab.org/modbase-download/projects/genomes/H_sapiens/2013/ModBase_H_sapiens_2013_GRCh37.70.pep.all.tar.xz -P ${tmpdir}
tar -C ${tmpdir} -xf ${tmpdir}/ModBase_H_sapiens_2013_GRCh37.70.pep.all.tar.xz ModBase_H_sapiens_2013_GRCh37.70.pep.all/m... |
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