sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 17k | content stringlengths 1 200k |
|---|---|---|---|---|
01cb61cca77cfd4ef33a3888f05e77bd768c7de7774175e5eee6ff90881daa6e | Shell | 488 | 11 | #!/usr/bin/env bash
pytest
docker run -e CTAT_GENOME_LIB='/genome' -v $(pwd):/data -v "$CTAT_GENOME_LIB":/genome --rm trinityctat/ctat_mutations:2.6.0-alpha.1 \
/bin/bash -c "cd /usr/local/src/ctat-mutations && pip install pytest && pytest"
singularity build -F ctat_mutations.simg docker://trinityctat/ctat_mutatio... |
85546bf12537e603c9deb22d1c28083f2d9c65f04f163937f62986bf45bbf149 | Shell | 496 | 12 | #!/usr/bin/env bash
previous_tag=0
for current_tag in $(git tag --sort=-creatordate); do
if [ "$previous_tag" != 0 ]; then
tag_date=$(git log -1 --pretty=format:'%ad' --date=short ${previous_tag})
printf "## ${previous_tag} (${tag_date})\n\n"
git log ${current_tag}...${previous_tag} --prett... |
c327b41c02947af82add5b650f1c42077be7d15e382237066e83bc9e750a7344 | Shell | 502 | 24 | #!/bin/bash
version="v0.1 - dd 29/11/2021"
kul_main_dir=$(dirname "$0")
script=$(basename "$0")
source /usr/local/KUL_apps/KUL_NIS/KUL_main_functions.sh
rm -rf KUL_LOG
mkdir -p KUL_LOG/$script
participant="John"
task_in[0]="echo hello0; echo hello1"
task_participant[0]="Stefan"
task_in[1]="sleep 10"
task_participa... |
7dc9565037a9d2bda488d8700f730e7867d3c48937b021299ff7ab7deff07ba1 | Shell | 503 | 18 | ROOT_DIR=$PWD/..
STAN_FNAME=exp10.57.14;
SAMPLING_ITERS=4000;
WARMUP_ITERS=1000;
NCHAINS=20;
DELTA=0.95;
MAX_DEPTH=20;
JITTER=0;
DATA_PATH=${ROOT_DIR}/Rfiles/fit_data.R
INIT_PATH=${ROOT_DIR}/Rfiles/param_init.R
RES_DIR=${ROOT_DIR}/samples
LOG_DIR=${ROOT_DIR}/logs
FNAME_SUFFIX="syn_cj"
for i in `seq 1 ${NCHAINS}`;do
... |
4369420d3d4663a3ef74014f347a9e3c528f9160118f6f4f3a32e9202d05a3f3 | Shell | 504 | 20 | CUDA_VISIBLE_DEVICES=5,6,7,8 python \
-m torch.distributed.launch \
--nproc_per_node 4 --nnodes=1 \
--node_rank=0 \
--master_addr="127.0.0.1" \
--master_port=9999 \
pretrain.py \
--exp_name TEST \
--epochs 0 \
--model v5 \
--sentence_shuffle false \
--validation true \
--valid_save_image_freq 10... |
90733b7a6ca5b712153117b61d9a2b032487ad5b388ae1afd631ed86dc4baec9 | Shell | 510 | 16 | ROOT_DIR="$(echo "$(cd ../ && pwd)")"
for nez in $(seq 3 1 5);
do
for snr in $(seq 0.1 0.1 2.5);
do
for i in $(seq 1 1 10);
do
sbatch run_optim.sh \
"${ROOT_DIR}/Rfiles/fit_data_snsrfit_ode_${nez}ez_snr${snr}_sample${i}.R" \
"${ROOT_DIR}/Rfiles/param_init_${nez}e... |
4e88c7460e9249ac5aa1238268b9383f9ae75d0a693e1d31504123af0edd0cbb | Shell | 512 | 20 | CUDA_VISIBLE_DEVICES=5 python \
-m torch.distributed.launch \
--nproc_per_node 1 --nnodes=1 \
--node_rank=0 \
--master_addr="127.0.0.1" \
--master_port=8668 \
zero_shot_cls.py \
--exp_name TEST_Zero \
--epochs 1 \
--model v5 \
--sentence_shuffle false \
--validation true \
--valid_save_image_fre... |
5287eac2a996754e08bc497d785a62fffc21199214e3ffa852b75576066c00ce | Shell | 512 | 15 | module load apps/matlab/2021b
cd /public/home/lishr2022/Project/Cross-modal/beta_estimate
subject=$1
#python step1_rescale.py
#matlab -nodisplay -r "step2_beta_estimate('${subject}'); exit;"
#matlab -nodisplay -r "run('test_onoff'); exit;"
#python unmatch_step1_rescale.py
#matlab -nodisplay -r "unmatch_step2_beta_es... |
87a0671a33ba4003b08f0acbf606076fcd157ef226a693a5e0541448d5c72178 | Shell | 517 | 20 | #!/bin/bash
# Example run configuration for Nanopore methylation analysis
# Set paths
INPUT_DIR="/data/nanopore/fastq_gpu_hac_mod"
OUTPUT_DIR="/data/nanopore/methylation_results"
REFERENCE_GENOME="/data/references/genome.fna"
# Submit job with custom thread count
sbatch scripts/NanoporeToBED.sh \
-i "$INPUT_DIR" \
... |
2078296e4a4c407ed7410239c63d71e300442e38fc6c1fb1e5e479956e56b1e9 | Shell | 518 | 15 | #!/bin/sh
# Choose the GHOME variable depending on your gurobi version
export GHOME_702="/opt/gurobi702/linux64"
export GHOME_752="/opt/gurobi752/linux64"
export GHOME_800="/opt/gurobi800/linux64"
export GHOME=$GHOME_800
if [ -d $GHOME ]; then \
#$GHOME/bin/grbgetkey $LICENSE_KEY && \
# Export path
echo "export G... |
5ec07a9eb258be8199e27f915ab3a9a66d1b47836f51a2243a634a6f05860c8e | Shell | 523 | 17 | #!/bin/bash
#
# Copyright (c) 2018 German Cancer Research Center (DKFZ).
#
# Distributed under the MIT License (license terms are at https://github.com/DKFZ-ODCF/AlignmentAndQCWorkflows).
#
#PBS -l nodes=1:ppn=1
#PBS -l walltime=5:00:00
#PBS -l mem=3g
#PBS -m a
[[ ! -f $DIR_METRICS ]] && mkdir -p $DIR_METRICS
cd $DI... |
3a89b4225b7d642cac2ca8ae441f51107bee7aa8948e2dbe95c8cc2cc2a94aef | Shell | 528 | 20 | CUDA_VISIBLE_DEVICES=5,6,7,8 python \
-m torch.distributed.launch \
--nproc_per_node 4 --nnodes=1 \
--node_rank=0 \
--master_addr="127.0.0.1" \
--master_port=9999 \
pretrain.py \
--exp_name v5,from_report_pretrain_e79 \
--epochs 50 \
--model v5 \
--sentence_shuffle false \
--validation true \
--... |
cc49f21ad92fb8c9ea819871455e5428eb2ac5026cb0c981ecbc5bee90640d7f | Shell | 528 | 16 | #!/usr/bin/env bash
# Check status of Slurm job
jobid="$1"
if [[ "$jobid" == Submitted ]]; then
echo smk-simple-slurm: Invalid job ID: "$jobid" >&2
echo smk-simple-slurm: Did you remember to add the flag --parsable to your sbatch call? >&2
exit 1
fi
output=$(sacct -j "$jobid" --format State --noheader | hea... |
dda77fee380d2300c88ec63dd3d64a2ca241c4ecca73c9e85f6bc0c8a748aef5 | Shell | 530 | 24 | #!/bin/bash
set -e
# Export environment variables
export PYTHONPATH=/workspace/truesight:$PYTHONPATH
# Run the finetuning daemon
source .venv/bin/activate
source .env
# Load .env file
if [ -f .env ]; then
export $(cat .env | grep -v '^#' | xargs)
fi
export VLLM_ALLOW_RUNTIME_LORA_UPDATING=True
vllm serve $VLLM_MOD... |
6561e8b96d3af0f8bad2ad0f3aadd692de71d1531685492475940f6817c2fba5 | Shell | 534 | 20 | #!/bin/bash
#SBATCH --job-name="P_Z"
#SBATCH --output=out
#SBATCH --error=err
#SBATCH --partition=accardi-gpu4
#SBATCH --nodes=1
#SBATCH --mem=250G #Large Request
#SBATCH --ntasks-per-node=16
#SBATCH --gres=gpu:1
#SBATCH -t 48:00:00
BASE_DIR=$(pwd)
PDB_FILE="$BASE_DIR/../step5_input.pdb "
XTC_FILE="$BASE_DIR/../ZFC_t... |
cbe0f4b854a85a8d14065efab4a291868536586f9d82b87c1378ca651f7e8228 | Shell | 534 | 20 | #!/bin/bash
#SBATCH --job-name="P_Z"
#SBATCH --output=out
#SBATCH --error=err
#SBATCH --partition=accardi-gpu4
#SBATCH --nodes=1
#SBATCH --mem=250G #Large Request
#SBATCH --ntasks-per-node=16
#SBATCH --gres=gpu:1
#SBATCH -t 48:00:00
BASE_DIR=$(pwd)
PDB_FILE="$BASE_DIR/../step5_input.pdb "
XTC_FILE="$BASE_DIR/../ZFA_t... |
37c9985f023f3d3f7e3e6c27d6498b1b8a1171bfafa09473d5c27188ba84d763 | Shell | 539 | 14 | #!/bin/bash
# Define radius (um)
r_mean=2.00
# Define MT induced effective T2 range and interval (ms)
mtmax=300
mtmin=10
mtstep=10
# Loop through MT values and run one simulation at each value
for mt in $(seq ${mtmin} ${mtstep} ${mtmax})
do
# use fsl_sub to submit a job described by the following arguments to a compu... |
45eb890d5819e2534cf85a8c4bd2b1d7e0555f277687aa5c69e69cbbf1d5ccf8 | Shell | 539 | 20 | #!/bin/bash
#SBATCH --job-name="CLA_Z"
#SBATCH --output=out
#SBATCH --error=err
#SBATCH --partition=accardi-gpu4
#SBATCH --nodes=1
#SBATCH --mem=37G #Large Request
#SBATCH --ntasks-per-node=16
#SBATCH --gres=gpu:1
#SBATCH -t 48:00:00
BASE_DIR=$(pwd)
PDB_FILE="$BASE_DIR/../step5_input.pdb "
XTC_FILE="$BASE_DIR/../ZFA_... |
a0f579ddaabbc50851225d2b3ba796100a0c39a03c512a0ecf870fc847ef0049 | Shell | 539 | 20 | #!/bin/bash
#SBATCH --job-name="POT_Z"
#SBATCH --output=out
#SBATCH --error=err
#SBATCH --partition=accardi-gpu4
#SBATCH --nodes=1
#SBATCH --mem=37G #Large Request
#SBATCH --ntasks-per-node=16
#SBATCH --gres=gpu:1
#SBATCH -t 48:00:00
BASE_DIR=$(pwd)
PDB_FILE="$BASE_DIR/../step5_input.pdb "
XTC_FILE="$BASE_DIR/../ZFC_... |
bbb12afc092fcfdeefc6907a31ade3abc2400c5103813c6bc172b4d328715d8e | Shell | 539 | 20 | #!/bin/bash
#SBATCH --job-name="POT_Z"
#SBATCH --output=out
#SBATCH --error=err
#SBATCH --partition=accardi-gpu4
#SBATCH --nodes=1
#SBATCH --mem=37G #Large Request
#SBATCH --ntasks-per-node=16
#SBATCH --gres=gpu:1
#SBATCH -t 48:00:00
BASE_DIR=$(pwd)
PDB_FILE="$BASE_DIR/../step5_input.pdb "
XTC_FILE="$BASE_DIR/../ZFA_... |
cfc77c4715bd442fecf23f208bd663ac39cbb8904744a7b2e124665d45a61ebf | Shell | 539 | 20 | #!/bin/bash
#SBATCH --job-name="CLA_Z"
#SBATCH --output=out
#SBATCH --error=err
#SBATCH --partition=accardi-gpu4
#SBATCH --nodes=1
#SBATCH --mem=37G #Large Request
#SBATCH --ntasks-per-node=16
#SBATCH --gres=gpu:1
#SBATCH -t 48:00:00
BASE_DIR=$(pwd)
PDB_FILE="$BASE_DIR/../step5_input.pdb "
XTC_FILE="$BASE_DIR/../ZFC_... |
08033373f3ac971df22314e725271c262337808db1d9437c212df121e499b117 | Shell | 546 | 20 | #!/bin/bash
#SBATCH --job-name="CL_Z"
#SBATCH --output=out
#SBATCH --error=err
#SBATCH --partition=accardi-gpu4
#SBATCH --nodes=1
#SBATCH --mem=50G #Large Request
#SBATCH --ntasks-per-node=16
#SBATCH --gres=gpu:1
#SBATCH -t 48:00:00
BASE_DIR=$(pwd)
PDB_FILE="$BASE_DIR/../step5_charmm2gmx.pdb"
XTC_FILE="$BASE_DIR/../s... |
26923e21dc9b7f5883734446cb85e544a40eafbd8ef4af6bb23d054888058bbe | Shell | 546 | 20 | #!/bin/bash
#SBATCH --job-name="NA_Z"
#SBATCH --output=out
#SBATCH --error=err
#SBATCH --partition=accardi-gpu4
#SBATCH --nodes=1
#SBATCH --mem=50G #Large Request
#SBATCH --ntasks-per-node=16
#SBATCH --gres=gpu:1
#SBATCH -t 48:00:00
BASE_DIR=$(pwd)
PDB_FILE="$BASE_DIR/../step5_charmm2gmx.pdb"
XTC_FILE="$BASE_DIR/../s... |
671704aca81f7db77c71704ee74b6d6ae9d4789d72737c0b1c44575caa94b719 | Shell | 547 | 13 | dir=$1
for file in "$dir"/*.sort.mdup.bam; do
echo "$file"
# samtools view -o "${file%.*}".chr21.bam "${file}" chr21
# samtools sort -n -o "${file%.*}".chr21.sort.bam "${file%.*}".chr21.bam
# bamToFastq -i "${file%.*}".chr21.sort.bam -fq "${file%.*}".1.fastq -fq2 "${file%.*}".2.fastq
# bgzip "${file%.*}".1.fa... |
797ec10f9fcddd662fd3e2ede724ded5b07cd261e1c11ab3b9cf0c9532296693 | Shell | 549 | 20 | #!/bin/bash
#SBATCH --job-name="PO4_Z"
#SBATCH --output=out
#SBATCH --error=err
#SBATCH --partition=accardi-gpu4
#SBATCH --nodes=1
#SBATCH --mem=50G #Large Request
#SBATCH --ntasks-per-node=16
#SBATCH --gres=gpu:1
#SBATCH -t 48:00:00
BASE_DIR=$(pwd)
PDB_FILE="$BASE_DIR/../step5_charmm2gmx.pdb"
XTC_FILE="$BASE_DIR/../... |
8a2ea21c8423e5de90f47264b6a72848a932d15f0f712a6e82152674f4941ae7 | Shell | 557 | 16 | #!/bin/sh
# this is temporary!
# will be replaced when https://github.com/ontodev/robot/issues/432
# this is adopted from Mondo
echo \#\# New Classes
echo
grep ^\+id: cl-diff.txt | perl -npe 's@...: CL:(\d+) . @ * [CL:$1](http://purl.obolibrary.org/obo/CL_$1) @'
echo
echo \#\# Obsoletions
echo
grep '\--> obsolete' cl-d... |
8eeb565bcee92875a8ed3ea28dd6e44802a4eee9f324758b9cda2fe2af870963 | Shell | 563 | 16 | ROOT_DIR="$(echo "$(cd ../ && pwd)")"
for nez in $(seq 3 1 5);
do
for sigma_prior in $(seq 0.1 0.1 1.0);
do
for i in $(seq 1 1 10);
do
sbatch run_optim.sh \
"${ROOT_DIR}/Rfiles/fit_data_snsrfit_ode_${nez}ez.R" \
"${ROOT_DIR}/Rfiles/param_init_${nez}ez_sigmaprior$... |
25413f52aada0ca056db5145af3146279013a7a0d3099c18224f021b30789dd2 | Shell | 570 | 14 | #!/bin/bash
# Define radius (um)
r_mean=2.00
# Define permeability range and interval
permmax=0.020
permmin=0.000
permstep=0.001
# Loop through permeability values and run one simulation at each value
for perm in $(seq ${permmin} ${permstep} ${permmax})
do
# use fsl_sub to submit a job described by the following arg... |
06115a192d14f6f4cf5e48f969b57314b7bbc416a63786b41271460b358191bb | Shell | 573 | 31 | #!/bin/bash
#
# Set the job name and wall time limit
#BSUB -J forcebal
#BSUB -W 12:00
#
# Set the output and error output paths.
#BSUB -o %J.o
#BSUB -e %J.e
#
# Set any gpu options.
#BSUB -q gpuqueue
#BSUB -gpu num=1:j_exclusive=yes:mode=shared:mps=no:
. ~/.bashrc
# Use the right conda environment
conda activate fo... |
5372a7b1e6654fd2d50af7ee304514f54d3cc254f0e63575e66fdda341bcaef4 | Shell | 573 | 24 | #!/usr/bin/env sh
GIST=$1
DIRNAME=${2:-./models}
if [ -z $GIST ]; then
echo "usage: download_model_from_gist.sh <gist_id> <dirname>"
exit
fi
GIST_DIR=$(echo $GIST | tr '/' '-')
MODEL_DIR="$DIRNAME/$GIST_DIR"
if [ -d $MODEL_DIR ]; then
echo "$MODEL_DIR already exists! Please make sure you're not overwriting ... |
efd40718d6dccddbfbb32ac7d786a2e2940b548a80f425c196280c92c856d177 | Shell | 573 | 16 | #!/usr/bin/env bash
##previous_tag=HEAD
previous_tag=0
FILTER="${1:-.*}"
NHEAD="${2:-999}"
for current_tag in $(git tag --sort=-creatordate | head -n ${NHEAD})
do
if [ "$previous_tag" != 0 ];then
tag_date=$(git log -1 --pretty=format:'%ad' --date=short ${previous_tag})
printf "### ${previous_tag} (${tag_date})... |
6aa4c73200b6e1b1ba267433228b17266ce1f4a980fa45bdad37cea9da5a905d | Shell | 587 | 14 | #!/bin/bash
python Model_training/MassSpecGym/Evaluation.py \
--datasetname "MassSpecGym" \
--Evaluation_mode "denovo" \
--dataset "./results/MassSpecGym/input_dataset.dataset" \
--config "./weights/generation/config.json" \
--vocab "./weights/generation/vocab.txt" \
--convert_dict "./weights/ge... |
074bc0266f7ca4ebf045f629a1b52b933b2cde8980abe7c0417f3771f3e8b036 | Shell | 596 | 20 | #!/bin/bash
#SBATCH --mail-user=alexandel91@zedat.fu-berlin.de
#SBATCH --job-name=c4
#SBATCH --mail-type=ALL
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --mem=30000 # specifies the maximum ... |
5e0129a72d260935153e5e045c3da1cb06edc5f5b3902b48880f622db8a273a8 | Shell | 596 | 20 | #!/bin/bash
#SBATCH --mail-user=alexandel91@zedat.fu-berlin.de
#SBATCH --job-name=c5
#SBATCH --mail-type=ALL
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=4
#SBATCH --mem=50000 # specifies the maximum ... |
4871ada543f649465cf0f0223f31ff84feec12878748222e9351d90af20cc8ef | Shell | 597 | 32 | # CMake configuration
mkdir -p build
cd build
ARGS="-DCMAKE_BUILD_TYPE=Release -DBLAS=Open"
if $WITH_PYTHON3 ; then
ARGS="$ARGS -Dpython_version=3"
fi
if $WITH_IO ; then
ARGS="$ARGS -DUSE_OPENCV=On -DUSE_LMDB=On -DUSE_LEVELDB=On"
else
ARGS="$ARGS -DUSE_OPENCV=Off -DUSE_LMDB=Off -DUSE_LEVELDB=Off"
fi
if $WITH... |
a504fbd6d167b61282f3633a986600ebce3e35fcc9f51fd8083cd6d65c2bca77 | Shell | 598 | 20 | #!/bin/bash
#SBATCH --mail-user=alexandel91@zedat.fu-berlin.de
#SBATCH --job-name=c10
#SBATCH --mail-type=ALL
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --mem=30000 # specifies the maximum... |
b4a8ab5297f258ec499241d514843f3d35dab2e49ef4b6d9dba61d007f07bf9d | Shell | 598 | 20 | #!/bin/bash
#SBATCH --mail-user=alexandel91@zedat.fu-berlin.de
#SBATCH --job-name=c11
#SBATCH --mail-type=ALL
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --mem=30000 # specifies the maximum... |
c28797356fce6caac1893ebbfbfaa7264e56074449c740533e51975e49ad0a9e | Shell | 600 | 14 | #!/bin/bash
python Model_training/MassSpecGym/Evaluation.py \
--datasetname "MassSpecGym" \
--Evaluation_mode "retrieval" \
--dataset "./results/MassSpecGym/input_dataset_retrieval.dataset" \
--config "./weights/generation/config.json" \
--vocab "./weights/generation/vocab.txt" \
--convert_dict ... |
f2ec0bcd301327c2b3c5134e2fbc21ba3944f7c48292d2bdd8d697b6980c5f67 | Shell | 602 | 20 | #!/bin/bash
#SBATCH --mail-user=alexandel91@zedat.fu-berlin.de
#SBATCH --job-name=time_gen
#SBATCH --mail-type=ALL
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --mem=10000 # specifies the ma... |
82fc2482a3cf5cfdcbff1fcfd5f377cba440e489d1d6e608026d72e8d7b260cb | Shell | 603 | 11 | REF="/g/korbel2/weber/MosaiCatcher_files/refgenomes_human_local/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna"
mkdir -p LITE/RPE-BM510/all/ LITE/RPE-BM510/selected/ TMP/
for file in *.bam; do
echo "$file" &&
cell=$(echo "${file}" | grep -P -o "PE[0-9]*") &&
samtools view "$file" chr21 -b -o TMP/"$cell".bam &&
... |
b6928597bfd914cadab4462023b82ede9e3c5761a68c64b70153174fd3683c74 | Shell | 603 | 20 | module add apps/fsl/6.0
source ~/anaconda3/etc/profile.d/conda.sh
conda activate tats
export FREESURFER_HOME=/public/home/lishr2022/freesurfer
export SUBJECTS_DIR=/public_bme/data/lishr/Cross_modal/subjects
export FSFAST_HOME=/public/home/lishr2022/freesurfer/fsfast
export MNI_DIR=/public/home/lishr2022/freesurfer/mni... |
c626c05a8e608d79aeb975518ba0ad986ccff467352cfee73ac3c57bfeed4790 | Shell | 603 | 26 | #!/bin/bash
FOLDER="./data"
OUTPUT_FILE="dataset.zip"
SERVER_URL="https://dataverse.harvard.edu"
PERSISTENT_ID="doi:10.7910/DVN/N8ITTG"
mkdir -p "$FOLDER"
echo "Created folder: $FOLDER"
echo "Downloading data..."
wget ${SERVER_URL}/api/access/dataset/:persistentId/?persistentId=${PERSISTENT_ID} -O $OUTPUT_FILE
echo... |
528e6706dc402a7959d61a076941769135442e1cfbc15208ff2ccb0867f6f24c | Shell | 604 | 16 | #!/bin/bash
#SBATCH -J im_proc
#SBATCH -o /oak/stanford/groups/menon/projects/branigan/2023_abcd_glm/jobs/preprocess/%x_%A_%a.out
#SBATCH -e /oak/stanford/groups/menon/projects/branigan/2023_abcd_glm/jobs/preprocess/%x_%A_%a.err
#SBATCH -t 0-16
#SBATCH -p normal,owners
#SBATCH --array=0-99
#SBATCH --ntasks=1
#SBATCH --... |
64a4e10590a497bea21c9d01016e29b1174ccdbf302c283685a6d6fe78087665 | Shell | 604 | 20 | #!/bin/bash
#SBATCH --mail-user=alexandel91@zedat.fu-berlin.de
#SBATCH --job-name=c7
#SBATCH --mail-type=ALL
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --mem=30000 # specifies the maximum ... |
ed3ca10c4f94172afb73e018c3f068ad45964560669c4be00cc906cfa9570259 | Shell | 607 | 18 | #!/bin/bash
#SBATCH --mail-user=alexandel91@zedat.fu-berlin.de
#SBATCH --job-name=c12
#SBATCH --mail-type=ALL
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --mem=10000 # specifies the maximum... |
32bf599cae57a4f6ab25f1971fa33380ff79698f0b5a6cacf03755ca4dd9ba52 | Shell | 609 | 20 | #!/bin/bash
#SBATCH --mail-user=alexandel91@zedat.fu-berlin.de
#SBATCH --job-name=c9_mini
#SBATCH --mail-type=ALL
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --mem=30000 # specifies the max... |
6b0ccc74a1ee3a0f5392449736a592f1e153b6775b3c02f1b188147e2effc957 | Shell | 613 | 20 | #!/bin/bash
#SBATCH --mail-user=alexandel91@zedat.fu-berlin.de
#SBATCH --job-name=c1_encoding
#SBATCH --mail-type=ALL
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --mem=32000 # specifies the... |
b80df46c34dbf0a95c4377a17d41e12bec993d6344ddfe0c0a60bf8f7ca66e9f | Shell | 613 | 20 | #!/bin/bash
#SBATCH --mail-user=alexandel91@zedat.fu-berlin.de
#SBATCH --job-name=c2_encoding
#SBATCH --mail-type=ALL
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --mem=32000 # specifies the... |
f990d73291a8caf45851c90e1de05f38f2d8bff58365e4967a86c5f927aa615d | Shell | 613 | 20 | #!/bin/bash
#SBATCH --mail-user=alexandel91@zedat.fu-berlin.de
#SBATCH --job-name=c3_encoding
#SBATCH --mail-type=ALL
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --mem=28000 # specifies the... |
31cd26a393fd00ce09e1306786cf24c472f06b56b882fcd47d9b0f3d878fc462 | Shell | 617 | 18 | #!/bin/bash
#SBATCH --mail-user=alexandel91@zedat.fu-berlin.de
#SBATCH --job-name=c6_2_mini
#SBATCH --mail-type=ALL
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --mem=32000 # specifies the m... |
91f4b87af54198ed0d6127a01b6df9309c440a5d8b6bdfaded48e214063ca399 | Shell | 617 | 17 | #!/usr/bin/env bash
#
# This script indexes the solr.json which is generated by dumps data pipeline
# Whenever you need to index or re-index your data you can use this script.
while getopts h:p:c: flag
do
case "${flag}" in
h) host=${OPTARG};;
p) port=${OPTARG};;
c) collection=${OPTARG};;
... |
e5540f22732d7e35567091645c0c8a91b4bc0d7093a0474164b31bfe288e89cd | Shell | 617 | 18 | #!/bin/bash
#SBATCH --mail-user=alexandel91@zedat.fu-berlin.de
#SBATCH --job-name=c6_1_mini
#SBATCH --mail-type=ALL
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --mem=32000 # specifies the m... |
a9e5df1dacb621da6c48775b23814c49f7a60ca338b25214bbeff2de62db4a56 | Shell | 619 | 19 | #!/usr/bin/env bash
for pp in "" /usr/bin; do
export PATH=$pp:$PATH
echo -e "\n# Switch environment to"
python -V
echo -e "\n# Test case 01"
cd /Users/qcc/Desktop/LaminarRivalry/comp_loc_epi/raw/S02
extract_physio.py -l -p 20170108_S18_ODC_S02_CQ_phy -d func*
echo -e "\n# Test case 02"
... |
e2546d4ee174cec1cb2605be7d4cc50bbe479ea3100d39714c2607c2d30b6724 | Shell | 625 | 31 | #! /bin/bash
## Small utility script used to search and replace text in all project files.
old=${1//|/\\|}
new=${2//|/\\|}
if [ -z "${old}" ]; then
echo "usage: $0 <old> <new>" 1>&2
exit 1
fi
if [[ `uname` == Darwin ]]; then
_replace()
{
sed -i '' "s|$2|$3|g" "$1"
}
else
_replace()
{
sed -i'' "s|$2|$3|g"... |
0e67a5761a7cc13c3613548f20bf93b8c25846c5875f3e476c69551dec1e4189 | Shell | 628 | 20 | #!/bin/bash
# Regenerate molecules (requires OpenEye toolkit)
rm -f *.mol2
# Parameterize CB7 from Tripos mol2.
rm -f CB7.gaff.mol2
cp ../molecules/CB7.tripos.mol2 .
antechamber -fi mol2 -i CB7.tripos.mol2 -fo mol2 -o CB7.gaff.mol2
parmchk -i CB7.gaff.mol2 -o CB7.frcmod -f mol2
# Parameterize viologen from Tripos mo... |
1d9242dd552d71d38cc4359e3094cb1e1a68fdf53e8490c0e7b0bec4320ab40c | Shell | 629 | 21 | #!/bin/bash
#SBATCH --mail-user=alexandel91@zedat.fu-berlin.de
#SBATCH --job-name=feat_extraction
#SBATCH --mail-type=ALL
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --mem=32000 # specifies... |
6ce9fb8d95058efbcaa9b74a676ff95685899f9bf5c675e0bab52328f486129c | Shell | 629 | 21 | #!/bin/bash
#SBATCH --mail-user=alexandel91@zedat.fu-berlin.de
#SBATCH --job-name=feat_extraction
#SBATCH --mail-type=ALL
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --mem=32000 # specifies... |
5b4076b316f6d5328046d216ea6307dd1818382f7f6daad65e89f0a826297fb6 | Shell | 634 | 19 | #!/bin/bash
# Regenerate molecules (requires OpenEye toolkit)
rm -f *.mol2
python generate-molecules.py
# Parameterize benzene from Tripos mol2.
rm -f benzene.gaff.mol2 benzene.frcmod
antechamber -fi mol2 -i benzene.tripos.mol2 -fo mol2 -o benzene.gaff.mol2
parmchk2 -i benzene.gaff.mol2 -o benzene.frcmod -f mol2
# P... |
d73abfc53ef9274ced64257a5e95f26a15372a11afb361d8ffa8ea8c835c3041 | Shell | 634 | 24 | module add apps/fsl/6.0
source ~/anaconda3/etc/profile.d/conda.sh
conda activate tats
export FREESURFER_HOME=/public/home/lishr2022/freesurfer
export SUBJECTS_DIR=/public_bme/data/lishr/Cross_modal/subjects
export FSFAST_HOME=/public/home/lishr2022/freesurfer/fsfast
export MNI_DIR=/public/home/lishr2022/freesurfer/mni... |
271d816933d6aff732f44cbb28cf6d4935e0fc8b325954b5a5f5b1cd0f202242 | Shell | 638 | 19 | #!/bin/bash
#SBATCH --mail-user=alexandel91@zedat.fu-berlin.de
#SBATCH --job-name=default_differences
#SBATCH --mail-type=ALL
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --mem=16000 # speci... |
ef9bb2a24c2bf889587ff8a674df0248deafa9c9c7d4d9526f8dc2216792ffab | Shell | 638 | 21 | #!/bin/bash
#SBATCH --mail-user=alexandel91@zedat.fu-berlin.de
#SBATCH --job-name=decoding_images
#SBATCH --mail-type=ALL
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --mem=20000 # specifies... |
ca3bb8fd3521df6501b3d9d7af6dcfa13d062e5055c5b1da6229c4d3c4e6d9fb | Shell | 639 | 21 | #!/bin/bash
#SBATCH --mail-user=alexandel91@zedat.fu-berlin.de
#SBATCH --job-name=feat_extraction
#SBATCH --mail-type=ALL
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --mem=32000 # specifies... |
5f10f939124c30e80a617b1b11d8382e91f338bbdda9ab6c632d5dbae244f0d6 | Shell | 640 | 23 | #!/bin/bash
#
# Copyright (c) 2018 German Cancer Research Center (DKFZ).
#
# Distributed under the MIT License (license terms are at https://github.com/DKFZ-ODCF/AlignmentAndQCWorkflows).
#
set -o pipefail
set -x
${PYTHON_BINARY} "${TOOL_MERGE_FILTER_CNV}" \
--inputfile "$FILENAME_COV_WINDOWS_ANNO" \
... |
185dce74eb361931ef9d9699a3b3a56e5bd270c08f8bb96831663f185cb95548 | Shell | 652 | 23 | #!/bin/bash
# Statistics and plots for the differences between the two conditions: images and miniclips
source /home/alexandel91/.bashrc
conda activate encoding
export LD_PRELOAD=$CONDA_PREFIX/lib/libstdc++.so.6
# First step: Bootstrapping
python ../EEG/Stats/encoding_difference_bootstrapping.py \
--config_dir .... |
685d25f6f9c65b52fea56aec2a9eda38be588ba0cdcecc4cb83e416fec6c15f5 | Shell | 665 | 20 | #!/usr/bin/env bash
#
# Copyright (c) 2018 German Cancer Research Center (DKFZ).
#
# Distributed under the MIT License (license terms are at https://github.com/DKFZ-ODCF/AlignmentAndQCWorkflows).
#
currentDir=$(dirname $(readlink -f "$0"))
runner=${SHUNIT2:?No SHUNIT2 variable. Point it to the shunit2 of https://githu... |
b8b7cdaa6b8d0b3aec8f59bbcdc82beec798fc25ce16b15e4e22918b352f7517 | Shell | 667 | 18 | #!/bin/bash
# Define radius range and interval (um)
rmax=5.50
rmin=0.30
rstep=0.10
# Define MT induced effective T2 range and interval (ms)
mtmax=150
mtmin=10
mtstep=10
# Loop through radius and MT values and run one simulation at each value pairs
for r_mean in $(seq ${rmin} ${rstep} ${rmax})
do
for mt in $(seq ${m... |
91b5bcbf145fdf24c4b8bb0194ded091d432d2d2a90b949b95e0bb5c0ed339d1 | Shell | 669 | 27 | #!/bin/bash
# Script to train the ResNet-18 on Kinetics-400 dataset.
num_workers=$1
gpus=$2
# Define variables
data_dir="/scratch/alexandel91/mid_level_features/kinetics_400"
batch_size=128
max_epochs=20
lr=3e-4
seed=42
save_dir="/scratch/alexandel91/mid_level_features/results/CNN/training/ResNet18"
weight_decay=0.0... |
a8ea3720f79577e3a72a6d532c5583d653843670083a3e39af27c7f0e57909b0 | Shell | 669 | 18 | #!/bin/bash
# nnUNetv2 for the segmentation of perivascular spaces in T2w MRI
# Author: William Pham
# Date: 2025-11-04
# Description: This script runs a nnUNet to label perivascular spaces in T2w MRI scans.
# Usage:
# Modify the script to include the INPUT_DIR and OUTPUT_DIR arguments, then run script:
# ./pvs_predic... |
38ceafb13f9687644eb32307702e8a7b6908e3cc56fd1f2653116d6b066b72b6 | Shell | 670 | 27 | #!/bin/bash
# Script to train the ResNet-18 on Kinetics-400 dataset.
num_workers=$1
gpus=$2
# Define variables
data_dir="/scratch/alexandel91/mid_level_features/kinetics_400"
batch_size=128
max_epochs=20
lr=3e-4
seed=42
save_dir="/scratch/alexandel91/mid_level_features/results/CNN/training/ResNet18"
weight_decay=1e-... |
fe4e23fcaa2213b29a61c5fa2a44076f4628962a823a2ef31de3d2e08dc0b9a1 | Shell | 686 | 19 | #!/bin/bash
#
# Copyright (c) 2018 German Cancer Research Center (DKFZ).
#
# Distributed under the MIT License (license terms are at https://github.com/DKFZ-ODCF/AlignmentAndQCWorkflows).
#
#PBS -l nodes=1:ppn=4
#PBS -l walltime=5:00:00
#PBS -m n
attachement=""
if [[ ${FILENAME} == *targetExtract* ]] && [[ -n ${TARGE... |
65455ed51618a548c4dd75e07b1ef8828ee6e7d79cd8480369cc1bfc35ca278f | Shell | 687 | 23 | #!/bin/bash
# Statistics and plots for the differences between the two conditions: images and miniclips
source /home/alexandel91/.bashrc
conda activate encoding
export LD_PRELOAD=$CONDA_PREFIX/lib/libstdc++.so.6
# # First step: Bootstrapping
# python ../../EEG/Stats/encoding_difference_bootstrapping.py \
# --con... |
204b520675625a0a1aff56d6bbcd6db5fd60e1431ae7b80a27fbdab0d0b6ab6a | Shell | 688 | 21 | #!/bin/bash
#SBATCH --mail-user=alexandel91@zedat.fu-berlin.de
#SBATCH --job-name=download_kinetics
#SBATCH --mail-type=ALL
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=2
#SBATCH --mem=50000 # specifie... |
4807f1c9f3b2f4ff367344faf398d48e4997a6b748e94226aa0c0a451f0999ea | Shell | 688 | 19 | #!/bin/bash
# nnUNetv2 for the segmentation of perivascular spaces in T1w MRI scans
# Author: William Pham
# Date: 2025-11-04
# Description: This script runs a nnUNet to label perivascular spaces in T1w MRI scans.
# Usage:
# Modify the script to include the INPUT_DIR and OUTPUT_DIR arguments, then run script:
# ./pvs_... |
0aff9e5fa4d3497f36c8784c7bd3136fac3d6014787dd007cf10afbd9afbc693 | Shell | 689 | 18 | #!/bin/bash
# Define radius range and interval (um)
rmax=5.50
rmin=0.30
rstep=0.10
# Define permeability range and interval
permmax=0.020
permmin=0.000
permstep=0.001
# Loop through radius and permeability values and run one simulation at each value pairs
for r_mean in $(seq ${rmin} ${rstep} ${rmax})
do
for perm in... |
0473ffdff7628f97f494bad4ef0ffca5aff706e70f5ae7c8c7bc9e93195ce7de | Shell | 690 | 31 | #!/bin/bash
# This wrapper script is for running GROMACS jobs on clusters.
COMMAND=$@
# Backup folder
export BAK=$HOME/temp/rungmx-backups
# Disable GROMACS backup files
export GMX_MAXBACKUP=-1
echo
echo "#=======================#"
echo "# STARTING CALCULATION! #"
echo "#=======================#"
echo
echo $@
# R... |
98c967270c0861d2b101be7a577d5060ad84b187adc1d86bd8d20c1fc3db0200 | Shell | 718 | 29 | #!/bin/bash
while getopts c:f:o: flag
do
case "${flag}" in
c) calc_in_percent=${OPTARG};;
f) vcffile=${OPTARG};;
o) outfile=${OPTARG};;
esac
done
echo "calc_in_percent: $calc_in_percent";
echo "vcffile: $vcffile";
echo "outfile: $outfile";
nsnps=$(bcftools view -H "$vcffile" |... |
524549c845d6a940d8b28884e45a6ea1883ec70029f529275318df14bb1fb80b | Shell | 720 | 26 | #!/bin/bash
# Statistics and plots for the differences between the two conditions: images and miniclips
source /home/alexandel91/.bashrc
conda activate encoding
export LD_PRELOAD=$CONDA_PREFIX/lib/libstdc++.so.6
# First step: Bootstrapping
python ../CNN/Stats/encoding_difference_bootstrapping_cnn.py \
--config_d... |
4b3552e2fa54bccac64f8a696905c3b1ddebfa579febba7f827cd952705d14ca | Shell | 734 | 23 | #!/usr/bin/env bash
#
# This script will be used at the end of pipeline deployment
# It indexes the solr.json which is generated by dumps data pipeline, configures
# the ontology schema by using solr_config.sh for partial search capability.
# Re-indexing is also takes place in order to generate newly added fields in th... |
57830d7104be82b45b58e2cae3d379573f6e9c719442ed0051cb3926f0384e6a | Shell | 737 | 25 | #!/bin/bash
#SBATCH --account=ich001m
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=30
#SBATCH --mem=120G
#SBATCH --time=24:00:00
#SBATCH --partition=normal
#SBATCH --constraint=mc
DATA_PATH="${PWD}/..";
RES_DIR="${PWD}/../samples";
LOG_DIR="${PWD}/../logs";
STAN_FNAME="vep-snsrfit-ode-rk4";
ITERS=20000;
for snr in $(s... |
18904b9e68679813bdef9ae42456aebd470e184bdeb3c9799c725ca30f784ce3 | Shell | 741 | 26 | #!/bin/bash
# Statistics and plots for the differences between the two conditions: images and miniclips
source /home/alexandel91/.bashrc
conda activate encoding
export LD_PRELOAD=$CONDA_PREFIX/lib/libstdc++.so.6
# First step: Bootstrapping
python ../../CNN/Stats/encoding_difference_bootstrapping_cnn.py \
--confi... |
370cb4becce7f195776a1c31f846422b38991d2ea6e452b57968a88c64a7432b | Shell | 752 | 21 | #!/bin/sh
# Copyright (C) 2025 Sotiris Lamrpinidis
#
# This program is free software and all terms of the GNU General Public License
# version 3 as published by the Free Software Foundation apply. See the LICENSE
# file in the root directory of the project or <https://www.gnu.org/licenses/>
# for more details.
mkdir ... |
f7c49c7b9942aebc4d3deb3571307b8e6981a0a5e3b8a7bdfc22b171bba7849a | Shell | 765 | 19 | #!/bin/bash
# nnUNetv2 for the segmentation of perivascular spaces in midbrain T1w MRI scans
# Author: William Pham
# Date: 2025-03-04
# Description: This script runs a nnUNet to label perivascular spaces in midbrain extracted T1w MRI scans.
# Usage:
# Modify the script to include the INPUT_DIR and OUTPUT_DIR argument... |
5d09862765bcdb7c8356d207eb3af15212c70d18fc8dfaf6e14cc178f2c683a2 | Shell | 767 | 40 | #!/bin/bash
# Pre-processing to build the main page document.
./make-option-index.py > option_index.txt
cat <<EOF > mainpage.py
"""
@mainpage
EOF
for i in "introduction.txt" "installation.txt" "usage.txt" "tutorial.txt" "glossary.txt" "option_index.txt"; do
cat $i >> mainpage.py
echo >> mainpage.py
done
c... |
97ef554727111af3df94b8b0dcfc82d2633bbea1f6171bac5076b5314c56a32a | Shell | 768 | 24 | #!/bin/bash
#wget https://dl.google.com/linux/direct/google-chrome-stable_current_amd64.deb
function install_chrome_browser() {
echo '>>> Installing Chrome'
wget -q -O - https://dl-ssl.google.com/linux/linux_signing_key.pub | apt-key add -
echo "deb [arch=amd64] http://dl.google.com/linux/chrome/deb/ s... |
e93fe4f075bd8b7424531e8e55fa5c9f9396a419dd2e5535b9b89b73cd7ba883 | Shell | 768 | 23 | #!/bin/bash
#SBATCH --mail-user=alexandel91@zedat.fu-berlin.de
#SBATCH --job-name=train_kinetics
#SBATCH --mail-type=ALL
#SBATCH --nodes=1
#SBATCH --ntasks=2 # 1 process per GPU
#SBATCH --cpus-per-task=16 # 16 CPU cor... |
6a85c111985481e0bfb9ab5a39685bd61ebb4253bdc638cbd10c0b40a50bebdb | Shell | 772 | 24 | #!/bin/bash
#SBATCH --job-name=model1_singleMod
#SBATCH --output=logs/ml_model_%A_%a.out
#SBATCH --error=logs/ml_model_%A_%a.err
#SBATCH --ntasks=1
##SBATCH --array=0-9##2303
#SBATCH --cpus-per-task=4 # Request only 1 CPU core
#SBATCH --mem=16G # Minimal memory for basic testing
#SBATCH --time=... |
0db6abe5c05543e3d7c161b126a8fd97ed733d6fd07830e97c09016ca6de3af5 | Shell | 774 | 19 | #!/bin/bash
# nnUNetv2 for the segmentation of perivascular spaces in hippocampal T1w MRI scans
# Author: William Pham
# Date: 2025-03-04
# Description: This script runs a nnUNet to label perivascular spaces in hippocampi extracted T1w MRI scans.
# Usage:
# Modify the script to include the INPUT_DIR and OUTPUT_DIR arg... |
18a2ad1ff31c8a128280f58528358327aa2c6be921ce24b7e5ac4b3b54ae4d7c | Shell | 778 | 18 | #!/bin/bash
#
# Copyright (c) 2018 DKFZ.
#
# Distributed under the MIT License (license terms are at https://github.com/DKFZ-ODCF/AlignmentAndQCWorkflows).
#
#PBS -l nodes=1:ppn=2
#PBS -l walltime=2:00:00
#PBS -m a
#PBS -l mem=4g
#PBS -j oe
readlen=`$SAMTOOLS_BINARY view ${FILENAME} | head -n 1 | awk '{print length($... |
32b6b38e79139aac60ccaf393a4be441daf6e01b08e34f22649114021e2e885a | Shell | 785 | 29 | #!/bin/bash
#SBATCH --job-name=model1_singleMod
#SBATCH --output=logs/ml_model_%A_%a.out
#SBATCH --error=logs/ml_model_%A_%a.err
#SBATCH --ntasks=1
##SBATCH --array=0-9##2303
#SBATCH --cpus-per-task=2 # Request only 1 CPU core
#SBATCH --mem=4G # Minimal memory for basic testing
#SBATCH --time=1... |
03c0bfc90819f3f668e17a434311643a2730e51515b50ed078b842eeefef6406 | Shell | 787 | 31 | #!/bin/env bash
# %%
cp topol_init.top topol.top
gmx editconf -f ./init.gro -o ./init_box.gro -c -d 4.0 -bt triclinic
gmx solvate -cp ./init_box.gro -o ./init_solv.gro -p ./topol.top
gmx grompp -f ./ions.mdp -c ./init_solv.gro -p ./topol.top -o ./ions.tpr
echo '13' | gmx genion -s ./ions.tpr -o ./init_solv_ions.gro ... |
df2193dfb2badd3be09999fa520817804d71e8fe4fde2844b7800c1785c06c2b | Shell | 787 | 23 | #!/bin/bash
# This script takes two arguments:
# 1. An indexed fasta genome file ($1)
# 2. The reference genome used ($2)
# conda activate facount
# Extract the first two columns from the input file and save them to a text file
cut -f 1,2 $1.fai >$2.txt
# Use BEDtools to create non-overlapping windows of 200 kb... |
455ef714803f5a401ea63bfa33ec333a33580ef024fd948d203fc7d5965573dd | Shell | 795 | 31 | #!/bin/bash
# Exit immediately if a command exits with a non-zero status.
set -e
# Create a virtual environment if it doesn't already exist
if [ ! -d "venv" ]; then
echo "Creating a virtual environment in venv..."
python3 -m venv venv
echo "Virtual environment created."
else
echo "Virtual environment already ... |
c047f5853c5599cfd80de08a53cb51dcc67537747261aaa75d535a1825d8ac8c | Shell | 796 | 25 | #!/bin/bash
# Copyright 2022 Google LLC.
#
# 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
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to... |
f00f02083cf79a37c1858a1bb81a593bd2e3781fa5b174fa13b5e563b4cd09b1 | Shell | 801 | 30 | #
# Copyright (c) 2018 German Cancer Research Center (DKFZ).
#
# Distributed under the MIT License (license terms are at https://github.com/DKFZ-ODCF/AlignmentAndQCWorkflows).
#
source ${TOOL_BASH_LIB:?No TOOL_BASHLIB}
testShellIsInteractive() {
export -f shellIsInteractive
assertEquals false "$(bash -c shell... |
cdda9b0551637070d8be7d9a2f9946b8e91b06a71fd76a37dad25caf5a187924 | Shell | 816 | 39 | #!/bin/bash
chr=$chr_train
# Load modules
module purge
module load R/4.2.2
# gene list
gene_list=$path_to_gene_list
n_row=`wc -l ${gene_list} | cut -d' ' -f 1`
for gene in $(seq 1 $n_row)
do
line=`head -n $gene ${gene_list} | tail -n 1`
gene_name=`echo ${line} | cut -d' ' -f 1`
geno_dir=$path_to_genotype_per_... |
3202a142539d69708e53e89ee67a326f0d218ecf2add596ea7ae32ca9f64412c | Shell | 823 | 25 | # Temporarily change directory to $HOME to install software
pushd .
cd $HOME
# Install Miniconda
MINICONDA=Miniconda3-latest-Linux-x86_64.sh
# Sed cuts out everything before the first digit, then traps the first digit and everything after
MINICONDA_HOME=$HOME/miniconda
MINICONDA_MD5=$(curl -s https://repo.continuum.io... |
7c229dbd8b56b93795450b4f0bf27e123446ce958f2e0abfd737d17d95cbed46 | Shell | 825 | 19 | #!/bin/bash
# nnUNetv2 for the segmentation of perivascular spaces in T1w with co-registered FLAIR MRI scans
# Author: William Pham
# Date: 2025-11-04
# Description: This script runs a nnUNet to label perivascular spaces and white matter hyperintensities in T1w and FLAIR MRI scans.
# Usage:
# Modify the script to incl... |
439abe549deca4cf560e1d3792b9e714dfc5ba21b6331c6c4e3a22c4e95977f7 | Shell | 827 | 19 | #!/bin/bash
# nnUNetv2 for the segmentation of perivascular spaces in T2w with co-registered FLAIR MRI scans
# Author: William Pham
# Date: 2025-11-04
# Description: This script runs a nnUNet to label perivascular spaces and white matter hyperintensities in T2w and FLAIR MRI scans.
# Usage:
# Modify the script to incl... |
560a4aabf15db372a58b1641ef8347bc16f39b293ce70441b75bb18516a21523 | Shell | 841 | 25 | ROOT_DATA_DIR=$PWD/..
ROOT_RES_DIR=$PWD/..
STAN_FNAME=vep-snsrfit-ode-rescaled-nointerp;
SAMPLING_ITERS=200;
WARMUP_ITERS=200;
NCHAINS=12;
DELTA=0.95;
MAX_DEPTH=15;
JITTER=0;
for PATIENT_ID in $(ls ${ROOT_DATA_DIR} | grep -i id*);
do
RES_DIR=${ROOT_RES_DIR}/${PATIENT_ID}/results;
LOG_DIR=${ROOT_RES_DIR}/${PA... |
abb510d5d0e6b5ab77311f7962cd73aaaeb6100f775c8d01ad3e04fc958661e0 | Shell | 848 | 27 | #!/bin/bash
#SBATCH --ntasks=1
#SBATCH -o slurm_logs/slurm-%j.out
#SBATCH --time=4-12:00:00
#SBATCH --partition rhu
DATA_PATH=${1};
INIT_PATH=${2};
RES_DIR=${3};
STAN_FNAME=${4};
SAMPLING_ITERS=${5};
WARMUP_ITERS=${6};
DELTA=${7};
MAX_DEPTH=${8};
JITTER=${9};
FNAME_SUFFIX=${10};
LOG_DIR=${11};
CHAIN_NO=${12}
./${STAN... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.