sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
c7b108755de6398075a0e547368d0df07e469c79c6295d6f238b3ababb70f873 | Shell | 706 | 26 | #!/usr/bin/env bash
set -o errexit
set -o pipefail
set -o nounset
__dir="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
#RAW DATA LOCATIONS
#field file should already be in cloud before running this. looks like
# field_id
# val1
# val2
# etc
# upload using gsutil cp fieldids.csv gs://ml4h/data/
# depending on access p... |
5109d293295d5290b5f0098e553bf8a6ad936a6ddeb35a60de69146c4527f94d | Shell | 708 | 33 | #!/usr/bin/env bash
set -e
set -x
# Save the current branch name
current_branch=$(git branch --show-current)
# Update main
git checkout main
git pull origin main
# Update develop
git checkout develop
git pull origin develop
# Check if develop is behind main
behind_count=$(git rev-list --left-right --count develop.... |
653bd02416bbe19def648d65d02ab3e984061762cb84ff9fbb4508a9a9efd1ad | Shell | 708 | 32 | #!/usr/bin/env bash
VM=${1:-sam-gpu2}
shift 1
ZONE=us-central1-a
MAX_TRIES=1000
COUNTER=0
while [[ $COUNTER -lt $(( $MAX_TRIES )) ]]; do
sleep 1s
gcloud compute instances start $VM --zone $ZONE
if [[ $? -eq 0 ]]
then
echo "Potentially started vm: ${VM} after ${COUNTER} attempts."
gcloud comp... |
62ac74ead815028c2daf85edb0f259371ff3df4a345c3e7fbc8924c94b95c6a2 | Shell | 709 | 19 | # You need load the required modules, in this case the intel
# compilers and intel mpi.
module load intel/2.144
module load impi/5.0.0.028
# It is very important putting number of the OMP variables
# on the correspondent system variable. In this case the value
# have to be equal to 1 (only one thread per MPI ... |
dd959855775fc5d4f9a18a6f391377234b4d261a09e35ab1e10502da9a5cf8ca | Shell | 711 | 9 | #!/bin/bash
container_name=$(basename $(dirname $(realpath $0)))
echo "Building seunglab/$container_name"
docker build . -f manylinux1.Dockerfile --tag "seunglab/$container_name:manylinux1"
docker build . -f manylinux2010.Dockerfile --tag "seunglab/$container_name:manylinux2010"
docker build . -f manylinux2014.Dockerfi... |
821fcf1cc2e6e804a31ebf2064ccce744ca54937f77b4d2e35116c2828552be0 | Shell | 718 | 15 | #!/usr/bin/bash
# --taxonomy /home/projects/cpr_10006/people/svekut/mmseq2/almeida_taxonomy.tsv \
# --taxonomy_predictions /home/projects/cpr_10006/projects/vamb/almeida_vaevaeout/results_taxonomy_predictor.csv \
run_id=$1
vamb taxometer \
--outdir /home/projects/cpr_10006/people/svekut/long_read_sludge_kfold_pred... |
6302dfee2ba3146d251dd747935f599649d19cd5eb04d6928302512c167f5a20 | Shell | 722 | 33 | #!/usr/bin/env bash
#
#SBATCH --time=48:00:00
#SBATCH --cpus-per-task=26
#SBATCH --array=2-5
#SBATCH --mem=10G
#SBATCH --partition=batch_48h
#SBATCH --output=logs/%x-%j.out
#
#### PARAMETERS
# Use this directory venv, reusable across RUNs
VENV_DIR=${HOME}/gym-sted
module load python/3.7
[ -d $VENV_DIR ] || virtuale... |
e7512d54a172b60b546db4deb74bb9939d8b9fb7b25eaee7cc4eac9a4b99298e | Shell | 723 | 21 | #!/bin/bash
#SBATCH --job-name=DeepTreeAttention # Job name
#SBATCH --mail-type=END # Mail events
#SBATCH --mail-user=benweinstein2010@gmail.com # Where to send mail
#SBATCH --account=ewhite
#SBATCH --nodes=1 # Number of MPI ran
#SBATCH --cpus-per-task=30
#SBATCH --mem=200GB
#SBATCH --t... |
0753b239b8a933b10d0e77a56096e7aaacac9a61523b25b2ae26a2a5bb453806 | Shell | 728 | 35 | #!/bin/bash
#SBATCH -t 1:55:00
#SBATCH -c 1
#SBATCH --mem-per-cpu 8G
#SBATCH --job-name=meta-eval
#SBATCH --output slurm_log/%j.log
LOGROOT=/tigress/qlu/logs/meta-model/log
# LOGROOT=/scratch/gpfs/qlu/logs/meta-model/log
DT=2023-10-29
# DT=freeze-ctx-test
# DT=new-mem
echo $(date)
srun python -u eval-group.py \
... |
948a51fc3ecbcd0d0d0aa8b52f0aeaeed836f05439046d387d131da969906c89 | Shell | 729 | 20 | ### compare test for STAR_RSEM pipeline
### usage: STAR_RSEM_testCompare.sh <testDir1> <testDir2>
### output: compared file names, no differences should be reported
echo Log.final.out
diff <(awk 'NR>4{print}' $1/Log.final.out) <(awk 'NR>4{print}' $2/Log.final.out) | head
echo Aligned.sortedByCoord.out.bam
diff <(sam... |
9bb23bbbad4fdd6270b58ba859981a405a7dd85ddd0c89a7549e97f5d6ad17ba | Shell | 729 | 40 | #!/bin/bash
#
# join_vcfs.sh
#
# Join VCFs which contain the same set of variants in different samples
#
set -e
vcflist=$1
prefix=$2
fout=${prefix}.vcf
base=$(head -n1 $vcflist)
if [[ ${base} == *.gz ]]; then
zcat $base | sed -n -e '/^##/p' > $fout
else
sed -n -e '/^##/p' $base > $fout
fi
# Paste final line ... |
99b5e4c3496c95307ebe877677d1a36297bafce9ec082d1605270f4a4f667571 | Shell | 734 | 18 | #! /bin/bash
# Get the FIMO motifs from JASPAR. Following the lead of the BBI at
curl https://jaspar.genereg.net/download/data/2018/CORE.backup-20220216/JASPAR2018_CORE_vertebrates_non-redundant_pfms_meme.txt -o fileOutputs/JASPAR2018_CORE_vertebrates_non-redundant_pfms_meme.txt
# Make a test file
cat fileOutputs... |
d14f6209df037689ffeee28b7151fcf8533ea210f162f3c34050a9a72702e88a | Shell | 738 | 23 | #!/usr/bin/env bash
# Set FSL Variable
OLD_FSLOUTPUTTYPE=$FSLOUTPUTTYPE
FSLOUTPUTTYPE=NIFTI
# Download Upstream Template
wget http://chymera.eu/distfiles/mouse-brain-atlases_rois_source.tar.xz
tar xf mouse-brain-atlases_rois_source.tar.xz
# Copy base ROIs
cp mouse-brain-atlases_rois_source/*nii .
# Make legacy vers... |
d297ffd3a97aff6d807cd4c9abcba85fa074eae2da682120fa91a7b8d00cede8 | Shell | 738 | 33 | #!/usr/bin/env bash
#
#SBATCH --time=48:00:00
#SBATCH --cpus-per-task=26
#SBATCH --array=2-5
#SBATCH --mem=10G
#SBATCH --partition=batch_48h
#SBATCH --output=logs/%x-%j.out
#
#### PARAMETERS
# Use this directory venv, reusable across RUNs
VENV_DIR=${HOME}/gym-sted
module load python/3.7
[ -d $VENV_DIR ] || virtuale... |
c3af4d17aecd2e88023f8cbd7670de80f09e23e5dfd290697cc7066adb44a309 | Shell | 742 | 16 | #!/usr/bin/bash
# --taxonomy /home/projects/cpr_10006/people/svekut/mmseq2/almeida_taxonomy.tsv \
# --taxonomy_predictions /home/projects/cpr_10006/projects/vamb/almeida_vaevaeout/results_taxonomy_predictor.csv \
run_id=$1
vamb \
--model taxonomy_predictor \
--outdir /home/projects/cpr_10006/people/svekut/alme... |
1c0f830483fe7ed2eb8ffc0d45d84fe5709e0931ec37342916968a03c316e46d | Shell | 744 | 13 | #!/bin/bash
# Point this macOS job's pip and uv at the CI package mirror. Source it, do not
# run it: it exports the index variables into the calling shell.
#
# macOS steps run directly on the agent, not in a container, so there is no
# /etc/profile.d being sourced; this entry point exists only to reach the shared
# de... |
ea5119c7cec9baf5b3c80dc04911fa3d9400a0bf03a090e7cf14c486ea2b46ad | Shell | 744 | 37 | #!/bin/bash
set -euo pipefail
set -x
# Sets RAY_COMMIT and RAY_VERSION
source .buildkite/release-automation/set-ray-version.sh
if [[ "${PYTHON_VERSION}" == "" ]]; then
echo "Python version not set" >/dev/stderr
exit 1
fi
export PYTHON_VERSION
export PATH="/usr/local/bin/miniforge3/bin:${PATH}"
source "/usr/loca... |
a57488318a88de4a3c1f86c7a88723935844048c815135d203125b16ea3ce22d | Shell | 749 | 36 | #!/bin/bash
#SBATCH -t 23:59:00
#SBATCH -c 1
#SBATCH --mem-per-cpu 2G
#SBATCH --job-name=meta-run-cgru
#SBATCH --output slurm_log/%j.log
LOGROOT=/tigress/qlu/logs/meta-model/log
# LOGROOT=/scratch/gpfs/qlu/logs/meta-model/log
DT=$(date +%Y-%m-%d)
# DT=freeze-ctx-test
echo $(date)
srun python -u train-lcn.py \
... |
68881584bb59377575873756d89de5461959a31a704145a53acca8f1c368ccc3 | Shell | 753 | 18 | #!/usr/bin/bash
dataset=$1
run_id=$2
keyword=$3
# --taxonomy /home/projects/cpr_10006/people/svekut/mmseq2/${dataset}_taxonomy.tsv \
# --taxonomy /home/projects/cpr_10006/people/svekut/mmseq2/${dataset}_taxonomy_${run_id}.tsv \
vamb taxometer \
--outdir /home/projects/cpr_10006/people/svekut/cami2_${datas... |
f8d1430db1322cefba1c25b71814a685312ed90f8e4a957fcf6eeb15238e6253 | Shell | 756 | 20 |
echo start `date`
outdir="./output_stage1"
train_list="./stage1_train_sample_lists/"
valid_list="./stage1_validation_sample_lists/valid_PDB_before2020_5.xls"
# users can use ./data/PDB_coord_seq.sh make hdf5 files for training and validation
coords_seq_hdf5="./data/xyz_tokens_label8_psi_phi_before2020_5.h5"
mkdir $... |
171e9094c58a8dbaf98624db4f26a41e465b3aa866dd5b30d59692c06d51e905 | Shell | 757 | 17 | #!/usr/bin/bash
# --taxonomy /home/projects/cpr_10006/people/svekut/mmseq2/almeida_taxonomy.tsv \
# --taxonomy_predictions /home/projects/cpr_10006/projects/vamb/almeida_vaevaeout/results_taxonomy_predictor.csv \
run_id=$1
# --cuda \
vamb taxometer \
--outdir /home/projects/cpr_10006/people/svekut/long_read_h... |
6040266bd90c60621c1dc99b5d891e96abbf093463116c31cd1a84214b22ebaf | Shell | 757 | 27 | #!/bin/bash
#
# Run script for GM matrix create #
# which creates the data matrix for input into OPNMF analyses #
# The R script requires 3 input arguments #
# 1 - Speceis investigated - "chimp" or "human"
# 2 - Name of the cohort phenotype data file e.g. chimp_meta_QC_n189.csv
# 3 - Name and relative path from projec... |
7dd9c69c5022da3b2338509207ea034d1e3ad7fc477523b3ede9abe2aa183542 | Shell | 757 | 31 | #!/bin/bash
#
# localize_bincov.sh
#
set -e
bed=$1
bincov_gs_path=$2
sort -k1,1V -k2,2n $bed | bedtools merge -i stdin -d 1000000 > merged.bed
export GCS_OAUTH_TOKEN=`gcloud auth application-default print-access-token`
while read chrom start end; do
echo "Fetching ${chrom}:${start}-${end}"
tabix -h ${bincov_gs... |
6f2ebaf1f6fc0a0b77b5b489d5e3a99e8ddd681dd3aac818b6feabf618ba02ca | Shell | 759 | 5 | SAMPLE=$1
tiecov -j /Users/chaokuan-hao/Documents/Projects/PR_SpliceNN/results/800bp/$SAMPLE/OUTPUT/SpliceAI_6_RB_p_n_nn_n1_TB_all_samples_thr_100_splitByChrom_L64_C16_L800_v21/BAM/$SAMPLE.cleaned.juncs /Users/chaokuan-hao/Documents/Projects/PR_SpliceNN/results/800bp/$SAMPLE/OUTPUT/SpliceAI_6_RB_p_n_nn_n1_TB_all_sampl... |
56c8d2eef5f15f56711be9e9196619b28d0d5886ab7dce3aac7354d31f45c1c2 | Shell | 761 | 26 | #!/usr/bin/env bash
set -euxo pipefail
install_strace() {
case "${OSTYPE}" in
linux*)
if ! strace -qq -k -e trace=exit /bin/true 2> /dev/null; then
(
set +x
echo "This Linux distribution doesn't appear to support strace -k." \
"Attempting to build & install a recent... |
92722c568b62eae1b41984fb16d6c5771b22030227f02f476aee204aa9fa0dc3 | Shell | 761 | 13 | #!/bin/bash
# Configure the PyPI index for the steps that no image can reach. Sourced from
# .buildkite/hooks/pre-command; it exports and must not be run.
#
# The images cover steps that run inside them: forge and manylinux carry
# ci/pypi_proxy_profile.sh as an /etc/profile.d hook. What they cannot cover is
# anything... |
e55eab4933df425530efab37e7397f0cb6acef0acaa1dd4a102a130a48f05cbf | Shell | 762 | 26 | #!/bin/bash
module unload matlab
module load matlab/2017a
log=compiled/commit_ids.txt
true > $log
echo "/N/u/brlife/git/jsonlab" >> $log
(cd /N/u/brlife/git/jsonlab && git log -1) >> $log
echo "/N/u/brlife/git/mba" >> $log
(cd /N/u/brlife/git/mba && git log -1) >> $log
echo "/N/u/brlife/git/wma_tools" >> $log
(cd /N/u... |
1f29723c47131d4b8abd212c8c904afc8544790d780a840988d84b614cef8fc9 | Shell | 764 | 23 |
mpirun -np 1 python3 train.py --inputfn input.xyz \
--box 15.6627 0 0 0 15.6627 0 0 0 15.6627 \
--committee_size 1 \
--fixed_seed \
> train.stdout 2> train.stderr
# using a previously trained aptnn on input.xyz should always yield the exakt same result
mpirun -np 1 python3 predict.py --trajectory input.xyz \
--a... |
0cfd1a8438846f0a2f217bf1d1c52eb7cb7df8ecea3388858bad3a398e0440e7 | Shell | 769 | 30 | #!/bin/bash
source 00_global_variables.sh
N_THREADS=16
export MKL_NUM_THREADS=$N_THREADS
export NUMEXPR_NUM_THREADS=$N_THREADS
export OMP_NUM_THREADS=$N_THREADS
OUT=./PRS
ref_1kg_eur=../ldblk_1kg_eur
UKB_bim=../ukb_eur_unrel_comb
for idx in "${!Phenotypes[@]}"
do
OUT2="${OUT}/${Phenotypes[$idx]}"
mkdir -p $O... |
9d591e915d814138522579531e4b330593d9098376ab3d14a7afdf58bae50fcd | Shell | 771 | 24 | #!/bin/bash
#SAMPLE=$1
M_VCF=s3://wanglab-play/leew8/17k_sv/manta_vcf/$SAMPLE.manta.diploidSV.vcf.gz
S_VCF=s3://wanglab-play/leew8/17k_sv/smoove_vcf/$SAMPLE\-smoove.genotyped.vcf.gz
WD=/mnt/data3/old-master/leew/17k_sv/scripts/tmp
OUT=/mnt/data3/old-master/leew/17k_sv/svimmer
aws s3 cp $M_VCF $WD
aws s3 cp $S_VCF $W... |
c05fb37bb497a091a9aae2d03b982b7a3aec53d9e581c2e8f0e2a3bf7c9517b8 | Shell | 774 | 29 | #!/bin/bash
#-------------------------------------------------------------------------------
ERROR=0
export PATH=/home/fmm/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:$PATH
PYTHON=python3
PYTHON_OPTIONS=
ARGV=
PYTHONPATH=.
APP_DIR=/mnt/c/Users/FMM/Documents/ProyectosVS/gtImputation/gtImpu... |
fcff44c17ea451bf5b2425e913ffabccecea81b32e48797cf46e5ef19c062306 | Shell | 775 | 23 | #!/bin/bash
#SBATCH -J CIForm
#SBATCH --output=slurm_out/CIForm_out.%j
#SBATCH --error=slurm_out/CIForm_err.%j
#SBATCH --partition=mcml-dgx-a100-40x8
#SBATCH --qos mcml
#SBATCH --gres=gpu:1
#SBATCH --time 3-00:00:00
#SBATCH --mem=200GB
#SBATCH --cpus-per-task=6
DSSFS02_HOME="/dss/dssfs02/lwp-dss-0001/pn36po/pn36po-ds... |
1f76811ea3144a48f6a5c8e41e9f36dfdd8f5b887e77c1c28f3a9558f529e703 | Shell | 784 | 30 | #!/bin/bash
source 00_global_variables.sh
N_THREADS=16
export MKL_NUM_THREADS=$N_THREADS
export NUMEXPR_NUM_THREADS=$N_THREADS
export OMP_NUM_THREADS=$N_THREADS
OUT=./PRS
ref_1kg_eur=../ldblk_1kg_eur
KoGES_bim=KCHIP.snp.imputed.HRC.rsID.rmdup
for idx in "${!Phenotypes[@]}"
do
OUT2="${OUT}/${Phenotypes[$idx]}"
... |
fb29275d210b09a4964974111db4b939485b8768d4e7a0fc7a4cedbced65e70a | Shell | 785 | 22 | #!/bin/bash
# Wrapper script for niivue-desktop CLI commands
# Usage: ./niivue-desktop-cli.sh segment --input mni152 --model tissue-seg-light --output output.nii.gz
# Resolve symlinks to find the real script location
SOURCE="${BASH_SOURCE[0]}"
while [ -L "$SOURCE" ]; do
DIR="$(cd "$(dirname "$SOURCE")" && pwd)"
SO... |
2c00d8e0e2c854da30f749345a687ed6e1cd20a90ba09ffe7b34b28950a4b5d3 | Shell | 790 | 41 | #!/usr/bin/env bash
#
#SBATCH --time=02:00:00
#SBATCH --cpus-per-task=11
#SBATCH --mem=16G
#SBATCH --partition=batch
#SBATCH --output=logs/%x-%j.out
#SBATCH --array=0-4
#
#### PARAMETERS
# Use this directory venv, reusable across RUNs
VENV_DIR=${HOME}/gym-sted
module load python/3.7
[ -d $VENV_DIR ] || virtualenv -... |
00a05c01d2442706ee7ef1b6984ad6aa520feabb18d3130a9d9a62aa597a1fcb | Shell | 791 | 22 | #!/bin/bash
#SBATCH -J xgboost
#SBATCH --output=slurm_out/xgboost_out.%j
#SBATCH --error=slurm_out/xgboost_err.%j
#SBATCH --partition=lrz-dgx-a100-80x8
#SBATCH --gres=gpu:1
#SBATCH --time 3-00:00:00
#SBATCH --mem=200GB
#SBATCH --cpus-per-task=12
DSSFS02_HOME="/dss/dssfs02/lwp-dss-0001/pn36po/pn36po-dss-0001/di93zer"... |
a3c64c0b019ecc59d83bee0e877e174e9fa86ac42d6975d9ccf5392092d4ea60 | Shell | 791 | 21 | #!/bin/bash
set -e
#local absolute path to where you want to download the dataset
LOCAL_DIR="your/path/to/BOLDMomentsDataset"
dataset_path="derivatives/versionA/MNI152/prepared_data/prepared_allvoxel_pkl"
TR_folder="TRavg56789"
#create directory paths that mimic the openneuro dataset structure
mkdir -p "${LOCAL_DIR}/${... |
ff32d9195cfdb068c8477b2959a67100b00e539b12b475c76f322992fb4cd2ac | Shell | 795 | 25 | export MODEL_NAME="runwayml/stable-diffusion-v1-5"
export OUTPUT_DIR="../../../models/alvan_shivam"
accelerate launch train_dreambooth.py \
--pretrained_model_name_or_path=$MODEL_NAME \
--pretrained_vae_name_or_path="stabilityai/sd-vae-ft-mse" \
--output_dir=$OUTPUT_DIR \
--revision="fp16" \
--with_prior_pre... |
f0ffa84f40b9eb0020ce251ad6126fa3fc91a45a4a7aba6661a6937f9fff33f1 | Shell | 799 | 27 | #!/bin/bash
metadata=./metadata_for_LDSC_rg.csv
outDIR=./rg_ldsc
mkdir -p $outDIR
while IFS=, read -r Category Trait MetSMunge TraitMunge
do
echo $Trait
if [ "$Category" == "Category" ]; then
continue
else
echo "LDSC rg calculation: ${Category} ${Trait}"
Trait_reformat=${Trait//[... |
6f2970a54feb2c03dac3e255434db15077ab19814e3819e99400924fdf664f42 | Shell | 807 | 25 | #!/bin/sh
python3 ../ntd/train_diffusion_model.py \
base.experiment=tycho_conditional_experiment \
base.tag=conv_wn \
dataset=tycho_conditional \
diffusion=diffusion_linear_200 \
diffusion_kernel=white_noise \
network=ada_conv_tycho \
optimizer=base_optimizer \
optimizer.lr=0.0004 \
... |
9519721907943f36e23e2548410fe5df91f0839acc93159465daf6df7e875890 | Shell | 808 | 21 | #!/bin/bash
#SBATCH -J scGPT
#SBATCH --output=slurm_out/scGPT_out.%j
#SBATCH --error=slurm_out/scGPT_err.%j
#SBATCH --partition=mcml-dgx-a100-40x8
#SBATCH --qos mcml
#SBATCH --gres=gpu:1
#SBATCH --time 3-00:00:00
#SBATCH --mem=90GB
#SBATCH --cpus-per-task=6
DSSFS02_HOME="/dss/dssfs02/lwp-dss-0001/pn36po/pn36po-dss-00... |
1eafc952fa6a5adcb738aec535f16f74e4772fe7fdc7dbaf2559022bfa5936fe | Shell | 810 | 25 | SAMPLE=$1
MODEL=$2
mkdir ./results
mkdir ./results/$SAMPLE/
mkdir ./results/$SAMPLE/assembly
touch ./results/$MODEL.txt
# echo samtools sort /Users/chaokuan-hao/Documents/Projects/PR_SPLAM/src_SPLAM/build/$SAMPLE/cleaned.bam -o ../results/800bp/$SAMPLE/cleaned.sort.bam
# samtools sort /Users/chaokuan-hao/Documents/Pr... |
fe61e8b43de939b75bd9d0d5bf04661b859df1d011587028a57a47f46b6f2e10 | Shell | 810 | 28 | #!/bin/bash
# This function looks at the status.csv log file backwards until reaching the last step of the analysis that was completed by MATLAB
# Returns empty nothing has been completed so far
folder_name=$1
log_name=${1%/}/status.csv
if ! test -w $log_name; then
# log file does not exist, create it and exit
Cre... |
0b76bef081efac2cf0e04d7b15ab9c6f2f93e8415f546912af32535238ca8ad9 | Shell | 811 | 29 | #!/bin/bash
date_folder=$1
start_point=$2
next_step=$(($start_point + 1))
if [ -f "$date_folder/labview_parameters.csv" ]; then
# this is a experiment folder
ProcessExperimentDirectory.sh $date_folder $start_point &
else
# this is not an experiment folder, repeat iteratively
# loop through all the directories i... |
480c169e0771cf1d4f523931338380b3275526a984c5bdef91f2e4f8edda7710 | Shell | 811 | 30 | #!/bin/bash
set -euo pipefail
# Clone pinned KubeRay commit to temporary directory, copy the CRD definitions
# into the autoscaler folder.
KUBERAY_BRANCH="v1.7.0"
OPERATOR_TAG="v1.7.0"
# Requires Kustomize
if ! command -v kustomize &> /dev/null
then
echo "Please install kustomize. Then re-run this script."
e... |
a7c0c4be7406ad8f9c9c03b4a9d201ade24b6a01b3cc874395f44750539d0e97 | Shell | 811 | 18 | #!/bin/bash
export ASM=$1
export TC=8
export CHR=chrX
export HG38=/home/tpesout/data/reference/hg38.fa
#export HG38=/home/ubuntu/data/human/reference/hg38/hg38.fa
minimap2 -ax asm20 -t $TC $HG38 $ASM | samtools view -hb >$ASM.unsorted.bam
samtools sort -@ $TC $ASM.unsorted.bam | samtools view -hb >$ASM.bam
samtools i... |
656dc9327554fecf643d14ee87150f92f4576cdd78912a4c761c94c103ed42af | Shell | 820 | 38 | #!/bin/bash
#SBATCH -p GPU
#Requesting one node
#SBATCH -N1
#SBATCH -n25
#Requesting 1 A100 GPU
#SBATCH --gres=gpu:a100:1
module purge
module load openmpi/4.1.0
module load gcc/8.3.0
module load cp2k/2024.3
#filter warnings
export OMPI_MCA_op=^avx
export OMPI_MCA_btl="^openib"
export OMPI_MCA_orte_base_help_aggregate... |
fdc19fab36c0e178f968c552b2efe7e0d5afee634ca030150d9af010f10b9167 | Shell | 820 | 23 | #!/bin/bash
#SBATCH -J DelSwitch
#SBATCH -p high
#SBATCH --exclude=node0[19-21,25]
#SBATCH --gres=gpu:1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=8
#SBATCH --mem=32G
#SBATCH --array=0-6
#SBATCH -o /homedtic/gjimenez/DADES/DADES/Delineator/Logs/%A-%a.out
#SBATCH -e /homedtic/gjimenez/DADES/DADES/Delineator/Logs/%A-%a.e... |
370dd25d8041189a650fe5a0f01ee1c9e4bb5b86d5b89447dfaef2b970eb190a | Shell | 822 | 26 | export MODEL_NAME="runwayml/stable-diffusion-inpainting"
export OUTPUT_DIR="../../../models/dress_inpainting"
accelerate launch train_inpainting_dreambooth.py \
--pretrained_model_name_or_path=$MODEL_NAME \
--pretrained_vae_name_or_path="stabilityai/sd-vae-ft-mse" \
--output_dir=$OUTPUT_DIR \
--with_prior_pres... |
ee9e3a00b4f5df71e1753bb3c7f10a7bd287f8a6e27bc49cc458ffa5e9bf3bd6 | Shell | 822 | 5 | SAMPLE=$1
samtools view /Users/chaokuan-hao/Documents/Projects/PR_SpliceNN/results/800bp/$SAMPLE/OUTPUT/SpliceAI_6_RB_p_n_nn_n1_TB_all_samples_thr_100_splitByChrom_L64_C16_L800_v21/BAM/$SAMPLE.cleaned.bam | grep -o "NH:i:[0-9]*" > /Users/chaokuan-hao/Documents/Projects/PR_SpliceNN/results/800bp/$SAMPLE/OUTPUT/SpliceAI... |
1aa01adb1b162639bd1a17c0b4851973c7ee6952abb5cb151218b031a307863b | Shell | 825 | 12 | #!/bin/bash
#SBATCH --time=24:00:00
#SBATCH --nodes=1
#SBATCH --account=rrg-mchakrav-ab
singularity run -B /scratch/m/mchakrav/desgab/rats/ds001981_inputs:/nii_inputs:ro \
-B /scratch/m/mchakrav/desgab/rats/rabies_ds001981_inputs_20211026:/rabies_out \
-B /home/m/mchakrav/desgab/atlases:/atlases:ro \
/home/m/mchakrav/d... |
e8fb0d486a806ddf7fb477153f1086d47a73dbe3a1affee27abc3a9ea03041e0 | Shell | 827 | 32 | #!/bin/bash
set -e
#local absolute path to where you want to download the dataset
LOCAL_DIR="your/path/to/BOLDMomentsDataset"
#put the un-preprocessed dataset in its own folder
mkdir -p "${LOCAL_DIR}/Nifti"
#download directory files
dataset_files=("participants.json"
"dataset_description.json"
"participants.t... |
6f8d0127ce45f5f9568419a64edcbdfe9dbc52ff546125c12507583e69bab343 | Shell | 828 | 34 | #!/bin/bash
# This script build Docker image one can run IsoNet inside.
# See interactive.sh to see how to run the built Docker image
set -Eeo pipefail
##############################
SELF_DIR="$(dirname "$(realpath "${0}")")"
REPO_ROOT="$(realpath "${SELF_DIR}/..")"
##############################
# Lower version ... |
b16da8a18a23b66f46ba6f4e54f2b35e54eea8f8083a513711d33164876398a5 | Shell | 828 | 24 | #!/bin/bash
eur=MetS_ukbincluded
eas=KoGES
s1=QC.MetS12_GWAS_MetS_maf0.01_popcornIN.tsv
s2=KoGES_MetS_logistic_plink.MetS.glm.logistic.hybrid.modified_maf0.01_popcornIN.tsv
score_file_eff=./precomputed_score/EUR_EAS_all_gen_eff.cscore
score_file_imp=/data1/jaeyoung/software/popcorn/EUR_EAS_all_gen_imp.cscore
fit_sc... |
c0c5785e4a1ef99bb47f30747785649cd46499c07c5d36c9e89c27845580433e | Shell | 830 | 12 | #!/bin/bash
#SBATCH --time=24:00:00
#SBATCH --nodes=1
#SBATCH --account=rrg-mchakrav-ab
singularity run -B /scratch/m/mchakrav/desgab/rats/ds003646_inputs:/nii_inputs:ro \
-B /scratch/m/mchakrav/desgab/rats/rabies_ds003646_20211026:/rabies_out \
-B /home/m/mchakrav/desgab/atlases:/atlases:ro \
/home/m/mchakrav/desgab/s... |
1759eb39f78c9859af31edd093db6c10f0fa5c877dc4226c841d59df7ff21c06 | Shell | 831 | 32 | #!/bin/bash
set -ex
git config --global core.symlinks true
git config --global core.autocrlf false
mkdir -p /c/rayci
git clone . /c/rayci
cd /c/rayci
{
echo "build --announce_rc";
echo "build --config=ci";
# Set a shorter output_base to avoid long file paths that Windows can't handle.
echo "startup --output_... |
8af29e520a64ff7dc743c7778e93b4e1e18994710116e800842ea5820c147c0d | Shell | 834 | 27 | #!/bin/bash
source 00_global_variables.sh
OUT=.
for idx in "${!Phenotypes[@]}"
do
sumstatPath="${Cleaned_sumstat_noUKB[$idx]}"
inDelimiter=tab
SelectedColumns='SNP A1 A2 Effect SE Pval'
RenamedColumns='MarkerName A1 A2 Beta SE P'
outDelimiter=tab
Suffix=.REFORMAT4PRS.GWAS
outExtension=tx... |
a75f777af34e39bd28b6a5d00e323169bf3daaceeefb0a374922301103ffcf46 | Shell | 835 | 40 |
echo $BASH_VERSION
subjs=( M9806 )
root=/mnt/labspace/Projects/MESO_v2.0/ALLSUBJS_2.0
for i in ${subjs[@]}; do
(
cd $root/$i
meso=(`ls | grep DIFF_meso_1.nii`)
research=(`ls | grep DIFF_meso_2.nii`)
pa=(`ls | grep DIFF_meso_pa.nii`)
if [ ${#research[@]} -eq 0 ]; then
continue
fi... |
e29d38ee712e9e1c3cecac8657febb43d45cdbcca3d1d45dac210f317319042e | Shell | 836 | 27 | #!/bin/bash
set -euxo pipefail
PERSISTENT_STACK_NAME=${PERSISTENT_STACK_NAME:-nm-persist}
GITHUB_REPO=${GITHUB_REPO:-neuron_morphology}
GITHUB_OWNER=${GITHUB_OWNER:-AllenInstitute}
BRANCH_TYPE=${BRANCH_TYPE:-dev}
DIR=$(dirname "$(readlink -f "$0")")
AWS_PROFILE=${AWS_PROFILE:-$(aws configure get profile)}
AWS_RE... |
54924971f5aac8e5e5590a0d80391b516d1e1f44e6622e3ae5b70a48819a358f | Shell | 837 | 46 | #!/bin/bash
SCRIPTNAME=$(basename $0)
USAGESTR="
NAME
${SCRIPTNAME} Evaluate repeats eye movements reconstructions with MS-SSIM and LPIPS
SYNOPSIS
${SCRIPTNAME} <config> <recons_path> <metrics_path>
Eric Wu, 2023-03-21
"
usage() {
echo "$USAGESTR"
}
if [[ $1 == "" ]]; then
echo "You must provide command line... |
857d837409dc5b41054a023f05bb3f110f6b76a50bdc270c92f8d550bd7b195f | Shell | 837 | 22 | #!/bin/bash
# Compare against the master branch, because most development is done against it.
base_commit="$(git merge-base HEAD master)"
if [ "$base_commit" = "$(git rev-parse HEAD)" ]; then
# Prefix of master branch, so compare against parent commit
base_commit="$(git rev-parse HEAD^)"
echo "Running clang-form... |
36c3ec25e7ac0db9d8b9b19fd680a5afb1ebdf7a361d969288e537b14ab46fa5 | Shell | 845 | 2 | python main.py --save_path experiments/evaluate_on_test_and_val --test_data_path data/train_val_test/test/data.json data/train_val_test/valid/data.json --load_model_path pretrained_models/DeltaSplice_models/model.ckpt-0 pretrained_models/DeltaSplice_models/model.ckpt-1 pretrained_models/DeltaSplice_models/model.ckpt-2... |
99f9bb551a1f6ae5a99ede8de864e0b8b9ff0bff17bdce44170d19bbe3699076 | Shell | 845 | 36 | #!/bin/bash
Phenotypes=('BMI'
'WC'
'T2D'
'FG'
'HTN'
'TG'
'HDL')
Cleaned_sumstat_noUKB=('CLEANED.BMI_GIANT2015.txt'
'CLEANED.WC_GIANT2015.txt'
'CLEANED.T2D_meta_FinngenR7_MVP.txt'
'CLEANED.FG_MAGIC.txt'
'CLEANED.HTN_Finngen_r7.txt'
'CLEANED.TG_GLGC_noUKB.txt'
'CLEA... |
f31817861db7fad4b6370eb29bac56d7079b786eb71359c3f90f367e62e1a554 | Shell | 845 | 27 | #!/bin/bash
# Re-install the package. By running './reinstall.sh'
#
# Note that CEBRA uses the build
# system specified in
# PEP517 https://peps.python.org/pep-0517/ and
# PEP518 https://peps.python.org/pep-0518/
# and hence there is no setup.py file.
set -e # abort on error
pip uninstall -y cebra
# Get version inf... |
ca78e73dc78dcabbad7ed7ebbfbe36cc0b682ffa93c564f9daab09de4a89c6ef | Shell | 847 | 17 | #!/usr/bin/bash
sample=/home/data/sample.list
OUT_DIR=/home/data/snp/vcfs
# get the basename of vcf
OUT_PREFIX=$(basename $VCF)
# remove ".vcf.gz" at the end of prefix
OUT_PREFIX=${OUT_PREFIX%%.vcf.gz}
THREADS=2
# remove everything except GT
bcftools annotate --threads $THREADS -x "FORMAT" -Oz -o $OUT_DIR/tmp/$OUT_PR... |
d1581484ef081f5e68f347e9bd20a774bf1c718fec4161105087d240b42df942 | Shell | 860 | 41 | #!/usr/bin/env bash
set -x
set -euo pipefail
ROOT_DIR=$(cd "$(dirname "${BASH_SOURCE:-$0}")"; pwd)
cd "$ROOT_DIR"
clean_up() {
ray stop --force
}
trap clean_up EXIT
CYPRESS_VERSION=14.2.1
(
cd ../client
npm ci
)
echo "Installing cypress"
if [[ -n "$BUILDKITE" ]]; then
apt-get update -qq
apt install -y li... |
7c954d8e42c7d221963debe5da14a3ad5c729a4bb2715e007216f34f0a853197 | Shell | 862 | 18 | echo "Initialazing Solr Indexing"
curl 'http://localhost:8983/solr/bioner-diseases/update/json?commit=true' --data-binary @data_processing/data/Disease/diseases.json -H 'Content-type:application/json'
echo "Disease Indexing finished!!"
curl 'http://localhost:8983/solr/bioner-drugs/update/json?commit=true' --data-bin... |
9366a5d820e2812636be830d2622493fdea1d739c896ce99f69dc18fe20dd41e | Shell | 862 | 17 | #!/usr/bin/env bash
# Checks that every py_test source file under python/ contains the
# `if __name__ == "__main__":` pytest snippet.
set -euxo pipefail
WORKSPACE_DIR="$(cd "$(dirname "${BASH_SOURCE:-$0}")" || exit; pwd)/../.."
cd "${WORKSPACE_DIR}"
# Read the team list from the team-owner checker rather than hardco... |
369ce5e260ac86f7c3f88d5975d846e038ba7c7119b0f7b175154ebbea572675 | Shell | 863 | 33 | #! /bin/bash
# FIMO needs a few things. It needs motifs in MEME format (already pulled from JASPAR)
MOTIF_FILE=./fileOutputs/JASPAR_2020_CORE_Vertebrates_non-redundant_meme.txt
inputSeqFile=$1
# cds_p_allHeartATAC_peakSeqsAsFasta.fa
# It also needs sequence to analyze. For this, I'm pulling a file (set here) of sequ... |
5b927bf966cc3960e1d35a58686edcbf8e41542ed2c315d64a6b7af88b93f214 | Shell | 864 | 21 |
echo start `date`
outdir="./output_stage1"
train_list="./stage1_train_sample_lists/"
valid_list="./stage1_validation_sample_lists/valid_PDB_before2020_5.xls"
# users can use ./data/PDB_coord_seq.sh make hdf5 files for training and validation
coords_seq_hdf5="./data/xyz_tokens_label8_psi_phi_before2020_5.h5"
SPIRED_sav... |
1bf1e06b4f242989e2252c282acd4c453846762c9f49aa4962ea5bd310e1467e | Shell | 865 | 23 | #!/bin/bash -e
if [ $# -lt 3 ] || [ $# -gt 4 ]; then
echo "usage v1: rampage_mad_qc.sh <quants_file_a> <quants_file_b> <out_root_name> [MAD_R_script]"
echo "Generages MAD QC scoring of 2 replicate quantification files and produces: *_plot.png/.json. Is independent of DX and encodeD."
exit -1;
fi
quants_fi... |
3d6976e8784db7890a1bed6d4f3006568ea030de906bbe688201b429d60fe2a9 | Shell | 865 | 32 | #!/usr/bin/env bash
NAME=${1:-jpp-1}
shift 1
INSTANCE_TYPE=${1:-n1-standard-1}
shift 1
DISK_SIZE=${1:-100GB}
shift 1
echo "Creating instance ${NAME} from family ml4h-image of type ${INSTANCE_TYPE}..."
echo "$@"
gcloud compute instances create ${NAME} \
--project broad-ml4cvd \
--zone us-central1-a \
--image-project... |
2db4ecce84d30a69b00ad1e05219624ba6e41adb27c62f3bd47edc41cfd0e5a7 | Shell | 866 | 34 | #!/bin/bash
cd /net/parasite/SchizConnect/Sites/COBRE/
#resample each WM and CSF segment into functional space
for i in $(cat havesmooth.txt)
do
cd ${i}/coReg/
3dresample -master ../func/s6w3*.nii -infile mwp2*.nii -prefix r3wm.nii -rmode NN
3dresample -master ../func/s6w3*.nii -infile mwp3*.nii -prefix r... |
4b50666e7ebd821f5cb3269a49fb1819dc2643c10c9f57afb1881b305d9ff9ae | Shell | 867 | 25 | #!/bin/bash
set -euo pipefail
OUTPUT_FOLDER="$HOME/fossa_output_folder"
mkdir -p "$OUTPUT_FOLDER"
FOSSA_API_KEY="$(
aws secretsmanager get-secret-value --region us-west-2 \
--secret-id oss-ci/fossa-api-key \
--query SecretString --output text
)"
export FOSSA_API_KEY
# run Full fossa analyze on entire ra... |
3681aef33f415ed2ec2d0ba229f9e0657d5a1c51b274a175c18b2141147c7d15 | Shell | 872 | 33 | #!/bin/sh
# script for execution of deployed applications
#
# Sets up the MATLAB Runtime environment for the current $ARCH and executes
# the specified command.
#
exe_name=$0
exe_dir=`dirname "$0"`
echo "------------------------------------------"
if [ "x$1" = "x" ]; then
echo Usage:
echo $0 \<deployedMCRroot\>... |
ea32098c405006869b00d66ef7e063f1f3975653d830af4ad4c4056fa590589c | Shell | 877 | 41 | #!/bin/bash
#####################################################
## List raw CMIP6 data files used in this analysis ##
#####################################################
proj_dir="/path/to/main_project_folder/" # edit this line
raw_data_path=${proj_dir}'input_data_CMIP6/raw_daily/'
EXPERIMENT_LIST=$(cat "LIST_E... |
fd9f9a18350969d77492e27fdee43ddfb6d74d23ebe8220ed9c1b884401f06a5 | Shell | 877 | 28 | #!/bin/bash
#SBATCH --job-name=DeepTreeAttention # Job name
#SBATCH --mail-type=END # Mail events
#SBATCH --mail-user=benweinstein2010@gmail.com # Where to send mail
#SBATCH --account=ewhite
#SBATCH --nodes=1 # Number of MPI ran
#SBATCH --cpus-per-task=1
#SBATCH --mem=50GB
#SBATCH --tim... |
be006e428e732adee7064fefd88efc05cb909bc2002ee784bc88f09a2fc93894 | Shell | 881 | 32 | #!/bin/bash
rscript=/snp_independence.R
trait1=MetS
trait2=BMI
gwas1_snplist=../COJO/extract_cojo/cojo_out_jma.MetS.snplist.chr_pos
gwas2=../COJO/cojo_input/CLEANED.BMI_GIANT2018.txt
r2_thres=0.01
p_thres=5e-8
window=500
n_thread=30
Rscript ${rscript} \
--gwas1-snplist ${gwas1_snplist} \
--delim-gwas1-snplis... |
090a835e1e4e3d914aaef3ec509d732cbb4de883c879785e819b3f69701e1c46 | Shell | 882 | 30 | #!/bin/bash
#
# reformat_metrics.sh
#
# TODO: do this as part of metric aggregation
#
set -e
blacklisted=$1
metricfile=$2
##remove duplicate lines## \
##create metric file remove variants where all samples are called to have a CNV## \
####fix BAF p-value to be on log scale to match others### \
####flip sign ... |
16db5016834f5d7aba3d5a81b26f008be9416af4256e9871af602ae6d88b12d4 | Shell | 884 | 33 | #!/bin/sh
# script for execution of deployed applications
#
# Sets up the MATLAB Runtime environment for the current $ARCH and executes
# the specified command.
#
exe_name=$0
exe_dir=`dirname "$0"`
echo "------------------------------------------"
if [ "x$1" = "x" ]; then
echo Usage:
echo $0 \<deployedMCRroot\>... |
c3f7a8f1ac14bac28f9714c9d676c7c7997e905f954bbd2c918e3903c53e4e26 | Shell | 887 | 23 | #!/bin/bash
set -e
prefix=$1
source_img="https://upenn.box.com/shared/static/yya0lvlur8aase29hvy630jd06r64tdn.jpg"
source_cnts="https://upenn.box.com/shared/static/kaoo8j31dx5lupyz8dctay7p5x3exqsa.tsv"
source_locs="https://upenn.box.com/shared/static/7nbnorlr2h6tkeyghjibqitztezkadwh.tsv"
source_radius="https://upenn.... |
5c0aa6d1249e22a5554f072a179d02a3b5e16b75fccdf4daa78baa42144f36dd | Shell | 888 | 21 | #!/usr/bin/env bash
set -eu
export PATH=/shared/utils.x86_64/anaconda2-4.3.1/bin:$PATH
export HOME=${bamboo_build_working_directory}/.home
export TMPDIR=${bamboo_build_working_directory}
export CONDA_PATH_BACKUP=${CONDA_PATH_BACKUP:-$PATH}
export CONDA_PREFIX=${CONDA_PREFIX:-}
export CONDA_PS1_BACKUP=${CONDA_PS1_BACKU... |
b7ea018a7d917022ab8254a7a11da000573895d0e5472392be16da3f65badaf3 | Shell | 891 | 33 | #!/bin/sh
# script for execution of deployed applications
#
# Sets up the MATLAB Runtime environment for the current $ARCH and executes
# the specified command.
#
exe_name=$0
exe_dir=`dirname "$0"`
echo "------------------------------------------"
if [ "x$1" = "x" ]; then
echo Usage:
echo $0 \<deployedMCRroot\>... |
0ec18ce85c1e719a7576b67b2af7bf816e399ce8d7152e5349a1df1677359816 | Shell | 893 | 12 | #!/bin/bash
#SBATCH --time=24:00:00
#SBATCH --nodes=1
#SBATCH --account=rrg-mchakrav-ab
singularity run -B /scratch/m/mchakrav/desgab/rats/upenn_data/inputs:/nii_inputs:ro \
-B /scratch/m/mchakrav/desgab/rats/rabies_upenn_20211026:/rabies_out \
-B /home/m/mchakrav/desgab/atlases:/atlases:ro \
/home/m/mchakrav/desgab/si... |
475980a964819481de9c93bf87102caf254722585a747e61d59a99d792cbcf46 | Shell | 899 | 19 | #!/bin/sh
#SBATCH --job-name=OCHiPerGator # Use the same name as the MATLAB program\
#SBATCH --mail-type=ALL # Mail events (NONE, BEGIN, END, FAIL, ALL)\
#SBATCH --mail-user=hannahanderson@ufl.edu # Where to send mail\
#SBATCH --account=tstepien
#SBATCH --qos=tstepien-b
#SBATCH --nodes=1 ... |
b5b19d02e5dc429d7ccbfd2c7e850a66ed2772229a8ad1902a332e28dedf73b6 | Shell | 901 | 24 | #!/bin/bash
#SBATCH -J DelBias
#SBATCH -p medium
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --mem-per-cpu=2G
#SBATCH --array=000-999
#SBATCH -o /homedtic/gjimenez/DADES/DADES/DelineationResults/BIAS_20_SEPARATE/LOGS/%A_%a.out
#SBATCH -e /homedtic/gjimenez/DADES/DADES/DelineationResults/BIAS_20_SEPARATE/LOGS/%... |
6ab1cb7ab3176e886601941a039035f117c6e9eaf0a183f60e651f75a2cf143a | Shell | 902 | 31 | #!/bin/bash
set -euo pipefail
WHEEL_NAME="$1"
SOURCE_IMAGE="$2"
DEST_IMAGE="$3"
PIP_FREEZE_FILE="$4"
RAY_VERSION="$(python python/ray/_version.py | cut -d' ' -f1)"
RAY_COMMIT="$(git rev-parse HEAD)"
CPU_TMP="$(mktemp -d)"
cp -r .whl "${CPU_TMP}/.whl"
cp docker/ray/Dockerfile "${CPU_TMP}/Dockerfile"
# Build the ima... |
6fde152ce1cc88194243278126c1e6cecb6228bbe689aa69788323c0f3e8f79f | Shell | 902 | 32 | #!/bin/bash
rscript=/snp_independence.R
trait1=MetS
trait2=WC
gwas1_snplist=../COJO/extract_cojo/cojo_out_jma.MetS.snplist.chr_pos
gwas2=../COJO/cojo_input/CLEANED.WC_UKB.txt
r2_thres=0.01
p_thres=5e-8
window=500
n_thread=30
/home/sanghyeon/.conda/envs/R4_HPC/bin/Rscript ${rscript} \
--gwas1-snplist ${gwas1_snpl... |
f35042baf5812b29ef0dfc874575b2027407b1d082026b1da9230191cea51b35 | Shell | 902 | 22 | #!/bin/bash
########################################################################################################
QCsumstat=MetS_noUKB_GWAS.csv
inDelimiter=comma
SelectedColumns='SNP A1 A2 est SE Pval_Estimate'
RenamedColumns='MarkerName A1 A2 Beta SE P'
outDelimiter=tab
Suffix=.REFORMAT4PRS.GWAS
outExtension=txt
o... |
76c04944449913ae9bcbe95fd09d56a348fc4f1bed070c9d3c0b2d22c8c00cd1 | Shell | 906 | 23 | source ~/anaconda3/bin/activate;
conda activate HPC;
cd ~/GitHub/DelineatorSwitchAndCompose;
# Get a list of all possible models
list_all_models=()
input="list_files.txt"
while IFS= read -r line
do
list_all_models+=("$line")
done < "$input"
for i in {0..108}
do
model=${list_all_models[$i]};
echo $((i+1))/10... |
824303cd3b28acba891429b4b9d5a1a3578cf8124a85867b39b87066c2c94af7 | Shell | 907 | 32 | #!/bin/bash
rscript=/snp_independence.R
trait1=MetS
trait2=TG
gwas1_snplist=../COJO/extract_cojo/cojo_out_jma.MetS.snplist.chr_pos
gwas2=../COJO/cojo_input/CLEANED.TG_GLGC_UKB.txt
r2_thres=0.01
p_thres=5e-8
window=500
n_thread=30
/home/sanghyeon/.conda/envs/R4_HPC/bin/Rscript ${rscript} \
--gwas1-snplist ${gwas1... |
222a8bd852239e43eff6771f8b1451a2645125270a92c5381a53d7c81df6d922 | Shell | 909 | 29 | #!/bin/bash
set -euo pipefail
CHAOS_FAULT="${1:-no_fault}"
CHAOS_WORKLOAD="${2:-test_potato_passer}"
bazel run //ci/ray_ci:build_in_docker -- docker \
--python-version 3.10 \
--platform cpu --canonical-tag kuberay-test
docker tag rayproject/ray:kuberay-test ray-ci:kuberay-test
bash python/ray/tests/chaos/pr... |
9dae41d947a8335ba727ed0b8fe29d840d7c39b24cdccaab407e42d1f90875c9 | Shell | 909 | 32 | #!/bin/bash
rscript=/snp_independence.R
trait1=MetS
trait2=HDL
gwas1_snplist=../COJO/extract_cojo/cojo_out_jma.MetS.snplist.chr_pos
gwas2=../COJO/cojo_input/CLEANED.HDL_GLGC_UKB.txt
r2_thres=0.01
p_thres=5e-8
window=500
n_thread=30
/home/sanghyeon/.conda/envs/R4_HPC/bin/Rscript ${rscript} \
--gwas1-snplist ${gwa... |
f1b93eea4a474a533bed48a80ca10b01dd01fc258ca04ad355b63c240a2c1f54 | Shell | 910 | 43 | ## 1. Write a slurm script (filename: plink_vcf_to_bed.sh) to convert VCFs to filtered BEDs
#!/bin/bash
# Set job time
#SBATCH --time=0-04:00:00
# Set a name for the job, visible in `squeue`
#SBATCH --job-name="plink_vcf_to_bed"
# One node
#SBATCH --nodes=1
# One task
#SBATCH --ntasks=1
# One CPU/core per task
#S... |
6c24104bffb89ca1b638de2bd580765737de25c0850aac9dfa9f46bdee236d5c | Shell | 914 | 32 | #!/bin/bash
if [[ "${TRAVIS_PULL_REQUEST}" != "false" ]]
then
echo "This is a pull request. Skipping release process"
exit 0
fi
if [[ "${TRAVIS_BRANCH}" != "master" ]]
then
echo "Not master branch. Skipping release process"
exit 0
fi
if .travis/version_updated.sh >/dev/null 2>&1
then
echo "Versio... |
19936c42fca8b49915d35fc34e0c5f533f4750d0f49390d4696f3826a8ec5979 | Shell | 917 | 25 | #!/bin/bash
#SBATCH -J mlp
#SBATCH --output=slurm_out/mlp_out.%j
#SBATCH --error=slurm_out/mlp_err.%j
#SBATCH --partition=mcml-dgx-a100-40x8
#SBATCH --qos mcml
#SBATCH --gres=gpu:1
#SBATCH --time 3-00:00:00
#SBATCH --mem=90GB
#SBATCH --cpus-per-task=6
DSSFS02_HOME="/dss/dssfs02/lwp-dss-0001/pn36po/pn36po-dss-0001/di9... |
c3b903f24af059e2ff44708bf324195b426d12caf2da73d540b3e7916f725eee | Shell | 917 | 17 | # polyA
for sample in R2826 R2835 R2839 R2845 R2855 R2857 R2869 R2874 R2894 R2895 ; do
echo mkdir ../results/polyA/$sample/assembly/AFTER/
mkdir ../results/polyA/$sample/assembly/AFTER/
echo stringtie -o ../results/polyA/$sample/assembly/AFTER/$sample.gtf ../results/polyA/$sample/$sample.cleaned.bam &
... |
88852d33dfbb235f39c0288d8d170c81e1509679c34113255333b812e0202d88 | Shell | 919 | 32 | #!/bin/bash
rscript=/snp_independence.R
trait1=MetS
trait2=HTN
gwas1_snplist=../COJO/extract_cojo/cojo_out_jma.MetS.snplist.chr_pos
gwas2=../COJO/cojo_input/CLEANED.HTN_meta_FinngenR7_UKB.txt
r2_thres=0.01
p_thres=5e-8
window=500
n_thread=30
/home/sanghyeon/.conda/envs/R4_HPC/bin/Rscript ${rscript} \
--gwas1-snp... |
a40df74688a64379814c5cb44966767844d4b1599bdc95e3df47ef7be9ff0af9 | Shell | 924 | 32 | #!/bin/bash
rscript=/snp_independence.R
trait1=MetS
trait2=F2
gwas1_snplist=../COJO/extract_cojo/cojo_out_jma.MetS.snplist.chr_pos
gwas2=../COJO/cojo_input/QC.MetS12_F2_GWAS.withQsnp.csv
r2_thres=0.01
p_thres=5e-8
window=500
n_thread=30
/home/sanghyeon/.conda/envs/R4_HPC/bin/Rscript ${rscript} \
--gwas1-snplist ... |
b9bed577fda71116161f31d41e2098d90b74df8080d6aafb0b41789a96a99be6 | Shell | 924 | 32 | #!/bin/bash
rscript=/snp_independence.R
trait1=MetS
trait2=F1
gwas1_snplist=../COJO/extract_cojo/cojo_out_jma.MetS.snplist.chr_pos
gwas2=../COJO/cojo_input/QC.MetS12_F1_GWAS.withQsnp.csv
r2_thres=0.01
p_thres=5e-8
window=500
n_thread=30
/home/sanghyeon/.conda/envs/R4_HPC/bin/Rscript ${rscript} \
--gwas1-snplist ... |
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