sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
b1d8d395dc6d1932d4ee7834361f118dd82e328a5495ccaa65da6a63c35ca2ab | Shell | 368 | 14 | #!/bin/bash
# Submits slurm batches to extract EDF files
# Created on 20200804 by Max B Wang
EDF_Dir="$1"
subjID="$2"
numEDFs=`ls "${EDF_Dir}/${subjID}/EDF/" | wc -l`
for (( i=0; i<${numEDFs}; i++)); do
python3 /home/maxwell.wang/WeekScripts/TestRun/WeekLongBrain-main/ExtractElectrodes.py ${EDF_Dir} ${subjID} ${i... |
c5228e21170a531149543ab7a9255e67f4d7fd9763790a88c22c99ae7b6f7c07 | Shell | 369 | 16 | #!/bin/bash
chr=$1
outdir=QTL_fsVars/out/mpra_LDblock
bfile=resources/1000G_EUR_Phase3_plink/1000G.EUR.QC.$chr
snp_file="mpra.$chr.txt"
out_prefix="LD_R2_mpra.$chr"
plink --bfile $bfile \
--r2 \
--ld-snp-list $outdir/$snp_file \
--ld-window-kb 1000 \
--ld-window 99999 \
--ld-w... |
54ac7afcf001eb41dfa240b39121dd21df9d80daf367a585b2c325c1eba253fb | Shell | 371 | 13 | #!/bin/sh
set -o allexport
sta_i_I_range=1
end_i_I_range=50 #50
for i_I_range in $(eval echo "{$sta_i_I_range..$end_i_I_range}")
do
echo "$i_I_range"
sbatch --partition=batch --job-name V0basin --output data/output/V0basin--i_I_range-"$i_I_range"-%j.txt --error data/output/V0basin--i_I_range-"... |
7131e6616b9b93295d3893310635e660a66dfdd2fa32a9f9fd5ada945cb12ef9 | Shell | 371 | 17 | #!/bin/bash
# define project directory and working directory
pd=/your/project/directory/
mkdir -p $pd/data/validations/POU5F1_CRISPRi_FASTQ
cd $pd/data/validations/POU5F1_CRISPRi_FASTQ
# download files
HOST=ftp.ncbi.nlm.nih.gov
USER=anonymous
URL="ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE29nnn/GSE298717/suppl/"
lftp... |
bae5fd5deaa38590c2cc6ebdb6f65e86907a2ead5f5ba96ad4813724ad656b91 | Shell | 371 | 24 | #!/bin/sh
prefix=/home/hegan/DeepDendrite
exec_prefix=/home/hegan/DeepDendrite/x86_64
NRNBIN=${exec_prefix}/bin
ARCH=x86_64
MODSUBDIR=x86_64
NEURONHOME=/home/hegan/DeepDendrite/share/nrn
cd $1
if [ -x ${MODSUBDIR}/special ] ; then
program="./${MODSUBDIR}/special"
else
program="${NRNBIN}/nrniv"
fi
hostname
pwd
shi... |
c4d8ea05647ca3bc83759c577c3a6f8cdd90979ec6197dc9bf6e4d36402bd848 | Shell | 371 | 9 | #!/bin/bash
rm -rf /share/python-virtual-environments/mesmerize-pip-testing &&
python3 -m venv /share/python-virtual-environments/mesmerize-pip-testing &&
source /share/python-virtual-environments/mesmerize-pip-testing &&
pip install --upgrade pip setuptools
pip install Cython numpy
pip install mesmerize --extra-index-... |
d916f5390c1127830c5af80868d9f90909e5d1e0a27b4e6b48219fb1dbc3ee92 | Shell | 371 | 9 | #!/bin/bash
#SBATCH --job-name=repeatmasker_macFas6
#SBATCH --cpus-per-task=16
#SBATCH --mem=12G
#SBATCH --output=repeatmasker_%j.log
pd=/your/project/directory/
RepeatMasker -pa 16 -gff -species primates -engine rmblast -dir $pd/data/validation/POU5F1_LTR7_enrichment $pd/data... |
66ef5fa78d6c6bdfc75fe0b3ca14fc21f187e51b20f46f2ba99029aa580457f3 | Shell | 373 | 15 | #!/bin/bash
EPHYS_PIPELINE_DIR=/allen/aibs/technology/sergeyg/ephys_pipeline
SPECIMEN_IDS_TXT=$EPHYS_PIPELINE_DIR/specimen_ids.txt
for p in $(<$SPECIMEN_IDS_TXT)
do
echo ${p}
JOB_NAME=cell_$p
JOB_OUTPUT_FILE=$EPHYS_PIPELINE_DIR/specimen_$p/cell_$p.out
qsub -N $JOB_NAME -o $JOB_OUTPUT_FILE -v SPECIME... |
d5060bc82a6442bc1e25a38c38bcd45bf4f98d593d30da573d26223389be9b49 | Shell | 373 | 15 | #!/bin/bash -l
#SBATCH --job-name=modelbuild
#SBATCH --time=24:00:00
#SBATCH --account=proj83
#SBATCH --partition=prod
#SBATCH --mem=0
#SBATCH --exclusive
#SBATCH --constraint=volta
source /gpfs/bbp.cscs.ch/home/pokorny/ToposampleKernel/bin/activate
python -u run_SSCx_model_building_order2_local.py
# EXAMPLE HOW TO ... |
03316ab06e8c7b10a20acef3bf830ab843470cfff0a066912a57d0670e563a9b | Shell | 374 | 18 | #!/bin/bash
cd $1
for dir in TestNI-* TestITC18-* TestITC1600-*
do
if [ ! -d $dir ]
then
continue
elif [ -n "$(find "$dir" -maxdepth 0 -type d -empty)" ]
then
continue
fi
tar --remove-files --use-compress-program=zstd -cvf $dir/NWB.tar.zst $dir/*nwb
tar --remove-files --use-compress-program=zs... |
2b8606c613599c08c5bf6f08cc1d01e286b17658647ca2e6f2f4a3a1a0aa4315 | Shell | 374 | 8 | #!/bin/bash
sudo apt-get install -y mesa-common-dev libglu1-mesa-dev libfuse2
sudo apt-get install -y make ninja-build patchelf libgmp-dev libmpfr-dev libxerces-c-dev
sudo apt-get install -y libtbb-dev
#needed by qt 5.15 on linux
sudo apt-get install libxkbcommon-x11-dev libxcb-icccm4-dev libxcb-image0-dev libxcb-key... |
39873a7c71930d03e387852b856659c49f6c9294f31a6f77baa28d4ac4b367fe | Shell | 374 | 27 | #!/bin/bash
#$ -cwd
#$ -S /bin/bash
ID=$1
ConfigFile=$2
source ${ConfigFile}
#####
DataPath=${AlignAllPath}
BAMFile="${ID}.bam"
OutPath=${HTseqPath}
#####
make_dir ${OutPath}
#### 01.HTseq
htseq-count \
-f bam \
-r name \
-s no \
-a 10 \
-t exon \
-m intersection-strict \
-i gene_name \
${DataPath}/${BAMFile} \
${G... |
b1b4cbe30185d27619a15e3497f83ae1eaf2eb64e27f64a9e101b0806dd3f163 | Shell | 374 | 18 | #!/usr/bin/env bash
set -ex
pushd ../../mlflow/R/mlflow
image_name="mlflow-r-dev"
docker build -f Dockerfile.dev -t $image_name . --platform linux/amd64
docker run \
--rm \
-v $(pwd):/mlflow/mlflow/R/mlflow \
-v $(pwd)/../../../docs/api_reference/source:/mlflow/docs/api_reference/source \
$image_name \
R... |
6974cc8367bbffd08c450d71a625783bb353cf8442d62f18a67ee4eeecbcb915 | Shell | 375 | 9 | #!/bin/bash
cd /lustre/atlas/proj-shared/nro101/BigNeuron/first2000/
for foldername in `ls *.v3draw`
do
mkdir /lustre/atlas/proj-shared/nro101/BigNeuron/first2000/images/$foldername
mv $foldername /lustre/atlas/proj-shared/nro101/BigNeuron/first2000/images/$foldername
mkdir /lustre/atlas/proj-shared/nro101/... |
e2e5e4e6c4057e72a22e6ba7974354dd6c0949433b76d1e39ba671aac3cee1d1 | Shell | 375 | 11 | #!/bin/bash -x
mkdir -p data
wget https://ndownloader.figshare.com/files/13612745 -O data/guacamol_v1_all.smiles
wget https://ndownloader.figshare.com/files/13612760 -O data/guacamol_v1_train.smiles
wget https://ndownloader.figshare.com/files/13612766 -O data/guacamol_v1_valid.smiles
wget https://ndownloader.figsh... |
7c48f8ec1a22f41cb5164f45b6723de1b0a274f2d27d68450c46639e174a5ad0 | Shell | 376 | 20 | #!/bin/bash
SERIES=$1 ## GSE123456
SCRIPT=$2
FQDIR=$3
GROUP=`id -gn`
CPUS=16
RAM=128000
QUE="normal"
WDIR=`pwd`
N=`cat $SERIES.sample.list | wc -l`
#################
bsub -G $GROUP -n$CPUS -q $QUE \
-R"span[hosts=1] select[mem>$RAM] rusage[mem=$RAM]" -M$RAM \
-J "starsolo.$SERIES.[1-${N}]" \
-o %J.%I.bsub... |
b7afce00e8544e2f4f24b02d8238a476fb0ce5bfd3d55bd64ab409773ccd7fa1 | Shell | 376 | 28 | #!/bin/bash
#$ -cwd
#$ -S /bin/bash
ID=$1
ConfigFile=$2
source ${ConfigFile}
#####
DataPath=${AlignAllPath_A}
BAMFile="${ID}.bam"
OutPath=${HTseqPath_A}
#####
make_dir ${OutPath}
#### 01.HTseq
htseq-count \
-f bam \
-r name \
-s no \
-a 10 \
-t exon \
-m intersection-strict \
${DataPath}/${BAMFile} \
${GTF_GRCm39_1... |
6a7b524ec33de53d9b26b0fff58d685be4ccae8dcade262b9a00588b57270df3 | Shell | 378 | 13 | #!/bin/sh
set -o allexport
sta_i_I_range=1
end_i_I_range=50 #50
for i_I_range in $(eval echo "{$sta_i_I_range..$end_i_I_range}")
do
echo "$i_I_range"
sbatch --partition=batch --job-name V0basinkm --output data/output/V0basin-km--i_I_range-"$i_I_range"-%j.txt --error data/output/V0basin-km--i_I... |
29e1376f1ef94f1c4dc8bdcccdc81c2c36c12d1c6e2c1099cd7efcee558dc077 | Shell | 379 | 28 | #!/bin/bash
#$ -cwd
#$ -S /bin/bash
ID=$1
ConfigFile=$2
source ${ConfigFile}
#####
DataPath=${AlignAllPath_A}
BAMFile="${ID}.bam"
OutPath=${HTseqPath_A}
#####
make_dir ${OutPath}
#### 01.HTseq
htseq-count \
-f bam \
-r name \
-s no \
-a 10 \
-t exon \
-m intersection-strict \
${DataPath}/${BAMFile} \
${GTF_mRatBN7_... |
d4c137b60e556395db5f5390d266db1f8bb521efca5ef072c52a0b8b02a8d0bf | Shell | 379 | 15 | #!/bin/bash -l
#SBATCH --job-name=modelbuild
#SBATCH --time=24:00:00
#SBATCH --account=proj83
#SBATCH --partition=prod
#SBATCH --mem=0
#SBATCH --exclusive
#SBATCH --constraint=volta
source /gpfs/bbp.cscs.ch/home/pokorny/ToposampleKernel/bin/activate
python -u run_SSCx_model_building_order2_midrange.py
# EXAMPLE HOW ... |
0653976d08e0bae651030e55a3a9c2ab7020b27d548c2a904b8cce93c51f3425 | Shell | 380 | 8 | #!/bin/bash
export TINKER9=/user/tinker-nn/build/path/
export CUDA_VISIBLE_DEVICES=0 # device number; can use 1 or 2 if there are multiple GPU cards
$TINKER9/dynamic9 start.xyz -k cu.key 5000000 2 2 4 200 1 N > npt.out &
echo $(hostname) > node.log
#number of steps; time step(fs); timee between saves(ps); ensenmble ... |
53e4838540540e7361af7a281f3a5f44a94143889275251026e1beebbf6f373f | Shell | 380 | 11 | pip install openxlab
pip install -U openxlab
openxlab login
openxlab dataset info --dataset-repo OpenDataLab/The_China_Physiological_Signal_etc
openxlab dataset get --dataset-repo OpenDataLab/The_China_Physiological_Signal_etc
openxlab dataset download --dataset-repo OpenDataLab/The_China_Physiological_Signal_et... |
5a2b3efb3bed6a272b7a69701397cd338a01ed3c7a7d1f09c44833c0b3833d2a | Shell | 380 | 1 | local_generate_classes.py --python_paths=/scratch/johnsonhj/src/NEP-11/NIPYPE --program_paths=/scratch/johnsonhj/src/NEP-11/bin:/usr/local/bin:/opt/ogs/bin/darwin-x64:/bin:/sbin:/usr/local/bin:/usr/bin:/usr/sbin:/usr/texbin:/Shared/sinapse/sharedopt/20120722/Darwin_i386/vv/bin:/usr/texbin:/scratch/johnsonhj/bin --outpu... |
8fd1b78e0760680622e70737f9d7dcc0f5d62508e2c0dbb1bf083c53054d7116 | Shell | 380 | 19 | #!/bin/bash
SERIES=$1 ## GSE123456
SCRIPT=$2
GROUP=`id -gn`
CPUS=16
RAM=4000
QUE="normal"
WDIR=`pwd`
N=`grep -w "BAM$" $SERIES.parsed.tsv | wc -l`
#################
bsub -G $GROUP -n$CPUS -q $QUE \
-R"span[hosts=1] select[mem>$RAM] rusage[mem=$RAM]" -M$RAM \
-J "bam2fastq.$SERIES.[1-${N}]" \
-o %J.%I.bsub... |
f739ec24138cf847d7c0dc3b543ffa9da396d8ac23bad23105463f9998923d8c | Shell | 380 | 23 | #!/bin/bash
echo "Installing NeuroDebian dependencies"
set -eu
echo "INSTALL_DEB_DEPENDENCIES = $INSTALL_DEB_DEPENDENCIES"
DEPS=(
fsl
# afni
# elastix
fsl-atlases
xvfb
fusefat
graphviz
)
if $INSTALL_DEB_DEPENDENCIES; then
bash <(wget -q -O- http://neuro.debian.net/_files/neurodebian-travis.sh)
... |
68d9c96124718fdc46fede07ac2c495a17f1bb89c3503f2ff0d5d65539991a1a | Shell | 382 | 19 | #!/bin/bash
SERIES=$1 ## GSE123456
SCRIPT=$2
GROUP=`id -gn`
CPUS=16
RAM=128000
QUE="normal"
WDIR=`pwd`
N=`grep -w "SRA$" $SERIES.parsed.tsv | wc -l`
#################
bsub -G $GROUP -n$CPUS -q $QUE \
-R"span[hosts=1] select[mem>$RAM] rusage[mem=$RAM]" -M$RAM \
-J "sra2fastq.$SERIES.[1-${N}]" \
-o %J.%I.bs... |
1a915dac59b394651e1da5a6631cab8dbb83e37d958f26fffe1f6f47c0526c9d | Shell | 383 | 14 | #!/bin/bash
# source run_all.sh
#
echo Press Esc at anytime to skip example, F1 to interrupt
for f in *.py; do
case $f in qt*.py) continue;; esac
case $f in wx*.py) continue;; esac
case $f in trame*.py) continue;; esac
case $f in *video*.py) continue;; esac
case $f in *napari*.py) continue;; esac
... |
3d2d0fde38b1a5e3db0dac954ab789536e0b2b2e32ed4b6675dbb172cca82658 | Shell | 384 | 16 | cd ~/catkin_ws/src
catkin_create_pkg midas_cpp std_msgs roscpp cv_bridge sensor_msgs image_transport
cd ~/catkin_ws
catkin_make
chmod +x ~/catkin_ws/devel/setup.bash
printf "\nsource ~/catkin_ws/devel/setup.bash" >> ~/.bashrc
source ~/catkin_ws/devel/setup.bash
sudo rosdep init
rosdep update
#rospack depends1 midas_... |
de1b17443d8e5811bf3b4060932d5a374490f047fd6aaf33c2b669f80bc22993 | Shell | 389 | 18 | #!/bin/bash
# Copyright (c) Meta Platforms, Inc. and its affiliates.
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
set -ex
git clone https://github.com/NixOS/patchelf
cd patchelf
git checkout 0.17.2
sed -i 's/serial/parallel/g' configure.a... |
9e7b4b30886cf2186a11cbe9f93edb705cc18d40ba8b1b6b5203e452d1b28641 | Shell | 392 | 11 | #!/bin/sh
#PBS -V
#PBS -q gpu
#PBS -N test_lammps_64
#PBS -l nodes=1:ppn=1
export CUDA_VISIBLE_DEVICES=[1,0]
export OMP_NUM_THREADS=1
source /share/home/bjiangch/group-zyl/.bash_profile
#export LD_LIBRARY_PATH=/usr/local/cuda/lib64:$LD_LIBRARY_PATH #for specify the cuda path to overcome error: failed to open libnvrtc-b... |
6eeffcbf5083b757e7a6dd00741056b85f7e878017d3ba81fc7c13f6f76efd83 | Shell | 393 | 12 | export BASE_URL=http://cvgl.stanford.edu/data2/ModelNet40/
# set progress option accordingly
wget --help | grep -q '\--show-progress' && \
_PROGRESS_OPT="-q --show-progress" || _PROGRESS_OPT=""
wget $_PROGRESS_OPT ${BASE_URL}/ModelNet40.tgz
tar -xzf ModelNet40.tgz
cd ModelNet40
wget ${BASE_URL}/train_modelnet40.txt... |
d98e4ee28e89ffa8cd2ebfbec8ce96d7a21ec30571a2d8628e81f6a0bb80c187 | Shell | 393 | 12 | #!/bin/sh
#PBS -V
#PBS -q testv5
#PBS -N h2o-0-reann
#PBS -l nodes=1:ppn=28
#export CUDA_VISIBLE_DEVICES="0,1"
export OMP_NUM_THREADS=1
source /public/home/group_zyl/.bashrc
#export LD_LIBRARY_PATH=/usr/local/cuda-11.1/lib64:$LD_LIBRARY_PATH #for specify the cuda path to overcome error: failed to open libnvrtc-builtins... |
205ba00c7215fc3be2199885ddda41c5658e7834ff5b5912497dc57b0a533b00 | Shell | 394 | 10 | # /bin/bash
# bash run_example.sh {file_to_run.py} {num_gpus}
# where file_to_run = example to run. Default = 'example.py'
# num_gpus = num local gpus to use (must be at least 2). Default = 2
# samples to run include:
# example.py
echo "Launching ${1:-example.py} with ${2:-2} gpus"
torchrun --nnodes=1 --nproc_per_nod... |
59110b2e614c73fb2040c623e83bda0627dc95a3d6ea7923e7a16686d568694e | Shell | 394 | 21 | CONFIG_DIR=$1
REPEAT=$2
MAX_JOBS=${3:-2}
SLEEP=${4:-1}
MAIN=${5:-main}
(
trap 'kill 0' SIGINT
CUR_JOBS=0
for CONFIG in "$CONFIG_DIR"/*.yaml; do
if [ "$CONFIG" != "$CONFIG_DIR/*.yaml" ]; then
((CUR_JOBS >= MAX_JOBS)) && wait -n
python $MAIN.py --cfg $CONFIG --repeat $REPEAT --mark_done &
ech... |
cfaf9c2fd98cc004a46944f5f9159b1e591bf0d057a685f4fed8872c6e083c66 | Shell | 394 | 9 | #!/bin/bash -l
num_gpus=4
# need to assign GPUs in reverse order due to topology
# See Polaris Device Affinity Information:
# https://www.alcf.anl.gov/support/user-guides/polaris/hardware-overview/machine-overview/index.html
gpu=$((${num_gpus} - 1 - ${PMI_LOCAL_RANK} % ${num_gpus}))
export CUDA_VISIBLE_DEVICES=$gpu
ech... |
d3e3ee29a5cf39703bf5ba52ae11e02acdb6e7e618529bac80716d098f3035bd | Shell | 394 | 16 | sbatch Atf3.2vs14.sh
sbatch Cldn9.2vs14.sh
sbatch Fibroblast.2vs14.sh
sbatch Immune_Cell.2vs14.sh
sbatch Mrgpra.2vs14.sh
sbatch Mrgprd.2vs14.sh
sbatch Neuron.2vs14.sh
sbatch Nppb.2vs14.sh
sbatch Red_blood_cell.2vs14.sh
sbatch S100b.2vs14.sh
sbatch Satellite_Cell.2vs14.sh
sbatch Schwann_Cell.2vs14.sh
sbatch Th_Fam19a4.2... |
691e6d3d72ba7eb8dc1b933c8603a85f330820457ac1b67baf24d6ea25bd68ae | Shell | 397 | 12 | #!/bin/sh
#removes specified .ffp files from merged_ffp directrory generated by step2. Run before step 3
export merged_ffp=$1
export remove_ffp_list_file=$2
#And remove all block files
awk -v working_dir=$merged_ffp '{print "rm "working_dir"/"$1".ffp"}' $remove_ffp_list_file > $merged_ffp/remove_specific_ffp.sh
chm... |
32c50a41ef40c11f2b9cbe458c909a4828676128e0772dca1360e22d5304bcba | Shell | 398 | 18 | for i in {0}
do
python ./train.py \
--gpu_ids '0,1' \
--wandb_entity [your_wandb_entity] \
--wandb_project SKD \
--model 'resnet18' \
--interval_rate 0.0 \
--dataset 'cifar100' &\
python ./train.py \
--gpu_ids '0,1' \
--wandb_entity [your_wandb_entity] \
--wandb_project SKD \
... |
7b3c40687deac3f3fd4e3160e415647d54b2718a1f3f4b96e7ac1806aeae053b | Shell | 399 | 20 | #!/bin/bash
#SBATCH -e logs/variant_filtering/mosdepth-%j.err
#SBATCH -o logs/variant_filtering/mosdepth-%j.out
#SBATCH --time=00-00:30:00
#SBATCH --mem=10G
#SBATCH --cpus-per-task=10
module load mosdepth
# input bam file
bam=$1
# sample name
sample=$(basename -a ${bam} | cut -d'_' -f1,2,3,4)
# output directory
out... |
abbe6e5ca3eb7e04c2dbb7964f04a09e0c8e2b19379b056ab746c78cce88e904 | Shell | 399 | 20 | #!/bin/bash
SERIES=$1 ## GSE123456 - need this for properly formatted job names only
SCRIPT=$2
URLS=$3
GROUP=`id -gn`
CPUS=1
RAM=100
QUE="transfer"
N=`cat $URLS | wc -l`
WDIR=`pwd`
#################
bsub -G $GROUP -n$CPUS -q $QUE \
-R"span[hosts=1] select[mem>$RAM] rusage[mem=$RAM]" -M$RAM \
-J "transfer.$SE... |
6289431b18d25f70477993a959aa28c37b39ab28c7a4c243823b8d709da2f184 | Shell | 401 | 15 | #!/bin/bash
echo "WARNING!!! This command will totally reset the Pisces2 caches (./feature_cache) and results directories (./results)."
echo "This action is irreversible."
echo -n "Type 'delete' to proceed: "
read input
if [ "$input" = "delete" ]; then
echo "Deleting ./results and ./feature_cache..."
rm -rf .... |
96919eccef414d2c3c0f78dda762e1b7ea519767d1a83a3d297591c73646d4dd | Shell | 401 | 13 | #!/bin/bash
set -Eeuo pipefail
base_dir=$(dirname $(dirname $0))
echo "Generating api directory with public APIs..."
# Generate API Files
python3 "${base_dir}"/api_gen.py
# Format code because `api_gen.py` might order
# imports differently.
echo "Formatting api directory..."
(SKIP=api-gen pre-commit run --files $(fi... |
aa9a00709638ae2bc39cdc31b71f04b5801e7e24c3a10540613eb07e11b21b9b | Shell | 402 | 22 | #!/bin/bash
export TEMP="$1"
shift
export N="$1"
shift
export NEURONHOME="$N"
export PATH="$N/bin:$N/mingw/usr/bin:$N/mingw/mingw64/bin:$PATH"
echo $N
echo $PATH
source set_nrnpyenv.sh
export PYTHONPATH="$PYTHONPATH:$N/lib/python"
export MINGW='yes'
$N/lib/mos2nrn1.sh "$1"
a=$?
if test $a -ne 0 ; then
echo'
mos2nrn... |
75670cc540a090084fd24e6a45c637e754760a042f12c306c0f49838f9d2fe52 | Shell | 404 | 9 | # get cpu clock
cd ../s2_lab_sw/host/units/s2_top/tc_s2app_qsar_19bill
echo "---------------------------------------------------------------------------"
echo "Measurement for 150MHz case"
python cnt_clk.py -l 1 -r log/measurement/150
echo "---------------------------------------------------------------------------"
ec... |
627bcc07c997c7ae634a5bcd078cf9dca370efcd88305b5b5d475089e1873c89 | Shell | 405 | 6 | #!/bin/bash
#Author: Yang Li <yal054@ucsd.edu>
#File: run.sh
#Create Date: 2019-02-13 23:19:14
snakemake -p --rerun-incomplete -k -j 128 --cluster "qsub -l {cluster.ppn} -l {cluster.time} -N {params.jobname} -m a -q {cluster.queue} -o pbslog/{params.jobname}.pbs.out -e pbslog/{params.jobname}.pbs.err" --jobscript jobs... |
7a5999bb92c34588c5e7aa6576d67c3133574aaf106d8fc9291d658a8cb78e45 | Shell | 405 | 17 | #/bin/bash
outdir="sam"
inp="fragments"
for sample in `cat list.86`
do
bam="$inp/$sample/outs/possorted_bam.bam"
if [ ! -f $outdir/header_${sample}.sam ]; then
echo "Processing sample: $sample"
echo "Input BAM: $bam"
samtools view -H "$bam" > "$outdir/header_${sample}.sam" # Extract header
samt... |
de462471085b43283b5fed41b73a89cec4a52ef1117a8d678fd407009167d006 | Shell | 405 | 14 | #!/bin/bash
target_dir="evaluation/with_results/"
# List all folders in the current directory
for folder in "$target_dir"*/; do
# Remove trailing slash from folder name
folder_name="${folder%/}"
# Run the Python script and pass the folder name as an argument
python eval.py --file_path "$folder_na... |
0014424dfb30d42acfd434b8013b251ad34385a191227ff1949b4f3f96245bd5 | Shell | 406 | 16 | #!/usr/bin/env bash
# Installs LASErMPNN and LigandMPNN repositories inside the NISE directory.
git submodule update --init --recursive
# Untar the REDUCE hetdict.
tar -xvf hetdict.tar.gz
# Install LigandMPNN weights
cd ./LigandMPNN
bash get_model_params.sh "./model_params"
cd ..
# Creates a virtual environment in ... |
56f9c13b8cc8cc4d619e424a2d4aea665e3a66ff01b30a84bfe33fa295408ae4 | Shell | 406 | 16 | #! /bin/sh
#
# test.sh
# Copyright (C) 2019 rkim <rkim@salk.edu>
#
# Distributed under terms of the MIT license.
#
for i in {1..10}; do \
python main_sequential.py --gpu 0 --gpu_frac 0.20 --n_trials 10000 --mode train \
--N 200 --P_inh 0.20 --som_N 0 --task go-nogo --gain 1.5 --P_rec 0.20 \
--act sigmoid --loss_... |
5c5a46419d1b7fdaa6db941e4fd906e46c90cefb83c1ef9f51f9130e07723e86 | Shell | 406 | 16 | #! /bin/sh
#
# test.sh
# Copyright (C) 2019 rkim <rkim@salk.edu>
#
# Distributed under terms of the MIT license.
#
for i in {1..5}; do \
python main_sequential.py --gpu 0 --gpu_frac 0.20 --n_trials 10000 --mode train \
--N 100 --P_inh 0.20 --som_N 0 --task go-nogo2 --gain 1.5 --P_rec 0.20 \
--act sigmoid --loss_... |
d0c706248ad9d338ea0fd9182809fa4c0bf0b020f101de6c5b32cfdf468254ce | Shell | 406 | 24 | #!/bin/bash
#$ -cwd
#$ -S /bin/bash
ID=$1
ConfigFile=$2
source ${ConfigFile}
#####
DataPath=${FastqPath_unzip}
OutPath=${FastpPath}
#####
make_dir ${OutPath}
#####
fastp \
--in1 ${DataPath}${FASTQ0_unzip} \
--out1 ${OutPath}${FASTP0} \
--html ${OutPath}${ID}.report.html \
--json ${OutPath}${ID}.report.json \
-... |
896a73b4dda94fd0c39521e1fd0bf6702a72fdc42e380405d81651e5d7488a85 | Shell | 407 | 11 | #!/bin/bash
# makeotf psf.dv otf.otf -angle -0.804300 -ls 0.2035 -na 1.4 -nimm 1.515 -fixorigin 3 20
parent_path=$( cd "$(dirname "${BASH_SOURCE[0]}")" ; pwd -P )
APP="$parent_path/../cmake_build/cudaSirecon/cudasirecon"
# test TIFF
$APP $parent_path raw $parent_path/otf.tif -c $parent_path/config-tiff
# test MRC
$A... |
376929f2252776fa9f1e7b20b829df421880d0a4007c7f68c12d4b1c78427e7e | Shell | 408 | 15 | #!/bin/bash
# Copyright (c) Meta Platforms, Inc. and affiliates.
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
export GLOG_minloglevel=2
export MAGNUM_LOG=quiet
set -x
python -u -m torch.distributed.launch \
--use_env \
--nproc_per... |
7a3a36b2fcc458d75859ca8f587c7c82fd1007fa06c6f58e173add804c0b0023 | Shell | 408 | 12 | #!/bin/bash
nohup python -m pipelines.pca \
-i 'chd_ukbb' \
-o 'file:///home/ubuntu/data/hail_data/sample_qc/pca_european_samples_03112021.ht' \
--n_pcs 10 \
--maf_threshold 0.01 \
--overwrite \
--write_to_file \
... |
dd4b59f82e880acf762d294791de70787c1e8b0e1f5139c2242dd3f776d22701 | Shell | 408 | 24 | #!/bin/bash
echo Creating isolated virtual environment
source tools/ci/env.sh
set -eu
# Required variables
echo SETUP_REQUIRES = $SETUP_REQUIRES
set -x
python -m pip install --upgrade pip virtualenv
virtualenv --python=python virtenv
source tools/ci/activate.sh
python --version
python -m pip install -U $SETUP_REQ... |
2a183e8572b9703929756183cc4af2f8368c2da2455f3641acf424a428674ac9 | Shell | 411 | 21 | #!/usr/bin/env bash
set -ex
mlflow_envs=$(
conda env list | # list (env name, env path) pairs
cut -d' ' -f1 | # extract env names
grep "^mlflow-[a-z0-9]\{40\}\$" # filter envs created by mlflow
) || true
if [ ! -z "$mlflow_envs" ]; then
for env in $mlflow_envs
do
conda... |
843c9546a1661e71b8da8593c2b45b2c62049c4753577877c05675f68bb738fe | Shell | 411 | 14 | #!/bin/bash
#SBATCH -c 2
#SBATCH -t 0-00:30
#SBATCH -p short
#SBATCH --mem=16G
#SBATCH -o jobs/test_l2_10ids_%j.out
#SBATCH -e jobs/test_l2_10ids_%j.err
# One-shot diagnostic: try fetching L2 skels for the 10 SeaTable neurons that
# came back without a region today (2026-05-15).
set -uo pipefail
cd /home/ab714/bancpipe... |
51b8721fdba5aa4f0a95b3c86c5b1c75205f8dd93d0a61c56ee4083954e81f7e | Shell | 413 | 21 | #!/usr/bin/env bash
set -euo pipefail
# Smoke test for CRN_Sim (R12-CROWN)
#
# Runs:
# 1) import checks
# 2) R12-CROWN/run_all.py
# 3) R12-CROWN/validate_checkpoints.py
python - <<'PY'
import sys
print('Python:', sys.version)
mods=['numpy','scipy','pandas','matplotlib','yaml']
for m in mods:
__import__(m)
p... |
875920655558c4a21e2a3b067ea96ca15b0da820cc59a5d0629061ed894b7fac | Shell | 414 | 24 | #!/bin/bash
#$ -cwd
#$ -S /bin/bash
ID=$1
ConfigFile=$2
source ${ConfigFile}
#####
DataPath=${FastqPath_unzip_A}
OutPath=${FastpPath_A}
#####
make_dir ${OutPath}
#####
fastp \
--in1 ${DataPath}${FASTQ0_unzip_A} \
--out1 ${OutPath}${FASTP0_A} \
--html ${OutPath}${ID}.report.html \
--json ${OutPath}${ID}.report.j... |
8b5656c274c20039d52cdb089c5b514252ff133a7c9fbd7bc570eb0114e1f854 | Shell | 414 | 7 | cd /data/share/htp/perturb-seq/TF94_combined/species_demultiplexing
for lane in `cat /data/share/htp/perturb-seq/TF94_combined/download_from_tuebingen/ids.txt`
do
sbatch -J hg38_${lane}_demux --output=hg38_${lane}_%j.out --exclude=gorilla4 run_cellsnp_supervised.sh hg38_${lane}
sbatch -J macFas6_${lane}_demux --ou... |
04f4f306a4c9384878e783ae6e7dd8a4d1b253916a2d60223af90069a97dc791 | Shell | 415 | 26 | #!/bin/bash
echo Installing dependencies
source tools/ci/activate.sh
source tools/ci/env.sh
set -eu
# Required variables
echo EXTRA_PIP_FLAGS = $EXTRA_PIP_FLAGS
echo DEPENDS = $DEPENDS
set -x
if [ -n "$EXTRA_PIP_FLAGS" ]; then
EXTRA_PIP_FLAGS=${!EXTRA_PIP_FLAGS}
fi
if [ -n "$DEPENDS" ]; then
pip install ... |
386a8efa469923f47c13fb618246c9e6b9b257cb7d38235086eea51d37e6768d | Shell | 415 | 11 | #!/bin/bash
nohup python -m vep.vep_parser \
--vcf_vep_path file:///home/ubuntu/data/chd_ukbb_vep/recal_snp_recal_indelgenome.sorted.test.vcf.bgz \
--tb_output_path file:///home/ubuntu/data/hail_data/hts/chd_ukbb.vep.split.ht \
--force_bgz \
--write_to_file \
... |
2e2971b64ad0425156b1968fec9c6208d542c8ec93f4e28d1c058c6ed7cd0799 | Shell | 417 | 7 | #!/usr/bin/env bash
aws --version
aws s3 ls s3://superconductive-public/static/gallery/ | grep staging
aws s3 cp s3://superconductive-public/static/gallery/expectation_library_v2--staging.json s3://superconductive-public/static/gallery/expectation_library_v2.json
aws s3 cp s3://superconductive-public/static/gallery/p... |
3c9b5510bb3334df372640bf36ea7bd7e31c0dbc51967ad52c38129ba7518646 | Shell | 418 | 8 | #!/bin/bash
for i in {1..164}
do
/lustre/atlas2/nro101/proj-shared/BigNeuron/Script_Vaa3D_svn_ORNL/script_MPI/gen_bench_pbs_scripts.sh 27 27 /lustre/atlas2/nro101/proj-shared/BigNeuron/zhi/bigneuron_annotation_consolidated_batch_run/gold166/pbs_all/gold166_$i.pbs /lustre/atlas2/nro101/proj-shared/BigNeuron/zhi/b... |
3fe55897d6dbbba5943defe4ae51e1c8eaa2ea0308bda908852353dd1c4536f4 | Shell | 418 | 8 | #!/bin/bash
for i in {1..164}
do
/global/project/projectdirs/m2043/BigNeuron/Script_Vaa3D_svn_LBNL/script_MPI/gen_bench_pbs_scripts.sh 27 27 /global/project/projectdirs/m2043/BigNeuron/zhi/bigneuron_annotation_consolidated_batch_run/gold166/pbs_all/gold166_$i.pbs /global/project/projectdirs/m2043/BigNeuron/zhi/b... |
5276cedd9dee35ae8177812220e7919591a1caf23b1859348ba6d4a9d6d45070 | Shell | 418 | 26 | #!/bin/bash
#SBATCH -A m2_jgu-funcpoll
#SBATCH -J run_racon
#SBATCH -C skylake
#SBATCH -p parallel
#SBATCH -n 1
#SBATCH -c 1
#SBATCH -t 04:00:00
#SBATCH -v
#SBATCH -o run_racon.%j.out
#SBATCH -e run_racon.%j.err
module purge
module load bio/Racon/1.5.0-GCCcore-11.2.0
PROJECT_DIR=/lustre/project/m2_jgu-funcpoll
F... |
4648e490c77f3d3b5f90e29cd8c5b669beafc43046f9908fccb6fb176adbce45 | Shell | 420 | 4 | # Estimate mean volumes and mean surface values inside ROI
/data/project/sleep_ENIGMA_insomnia/Tools/CAT12.8.1_r2040_R2017b_MCR_Linux/standalone/cat_standalone.sh -m /data/group/sysmed/TOOLS/MCR/v93 \
-b /data/project/sleep_ENIGMA_insomnia/Tools/CAT12.8.1_r2040_R2017b_MCR_Linux/standalone/cat_standalone_get_ROI_value... |
7531c71f9c2230f94162498b2637da736199f8211d13bcd888eb9e8663b1296a | Shell | 420 | 29 | #!/usr/bin/env bash
# Get top level of git repo
git --version > /dev/null
if [ $? -ne 0 ]
then
echo "Could not find git executable"
exit 1
fi
top_level=$(git rev-parse --show-toplevel)
if [ -z "$top_level" ]
then
echo "This is not a git repository"
exit 1
fi
case $(uname) in
Linux)
IPT=$top_level/... |
a444a3401f8efadfbd4c300fc90d74e19f51c46af3baf75d5e4556d1de80ef30 | Shell | 420 | 8 | #!/bin/bash
cd /data/mat/zhi/BigNeuron/first2000/images/
for filename in `ls -d *`
do
/local1/work/vaa3d_tools/hackathon/zhi/neuron_comparison_script/batch_reconstruction.test /data/mat/zhi/BigNeuron/Vaa3D_BigNeuron_version1/vaa3d "/data/mat/zhi/BigNeuron/first2000/images/"$filename"/"$filename "/data/mat/zhi/BigNeuro... |
ca218adce7143cef81e59fb0ae6b4f0535a3205d924c72e6bd484900ad021631 | Shell | 420 | 14 | #!/bin/bash
cd /lustre/atlas2/nro101/proj-shared/BigNeuron/data/taiwan16k/img_anisosmooth/
for filename in `ls -d *`
do
cd $filename
echo $filename
for file in `ls *.swc`
do
mv $file /lustre/atlas2/nro101/proj-shared/BigNeuron/data/taiwan16k/reconstructions_for_img_anisosmooth/$filename/
done
cd ..
# /lustr... |
051b56712c4420b75f6654446ffec4586e90685c8b0c813444f21817b071f8d6 | Shell | 421 | 18 | #!/bin/bash
# set the pisces data dir
if [ -z "$1" ]; then
echo "Usage: $0 <host_pisces_data_dir>" >&2
exit 1
fi
HOST_PISCES_DATA_DIR=$1
docker run -it --gpus all --ipc=host --security-opt label=disable \
--rm \
-e PISCES_DATA_DIR=/home/ubuntu/data \
-v "$PWD":/home/ubuntu/workspace \
-v "$HOST_PISCES_DA... |
180698eb7fed27b4c306398e65d63eaeffa2e8e83bf49684ac04e388a46f4130 | Shell | 421 | 16 | #!/bin/bash
tools_dir=$(realpath $(dirname $(command -v $0)))
[[ -d $tools_dir/pkg/workbench ]] && rm -rf $tools_dir/pkg/workbench
mkdir -p $tools_dir/pkg
pushd $tools_dir/pkg > /dev/null
# download workbench
if [[ ! -f workbench-linux64-v1.5.0.zip ]]; then
wget https://www.humanconnectome.org/storage/app/media/w... |
724e3cd8fdae834ea64dcd21ef4fb1ef54db20c8c355b7d85451dfff862700c9 | Shell | 421 | 20 | #!/bin/bash
#SBATCH --time=1-00:00:00
#SBATCH --mem=40G
#SBATCH --cpus-per-task=12
module load repeatmasker
# read reference genome as first argument
ref=$1
# dir is created in the same directory as the reference genome
ref_dir=$(dirname $ref)
if [ ! -d ${ref_dir}/repeatmasker ]; then
mkdir ${ref_dir}/repeatmask... |
aa7441eb7404f232ba6b93b44434ebf7e3f02c42a0573b38a6961c2c36b427f7 | Shell | 422 | 15 | python ./train_kfold/train.py \
--xlsx ./data/revision/descriptors_all.xlsx \
--mapping ./descriptors_group/descriptorsMap/descriptorsMapping.json \
--k 10 \
--a 0.1 \
--epochs_embed 200 \
--trials 2 \
--epochs_tr 500 \
--patience 50 \
--bs_tr 512 \
--only_sheet EOV \
--only_... |
d382c2ed4092215f678c5a663af1ecc47ce3611e86e0a3322e2732a255b2e757 | Shell | 422 | 13 | #!/bin/bash
set -e
input_dir=$(readlink -f "$1")
output_dir="$(pwd)/pod5-benchmark-outputs"
mkdir -p "${output_dir}"
script_dir=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )
echo "Running benchmark on input '${input_dir}'"
docker run --rm -it -v"${input_dir}":/input -v"${output_dir}":/output... |
079a46d60fd62d83755dbc1745bd93b56451c95889085bf5b825c9f5ea6b27bd | Shell | 426 | 15 | #!/bin/bash
# define project directory and working directory
pd=/your/project/directory/
wd=$pd/data/neural_differentiation_dataset/genomes
# create STAR indices for all genomes
for genome in hg38 gorGor6 macFas6
do
sbatch --cpus-per-task=15 \
--mem=30G \
--job-name=${genome}_bwa_mem2 \
... |
cda9f5de75e46988b7b180692209c36241a357d707011bfacffa8584bbbab55d | Shell | 427 | 15 | #!/usr/bin/env bash
set -e
./dev/generate-protos.sh
GIT_STATUS="$(git status --porcelain)"
if [ "$GIT_STATUS" ]; then
echo "Protobufs were not generated with protoc. Please run './dev/generate-protos.sh' or comment '/autoformat' on the PR"
echo "Git status is"
echo "------------------------------------------------... |
142304b4a128b6044b3fee4d67039f50cdc336d1f204ba9e2fa59da1b7361ab6 | Shell | 429 | 9 | # get power and energy
cd ../s2_lab_sw/host/units/s2_top/tc_s2app_qsar_19bill
echo "---------------------------------------------------------------------------"
echo "Measurement for 150MHz case"
uv run python calc_energy.py -r power_record_150_0.log
echo "---------------------------------------------------------------... |
0febc65e96db60aa454509c297ddd504e5f6c7e79389f72483679084e270c50b | Shell | 430 | 17 | sam=$1
out=$2
#chrom=$3
#start=$4
#end=$5
vicin=100000
samtools view $sam | cut -f3,4 | uniq | awk '{print $0"\t"$2}' > $out
# Filtering regions in vicinity:
#samtools view $sam | awk -v awkchrom="$chrom" -v awkstart=$start -v awkend=$end -v awkvicin=$vicin\
# '($3 != awkchrom) || (($3 == awkchrom) && (($4 < awksta... |
8f0e94319b3f79e66c61cce3f2e16d43760b8b870a9ce13346a74ae62e18aedb | Shell | 430 | 29 | #!/bin/bash
# HTSlib first
cd htslib
if [ ! -f libhts.a ]; then
make
fi
cd $DEPS
#Bio::DB::HTS
cd Bio-HTS
perl Build.PL
./Build
./Build test
./Build install
cd $DEPS
# kent src
export MACHTYPE=$(uname -m)
export MYSQLINC=`mysql_config --include | sed -e 's/^-I//g'`
export MYSQLLIBS=`mysql_config --libs`
# Build ... |
ae8192ac7668d4651f9d25c0848a3b820028c455120b084774f64ffe3ac9d8b0 | Shell | 430 | 21 | #!/bin/bash
# BA-Pred Example Inference Script
if command -v bapred &> /dev/null; then
bapred \
-r 1KLT.pdb \
-l ligands.sdf \
-o result.tsv \
--batch_size 64 \
--device cuda
else
cd ..
python -m bapred.inference \
-r example/1KLT.pdb \
-l example/li... |
77a34ad829c1c840c1907cceeb9c5b48101e0c010f0ab68bc5c5ea8fd4c84e9e | Shell | 431 | 20 | ##DIRECTORY
workdir=/Volumes/DJICopilot/REST-meta-PD
CCS_DIR=/Users/mac/Projects/CCS
##LOOP GLOBAL METRICS
for metric in alff
do
echo "Estimating normative charts for ${metric} ..."
metricdir=${workdir}/nmm/data/${metric}
cd ${metricdir}
if [ ! -f centiles_estimate.R ]
then
cp ${workdir}/scripts/t... |
393e5f8b698b9f59f08ea2b95497e08e374759cd49c43f54ecad5eb3340f36e7 | Shell | 432 | 5 | # Preprocessing
/data/group/sysmed/TOOLS/CAT12.8.1_r2040_R2017b_MCR_Linux_HB/standalone/cat_standalone.sh -m /data/group/sysmed/TOOLS/MCR/v93 \
-b /data/group/sysmed/TOOLS/CAT12.8.1_r2040_R2017b_MCR_Linux_HB/standalone/cat_standalone_segment_enigma.m \
/data/project/sleep_ENIGMA_insomnia/Data/KUMS_Iran_20.07.2021/KU... |
cea2df5b755429e6848f77dfced4fa029d048c8cb3461aad449c7cd878cbeb70 | Shell | 432 | 19 | #!/bin/bash
#SBATCH --output=logs/alignment/qualimap-%j.out
#SBATCH --error=logs/alignment/qualimap-%j.err
#SBATCH --time=02:45:00
#SBATCH --mem=20G
#SBATCH --cpus-per-task=10
module load qualimap
bam=$1
out_dir=$2
sample=$(echo $bam | rev | cut -d'/' -f1 | rev | cut -d'_' -f1,2,3,4)
qualimap bamqc \
-bam ${bam} \... |
0e4fda01a9cf50e81f2fb8e6b4c5478da442e7a175721daf6763a3ec8e09922e | Shell | 433 | 15 | #!/bin/sh
juliapath=`which julia`
compiled_code="./SimplicialTS/Simplicial.so"
nthreads=6
input_file="./SimplicialTS/data/TS_Schaefer60S_gsr_bp_z.mat"
###Launching the code
#time julia -J ${compiled_code} --threads ${nthreads} simplicial_multivariate.jl ${input_file}
##Launching the code only for time 1-20 using ... |
0d617221939b75164c4fa71b55e7e2820a4b8f6d238c2f6fbdae9cbdfa8f1933 | Shell | 435 | 13 | #!/bin/bash
#SBATCH --job-name=ucb-model_%a
#SBATCH --output=logs/ucb-model/estimate_%A_%a.out
#SBATCH --error=logs/linear-model/estimate_%A_%a.err
#SBATCH --array=1-20%20
#SBATCH --time=00:10:00
#SBATCH --cpus-per-task=1
#SBATCH --mem=4G
# Run the Julia script
cd /vols/Scratch/jdf650/DPhil-Human-fMRI-HybridModellingR... |
0ef1c2fa5ce89ea70488b39c99465a0bf9182bab3633ea487021ee75bbb297a7 | Shell | 435 | 14 | #!/bin/bash
python3 ./prepare_sensitivity.py
# python3 ./standalone_stage2.py -f 0 --split sensitivity
# python3 ./standalone_stage2.py -f 1 --split sensitivity
# python3 ./standalone_stage2.py -f 2 --split sensitivity
# python3 ./standalone_stage2.py -f 3 --split sensitivity
# python3 ./standalone_stage2.py -f 4 --sp... |
f766daae5bcbbb7a8fb2bc5d999c4a7796ba68e306c8e623e136f580126c6349 | Shell | 437 | 15 | #!/bin/bash
# LSTM
python run_config.py \
-pc config/processing/spectrogram.json \
-mc config/models/lstm.json \
-cvc config/cv/tr_h_test_cdw_mc3.json \
-tc config/training/lstm.json \
-extn LSTM-tr-healthy
python run_config.py \
-pc config/processing/spectrogram.json \
-mc config/models/ls... |
dfff2bf57ee24e391614735d2bc8c1cbcb953f2ece392c8708399e381d2ee47b | Shell | 438 | 9 | python ./load_model/kfold_predict.py \
--fold_dir ./train_kfold/lg_transformer_kfold_runs/sheet_EOV/fold_1 \
--xlsx_train ./data/revision/descriptors_all.xlsx \
--sheet_train EOV \
--xlsx_new ./data/predict_data/new_test_descriptors.xlsx \
--sheet_new EOV \
--mapping ./descriptors_... |
81f1e5603f4172fbb882f25f4e9f2da431ab0eb55a348e65ed4c4a2ae72713ab | Shell | 439 | 26 | #!/bin/sh
git --version > /dev/null
if [ $? -ne 0 ]
then
echo "Could not find git executable"
exit 1
fi
top_level=$(git rev-parse --show-toplevel)
if [ -z "$top_level" ]
then
echo "This is not a git repository"
exit 1
fi
cd $top_level/Packages/doc/dot
for i in $(ls *patch-seq*.dot auto-testpulse.dot async-... |
4e128663042484507407aaa97ca4564f6303a9e0b71c9204340580e637b77108 | Shell | 441 | 21 | #!/bin/bash
#
# compiles the binaries for rwt(Plus)
# (C) Alle Meije Wink (a.wink@vumc.nl)
#
# rwt mex files -largeArrayDims
mex mdwt.c mdwt_r.c
mex midwt.c midwt_r.c
mex mrdwt.c mrdwt_r.c
mex mirdwt.c mirdwt_r.c
# Rice Wavelet Toolbox 1D extensions
mex multi1Drdwt.c
mex multi1Dirdwt.c
# Frequency domain shift-invar... |
31a8191198b79f6d8b5f1d8efe8224480d458c6b483f5fac474daacd427f95a0 | Shell | 442 | 8 | image1=/home/fs0/jdf650/scratch/InfoSamplingTask/data/masks/mask2add.nii.gz
image2=/home/fs0/jdf650/scratch/InfoSamplingTask/data/masks/Septal_Nuclei.nii.gz
out=/home/fs0/jdf650/scratch/InfoSamplingTask/data/masks/resampled_mask2add.nii.gz
flirt -in $image1 -ref $image2 -out $out -applyisoxfm 1
out2=/home/fs0/jdf650/s... |
3ee312a669272c6c172566e526455913da042a92b2fb7787881cd41c728454a8 | Shell | 442 | 23 | rm -rf cmake_build
if [ ! -d "src/IVE" ]
then
wget src/ https://www.dropbox.com/s/2twvw0go3dr3aim/IVE.zip
unzip -o -d src IVE.zip
rm IVE.zip
fi
mkdir cmake_build
cd cmake_build
CXXFLAGS="$CXXFLAGS -Wfatal-errors -Wno-deprecated-declarations"
cmake ${CMAKE_ARGS} \
-DBUILD_MRC=ON \
-DBUILD_OTF_VI... |
7c0477cfa94ad2d69b1f66d900b211438d6e70590d4e29a38ccfb2bc2f8079ce | Shell | 442 | 16 | #!/bin/bash
conda activate cyclegan_ulf
python /gpfs/data/johnsonplab/data/hyperfine/cyclegan_model/test.py \
--image ../data/CycleGAN/ULF_Tomo_KCL/val/ \
--result ../output/CycleGAN_val/ \
--batch_size 1 \
--patch_size 128 128 128 \
--netG resvit \
--name cyclegan_model_1 \
--checkpoints_d... |
3187cba5d04b4319da96c695b3ce879a980b5d6730e2765aeb28f43b04567fa7 | Shell | 443 | 19 | #!/usr/bin/env bash
error=0
for DIR in camera cmf illuminant training; do
for FILE in ./data/$DIR/*; do
echo "Processing file $FILE"
if ! check-jsonschema --schemafile ./schema/spectral_1.0.0.json $FILE; then
error=1
fi
done
done
echo "Processing file ./data/aliases.json"
... |
d66d739749ac4b200efd9b185fc17d409bac3ea4f0133a78cb68a508c35e33e3 | Shell | 444 | 13 | #!/bin/bash
#SBATCH --job-name=linear-model_%a
#SBATCH --output=logs/linear-model/estimate_%A_%a.out
#SBATCH --error=logs/linear-model/estimate_%A_%a.err
#SBATCH --array=1-20%20
#SBATCH --time=00:10:00
#SBATCH --cpus-per-task=1
#SBATCH --mem=4G
# Run the Julia script
cd /vols/Scratch/jdf650/DPhil-Human-fMRI-HybridMode... |
f979d45bb410918965996439429d3ff46d85ca78534daab79c20720d99d024ca | Shell | 444 | 15 | #!/bin/bash
cd /lustre/atlas2/nro101/proj-shared/BigNeuron/data/taiwan16k/img_gaussiansmooth/
for filename in `ls -d *`
do
cd $filename
echo $filename
for file in `ls *.swc`
do
# echo $file
mv $file /lustre/atlas2/nro101/proj-shared/BigNeuron/data/taiwan16k/reconstructions_for_img_gaussiansmooth/$filename/
don... |
599dd7bb3d21fdda10f1c9dcb1cafbd5bfe5deaf3966d418bb988b5c06ef6671 | Shell | 446 | 5 | #!/bin/bash
matlab -nojvm -nodesktop -r "m=importdata('../ants/00_fsl_to_fmriprep_subctx_AffineTransform.mat'); mm=ea_antsmat2mat(m.AffineTransform_double_3_3,m.fixed); csvwrite('../spm/00_fsl_to_fmriprep_subctx_AffineTransform.csv',mm);\
m=importdata('../ants/01_fmriprep_to_fsl_subctx_AffineTransform.mat'); mm=ea_ant... |
8fef8ac4e7a7a0b7c10961b2acebc1e465351c2667ba1a03e690187ce62a38f7 | Shell | 448 | 22 | #!/bin/bash
#SBATCH -c 10
#SBATCH --mem=40G
#SBATCH -t 03-00:00:00
# load the necessary modules
module load cesga/system miniconda3/22.11.1-1
source activate /mnt/netapp1/Store_CSIC/home/csic/eye/eba/gadma2
cd data/demographic_inference
# define the pair, the iteration number and the folder
pair=$1
n=$2
folder=$3
#... |
5545f89d69ca71c24adef2bfc38282403924c511be83edb1d3974a46fb7cd0fd | Shell | 449 | 10 | #!/bin/bash
for i in {1..27}
do
j=16
# for j in {1..16}
# do
/global/project/projectdirs/m2043/BigNeuron/Script_Vaa3D_svn_LBNL/script_MPI/gen_bench_pbs_scripts.sh 921 200 /global/project/projectdirs/m2043/BigNeuron/zhi/taiwan_16k_valid_batch_run/anisosmooth/pbs_all/taiwan16_aniso_${i}_part${j}.pbs /global/pro... |
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