sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
cdfc1e9dc245aa7c037b227d085cc13bed304ae113ae407b9ef09bd08c559657 | Shell | 540 | 18 | #!/bin/sh
#SBATCH -p sapphire
#SBATCH -t 0-71:00
#SBATCH --mem 60G
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=20
#SBATCH -o /n/holyscratch01/davis_lab/pflynn/soil/Ma_images_varKode.%A.out
#SBATCH -e /n/holyscratch01/davis_lab/pflynn/soil/Ma_images_varKode.%A.err # File to which standard err will ... |
a98663480fe46414ccebd11bf02a2ce04a6332250dd58c480ca15e12b5eebaf2 | Shell | 541 | 17 | #!/bin/sh
# Run at FMNH server
conda deactivate
conda activate varKoder
#now do query
VARKODER_PATH=/home/bdemedeiros/varKoder_test/varKoder/varKoder.py
#create folder with query images
time python $VARKODER_PATH image -k 7 -m 500K -M 10M -n 20 -c 2 -i varkoder_int_SRA/ -o varkoder_images_SRA_notincluded/ -f image_s... |
87f7c7f7f36a94e56bba4f9ff39a8812bf39e4374dd377615d0831f91ca0aa08 | Shell | 542 | 10 | arch=$(uname -m)
project=$1
# install miniforge to install pre-built gsl (faster than building it)
# (TODO: miniforge can also be used to install cuda toolkit for platforms
# for which cuda manylinux is not available)
curl -L -O "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-$arch.s... |
b1e8c637dab8f5a4bd4f7b9cc5ec19c7e82a7a8a8ac48d7eb4481cf7cccfc65a | Shell | 543 | 25 | #!/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=$(pwd -P)
logfile=$currdi... |
aed5d37b7ae55021a971b44e9acf9c0d9e255db8902e928bd09390cdd8415257 | Shell | 544 | 31 | #!/bin/bash
set -e
SCRIPT=`realpath $0`
SCRIPTPATH=`dirname $SCRIPT`
PYPROF="$SCRIPTPATH/../.."
parse="python $PYPROF/parse/parse.py"
prof="python $PYPROF/prof/prof.py"
for f in *.py
do
base=`basename $f .py`
sql=$base.sql
dict=$base.dict
#NVprof
echo "nvprof -fo --profile-from-start off $sql python $f"
nvpr... |
a050f93825b777665a535476a2ef4848d32ff3e40f0d6aebab25f64622f6fa86 | Shell | 545 | 20 | CUDA_VISIBLE_DEVICES=0,1,3 python src/ms_pred/scarf_pred/gen_hyperopt.py \
--seed 5 \
--num-workers 10 \
--max-epochs 200 \
--dataset-name nist20 \
--dataset-labels labels.tsv \
--loss-fn bce \
--formula-folder magma_subform_50 \
--split-name hyperopt.tsv \
--gpu \
--save-dir results/scarf_hyperopt_v3 \
--cpus-p... |
c04f6b1599aa4aacf5d9b71e06876e84854f478a308c508ccc99688a49a2250b | Shell | 546 | 23 | #!/bin/bash
# Parameters
expe_name="pipeline_transition"
main_script=/srv/tempdd/egermani/hcp_pipelines/src/singularity_launcher_groups.sh
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 "path... |
37aebf2dcecb69697748f92240052bde61cffd4c6e63366ee0d4acbad751150b | Shell | 547 | 23 | #!/usr/bin/env bash
set -x
PARTITION=$1
JOB_NAME=$2
CONFIG=$3
GPUS=${GPUS:-8}
GPUS_PER_NODE=${GPUS_PER_NODE:-8}
CPUS_PER_TASK=${CPUS_PER_TASK:-5}
PY_ARGS=${@:4}
SRUN_ARGS=${SRUN_ARGS:-""}
PYTHONPATH="$(dirname $0)/..":$PYTHONPATH \
srun -p ${PARTITION} \
--job-name=${JOB_NAME} \
--gres=gpu:${GPUS_PER_NODE} \... |
94e1446f9312926edfa0741742692c3c43b3198c7a780f4ef037232dc9b53b05 | Shell | 548 | 19 | #!/bin/bash
#
#
# copies rsfMRI time series into a target directory
#
# Inputs:
# $1 : source directory
# $2 : target directory
#
#
# 2025 Mark C Nelson, McConnell Brain Imaging Centre, MNI, McGill
#-------------------------------------------------------------------------------------------------------------------------... |
4d1f65cc2c6f5439a72b6a0507b679010d00d7e14acbd5552fa6ff8a79240129 | Shell | 551 | 19 | #!/bin/bash
#
#
# copies tSNR files related to rsfMRI time series into a target directory
#
# Inputs:
# $1 : source directory
# $2 : target directory
#
#
# 2025 Mark C Nelson, McConnell Brain Imaging Centre, MNI, McGill
#---------------------------------------------------------------------------------------------------... |
d9e8c8b10eda1217f733ce6a28db9a8a1987fbc2b5d786df6e30c7bd57934370 | Shell | 552 | 23 | #!/usr/bin/env bash
set -x
PARTITION=$1
JOB_NAME=$2
CONFIG=$3
GPUS=$4
GPUS_PER_NODE=${GPUS_PER_NODE:-8}
CPUS_PER_TASK=${CPUS_PER_TASK:-2}
PY_ARGS=${@:5}
SRUN_ARGS=${SRUN_ARGS:-""}
PYTHONPATH="$(dirname $0)/..":$PYTHONPATH \
srun -p ${PARTITION} \
--job-name=${JOB_NAME} \
--gres=gpu:${GPUS_PER_NODE} \
--n... |
f07ce200b99d1e5dbe18a313c7334082aec01c84a37501e5a4758e82e5e87f27 | Shell | 553 | 12 | #!/bin/sh
echo "Building directory and getting package version"
mkdir -p build
AIND_DATA_TRANSFER_VERSION=$(grep -Eo '[0-9]+\.[0-9]+\.[0-9]+' src/aind_data_transfer/__init__.py)
echo ${AIND_DATA_TRANSFER_VERSION}
echo "Building docker container"
docker build -t singularity-builder:latest --build-arg AIND_DATA_TRANSFE... |
470d2c89d3b2d6c78f1dbf01c8517630121aa9d2e84143195cb95880644ef103 | Shell | 556 | 19 | #!/bin/bash
conda activate skmer
#Because skmer fails to do sketches for very low coverage samples sometimes,
#we will resume but first delete folders for samples that failed
#The following deletes folders that do not contain a *.msh file:
echo deleting folders that do not contain *.msh file
find ./skmer_ref/ -mind... |
a9418f9eb301aa7e834f24377b128eb4e5f7176b1033e243c9f272b01409c01e | Shell | 557 | 13 | #!/bin/bash
#Paired
while read j; do
echo $j
fastp --in1 "../data/2_SRA/"$j"_1.fastq" --in2 "../data/2_SRA/"$j"_2.fastq" --out1 "../data/3_trimmed/"$j"_1.trimmed.fastq" --out2 "../data/3_trimmed/"$j"_2.trimmed.fastq" --cut_tail --html $j".html" --json $j".json" 2> $j".log"
done <../data/1_ids/paired_id... |
0fde60387c9995149f2c511da9ac37a83d13a7c4423eeb92a5ca871fa96922f5 | Shell | 561 | 26 | #!/bin/bash -x
#SBATCH --job-name=ctd-pep
#SBATCH --nodes=1
# Production: Always use all GPUs per node
#SBATCH --ntasks-per-node=1
# Budget account where contingent is taken from
#SBATCH --account=chemtrain-deploy
# Share CPUs equally among four tasks
#SBATCH --cpus-per-task=72
# Run for at most 10 minutes
#SBATCH ... |
165d7b3b1e07648551f81ac4e3d6d6ffe1ef7ef57a8d1ee1b1f1db430eba873a | Shell | 561 | 16 | #!/bin/bash
set -e
di=/media/athena-admin/FastSSD1/Athena/francesca_202203/data
do=/media/athena-admin/FastSSD1/Athena/francesca_202203/out_filter647_01
samples=("340258_2LD_5" "840298_52_P_20" "340299_35_22_HD" "840298_16_P_17" "840298_50_P_19" "840295_42_HD" "840295_40_HD_27" "454371_17_LD_7" "840258_3_LD_6")
#sampl... |
3d2f356e9393605c9ac56ddd083ffbb169e57be8e0219fcfaacf6cc9adcbba3c | Shell | 561 | 26 | #!/bin/bash -x
#SBATCH --job-name=ctd-al
#SBATCH --nodes=8
# Production: Always use all GPUs per node
#SBATCH --ntasks-per-node=4
# Budget account where contingent is taken from
#SBATCH --account=chemtrain-deploy
# Share CPUs equally among four tasks
#SBATCH --cpus-per-task=72
# Run for at most 10 minutes
#SBATCH -... |
5fcac832870ab688022cdcdb631ea25230414fdc08c33690bf0d1d6e65775c5f | Shell | 561 | 26 | #!/bin/bash -x
#SBATCH --job-name=ctd-wat
#SBATCH --nodes=1
# Production: Always use all GPUs per node
#SBATCH --ntasks-per-node=1
# Budget account where contingent is taken from
#SBATCH --account=chemtrain-deploy
# Share CPUs equally among four tasks
#SBATCH --cpus-per-task=72
# Run for at most 10 minutes
#SBATCH ... |
65f159baf0076bc263281e8293c5aa159f9490728f406acf1d420b24f4f458c1 | Shell | 562 | 26 | #!/bin/bash -x
#SBATCH --job-name=ctd-pep
#SBATCH --nodes=8
# Production: Always use all GPUs per node
#SBATCH --ntasks-per-node=4
# Budget account where contingent is taken from
#SBATCH --account=chemtrain-deploy
# Share CPUs equally among four tasks
#SBATCH --cpus-per-task=72
# Run for at most 10 minutes
#SBATCH ... |
b43cf85815c286971bd220f0c727ed3c8d43aa5e419364456b0db83c674397c3 | Shell | 562 | 26 | #!/bin/bash -x
#SBATCH --job-name=ctd-wat
#SBATCH --nodes=4
# Production: Always use all GPUs per node
#SBATCH --ntasks-per-node=4
# Budget account where contingent is taken from
#SBATCH --account=chemtrain-deploy
# Share CPUs equally among four tasks
#SBATCH --cpus-per-task=72
# Run for at most 10 minutes
#SBATCH ... |
95a57917a6740a7b1ede28f5bd133edcece5fd12166c309ff85f6fa4b5a374cb | Shell | 563 | 26 | #!/bin/bash -x
#SBATCH --job-name=ctd-pep
#SBATCH --nodes=16
# Production: Always use all GPUs per node
#SBATCH --ntasks-per-node=4
# Budget account where contingent is taken from
#SBATCH --account=chemtrain-deploy
# Share CPUs equally among four tasks
#SBATCH --cpus-per-task=72
# Run for at most 10 minutes
#SBATCH... |
9729aaa00361b4811b5ea11e9fc9738d94f064d464a664152682379d6efc4618 | Shell | 564 | 13 | # argument 1 is either BASELINE, NAIVE, RTLC, PERCEPTION
# argument 2 is NITER
# argument 3 is fsl location
ls -R ../../../results/searchlight/*/map_$2iter_12mm_$1_centered_mni.nii.gz > list.txt
files=$(cat list.txt)
echo "$files"
fslmerge -t ../../../results/searchlight/$1 $files;
randomise -i ../../../results/searc... |
4d553dcdebe27c0c6370b9a776fdf97b7924659d7fde37d58bc281b3ad44660a | Shell | 566 | 23 | #!/bin/bash
# Parameters
expe_name="hcp_pipelines"
main_script=/srv/tempdd/egermani/hcp_pipelines/src/singularity_launcher.sh
echo "Create dir for log"
CURRENTDATE=`date +"%Y-%m-%d"`
echo "currentDate :"
echo $CURRENTDATE
PATHLOG="/srv/tempdd/egermani/Logs/${CURRENTDATE}_OARID_${OAR_JOB_ID}/"
echo "path log :"
echo ... |
11487f903ba36f90a0439126015c9ad3d505bb711148150225705a683a0844bc | Shell | 567 | 10 | #!/usr/bin/env bash
set -e
# device specifier given from first argument, default value is -1
device=${1:--1}
for method in nfp ggnn schnet weavenet rsgcn relgcn megnet
do
python train_own_dataset.py --datafile dataset_train.csv --method ${method} --label value1 --conv-layers 1 --device ${device} --epoch 1 --unit-n... |
a375d941f2b8a48df2c469b4f97c963a6cd8f372d09fee68e75c594b3aee33dd | Shell | 575 | 26 | #!/bin/sh
#SBATCH -p shared
#SBATCH -t 7-00:00
#SBATCH --mem 10G
#SBATCH -n 1
#SBATCH -c 1
#SBATCH -o 3_download_SRA.%A.out
sleep 30
scontrol show jobid=$SLURM_JOBID
module load Anaconda3/2020.11
source activate sra
cat runs_to_download.txt | while read line
do
echo working on $line
accession=$(echo $line | cut ... |
0e4ad8ac03ced45099ead387f4ed4658c78b06de606a6a4da1ed758407b883f6 | Shell | 580 | 11 | #!/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... |
6bd338a24bd50fa241c22241d38d171bd62c7d4a7c17937ce905138b90c426e8 | Shell | 584 | 17 | #!/bin/bash
#SBATCH --cpus-per-task=4
#SBATCH --mem-per-cpu=20G
#SBATCH --time=2-00:00
#SBATCH --account=def-barrett
#SBATCH --mail-type=ALL
#SBATCH --mail-user=janay.fox@mail.mcgill.ca
################################################################################
### Goal: Read alignment files into methylKit and fi... |
1a98e0043387611589b614c6a8f0940a772624485c539210ca7c8213791f7961 | Shell | 585 | 11 | #!/bin/bash
awk '{print $1}' dropoutDIV_sig > adapt
while read j; do
p=$(cat /Users/bill/project_Adult_EVE/data/step1_transcripts2genes/keys/hypot/no_pap/bos_key | grep $j| awk '{print $1'})
cat /Users/bill/project_Adult_EVE/data/step1_transcripts2genes/keys/hypot/no_pap/final_sor_key | grep $p >> shrew_sigShrewDO... |
2cb29463446b8c3a83e944a64542fe9e43ae6dc08f6349702757294b6e59d9b7 | Shell | 587 | 17 | #docker pull atbigdawg:5000/fcollman/render-python-apps:reorg
#docker tag atbigdawg:5000/fcollman/render-python-apps:reorg fcollman/render-python-apps
docker build -t sharmishtaas/render_modules .
#docker tag sharmishtaas/luigi-scripts atbigdawg:5000/sharmishtaas/luigi-scripts
#docker push atbigdawg:5000/sharmishtaas/l... |
343654820345b7fb56dc4b94322f6bbc76858c29db45a468e8c9bf86db9940b6 | Shell | 587 | 21 | #!/usr/bin/env bash
python run_asr.py \
--output_dir="./wav2vec2-base-100h" \
--num_train_epochs="30" \
--per_device_train_batch_size="32" \
--per_device_eval_batch_size="32" \
--evaluation_strategy="steps" \
--save_total_limit="3" \
--save_steps="500" \
--eval_steps="100" \
--logging_steps="50" \
--learning_rate="5e-4... |
f0fd8c3574bf65c48ecb634c9e473fde962cf9dcf5b2b1ad40e449d5e060e5af | Shell | 588 | 27 | #!/bin/bash
#SBATCH -n 1
#SBATCH -t 1-18:00:00
#SBATCH -J ms
#SBATCH --output=logs/ms_run_%j.log
#SBATCH -p mit_preemptable
#SBATCH --requeue
#SBATCH --gpus=l40s:1
#SBATCH --cpus-per-task=16
#SBATCH --mem=160G
# Use this to run generic scripts:
# sbatch --export=CMD="python my_python_script --my-arg" launcher_scripts/... |
6b3230735d5beada3c19ef60c34a31e03860c7f4c80f8e37167183199a3bf565 | Shell | 590 | 21 | #!/bin/bash
cd ..
#source ~/.bashrc
#source ./scripts/utils.sh
#source /GPUFS/paratera/scripts/cn-module.sh
#module load CUDA/10.2 compiler/CUDA/10.2
#module load anaconda/2020.11
#module load nccl/2.9.6-1_cuda10.2
#module load cudnn/7.6.5.32_cuda10.2
module load cuda/11.3
source activate paddlehelix
export PYTHONUN... |
d670a9d4c1cf5b1b1417d8bba1454bedf992ce1d75c3f326708a80cbb8eec80b | Shell | 592 | 24 | #!/bin/bash
OUTPUT_DIRECTORY="output/single_pdb/"
UPLOADED_FILE="data/pdbs/6y1l_imgt.pdb"
HEAVY_CHAIN="H"
LIGHT_CHAIN="L"
SAMPLE_NUMBER=20
SAMPLING_TEMP=0.20
REGIONS="CDRH2 CDRH3"
LIMIT_VARIATION_STRING=""
python antifold/main.py \
--out_dir "$OUTPUT_DIRECTORY" \
--pdb_file "$UPLOADED_FILE" \
--heavy_chain "$HEAVY_CHA... |
83a8143b79ecef2939b377d1f2065c8caaed4aa01af5600c3f3a8d31afcbf837 | Shell | 594 | 29 | #!/bin/bash
set -e
# dedup_umi.py requires pysam.
FILE=$1
BASE=`basename ${FILE%.bam}`
OUTDIR=bam-rmdup-umi
mkdir -p $OUTDIR
if [ ! -s $FILE ]
then
echo "File is missing or empty: $FILE"
exit 65
fi
if [ -s $OUTDIR/$BASE.rmdup.bam ]
then
echo "Output file already exists: $OUTDIR/$BASE.rmdup.bam"
exit 64
fi
... |
a50ac8eed96a448fc2c88103be80e1bc1f30e791a020d973c44712129c8cf891 | Shell | 597 | 30 | #!/bin/bash
set -e
FILE=$1
BASE=`basename ${FILE%.bam}`
OUTDIR=bam-processed
mkdir -p $OUTDIR
if [ ! -s $FILE ]
then
echo "File is missing or empty: $FILE"
exit 65
fi
if [ -s $OUTDIR/$BASE.sorted.bam ]
then
echo "Output file already exists: $OUTDIR/$BASE.sorted.bam"
exit 64
fi
echo "Sorting file..."
samtoo... |
15296b713b3a547bbc0dc98599ccac294ee99e9c6d4b3cfa65c2a5daa24054fb | Shell | 598 | 18 | #!/usr/bin/env bash
export PYTHONPATH="../":"${PYTHONPATH}"
python finetune.py \
--learning_rate=3e-5 \
--fp16 \
--do_train \
--val_check_interval=0.25 \
--adam_eps 1e-06 \
--num_train_epochs 6 --src_lang en_XX --tgt_lang ro_RO \
--data_dir $ENRO_DIR \
--max_source_length $MAX_LEN --max... |
5d55272197d2e2d0e189b393cbaafec65d74f4ad6fd9960ba42c145382262403 | Shell | 598 | 19 | mkdir results/ffn_hyperopt
CUDA_VISIBLE_DEVICES=1,2,3 python src/ms_pred/ffn_pred/ffn_hyperopt.py \
--seed 1 \
--num-workers 8 \
--max-epochs 200 \
--dataset-name nist20 \
--dataset-labels labels.tsv \
--form-dir-name no_subform \
--loss-fn cosine\
--split... |
9959ef355d283bcc9037c9a472944233751eb12025f5a318be4529ccf2f2b59b | Shell | 598 | 18 | sif=/mnt/data1/workspace/Anders/MelBrM/Containers/cibersortx_fractions.sif
username=<your.email>
token=<token.from.cibersortx.website>
sigmatrix=/mnt/data1/workspace/Anders/MelBrM/Code/Duke_ms/RNASeq/signature_lm22_ensembl.txt
mixture=/mnt/data1/workspace/Anders/MelBrM/Proc/Duke/RNASeq/CIBERSORTx/cibersortx_mixture.t... |
0088de30fe1da456cc950fb48b1669d05f3f0f13f77e0c2c15296d64ae52e9f1 | Shell | 599 | 21 | #!/usr/bin/env bash
python run_asr.py \
--output_dir="./wav2vec2-large-lv60-100h" \
--num_train_epochs="30" \
--per_device_train_batch_size="16" \
--per_device_eval_batch_size="16" \
--evaluation_strategy="steps" \
--save_total_limit="3" \
--save_steps="500" \
--eval_steps="100" \
--logging_steps="50" \
--learning_rate... |
46bcf9e760347468ae939af62dc31bb9d9d9ef7c55e067e8db87c0f8d3325138 | Shell | 600 | 18 | sif=/mnt/data1/workspace/Anders/MelBrM/Containers/cibersortx_fractions.sif
username=<your.email>
token=<token.from.cibersortx.website>
sigmatrix=/mnt/data1/workspace/Anders/MelBrM/Code/MDACC_ms/RNASeq/signature_lm22_ensembl.txt
mixture=/mnt/data1/workspace/Anders/MelBrM/Proc/MDACC/RNASeq/CIBERSORTx/cibersortx_mixture... |
b63c6cfacada699f34b0f0af9a817b81f2027bd35168e967e443b56a92bfb8b8 | Shell | 600 | 12 | #!/bin/bash
#SBATCH --cpus-per-task=32
#SBATCH --time=24:00:00
module load bowtie2
module load samtools
module load bedtools
module load dimelo
cd /data1/czhao/xiaodong/NCI_H660_DiMeLo/result/pass
dimelo-plot-enrichment-profile -f NCI_H660_DiMeLo_sorted.bam -s NE_CREs AD_CREs -b /data1/czhao/xiaodong/NE_hg38.bed /da... |
41f61627b803597dc8418c32f28048804ecf5fd275571328ab635769987c12a4 | Shell | 605 | 9 | #!/bin/bash
#need to run the below for each species, changing the amount of columns you keep dependent on how many individuals per species you have
#only bos keeps the var2, the rest remove var2 from awk output as they will not be pasted in the next step
while read j; do
f=$(awk -v var=$j '$1 == var {print $2}... |
d40e813159bbb2c38be97c841ef784fb58fc6cf47deb76ce60f734286a3dd6de | Shell | 605 | 28 | #!/bin/sh
# Usage:
#
# mri_convert_batch.sh <<subj1 dir> <subj2 dir> ... <subN dir>>
#
# Example:
#
# ../scripts/mri_convert_batch.sh WELM34 YESB65
#
# Run this in this script root subject sirectory
for i in $*
do
if [ ! -f $i/mri/T1.nii ] ; then
mri_convert $i/mri/T1.mgz $i/mri/T1.nii
... |
a86c4c66136bd065c063db2fcbb5a656f045bc10b5ce72d06f81dbaa82a99e74 | Shell | 607 | 32 | #!/bin/bash
set -e
FILE=$1
BASE=`basename ${FILE%.fastq.gz}`
OUTDIR=fastqc
mkdir -p $OUTDIR
if [ ! -s $FILE ]
then
echo "File is missing or empty: $FILE"
exit 65
fi
if [ -s $OUTDIR/$BASE.count.txt ]
then
echo "Output file already exists: $OUTDIR/$BASE.raw.count.txt"
exit 64
fi
# Unzip file (fastqc throws e... |
95e62f93d861ed72e9ebcb071830f1a30d867554dfcd07767e5f14e97c9d16b7 | Shell | 614 | 24 | #!/bin/bash
set -e
source ../paths.sh
if [ -z "${FLANG_PATH}" ]; then
echo "this test is not run when not using --with-flang"
# Exit with 77 to mark the test skipped
# https://www.gnu.org/software/automake/manual/html_node/Scripts_002dbased-Testsuites.html
exit 77
fi
verificarlo-f -c vfc_probes_test.... |
ed2a3d41f2a28fc6c684e4731c7b2ae49668d12f5d1e2cf62edd68ce7fd916dc | Shell | 615 | 26 | #!/bin/bash
# Determine the relevant directories based on hostname
if [ "$(hostname)" == "PC085765" ]; then
home_directory="/home/iml/hannah.eichhorn/"
anaconda_directory="/home/iml/hannah.eichhorn/anaconda3/"
code_directory="/home/iml/hannah.eichhorn/Code/_OWN_PUBLIC_REPS/ImageQualityMetricsMRI/"
host... |
2cd07ed19b7a7c039c390f777a6f5ba33c856c19da0a9541428532dfc259d417 | Shell | 616 | 21 | echo baseline-early-exit
python cdq_test_clotho_baseline_early_exit.py > ./logs/baseline-early-exit.log 2>&1
# sleep 60
echo baseline-full-bs-32
python cdq_test_clotho_baseline_full.py --bs 32 --ee 11 > ./logs/baseline-full-bs-32.log 2>&1
# sleep 60
echo baseline-full-bs-1
python cdq_test_clotho_baseline_full.py --... |
bf7a5a056e7b0c0bb9fb6318e91cdb8c323e677db2440de52443b915d365dbcb | Shell | 617 | 41 | #!/bin/bash
CURRENT_REP=$PWD
BUILD_REP=$1
INSTALL_REP=${CURRENT_REP}/$1/install
VALGRIND_ARCHIVE=$2
FLAGS=$3
echo "BUILD_REP:" ${BUILD_REP}
echo "VALGRIND_ARCHIVE:" ${VALGRIND_ARCHIVE}
echo "VALGRIND_NAME: "${VALGRIND_NAME}
echo "FLAGS:" ${FLAGS}
mkdir ${BUILD_REP}
tar xvfz ${VALGRIND_ARCHIVE} --directory ${BUIL... |
ea6c8cc8e89a44cb69d4d189c49f4485888a6cac426c7cc981d1152b35173a31 | Shell | 617 | 18 | #!/bin/sh -e
# # Get files and create one file for all chromosomes
# echo Download files
# cd ~/snpEff/data/spombe
# wget ftp://ftp.sanger.ac.uk/pub/yeast/pombe/Chromosome_contigs/chromosome1.contig.embl
# wget ftp://ftp.sanger.ac.uk/pub/yeast/pombe/Chromosome_contigs/chromosome2.contig.embl
# wget ftp://ftp.sanger.ac... |
7fac2d0b13a3630417360d0ebf576ba553ea61ac671ad8aaf3572c0b108b0137 | Shell | 619 | 18 | #!/bin/bash
subj=sub-PCM003
dirHere=/gpfs/milgram/project/holmes/PsychConnectome/MRI_Data/fmri_analysis/${subj}/func/
funcRunNames_AllPossible=( restAP_run-01 restPA_run-01 restAP_run-02 restPA_run-02 stroopAP_run-01 stroopPA_run-01 hammerAP_run-01 )
funcRunNames_Present=()
for runName in "${funcRunNames_AllPossible... |
0405ff86d0c16bdf190bc5dd8a27bd1a989ea7da5276378b6c27a1a6f580c33b | Shell | 622 | 8 | #!/bin/sh
cd reconstruction
# 5.1. Feature extraction for evaluation
python feature_extraction_melception_from_reconsound.py config/recon_vggsound_fmriprep_rep4_500voxel_vggishish_allunits_fastl2lir_alpha100.yaml
python feature_extraction_melception_from_reconsound.py config/recon_vggsound_attention_fmriprep_rep4_500vo... |
78d4b78836000323d6e7f8396303de6b0bda57f4eecaa82962911bb4e7467df0 | Shell | 622 | 15 | module restore tools
for i in 1 2 3 4 5 6 7
do
bedtools intersect -u -a h1embryonicstsemcellENCODEhg38.bed -b {DIR}/peak_subset_cluster_${i}.bed > ${OUTPUT_DIR}/cluster${i}_ESCchromHMMhg38.bed
bedtools intersect -u -a h9neuralstemcellENCODEhg38.bed -b {DIR}/peak_subset_cluster_${i}.bed > ${OUTPUT_DIR}/cluster${i}_... |
7d91c252ab5ee71f62532417fe04dc41213328c4f419c43cab1575509ea37ae2 | Shell | 624 | 16 | #!/bin/bash
#SBATCH --job-name=dmsfold_test_1pwt_A
#SBATCH --time=00:30:00
#SBATCH --nodes=1 --ntasks=1
#SBATCH --cpus-per-task=8
#SBATCH --gpus-per-node=1
#SBATCH --error=1PWT_A_error.txt
#SBATCH --output=1PWT_A_log.txt
set -vx
module load miniconda3
conda activate openfold
repo_location = '/users/drake463/DMS-Fold/... |
374ef646c27d04954f0049b2dceea1059cd41c99d4cc2a85749201c0718ffc48 | Shell | 625 | 26 | #!/bin/bash
BIN=${1}
MODE=${2}
OP=${3}
TYPE=${4}
NB_TESTS=${5}
ABS_ERR=${6}
echo
echo "--- Running test ---"
echo "Binary: ${BIN}"
echo "Mode: ${MODE}"
echo "Operation: ${OP}"
echo "Type: ${TYPE}"
echo "Number of tests: ${NB_TESTS}"
echo "Absolute error: ${ABS_ERR}"
# Set the VFC_BACKENDS environment variable
export... |
547f5d994c6681b2545ae43bab7f7b7f0d0735dc6f2545bbd3e57aff170ff72d | Shell | 625 | 12 | #!/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... |
ce1db82dcdee10b0a2c34da26b692764eb0ec7f3b53b79575b2b38d868646003 | Shell | 626 | 26 | #!/bin/sh
# wget ftp://ftp.solgenomics.net/genomes/Solanum_lycopersicum/wgs/assembly/build_2.40/S_lycopersicum_chromosomes.2.40.fa.gz
# GFF has to be downloaded manually from
#
# http://solgenomics.net/itag/release/2.3/list_files#
# File ITAG2.3_gene_models.gff3
#
#
# Create genes.gff
echo Decompressing th... |
157ed1936f0ed4d8d7d6427c9599eb36c786c2dda922a1fb746aa3849ef2c827 | Shell | 629 | 27 | set -e
RES=$1
CHROM=$2
DATA_DIR=hic_data
mkdir -p $DATA_DIR
PREFIX=GM12878_combined
TAR=$DATA_DIR/GSE63525_${PREFIX}_intrachromosomal_contact_matrices.tar.gz
test ! -s $TAR && (curl ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE63nnn/GSE63525/suppl/GSE63525%5FGM12878%5Fcombined%5Fintrachromosomal%5Fcontact%5Fmatrices%2E... |
89d1bc2a95434672221e3c3a5c7bb6728c7e4b72aad509387b526eb17c4d792f | Shell | 630 | 17 | #!/usr/bin/env bash
export PYTHONPATH="../":"${PYTHONPATH}"
export WANDB_PROJECT=dmar
export MAX_LEN=128
export m=sshleifer/student_marian_en_ro_6_1
python finetune.py \
--learning_rate=3e-4 \
--do_train \
--fp16 \
--data_dir wmt_en_ro \
--max_source_length $MAX_LEN --max_target_length $MAX_LEN --val_max_targ... |
d4912b0003e4987ea4a9640fadc429e350f557c5e2040fc26b2170035bf8fe57 | Shell | 631 | 35 | #!/bin/bash
dropbox='../../dropbox'
data=uspto_full
tpl=new
tpl_min_cnt=4
fp_degree=2
num_parts=40
cooked_root=../../cooked_data
save_dir=$cooked_root/$data/tpl-$tpl-mincnt-$tpl_min_cnt
N=$num_parts
(
for ((s=0;s<40;s+=1))
do
((i=i%N)); ((i++==0)) && wait
python dump_graphs.py \
-dropbox $dropbox \
-dat... |
6dc07951e1ec5512e9b3ddbd7203afb8d6cc8909f3b92d065c46c78874c84d91 | Shell | 632 | 14 | #!/bin/sh
# ____________________________________________________________________________________
#
# Pyomo: Python Optimization Modeling Objects
# Copyright (c) 2008-2026 National Technology and Engineering Solutions of Sandia, LLC
# Under the terms of Contract DE-NA0003525 with National Technology and Engineering
# So... |
752939689925db7588b5e0bfbc56c573a363991c167dbf45806cd964152e7720 | Shell | 632 | 22 | CUDA_VISIBLE_DEVICES=0
NPROC=1
LOADER=Noisy
ANATOMY=brain
DATA=noisy
SNR=32dB
ROOT=/path/to/root/
ROOT_DATA=/path/to/data/
BATCH_SIZE=1
NORMALIZE=0
PRECOND=edm
AUGMENT=0
torchrun --standalone --nproc_per_node=$NPROC train.py \
--outdir=$ROOT/models/$PRECOND/$ANATOMY/$SNR \
--data=$ROOT_DATA/$ANATOMY/train/$SNR/$DATA... |
98d16c4f2c9c2a2329bd4c07e7501011357a23ba2bb70fc4b47eac9a3fdd0fa5 | Shell | 633 | 25 | #!/bin/bash
# Set VIRTUAL_ENV to the /usr/local directory if it is not set
if [ -z "$VIRTUAL_ENV" ]; then
export VIRTUAL_ENV=/usr/local
fi
gcc test_blas.c -o test_blas -lblas -llapack -L$VIRTUAL_ENV/lib -I$VIRTUAL_ENV/include
for i in {1..10}; do
./test_blas >test_blas.$i.txt
done
for i in {1..10}; do
f... |
5719ea0110f8b55f5f075a8cca075319caa16f5306a8d2dfeff8271b4e5492fb | Shell | 634 | 22 | #!/bin/bash
# Extracts the index sequences from multiple fastq.gz files and writes them
# in fasta format.
FILES=`find /rawdata/Illumina_Runs/141030_SN_0795_0391_AHAV20ADXX/Unaligned -name "*fastq.gz"`
#FILES=/rawdata/Illumina_Runs/141030_SN_0795_0391_AHAV20ADXX/Unaligned/Project_N/Sample_19239_LCL_01/19239_LCL_01_CG... |
c275f5e1b458761d8eb9846f9d95d76a0aa37ad02cb85cf1c8af35f4a886bbe4 | Shell | 634 | 22 | CUDA_VISIBLE_DEVICES=0
NPROC=1
LOADER=Noisy
ANATOMY=brain
DATA=noisy
SNR=32dB
ROOT=/path/to/root/
ROOT_DATA=/path/to/data/
BATCH_SIZE=1
NORMALIZE=0
PRECOND=gsure
AUGMENT=0
torchrun --standalone --nproc_per_node=$NPROC train.py \
--outdir=$ROOT/models/$PRECOND/$ANATOMY/$SNR \
--data=$ROOT_DATA/$ANATOMY/train/$SNR/$DA... |
486e3dc3d6edd89659be74676b28716ccf051eca2a627765ab645c92561a874b | Shell | 635 | 21 | #!/usr/bin/env bash
echo "Indexing Script Called"
while getopts ':i:o:n:g:f:l:' flag; do
case "${flag}" in
i) UnIndexed_FA=${OPTARG} ;;
o) Index_Destination=${OPTARG} ;;
n) nThreads=${OPTARG} ;;
g) Annotation=${OPTARG} ;;
f) Index_Flags="${OPTARG}" ;;
l) LogOut_Destination=${... |
91e643780a81da27c40296b1ae4e87d0a2d15ea215bc7221070079007502c3e5 | Shell | 636 | 13 | arch=$(uname -m)
project=$1
# install miniconda to install pre-built gsl (faster than building it)
# (TODO: miniconda can also be used to install cuda toolkit for platforms
# for which cuda manylinux is not available)
curl -s -O https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-$arch.sh
bash Miniconda3-latest... |
d0ca38f55c1988c072dc8d4579ed739226ed3f79f9aa9b0fc91a6be73502167a | Shell | 637 | 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... |
bb76e2d5c4238a4e17c8d5c64f03cc8a0bd27d452dcd61445e9bde2e920f7679 | Shell | 638 | 31 | #!/bin/bash
#SBATCH -A p20023
#SBATCH -p normal
#SBATCH -n 1
#SBATCH --mem=40G
#SBATCH -t 48:00:00
#SBATCH --mail-user=viriyakeo2023@u.northwestern.edu
#SBATCH --mail-type=END,FAIL
#SBATCH --job-name=z_mustache
#SBATCH -o "%x.o%j"
source ~/.bashrc
conda activate mustache
/home/vkp2256/mustache/mustache/diff_mustac... |
e8000aad5dbfd970753815da659e1c68c530e1c1277e0ca23b0de121f6b49f95 | Shell | 639 | 28 | #!/bin/bash
picard=/nfs/software/helmod/apps/Core/picard-tools/2.4.1-gcb01/picard.jar
outdir=/data/anderslab/MelBrM/Proc/MDACC/bam2fastq/
tmpdir=/data/anderslab/MelBrM/tmp/
bam=("$@")
echo "Processing... ${bam}"
#CleanSam-MAPQ
cleaned="$(basename -- $bam)"
java -Djava.io.tmpdir=${tmpdir} -Xmx8G -jar ${picard} Clean... |
89a9cb9620151eafb350f1303e79d6e07ca68709489a35e92ae1de0d06d37328 | Shell | 640 | 17 | #!/bin/bash
#SBATCH --job-name=dmsfold_test_1pwt_A
#SBATCH --time=00:30:00
#SBATCH --nodes=1 --ntasks=1
#SBATCH --cpus-per-task=8
#SBATCH --gpus-per-node=1
#SBATCH --error=1PWT_A_error.txt
#SBATCH --output=1PWT_A_log.txt
set -vx
module load miniconda3
conda activate openfold
repo_location = '/users/drake463/DMS-Fold/... |
5706fc2b95a8b0ee43160aad7367d82cb650699b6a39e9149f9771322eec9a95 | Shell | 643 | 13 | #!/bin/sh
# ____________________________________________________________________________________
#
# Pyomo: Python Optimization Modeling Objects
# Copyright (c) 2008-2026 National Technology and Engineering Solutions of Sandia, LLC
# Under the terms of Contract DE-NA0003525 with National Technology and Engineering
# So... |
16cf91b228470f6b5c58d08fe1949929387581a970b38763cdd62d4caa07b579 | Shell | 645 | 29 | #!/bin/bash
set -e
source ../paths.sh
if [ -z "${FLANG_PATH}" ]; then
echo "this test is not run when not using --with-flang"
# Exit with 77 to mark the test skipped
# https://www.gnu.org/software/automake/manual/html_node/Scripts_002dbased-Testsuites.html
exit 77
fi
export VFC_BACKENDS="libinterflop... |
efe24ffba4977aa71eefc376ceedc4b0e0e8075f4586e557fc49a23c9b176bc3 | Shell | 645 | 13 | #!/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... |
087598696388ef4c53aa244fd82f09242a8ad077853c0aa4d44beb1d577147cf | Shell | 646 | 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... |
33c74acace6fabe6b8d4e27de96a156c0ccbe55c51bb06c742e4d48f96e84b6a | Shell | 646 | 28 | #!/bin/bash
set -euo pipefail
RED='\033[0;31m'
GREEN='\033[0;32m'
NC='\033[0m'
die() { echo -e "${RED}$1${NC}"; exit 1; }
ok() { echo -e "${GREEN}$1${NC}"; }
BACKEND_URL="${1:-http://localhost:8080}"
SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
PROJECT_ROOT="$(dirname "$SCRIPT_DIR")"
cd "$PROJECT_ROO... |
3e6bb72a6d5cfc39eb5ab5398f8c03c77d9c670569e9240225cb905fd7bb9e9e | Shell | 646 | 15 | #!/usr/bin/env bash
# This script should be run from the repository root.
set -euo pipefail
source scripts/linux-target.sh
PROJECTS=(Noise2Map Noise2Mic Noise2Tomo Noise2Half EstimateWeights Frankenmap MrcConverter WarpWorker WarpWorker2 WarpTools MTools MCore)
for PROJECT in "${PROJECTS[@]}"; do
dotnet publish \
... |
6add66ed7d4a4586dcbadf40f18bb202df529d9dd9c023904b2d2653d9a2365c | Shell | 646 | 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... |
77231551dd433c11e63271388b6cb276effc807b9288d5e2d14c13e9139500a6 | Shell | 646 | 12 | #! /bin/bash
# ____________________________________________________________________________________
#
# 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
#... |
89eea72874d019bd4f4e8ea8870710081e26e0665aaa8de8485f9d4c54804f12 | Shell | 646 | 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... |
95075d31e9cbca56ac65e2b6b99673468d42a0db739a6df7bf4e3a583dabf018 | Shell | 646 | 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... |
9a35801fae16f544740a59b196e0b6c0c747c719c4dd452900d778d6fbc58851 | Shell | 646 | 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... |
36c23878f4cc3d47260bd1d281e9d5191b7ae9392e33b63d3c11e624c1bd1275 | Shell | 647 | 12 | #!/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... |
47561d9e84a82773f2eabb47d0a07470152ad45f817d4adc62f0bdfe56fabdce | Shell | 647 | 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... |
c27d479f37578225cdab28d8233f05da1f9fc2c76159d4e0aef2d48e90552292 | Shell | 647 | 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... |
3c2ccee4548df23ed198e8022aee4329619edb672e72670e93b79df5af41e6c4 | Shell | 648 | 13 | #!/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... |
ad312cbbae89bce6bc0ba24fc5456d605711e21f1eb748f25e21207203ab4476 | Shell | 648 | 23 | #!/bin/bash
# set -e
export VFC_BACKENDS_LOGGER=False
make clean
make dd
echo "=============================================================="
echo "Ok instructions are:"
cat dd.line/rddmin-cmp/dd.line.include
echo "=============================================================="
echo "Problematic instructions are:"
... |
9ede433712170fc9188bd9b0ac3c5a6addd33aa53262435dbacaa7af8a64a975 | Shell | 649 | 24 | #!/usr/bin/env bash
export PYTHONPATH="../":"${PYTHONPATH}"
export BS=32
export GAS=1
python finetune.py \
--learning_rate=3e-5 \
--fp16 \
--gpus 1 \
--do_train \
--do_predict \
--val_check_interval 0.25 \
--n_val 500 \
--num_train_epochs 2 \
--freeze_encoder --freeze_embeds --data... |
cb5d1049c97bac2bf3730f81f6841b620cf1668b5a68f60321bf75b8f3ed55d7 | Shell | 650 | 13 | #!/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... |
4dece457f53acf552f1ec899db73e1bae2cefa38d7b717fa2ae632cc43b554fd | Shell | 651 | 13 | #!/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... |
9e602917fe6cdff82e9129a5ae7d730554a7fae2e586651d836160a62a519d90 | Shell | 654 | 12 | #!/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... |
8f50491a53a05cab3f17de76952d20c50b50fc165b0fb1e1a6565cd7d8c3b802 | Shell | 655 | 13 | #!/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... |
808bcd9998228a398cc34a9398638f522f9fb6432d738b1785311a0ad294bfb3 | Shell | 656 | 31 | #!/bin/bash
# Function to run the commands in parallel batches of 5
run_batch() {
local batch=()
for cmd in "$@"; do
batch+=("$cmd")
if [ ${#batch[@]} -eq 1 ]; then
for b in "${batch[@]}"; do
eval "$b" &
done
wait
batch=()
... |
71cf4a8c3c1fa67ef9c06d0fad1d82af4711bba74a5a0cf3eb27e051be4ab779 | Shell | 657 | 18 | #!/usr/bin/env bash
export PYTHONPATH="../":"${PYTHONPATH}"
export WANDB_PROJECT=dmar
export MAX_LEN=128
python finetune.py \
--learning_rate=3e-4 \
--do_train \
--do_predict \
--fp16 \
--val_check_interval 0.25 \
--data_dir $ENRO_DIR \
--max_source_length $MAX_LEN --max_target_length $MAX_LEN --val_max_t... |
f8417cebca1fe84b229231a48a83de77e0a01e9590bd9ef05cd3b4c3f80872eb | Shell | 657 | 13 | #!/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... |
10ff195dda5aea9b1e8fab173327ec2ff4fe269ed59ad3b7f1289d20b8b6f81d | Shell | 658 | 13 | #!/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... |
ae235b43c99c32df326f27d895a9671db830c9e30a451d03f15aa1a2652c66ad | Shell | 658 | 22 | #!/bin/bash -eu
set -o pipefail
# ClinVar
mkdir $HOME/snpEff/data/GRCh38/clinvar
cd $HOME/snpEff/data/GRCh38/clinvar
wget https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/clinvar.vcf.gz
# DbSnp
mkdir $HOME/snpEff/data/GRCh38/dbSnp
cd $HOME/snpEff/data/GRCh38/dbSnp
wget https://ftp.ncbi.nih.gov/snp/archive/b154/VCF... |
6962bd6844537dfe051d30aa3d849862efec6d285563d1922923cf0c23766231 | Shell | 659 | 22 | #!/usr/bin/env bash
workers=${workers:-32}
subform_file="data/spec_datasets/msg_all_iceberg/subformulae/no_subform.hdf5"
if [ -f "$subform_file" ]; then
echo "$subform_file exists; skipping"
exit 0
fi
if [ -L data/spec_datasets/msg_all_iceberg/subformulae ]; then
rm data/spec_datasets/msg_all_iceberg/subformul... |
19973fc34d5447f7268e5575bccad7b9375b90e07c0c5d6774feeaad99b06314 | Shell | 661 | 31 | #!/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 "$b" &
done
wait
batch=()
... |
ea08d4b5e685febc1effe37a3b0d27aac5a33362a2325c15545a193a75cbcaca | Shell | 662 | 19 | #!/bin/sh
# Run at FMNH server
conda deactivate
conda activate varKoder
export CUDA_VISIBLE_DEVICES=3
#create folder with query images (i. e. those chosen as validation)
mkdir -p varkoder_query_images
cat validation_samples_SL.txt | tr ',' '\n' | xargs -L 500 -I {} bash -c 'for sample in "$@"; do for file in $(find ... |
cbda68e5aa0c5fb283715aa46547b4d0dd2d4212060cfcf05d6d227d5f2f5b29 | Shell | 663 | 13 | #!/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... |
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