sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
2f9fcf77be129df513df031e51e96278ce3586def338bbe049b9fbd524921308 | Shell | 386 | 12 | #!/bin/bash
set -Ceu
outdir=$(mktemp -d)
gpu="$1"
# gym/categorical_dqn
python examples/gym/train_categorical_dqn_gym.py --steps 100 --replay-start-size 50 --outdir $outdir/gym/categorical_dqn --gpu $gpu
model=$(find $outdir/gym/categorical_dqn -name "*_finish")
python examples/gym/train_categorical_dqn_gym.py --de... |
bdcb95e735bf3d64cb5f92c15512ccf6a9080d2b42e6dc12dccf3c5a4433d051 | Shell | 386 | 12 | #!/bin/bash
set -Ceu
outdir=$(mktemp -d)
gpu="$1"
# atari/dqn
python examples/atari/train_dqn_ale.py --env PongNoFrameskip-v4 --steps 100 --replay-start-size 50 --outdir $outdir/atari/dqn --gpu $gpu
model=$(find $outdir/atari/dqn -name "*_finish")
python examples/atari/train_dqn_ale.py --env PongNoFrameskip-v4 --de... |
2948b4ff617257ab2d8814cbf32d43d4f17f91ce8aa3fc7b4e5beb559f0395cf | Shell | 388 | 19 | #!/bin/bash
#SBATCH -p general
#SBATCH -N 1
#SBATCH --mem=96g
#SBATCH -n 18
#SBATCH -t 1-
module use /proj/mnhallqlab/sw/modules
module load r/4.0.1
module load fsl/6.0.4
module load afni/20.1.05
#export atlas #pass through env variable
#suffix=$( basename $atlas )
#suffix=${suffix/.nii.gz/}
export ncores=18
R CMD ... |
7eaa737164a8f6d54448e1f8397f9de8a94dab1e19c5ae6de1ca64fd0dcca7aa | Shell | 388 | 13 | #!/bin/bash
python run_validation.py \
--checkpoint_path "<path-to-checkpoint>" \
--trajectory_path "<path-to-OC20NEB-trajs>" \
--k 1 \
--output_file_path "<path-to-your-output>" \
--batch_size 8 \
--delta_fmax_climb 0.4 \
--get_ts_sp \
--vasp_command "<vasp-command>" \
--fmax 0.05 ... |
927c753c14220a1f3c488f73080bc2f29ec6cc46bde88f17d7e448f275b7afda | Shell | 389 | 11 | #! /bin/bash
# Get the chrom file from the BBI directory used in the ATAC pipeline
cp /net/bbi/vol1/data/genomes_stage/human/human_atac/chromosome_sizes_fasta_finished.txt ./chromosome_sizes_fasta_finished.txt
# Add "chr" to front of the chrom names files
cat ./chromosome_sizes_fasta_finished.txt | awk '$1="chr"$1' ... |
e46b96b875934b147e5c145966b51ef5b2da6f92a1934efc87a6b3c1c45c9d41 | Shell | 390 | 3 | SAMRI bru2bids -o /var/tmp/samri_testing/bash/mouse -f '{"acquisition":["EPI"]}' -s '{"acquisition":["TurboRARE"]}' /usr/share/samri_bindata
SAMRI bru2bids -o /var/tmp/samri_testing/bash/rat -f '{"acquisition":["seEPI"]}' /usr/share/samri_bindata
SAMRI bru2bids -o /var/tmp/samri_testing/bash/lemur -f '{"acquisition":["... |
01c87e713b567694c319e3debe78d80fc013da9e8114e8dbd22fbf0e55f437de | Shell | 391 | 20 | #! /bin/bash
image_name="srp33/bio_image_colorblindness"
version=1
container_name="bio_image_colorblindness"
docker build -t ${image_name}:version$(cat VERSION) \
-t ${image_name}:latest \
.
mkdir -p TempResults
docker run \
-i -t \
--rm \
--name ${container_name} \
--user $(id -u)... |
88bf2482f0325bee5d79fa7267cdaf785402afb6acb71948beffc13d33901154 | Shell | 391 | 11 | #!/bin/bash
echo $PKG_VERSION > conda/.version
$PYTHON setup.py install --single-version-externally-managed --record record.txt
if [[ $(uname -o) != Msys ]]; then
rm -rf "$SP_DIR/conda/shell/*.exe"
fi
$PYTHON -m conda init --install
if [[ $(uname -o) == Msys ]]; then
sed -i "s|CONDA_EXE=.*|CONDA_EXE=\'${PREFIXW//\... |
d313f0db49ea134d7266914fa513b6597dfd11f425609b553f8f287e7e121faf | Shell | 393 | 4 | for sample in R2826 R2835 R2839 R2845 R2855 R2857 R2869 R2874 R2894 R2895; do
echo scp /Users/chaokuan-hao/Documents/Projects/PR_SPLAM/results/polyA/$sample/junction_score.bed s3:/ccb/salz3/kh.chao/SPLAM/results/polyA/$sample/
scp /Users/chaokuan-hao/Documents/Projects/PR_SPLAM/results/polyA/$sample/ju... |
9fbb5d351e8c238ae734f98acdad053ba35bda6302e92f0814dd27773f9b38b0 | Shell | 394 | 16 | #!/bin/bash
gwas=MetS_GWAS.txt
ref_random_ukb=.test.rand10k
eqtl_besd=./BrainMetaV2/BrainMeta_cis_eQTL_chr
for chr in {1..22};do
smr_Linux --bfile ${ref_random_ukb} \
--gwas-summary ${gwas} \
--beqtl-summary ${eqtl_besd}${chr} \
--out ./smr.MetS.BrainMetaV2 \
--smr-multi \
... |
c404630828e6c3e637841c766836f7ed607351ac759d9acede56d3fab8c8de6a | Shell | 395 | 15 | #!/bin/bash
OMP_NUM_THREADS=64 mpirun -np 1 python3 train.py --inputfn train.xyz \
--box 15.6627 0 0 0 15.6627 0 0 0 15.6627 \
--committee_size 1 \
--fixed_seed \
--num_epochs 500 \
> train.stdout 2> train.stderr
OMP_NUM_THREADS=64 python3 compare.py \
--infile test.xyz \
--box 15.6627 0 0 0 15.6627 0 0 0 15.6... |
a802d28d2b2d5fb18abba73e4c8c1450b48b97d1a984e8d224c7a4b848cad38c | Shell | 396 | 15 | #!/bin/bash
module load matlab/2017a
mkdir compiled
cat > build.m <<END
addpath(genpath('/N/u/brlife/git/vistasoft'))
addpath(genpath('/N/u/brlife/git/jsonlab'))
addpath(genpath('/N/u/brlife/git/encode'))
addpath(genpath('/N/u/brlife/git/spm'))
addpath(genpath('/N/u/brlife/git/wma_tools'))
mcc -m -R -nodisplay -d com... |
da23e6d2b748f563002ab1851e1d025df4b2cec237c3356a60d16f35878c081d | Shell | 398 | 14 | #!/usr/bin/env bash
# Checks front-end code format
set -euxo pipefail
ROOT_DIR="$(cd "$(dirname "${BASH_SOURCE:-$0}")" || exit; pwd)/.."
WORKSPACE_DIR="${ROOT_DIR}/.."
cd "${WORKSPACE_DIR}"/python/ray/dashboard/client || exit
npm ci
FILENAMES=($(find src -name "*.ts" -or -name "*.tsx"))
node_modules/.bin/prettier -... |
11caa66f46179a50a805e53eed08cb6a016ca6e6ae0e5f252fcca27578fdc672 | Shell | 400 | 15 | #!/bin/bash
module load matlab/2017a
mkdir -p compiled
cat > build.m <<END
addpath(genpath('/N/u/brlife/git/vistasoft'))
addpath(genpath('/N/soft/mason/SPM/spm8'))
addpath(genpath('/N/u/brlife/git/jsonlab'))
addpath(genpath('/N/u/brlife/git/wma_tools'))
addpath(genpath('/N/soft/rhel7/mrtrix/3.0/mrtrix3/matlab'))
mcc ... |
619f6223dab4264e9a768701e547489b76babbfb60f398792108fb26d75d7c20 | Shell | 400 | 15 | #!/bin/bash
gwas=MetS_GWAS.txt
ref_random_ukb=.test.rand10k
eqtl_besd=./Brain_Anterior_cingulate_cortex_BA24/Brain_Anterior_cingulate_cortex_BA24
smr_Linux --bfile ${ref_random_ukb} \
--gwas-summary ${gwas} \
--beqtl-summary ${eqtl_besd} \
--out ./smr.MetS.GTEx.Brain_Anterior_cingulate_cortex_BA24 \
-... |
6ce32b5f7dcdb6f2bfa48ebddbe116c0090aef73653ca10a8962986102be68b1 | Shell | 400 | 14 | #!/bin/bash
set -Ceu
outdir=$(mktemp -d)
gpu="$1"
# atari/acer (only for cpu)
if [[ $gpu -lt 0 ]]; then
python examples/atari/train_acer_ale.py 4 --env PongNoFrameskip-v4 --steps 100 --outdir $outdir/atari/acer
model=$(find $outdir/atari/acer -name "*_finish")
python examples/atari/train_acer_ale.py 4 --env P... |
bfb05af26dc7f998d0096d30f5134c542a4234ba8613d40e2af131179bda4060 | Shell | 402 | 9 | #!/bin/bash
MungeName=MetS_GWAS_munge
python2 ./ldsc/ldsc.py --h2 ${MungeName}.sumstats.gz \
--ref-ld-chr ./baseline_v1.2/baseline. \
--w-ld-chr ./1000G_Phase3_weights_hm3_no_MHC/weights.hm3_noMHC. \
--overlap-annot \
--frqfile-chr ./1000G... |
d7ff7ef426e4ab2cf35b5d87fe1db644b77235e4ddc1ba76f845061fd9670f7e | Shell | 402 | 13 | #!/usr/bin/env bash
#Cause the script to exit if a single command fails.
set -e
ROOT_DIR="$(cd "$(dirname "${BASH_SOURCE:-$0}")" || exit; pwd)"
bazel --nosystem_rc --nohome_rc build //:example
if [[ "$OSTYPE" == "darwin"* ]]; then
DYLD_LIBRARY_PATH="$ROOT_DIR/thirdparty/lib" "${ROOT_DIR}"/bazel-bin/example
else
... |
1579a99c15d456df70ba61cb42d4f4e9af7558a13203c636190b243b35b16834 | Shell | 403 | 4 | for sample in R2826 R2835 R2839 R2845 R2855 R2857 R2869 R2874 R2894 R2895 ; do
echo samtools merge ../results/polyA/$sample/$sample.cleaned.bam ../results/polyA/$sample/cleaned.sort.bam ../results/polyA/$sample/cleaned_2stage.sort.bam &
samtools merge ../results/polyA/$sample/$sample.cleaned.bam ../results/poly... |
8287ded38ff9d67a18fe5cc54602f29022ad1e21ce0b04677a7e0ab039fcccaa | Shell | 405 | 10 | #!/bin/bash
R_INSTALL_PATH=${1:-/opt/R}
R_LIB_PATH=$(find $R_INSTALL_PATH -name lib -type d -print -quit)
find $R_LIB_PATH \
-type d \
\( -name "help" -o -name "doc" -o -name "html" -o -name "htmlwidgets" -o -name "demo" -o -name "demodata" \
-o -name "examples" -o -name "exampleData" -o -name "unitTests... |
c6a212fa63f88e7279b46008da9155e2c6dd5d048d85e2ed95ce98acc23373b9 | Shell | 405 | 18 | #!/bin/bash
folder_name=$1
script_name=$2
job_ID=$3
log_name=${1%/}/status.csv
master_log_name=~/logs/masterlog.csv
current_time=$(date +%F_%T)
log_header=Script_Name,Status,Time,Folder_Name,JobID,Computer_Name,Comment
log_entry=CreateLog,COMPLETE,$current_time,$folder_name,$job_ID,$(hostname),Log_Initialized
echo... |
d6ef3a27c096181ed1876e03c806170cf141f2bea438790dc4cbe5d061029c6d | Shell | 406 | 5 | threshold=5
SEQ_LEN=800
bedtools getfasta -s -fi ../../../Dataset/hg38_p12_ucsc.no_alts.no_fixs.fa -bed ./NEG_rev_junctions/${SEQ_LEN}bp/donor/donor.bed -fo ./NEG_rev_junctions/${SEQ_LEN}bp/donor/donor_seq.fa
bedtools getfasta -s -fi ../../../Dataset/hg38_p12_ucsc.no_alts.no_fixs.fa -bed ./NEG_rev_junctions/${SEQ_LEN}... |
abbff18139a5c1481bc01c0e6e0a2ebec80f71625ee46c7887a5e770e93fc8a9 | Shell | 410 | 12 | #!/bin/bash
set -Ceu
outdir=$(mktemp -d)
gpu="$1"
# atari/ppo
python examples/atari/train_ppo_ale.py --env PongNoFrameskip-v4 --steps 100 --update-interval 50 --batchsize 16 --epochs 2 --outdir $outdir/atari/ppo --gpu $gpu
model=$(find $outdir/atari/ppo -name "*_finish")
python examples/atari/train_ppo_ale.py --env... |
2911a37c7ba5133aa9b0c4535b5d7e66d73ff49692e3f7219635259f256900cf | Shell | 413 | 21 | #!/usr/bin/env bash
set -o errexit
set -o pipefail
set -o nounset
#pass in
BUCKET=$1 #e.g. "gs://ml4cvd/projects/jamesp/bigquery/201903"
DATASET=$2 #e.g. "ukbb7089_201903"
#specific to this func
GEO="US"
NAME="sample"
bq --location=${GEO} load \
--field_delimiter "\t" \
--replace \
--quote "" \
--source_format=C... |
71c820d11d8c5eebf68240cc8b9f0444027dea10b3dfb5c095fc11964d3c9c44 | Shell | 416 | 12 | #!/bin/bash
set -Ceu
outdir=$(mktemp -d)
gpu="$1"
# atari/dqn_batch
python examples/atari/train_dqn_batch_ale.py --env PongNoFrameskip-v4 --steps 100 --replay-start-size 50 --outdir $outdir/atari/dqn_batch --gpu $gpu
model=$(find $outdir/atari/dqn_batch -name "*_finish")
python examples/atari/train_dqn_batch_ale.py... |
d420d659bd9d2384fea9f45d8d23a773d2b20e5a406c8311c20d112df36ae7bf | Shell | 416 | 4 | for sample in R12258 R12260 R12263 R12265 R12266 R12277 R12278 R12280 R12285 R12287 ; do
echo scp /Users/chaokuan-hao/Documents/Projects/PR_SPLAM/results/ribozero/$sample/junction_score.bed s3:/ccb/salz3/kh.chao/SPLAM/results/ribozero/$sample/
scp /Users/chaokuan-hao/Documents/Projects/PR_SPLAM/results... |
572ff724327106fa6f976ad90c8cf2cc6e1526ee2ecffbccec19054fc5639178 | Shell | 417 | 23 | #!/usr/bin/env bash
set -e
set -x
rm -rf $(find . -name __pycache__)
rm -f $(find . -type f -name '*.py[co]')
rm -f $(find . -type f -name '*~')
rm -f $(find . -type f -name '.*~')
rm -rf .pdm-build
rm -rf .mypy_cache
rm -rf .cache
rm -rf .pytest_cache
rm -rf .ruff_cache
rm -rf htmlcov
rm -rf *.egg-info
rm -f .covera... |
c12f8a29e5c9ee460a21854d7fae2013767c18c11610010cd30eff03e830463b | Shell | 417 | 9 | #! /bin/bash
# Get the FIMO motifs from JASPAR. Following the lead of the BBI at
curl http://jaspar.genereg.net/download/CORE/JASPAR2020_CORE_vertebrates_non-redundant_pfms_meme.txt -o fileOutputs/JASPAR_2020_CORE_Vertebrates_non-redundant_meme.txt
# Make a test file
cat fileOutputs/JASPAR_2020_CORE_Vertebrates_non-... |
d63a88b70e447c3e247a239df7e9ad60b90b63dc47bcc2da3151abb724e9d0ec | Shell | 419 | 4 | #! /bin/bash
Rscript /net/trapnell/vol1/home/readdf/trapLabDir/hubmap/results/2021_11_08_motifInPeaksRegression_nobackup/runMotifCelltypeRegression.R --cellType $1 --fixedEffects $2 --ATACprocNote FRIP=0.2_FRIT=0.05UMI=1000DL=0.5_useMNN_Peak_CDS_50k_20 --groupColumn Assigned_Cell_Type --cdsPath /net/trapnell/vol1/home... |
f35963da31bf862a0389f3cf41b741e6fc39d227e6e965f14822a3abe2bf5ad2 | Shell | 419 | 2 | python -m experiments.eval_fas.generate_data
python main.py --save_path experiments/eval_fas --mut_data_path data/FAS/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 pretrained_models/Delta... |
7b57ce1e757d4d3fb2b3d4dffdcea95d140bc05ebceee61aed10a8ef995671ea | Shell | 421 | 12 | #!/usr/bin/env bash
cd ../deepface/api/src
# run the service with flask - not for production purposes
# python api.py
# run the service with gunicorn - for prod purposes
if ! command -v gunicorn > /dev/null 2>&1; then
echo "gunicorn is required to run the deepface api. Please run \`pip install \"deepface[api]\"\` t... |
8001b387ce8183fd31aef3d171e5fd17889f0f218ce7bf213ae3495070d35d76 | Shell | 424 | 24 | set -ex
USERNAME=dekkerlab
IMAGE=cworld_env
cp -r ../lib ./
cp -r ../scripts ./
cp ../Build.PL ./Build.PL
cp ../VERSION ./VERSION
cp ../cworld_environment.yml ./cworld_environment.yml
cp ../MANIFEST ./MANIFEST
function cleanup {
rm ./VERSION
rm ./MANIFEST
rm -r ./lib
rm -r ./scripts
rm ./Bui... |
06ad1ca767f7f0420f751b7350f31f829149874b98c502ed52bb67aeb5d31c97 | Shell | 426 | 12 | #!/bin/bash
output_file_name=~/logs/viewoutput.csv
sorted_output_file_name=~/logs/sortedviewoutput.csv
#sort the ouputs
sort -k2,2 -k3,3 -k4,4 -k5,5 -k6,6 $output_file_name>$sorted_output_file_name
#add header
echo 'Folder_Name Progress_Bar Script_Name Status Comment Time_Since JobID' | cat - $sorted_output_file_name... |
c33decb5e49b16a6ae061cf150c238875bfc905db245ffbd8e6043dfbce3276f | Shell | 426 | 12 | #!/bin/bash
set -eu -o pipefail
MODULE_ARCHIVE_URL=$1
# override for debugging purposes
QUIET=${QUIET:-TRUE}
ARCHIVE_DIR=$(mktemp -d "${TMPDIR:-/tmp/}$(basename $0).XXXXXXXXXXXX")
trap "rm -rf $ARCHIVE_DIR" EXIT
MODULE_ARCHIVE_DEST="$ARCHIVE_DIR/$(basename "$MODULE_ARCHIVE_URL")"
curl "$MODULE_ARCHIVE_URL" --output "... |
0461d8817bf6d73af92d0f0c7f9783ca795f49e783657630734c8b3b68b7a299 | Shell | 427 | 4 | for sample in R2826 R2835 R2839 R2845 R2855 R2857 R2869 R2874 R2894 R2895 ; do
echo python Step_1_splam_prediction.py -f ../results/polyA/$sample/fasta/junction.fa -o ../results/polyA/$sample/junction_score.bed -m ../src/MODEL/SPLAM_v11/splam_14.pt
python Step_1_splam_prediction.py -f ../results/polyA/$sample/f... |
03cf7c29527c7076ef5836f217e7e33c6fbb7e878e4aafea004f63effa8e6d4e | Shell | 428 | 24 | set -ex
USERNAME=dekkerlab
IMAGE=cworld_bioperl
cp -r ../lib ./
cp -r ../scripts ./
cp ../Build.PL ./Build.PL
cp ../VERSION ./VERSION
cp ../cworld_environment.yml ./cworld_environment.yml
cp ../MANIFEST ./MANIFEST
function cleanup {
rm ./VERSION
rm ./MANIFEST
rm -r ./lib
rm -r ./scripts
rm .... |
8f71830d0264fa38d35a9d4ec75daa4804dd52eb47a262a3f2087afbea398bc6 | Shell | 429 | 4 | for sample in R2826 R2835 R2839 R2845 R2855 R2857 R2869 R2874 R2894 R2895 ; do
echo samtools sort ../results/polyA_STAR/$sample.bamAligned.sortedByCoord.out/cleaned.bam -o ../results/polyA_STAR/$sample.bamAligned.sortedByCoord.out/cleaned.sort.bam &
samtools sort ../results/polyA_STAR/$sample.bamAligned.sortedB... |
2b842cfab0060bddad7cf2287de51addce3b4afdef0459618a26c097781445d3 | Shell | 430 | 21 | #!/bin/bash
cd /E-P-INs/Scripts/
module purge
source ~/.bashrc
conda activate Enhancer-Interactions-Project
export LC_ALL="en_US.UTF-8"
# DESeq2 Analysis
cd /E-P-INs/Scripts/DESeq2/
srun Rscript ATACSeq_DESeq2.R
srun Rscript H3K27ac_DESeq2.R
srun Rscript RNASeq_DESeq2.R
# ImpulseDE2 Analysis
cd /E-P-INs/Scripts/Imp... |
c1cca74691511c8e227d9ec6a4affa1dede0b6479c263d4fe309121eb9375bd7 | Shell | 430 | 10 | #!/bin/sh
#$ -S /bin/sh
#Version1.0 hewm@genomics.cn 2020-01-10
echo Start Time :
date
#../../bin/LDBlockShow -InVCF Test.vcf.gz -OutPut out -Region chr11:24100000:24200000 -OutPng -SeleVar 1
../../bin/LDBlockShow -InVCF Test.vcf.gz -OutPut out -Region chr11:24100000:24200000 -OutPng -SeleVar 2
# [-... |
1626b5e493c86ce9a0cdff7bca1c69fc49554b406b888ee137a48916949a4b8e | Shell | 431 | 22 | #!/usr/bin/env bash
# This scripts creates a kind cluster and verify it works
set -euo pipefail
# Install k8s tools
bash ci/k8s/install-k8s-tools.sh
set -x # Be more verbose now.
# Delete dangling clusters
kind delete clusters --all
kind create cluster --wait 120s --config ci/k8s/kind.config.yaml
# Verify the ku... |
bec75bcfb38d736ae57c56f5151ee3539bbfe12532b70211a40a9d8fbfcc1d01 | Shell | 431 | 8 | for DATABASE in "GRCm39" "Mmul_10" "NHGRI_mPanTro3" "TAIR10"
do
echo Generating scores for $DATABASE
mkdir -p ./4_output/${DATABASE}/
echo python 4_splam_predict.py -f ./2_output/${DATABASE}/input_pos.fa -o ./4_output/${DATABASE}/score.bed -m ../../../model/splam_script.pt
python 4_splam_predict.py -f ... |
c36b11ff4ed348901bf6d8741b5e08d5d806b2f8790f00a1e15e2d346c51e62a | Shell | 432 | 21 | #!/bin/bash
echo -e "chr\tstart\tend\ttotal\tmini_percent" > $table_output
cat $pred_dir/*final.csv | grep "^data" -v \
| sed 's/[,:-]/\t/g' | sed 's/.gz//g' \
| cut -f 1,2,3,4,7 | sort -k1,1 -k2n,2 \
>> $table_output
# plot
module load R
Rscript $rplot_script \
$table_output \
${fasta}.fai \
$outdir \
$prefix ... |
90cdf18f45fd84fe56e233730a4547c8204f8bc28307dc9b8024324fd651836b | Shell | 433 | 23 | #!/bin/bash
# This script can be used to run interactive Docker session of IsoNet.
set -Eeo pipefail
##############################
SELF_DIR="$(dirname "$(realpath "${0}")")"
REPO_ROOT="$(realpath "${SELF_DIR}/..")"
##############################
"${SELF_DIR}/build.sh"
docker run \
-it \
--rm \
--gpu... |
a4269b728ae419bf46ef62d9a09b8ec4a425f19293f010108c0ae76559793462 | Shell | 433 | 15 | # Get all the files
wget -r -np -nH --cut-dirs=3 -e robots=off -R "index.html*" https://data.broadinstitute.org/alkesgroup/UKBB/UKBB_409K/
mkdir -p ldsc_sumstats_files
module unload python
module load python/2.7.3
for fn in *.sumstats.gz; do
output_prefix=ldsc_sumstats_files/${fn%.sumstats.gz}
python ~ajh24/b... |
54656b5c6254127760f5fe90a8a5c76cb71cace1c0782fec3af16f45a337c955 | Shell | 434 | 4 | julia --project=. -e 'cd("examples"); using NBInclude; @nbinclude("fit_choice_synthetic_data.ipynb"); exit();'
julia --project=. -e 'cd("examples"); using NBInclude; @nbinclude("fit_joint_synthetic_data.ipynb"); exit();'
julia --project=. -e 'cd("examples"); using NBInclude; @nbinclude("fit_neural_real_data.ipynb");... |
107b69cb1f93f8e774698abe339d9157d3495df575737f04f2f576835f8ff08c | Shell | 438 | 19 | for rsb in 1 2 3
do
rsg=5
echo python splam_albation_train.py --rsg $rsg --rsb $rsb
python splam_albation_train.py --rsg $rsg --rsb $rsb
done
for rsg in 1 2 3 4
do
rsb=4
echo python splam_albation_train.py --rsg $rsg --rsb $rsb
python splam_albation_train.py --rsg $rsg --rsb $rsb
done
rsg=5
... |
90034488f120131a4e04ee97e1c235b5a1f3d04c9b6fbf5040274fe27a846226 | Shell | 438 | 3 | conda activate basenji
/home/arthur/basenji/bin/basenji_sad.py -f /home/arthur/lauren/basenji_training/data/fasta/GRCh38.primary_assembly.genome.fa -o /home/arthur/sandbox/sadness/chr3_sad_2023 --rc --shift "1,0,-1" -t /home/arthur/lauren/basenji_training/data/cn-wigs.txt /home/arthur/lauren/basenji_training/models/cn... |
c6605ae48680991652f0003a9370110346ffd49b5932c7fbe994ee162f8b1757 | Shell | 439 | 4 | for sample in R12258 R12260 R12263 R12265 R12266 R12277 R12278 R12280 R12285 R12287; do
echo samtools merge ../results/ribozero/$sample/$sample.cleaned.bam ../results/ribozero/$sample/cleaned.sort.bam ../results/ribozero/$sample/cleaned_2stage.sort.bam &
samtools merge ../results/ribozero/$sample/$samp... |
3e32deeda08ceac9867a7a1910b2ee1c45daac2e2e4df2715f194364b11a9610 | Shell | 440 | 23 | #!/usr/bin/env bash
cd "$(dirname "$0")"
# gs will succeed even if pointed to an empty file.
set -eu
SHOWCASE_PDF=${1}
# Cropbox is:
# - left boundary (from left)
# - lower boundary (from bottom)
# - right boundary (from left)
# - top boundary (from bottom)
gs \
-o ../figs/diff_date.pdf \
-dFirstPage=1 -dL... |
88245b9e6705a165e0ba9bb99045625411aaf9c2d64e8339852fd1d98ddc26fd | Shell | 440 | 21 | #! /bin/bash
#Define locations
#CHR="17"
#REGION="chr17:45500000-46500000"
SV_DIR=chrs_union;
GENO_DIR=output_union;
VCF=$SV_DIR/${CHR}_no_BND.vcf.gz;
CRAM_DIR=crams;
#Define files
REF=GRCh38_full_analysis_set_plus_decoy_hla.fa;
SAM=$CRAM_DIR/cram.list;
cd $GENO_DIR;
graphtyper genotype_sv $REF $VCF --max_files... |
665ffec8f1e888bd4dede716d474d6607d5e8ea4913e93923d1dc988dce3206b | Shell | 441 | 17 | curl -X POST -H 'Content-type:application/json' --data-binary '{
"add-field":{
"name":"section_s",
"type":"string" },
"add-field":{
"name":"text_t",
"type":"text_general" },
"add-field":{
"name":"article_id_s",
"type":"string" },
"add-field":{
"name":"size_i",
"type":"pin... |
893c0560509d158dba0411e6f33ada684b393cc75653b7a7aafeb7a66f1f8257 | Shell | 441 | 23 | #!/usr/bin/env bash
cd "$(dirname "$0")"
# gs will succeed even if pointed to an empty file.
set -eu
SHOWCASE_PDF=${1}
# Cropbox is:
# - left boundary (from left)
# - lower boundary (from bottom)
# - right boundary (from left)
# - top boundary (from bottom)
gs \
-o ../figs/diff_text.pdf \
-dFirstPage=4 -dL... |
d644c46d8816e68465bdd605bbaf6148a7ccd91eb525c15657c9e1e14af15279 | Shell | 441 | 23 | #!/usr/bin/env bash
cd "$(dirname "$0")"
# gs will succeed even if pointed to an empty file.
set -eu
SHOWCASE_PDF=${1}
# Cropbox is:
# - left boundary (from left)
# - lower boundary (from bottom)
# - right boundary (from left)
# - top boundary (from bottom)
gs \
-o ../figs/diff_fig.pdf \
-dFirstPage=14 -dL... |
2f441248f271f41c15aab1a14a0a0de69b9a6dcc31ac5b24044874e0dd4e8da8 | Shell | 442 | 21 | #!/bin/bash
set -exuo pipefail
# Do not upload results to remote cache for pull requests
if [[ "${BUILDKITE_CACHE_READONLY:-}" == "true" ]]; then
echo "build --remote_upload_local_results=false" >> ~/.bazelrc
fi
# Build ray java
if [[ "${RAY_INSTALL_JAVA}" == "1" ]]; then
bazel run //java:gen_ray_java_pkg
fi
exp... |
ef99a5f7f755fa380eb4a6c1aeb1047b3873e626799013cb9b87f1d08bf09d16 | Shell | 443 | 12 |
cd /lustre/projects/Research_Project-MRC148213/lsl693/rTg4510/H_Sorted_Nuclei/2_cutadapt_merge/DN
for i in *_merged_combined.fasta*; do
count=$(grep -c description "$i")
echo -e "$i\t$count" >> read_numbers.txt
done
cd /lustre/projects/Research_Project-MRC148213/lsl693/rTg4510/H_Sorted_Nuclei/2_cutadapt_merge/Neu... |
b45d067e13dd627a57e39c46d5a77da2b429af0a21921aca1b2e943ef7ec2873 | Shell | 444 | 8 | for DATABASE in "GRCm39" "Mmul_10" "NHGRI_mPanTro3" "TAIR10"
do
echo Generating scores for $DATABASE
mkdir -p ./4_output/${DATABASE}/
echo python 4_splam_predict.py -f ./2_output/${DATABASE}/input_neg_random.fa -o ./4_output/${DATABASE}/score.bed -m ../../../model/splam_script.pt
python 4_splam_predict... |
bfdda6fde4d2606c8622e21e4260da48f2a50aea238850b316be1e2de6088455 | Shell | 444 | 14 | #!/bin/bash
out_dir=xai_output
# timestamp = scaling_experiment
# i = num_experiments
for ((i=0;i<=0;i++)); do
for scenario in linear multiplicative translations_rotations xor; do
for background in uncorrelated correlated imagenet; do
pipenv run python -m eval.quantitative_metrics $scenario $b... |
9c700c72caa3ebb70f5b9a24d2f9fee6ba4ef19032a92d229d66e4bb30b0ec69 | Shell | 445 | 7 | SEQ_LEN=$1
project_root=/ccb/cybertron/khchao/splam-analysis-results/
output_dir=${project_root}train/results/MANE/BAM_REF_Intersection/${SEQ_LEN}bp/100_juncs/
bedtools getfasta -s -fi ${project_root}Dataset/hg38_p12_ucsc.no_alts.no_fixs.fa -bed ${output_dir}donor.bed -fo ${output_dir}donor_seq.fa
bedtools getfasta -... |
5248e2d701becd2f79ab3f504bc7f48cf1409cb1474d01e09a1dbf7116a7aba3 | Shell | 446 | 12 | #!/bin/bash
set -Ceu
outdir=$(mktemp -d)
gpu="$1"
# atari/categorical_dqn
python examples/atari/train_categorical_dqn_ale.py --env PongNoFrameskip-v4 --steps 100 --replay-start-size 50 --outdir $outdir/atari/categorical_dqn --gpu $gpu
model=$(find $outdir/atari/categorical_dqn -name "*_finish")
python examples/atar... |
0c3a84a56d3375c4e0ec0118d1aae7b4ef50486f957ad9b219210aed86bc981b | Shell | 447 | 4 | for sample in R2826 R2835 R2839 R2845 R2855 R2857 R2869 R2874 R2894 R2895 ; do
echo python Step_1_splam_prediction.py -f ../results/polyA_STAR/$sample/fasta/junction.fa -o ../results/polyA_STAR/$sample/junction_score.bed -m ../src/MODEL/SPLAM_v11/splam_14.pt
python Step_1_splam_prediction.py -f ../results/polyA... |
2b8189d729af25995b5f4a040f90a59a6e64f76e3a073779cc79867dcc4247c1 | Shell | 448 | 10 | wget -O ftp://ftp.ebi.ac.uk/pub/databases/RNAcentral/current_release/sequences/rnacentral_active.fasta.gz
gunzip rnacentral_active.fasta.gz
# deduplication (mmseqs2 required)
mmseqs createdb rnacentral_active.fasta rnacentral_db
mmseqs cluster rnacentral_db rnacentral_cluster tmp --min-seq-id 0.8 -c 0.8
mmseqs create... |
a005b253ab224d5b0d89654cb7f7aa41a746b64d1233efc7ef7777ffe42494c4 | Shell | 449 | 17 | #!/bin/bash
set -euxo pipefail
# create data directory
mkdir -p 'data/mtx'
# fetch counts
curl 'https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE258835&format=file' -o 'data/mtx/GSE258835.tar'
tar -xvf 'data/mtx/GSE258835.tar' -C 'data/mtx'
rm 'data/mtx/GSE258835.tar'
for f in 'data/mtx/'*'.tar.gz'; do
exdir="data... |
4dd623166ff6f5f2f6eab909bd4b4a8f2823256cfc513be2bf3d66a8d62619cb | Shell | 451 | 15 | target=$1
# for target in "GRCm39" "Mmul_10" "NHGRI_mPanTro3" "TAIR10"
# do
for SPLICEAI_VERSION in 1 2 3 4 5
do
echo ./5_spliceai_prediction_all_seq_noN.sh $target $SPLICEAI_VERSION &
./5_spliceai_prediction_all_seq_noN.sh $target $SPLICEAI_VERSION &
echo -e "\n"
echo ./5_spliceai_prediction_all_seq... |
7c4adec7dd14bd116914fe32e470ff84d06fdb2b8a2182dca411742806f17ff9 | Shell | 451 | 7 | SEQ_LEN=$1
project_root=/ccb/cybertron/khchao/splam-analysis-results/
output_dir=${project_root}train/results/ALL_RefSeq/BAM_REF_Intersection/${SEQ_LEN}bp/100_juncs/
bedtools getfasta -s -fi ${project_root}Dataset/hg38_p12_ucsc.no_alts.no_fixs.fa -bed ${output_dir}donor.bed -fo ${output_dir}donor_seq.fa
bedtools getf... |
17dee3c19ca4aeb5441046d19d86d1fd615006bff43e4f7962f2cfca68a9250b | Shell | 452 | 7 | SEQ_LEN=$1
project_root=/ccb/cybertron/khchao/splam-analysis-results/
output_dir=${project_root}train/results/RefSeq_ALTS/BAM_REF_Intersection/${SEQ_LEN}bp/100_juncs/
bedtools getfasta -s -fi ${project_root}Dataset/hg38_p12_ucsc.no_alts.no_fixs.fa -bed ${output_dir}donor.bed -fo ${output_dir}donor_seq.fa
bedtools get... |
1aabf1b859d29f4e833d8b72d1cb2e603984d0e58167f144134abedb3746b988 | Shell | 455 | 13 | #!/bin/bash
set -Ceu
outdir=$(mktemp -d)
gpu="$1"
# slimevolley/rainbow
# Use CartPole-v0 to test without installing slimevolleygym
python examples/slimevolley/train_rainbow.py --gpu $gpu --steps 100 --outdir $outdir/slimevolley/rainbow --env CartPole-v0
model=$(find $outdir/slimevolley/rainbow -name "*_finish")
py... |
2610cc246192c1745d31e52bbc5d775020a5e74dde9b23b36a7325db40109613 | Shell | 455 | 12 | #!/bin/bash
set -Ceu
outdir=$(mktemp -d)
gpu="$1"
# atari/drqn
python examples/atari/train_drqn_ale.py --env PongNoFrameskip-v4 --steps 100 --replay-start-size 50 --outdir $outdir/atari/drqn --gpu $gpu --recurrent --flicker
model=$(find $outdir/atari/drqn -name "*_finish")
python examples/atari/train_drqn_ale.py --... |
450fa260d6ab2a0445a9026ea4acb31a2d77075f4c88b8d879243138c64e90a2 | Shell | 455 | 7 | #!/bin/bash
awk -v no=$2 '{if(no==""&&$1!="."){print $1} else {if($no!="."){print $no}}}' $1 > /tmp/coucoufromsarah.txt
echo 'l<-scan("/tmp/coucoufromsarah.txt");summary(l)' | R --vanilla > /tmp/coucoufromsarahout.txt 2> /tmp/coucoufromsaraherr.txt
cat /tmp/coucoufromsaraherr.txt | awk '{print "#", $0}'
awk 'NR==21||... |
8535e68145c900ac16ff7b8834dc56c425c2cc1a9a8b4cfc49e53d13580d42fa | Shell | 456 | 20 | #!/usr/bin/env bash
set -o errexit
set -o pipefail
set -o nounset
#pass in
BUCKET=$1 #e.g. "gs://ml4cvd/projects/jamesp/bigquery/201903"
DATASET=$2 #e.g. "ukbb7089_201903"
#specific to this func
GEO="US"
__dir="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
bq --location=${GEO} load \
--field_delimiter "\t" \
--rep... |
eabf12f5268d3974005d9e49f3ef75c5cd263fa810d397218e75ee5fd16b0cd1 | Shell | 457 | 9 | #first install openneuro-py at https://github.com/hoechenberger/openneuro-py
pip install openneuro-py
#second log into openneuro with your personal API key
openneuro-py login
#third run download command
#Reminder that the stimulus set .mp4 files and jpg frames must be downloaded from a separate link, detailed in the ... |
f7c0bd46fd430355ff09ee1df66fb063ef33ec4232ede9938a892222fd60cd43 | Shell | 458 | 4 | for sample in R12258 R12260 R12263 R12265 R12266 R12277 R12278 R12280 R12285 R12287 ; do
echo python Step_1_splam_prediction.py -f ../results/ribozero/$sample/fasta/junction.fa -o ../results/ribozero/$sample/junction_score.bed -m ../src/MODEL/SPLAM_v11/splam_14.pt
python Step_1_splam_prediction.py -f .... |
45b1a3b4155f54332ce0f6d63e51871c4e9a9b258494ddeb6836cb9ba52f48e0 | Shell | 459 | 4 | for sample in R12258 R12260 R12263 R12265 R12266 R12277 R12278 R12280 R12285 R12287; do
echo samtools sort ../results/ribozero_STAR/$sample.bamAligned.sortedByCoord.out/cleaned.bam -o ../results/ribozero_STAR/$sample.bamAligned.sortedByCoord.out/cleaned.sort.bam &
samtools sort ../results/ribozero_STAR... |
85d07f4f09250bc90f55cae59f08f71c52c2983d526638c7afc917b2144ae45f | Shell | 459 | 4 | for sample in R2826 R2835 R2839 R2845 R2855 R2857 R2869 R2874 R2894 R2895 ; do
echo samtools sort ../results/polyA_STAR/$sample.bamAligned.sortedByCoord.out/cleaned_2stage.bam -o ../results/polyA_STAR/$sample.bamAligned.sortedByCoord.out/cleaned_2stage.sort.bam &
samtools sort ../results/polyA_STAR/$sample.bam... |
56256b7251b715b61e5eca47d7938d138f031d68589e3078e46f777d3f473d19 | Shell | 462 | 19 | # for rsb in 1 2 3
# do
# rsg=5
# echo python splam_albation_train.py --rsg $rsg --rsb $rsb
# python splam_albation_train.py --rsg $rsg --rsb $rsb
# done
for rsg in 1 2 3 4 5
do
rsb=4
echo python splam_albation_train.py --rsg $rsg --rsb $rsb
# python splam_albation_train.py --rsg $rsg --rsb $... |
760dc3325b7a13b930400c09691f130bdbbad07c05513852d07573375ae6cd4c | Shell | 463 | 18 | #!/bin/bash
# Remove old consensus directory
if [ -d vcf_consensus ]
then
rm -rf vcf_consensus
fi
# Make consensus dir
mkdir -p vcf_consensus
# Link in all the consensus files with samplename instead of lenghty bam samplename
for f in Projects/*/*.consensus.fasta
do
# Base name of file
bn=$(basename $f);
... |
dc198b3d704e37415c52a138232d4e5a928437aaf9e50c5e70f53c6b8fafbd6b | Shell | 463 | 6 | PARTITION=$1
WORK_DIR=$2
CPUS_PER_TASK=${3:-4}
echo 'configs/detection/detector_with_enhance_head/faster-rcnn_r50_fpn_basic-enhance_1x_coco.py' &
GPUS=8 GPUS_PER_NODE=8 CPUS_PER_TASK=$CPUS_PRE_TASK ./tools/slurm_train.sh $PARTITION example-1 configs/detection/detector_with_enhance_head/faster-rcnn_r50_fpn_basic-enha... |
e57f9949370bcda8bcd83b4a41e4b1dc6c476ce5d1a92fc7b4d56726bc5a24d8 | Shell | 463 | 14 | #!/bin/bash
out_dir=xai_output
# timestamp = scaling_experiment
# i = num_experiments
for ((i=0;i<=0;i++)); do
for scenario in linear multiplicative translations_rotations xor; do
for background in uncorrelated correlated imagenet; do
pipenv run python -m xai.calculate_explanations $scenario $... |
24e4fecc17067a1f223156462fe96562beb9650a66caa7c3289cfcaf79f36e65 | Shell | 464 | 20 | #!/bin/bash
#SBATCH -p general
#SBATCH -N 1
#SBATCH --mem=72g
#SBATCH -n 18
#SBATCH -t 3-
module use /proj/mnhallqlab/sw/modules
#module load r/4.0.1
module load r/4.0.3_depend
module load gsl/2.6
module load fsl/6.0.4
module load afni/20.1.05
export atlas #pass through env variable
suffix=$( basename $atlas )
suffi... |
e253245bb2c6d2544306843645e8bcc3151670257e3ea46338fdafa2b8d88516 | Shell | 465 | 12 | SPLICEAI_VERSION=$1
for target in "pos_MANE" "pos_ALTS" "neg_1" "neg_random"
#for target in "pos_MANE" "pos_ALTS"
do
echo ./Step_6_spliceai_prediction_all_seq_noN.sh $target $SPLICEAI_VERSION &
./Step_6_spliceai_prediction_all_seq_noN.sh $target $SPLICEAI_VERSION &
echo "\n\n"
echo ./Step_6_spliceai_pr... |
6666262bb727c1490481a69ce22bdf34581ffabfe32471d169b2a8ee9d100153 | Shell | 466 | 15 | #!/usr/bin/env bash
set -o errexit
set -o pipefail
set -o nounset
#this script takes a folder of .enc files from UKBB, keys, and produces .csv.gz
__dir="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
enc_directory=${__dir}/uk_biobank_4_1_2019
for file in 28112 23300 23301 23302
do
${__dir}/ukbunpack ${enc_directory... |
f7bccfb918c106ffab8a25d0b6638caf98b2d824710eb91f05a1adbd19760b56 | Shell | 466 | 20 | #!/bin/bash
date_folder=$1
if [ -f "$date_folder/labview_parameters.csv" ]; then
# this is a experiment folder
ZipExperimentDirectory.sh $date_folder &
else
# this is not an experiment folder, repeat iteratively
# loop through all the directories in a date folder
for folder_name in $date_folder*; do
if [ ... |
45582e6eb2b67dc8c72f8bf6f586100735532199fd85e8303a25fac39d9e98d1 | Shell | 467 | 21 | #!/bin/bash
# Load bedtools
module load bedtools/2.29.2
cd /net/trapnell/vol1/home/readdf/trapLabDir/hubmap/results/2021_07_15_Greg_ATAC_Code_nobackup/archr/results/NB12/
bedFileToUse=$1
# nb12Dir=/net/trapnell/vol1/home/readdf/trapLabDir/hubmap/results/2021_07_15_Greg_ATAC_Code_nobackup/archr/results/NB12/
bedtoo... |
05ba8a02fef8dca2b2367eaf70584ffbe632b8e955b008b8c163aeb071536cd5 | Shell | 468 | 13 | #!/usr/bin/env bash
# Checks bazel buildifier format
set -euxo pipefail
ROOT_DIR="$(cd "$(dirname "${BASH_SOURCE:-$0}")" || exit; pwd)/.."
LINT_BAZEL_TMP="$(mktemp -d)"
curl -sl "https://github.com/bazelbuild/buildtools/releases/download/v6.1.2/buildifier-linux-amd64" \
-o "${LINT_BAZEL_TMP}/buildifier"
chmod +x ... |
41c1e44367c3be2a5729b450b87622c97de836a1a235918fd4fbc4abf933026a | Shell | 468 | 19 | #!/usr/bin/env bash
ROOT="$(realpath "$(dirname "$0")")"
function localexec(){
prog="$1"
shift
#PORTDIR_OVERLAY="$ROOT" DOTGENTOO_PACKAGE_ROOT="$ROOT/../" $prog "$@"
PORTDIR_OVERLAY="${ROOT}/overlay" DOTGENTOO_PACKAGE_ROOT="$ROOT/../" $prog "$@"
#echo $PORTDIR_OVERLAY
#echo $DOTGENTOO_PACKAGE_ROOT
}
EBUILD="$(... |
b96820439a7a73180a1afd09b1e20868fdf44a390ce05b57482a6a23837ac1b4 | Shell | 469 | 14 | #!/bin/bash
out_dir=training_output_8by8
# timestamp = scaling_experiment
# i = num_experiments
for ((i=0;i<=0;i++)); do
for scenario in linear multiplicative translations_rotations xor; do
for background in uncorrelated correlated imagenet; do
pipenv run python -m training.train_models $scena... |
4f8d69fd0c6453edb1c72e09c4be8e835f352248fcb94609d5ef353f4c440361 | Shell | 470 | 20 | #!/bin/bash
date_folder=$1
if [ -f "$date_folder/labview_parameters.csv" ]; then
# this is a experiment folder
UnZipExperimentDirectory.sh $date_folder &
else
# this is not an experiment folder, repeat iteratively
# loop through all the directories in a date folder
for folder_name in $date_folder*; do
if ... |
8ecae1784ceba48203bada71c5f5427c1a66f96c96a7e318e36e091884b133ed | Shell | 471 | 4 | for sample in R2826 R2835 R2839 R2845 R2855 R2857 R2869 R2874 R2894 R2895; do
echo scp /Users/chaokuan-hao/Documents/Projects/PR_SPLAM/results/polyA_STAR/$sample/junction_score.bed s3:/ccb/salz3/kh.chao/SPLAM/results/polyA_STAR/$sample.bamAligned.sortedByCoord.out/
scp /Users/chaokuan-hao/Documents/Pro... |
107540df741a8d18571e6f0a1c03f05b6a75e46aadf30334261f51692f7f8924 | Shell | 472 | 8 |
module load bedtools/2.29.2
# echo "Starting peak matching and sequence extraction"
# # First, set wd
cd /net/trapnell/vol1/home/readdf/trapLabDir/hubmap/results/2022_04_07_redoATACtoExprData_nobackup
# # For a defined promoter size and cicero linking hyperparams, get site info for each gene
Rscript definedPro... |
535644b5f158e2eaded7681fb8e16e2de18688397bd69238fe7953a1170129c5 | Shell | 474 | 12 | #!/usr/bin/env bash
set -eu
export PATH=/shared/utils.x86_64/anaconda2-4.3.1/bin:$PATH
export TMPDIR=${bamboo_build_working_directory}/.tmp
export CONDA_PATH_BACKUP=${CONDA_PATH_BACKUP:-$PATH}
export CONDA_PREFIX=${CONDA_PREFIX:-}
export CONDA_PS1_BACKUP=${CONDA_PS1_BACKUP:-}
source activate ${bamboo_build_working_dir... |
1f66bc961023cbcf5e77bf5f146c0e2b7edd2cd145e8541957c0d3bd1d1439c5 | Shell | 477 | 21 | #!/usr/bin/env bash
set -o errexit
set -o pipefail
set -o nounset
#pass in
BUCKET=$1 #e.g. "gs://ml4cvd/projects/jamesp/bigquery/201903"
DATASET=$2 #e.g. "ukbb7089_201903"
#specific to this func
GEO="US"
__dir="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
bq --location=${GEO} load \
--field_delimiter "\t" \
--quo... |
0783a9d43dc88a2480b8596e9477a4adaecfc46b0d2a74b505faf4815448c954 | Shell | 478 | 30 | #!/bin/bash
STATUSFILE=run_repetition.sh.status
CURRENT_DIR=$(pwd)
REP=${CURRENT_DIR##*/}
EXP=${CURRENT_DIR%/*}
EXP=${EXP##*/}
echo "Run ${REP} of ${EXP} ..."
STATE='Running'
date "+%Y/%m/%d %H:%M:%S" >> $STATUSFILE
echo $STATE >> $STATUSFILE
python run_repetition.py
RETURN_CODE=$?
echo "Write status file ..."
i... |
389ebcd47d316e81917ee84f14772e0394476b57b725adfed3ca0da593a16fa4 | Shell | 479 | 13 | #!/bin/bash
set -Ceu
outdir=$(mktemp -d)
gpu="$1"
# atlas/soft_actor_critic
# Use Pendulum-v0 to test without installing roboschool
python examples/atlas/train_soft_actor_critic_atlas.py --gpu $gpu --steps 100 --outdir $outdir/atlas/soft_actor_critic --env Pendulum-v0
model=$(find $outdir/atlas/soft_actor_critic -n... |
04ecf9b401603d032e9a3aaf01c569fefefafd3770c2d1e25e00a72facefc281 | Shell | 484 | 21 | #!/bin/bash
trait=F3
n_thread=5
###
exe_gcta=gcta-1.94.1
bfile=UKB_random10k_noqc
file_leadsnp=../leadSNP/leadSNP_list.${trait}.txt
dir_cojo_input=../cojo_input
dir_out=cojo_out.${trait}
mkdir -p ${dir_out}
${exe_gcta} --bfile ${bfile} \
--diff-freq 0.2 \
--cojo-file ${dir_cojo_input}/cojo_i... |
61d687b8c54ff0f2212f08bfa84de99c05b297aea57425862ffb59c82c673e5d | Shell | 484 | 21 | #!/bin/bash
trait=F2
n_thread=5
###
exe_gcta=gcta-1.94.1
bfile=UKB_random10k_noqc
file_leadsnp=../leadSNP/leadSNP_list.${trait}.txt
dir_cojo_input=../cojo_input
dir_out=cojo_out.${trait}
mkdir -p ${dir_out}
${exe_gcta} --bfile ${bfile} \
--diff-freq 0.2 \
--cojo-file ${dir_cojo_input}/cojo_i... |
70f93f771e67085193f8c35a5735a4af8f2c951faab7afa9b031db85b9ff191c | Shell | 485 | 21 | #!/bin/bash
set -euxo pipefail
# Install Python dependencies
pip3 install --no-cache-dir \
"numpy>=1.24.0,<2.0" \
"torch>=2.0.0" \
"transformers>=4.35.0" \
"accelerate>=0.25.0" \
"sentencepiece>=0.1.99" \
"httpx>=0.25.0" \
"aioboto3>=12.0.0" \
"pillow>=10.0.0"
sudo apt-get update && ... |
3f2e2fdfb67c446d16514626c5b9d04d609de505e18f42814a90e1bf8db9715f | Shell | 486 | 21 | #!/bin/bash
trait=F1
n_thread=5
###
exe_gcta=gcta-1.94.1
bfile=UKB_random10k_noqc
file_leadsnp=../leadSNP/leadSNP_list.${trait}.txt
dir_cojo_input=../cojo_input
dir_out=cojo_out.${trait}
mkdir -p ${dir_out}
${exe_gcta} --bfile ${bfile} \
--diff-freq 0.2 \
--cojo-file ${dir_cojo_input}/cojo_i... |
7cd0ede718238698f98a5dba70b5f137d8f29a10538a9ce37beba9ecd0fc1444 | Shell | 486 | 21 | #!/bin/bash
date_folder=$1
if [ -f "$date_folder/labview_parameters.csv" ]; then
# this is a experiment folder
echo $date_folder/
delete_tracks.sh $date_folder &
else
# this is not an experiment folder, repeat iteratively
# loop through all the directories in a date folder
for folder_name in $date_folder*; do... |
c51b277fa175372838443ea45f4fb807eef071e559dfa9a6bf43718403e92c63 | Shell | 486 | 17 | #! /bin/bash
# Commands to set up R 4.1.2 to use
module unload R/4.0.0
module unload pcre2/10.35
module unload proj/4.9.3
module unload gdal/2.4.1
module unload hdf5/1.10.1
#module load pcre2/10.39
#module load R/4.1.2
module add sqlite/3.32.3 proj/7.1.0 gdal/3.5.2 hdf5/1.10.5 pcre2/10.39 R/4.1.2
Rscript /net/tra... |
68fe0324329be94e4d7597feda955f200961623b9f1c39f2d2431d6bfc148945 | Shell | 488 | 8 | # Step 1: extract introns in the annotation
splam extract lncs_and_exons.gff -o tmp_out_annotation_lncRNA -F feature_transcript.txt
# Step 2: score introns in the annotation
splam score -G ~/Documents/Projects/ref_genome/homo_sapiens/NCBI_Refseq_chr_fixed/GCF_000001405.40_GRCh38.p14_genomic.fna -m ../model/splam_scrip... |
1c98a044c0e8fcb62a1fe53e1f04b3e69d96e9a99e4a311e60a5678cfc7978c5 | Shell | 489 | 12 | #!/usr/bin/bash
vamb \
--model taxonomy_predictor \
--outdir /home/projects/cpr_10006/people/svekut/cami2_rhizo_500_predictor \
--fasta /home/projects/cpr_10006/people/svekut/rhizo_data/rhizo.fna.gz \
--rpkm /home/projects/cpr_10006/people/svekut/rhizo_data/abundance.npz \
--taxonomy /home/projects/... |
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