sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
bea7a1e63e17c87842d560337687699f99c919f8bacab23c0867fc3729692bbc | Shell | 400 | 12 | #!/bin/bash
set -e
set -o pipefail
# Set the working directory to the directory of this file
cd "$(dirname "${BASH_SOURCE[0]}")"
# Run R script to generate json file containing pathology_diagnosis for neurocytoma subsetting
Rscript 00-neurocytoma-select-pathology-dx.R
# Run notebook to get molecular subtype for Neur... |
6e7cfab73185ca7f1831c2efca35f479372d28f723e11027ec0bbefc07e8fddc | Shell | 401 | 16 | #!/bin/bash
#SBATCH --job-name=cebra_train
#SBATCH --partition=gpu
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --gres=gpu
#SBATCH --output=./outputs/cebra_train.o%j
#SBATCH --error=./error/cebra_train.e%j
source /etc/profile.d/conda.sh
eval "$(/opt/conda/bin/conda shell.bash hook)"
conda activate cebra_cuda
python ~... |
17bc8c007d9aaf0587402a0a5198c61b37ac36f72ad4e3b3bd4ddb6e997b6ce6 | Shell | 403 | 7 | ############### CRN2017 TASK1 and IKACh #####################################################
MODEL_FILE_CPU="CRN2017_TASK1_IKACh.c"
MODEL_FILE_GPU="CRN2017_TASK1_IKACh.cu"
COMMON_HEADERS="CRN2017_TASK1_IKACh.h"
COMPILE_MODEL_LIB "CRN2017_TASK1_IKACh" "$MODEL_FILE_CPU" "$MODEL_FILE_GPU" "$COMMON_HEADERS"
############... |
431364514937667d26f05c59398d8931d5da09c5d1d06a87a0ee3f46d9680be2 | Shell | 405 | 16 | #!/bin/bash
#SBATCH --job-name=parallel_nm
#SBATCH --partition=compute
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --array=1-184
#SBATCH --cpus-per-task=1
#SBATCH --output=./outputs/parallel_nm.o%j
#SBATCH --error=./error/parallel_nm.e%j
eval "$(/opt/conda/bin/conda shell.bash hook)"
source /etc/profile.d/conda.sh
c... |
22de03ea89791bfbfaaec47d0f1d5858dbaebe65b1574cc3f819dbcd64fdd3a0 | Shell | 406 | 20 | #!/bin/bash
#SBATCH --time=16:00:00
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --job-name=gnn_eve_data
#SBATCH --output=logs/gnn_eve_data-%j.log
#SBATCH --mem=500MB
#SBATCH --partition=regular
# Assign command line arguments to variables
name=$1
beta_phi=$2
batch=$3
index=$4
ml R
# Call the R script with the nece... |
49389e6d3a1a6c2ed6e26b70f84e90ce6a2070c3dbdc1dbd626a736b2a27917f | Shell | 407 | 15 | #!/bin/bash
#SBATCH --job-name=parallel_nm
#SBATCH --partition=compute
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --array=1-184
#SBATCH --cpus-per-task=1
#SBATCH --output=./outputs/parallel_nm.o%j
#SBATCH --error=./error/parallel_nm.e%j
eval "$(/opt/conda/bin/conda shell.bash hook)"
source /etc/profile.d/conda.sh
co... |
780206be0487736b5dd522c7d194293a7891c1186eacc9dcbfb453a9128fe022 | Shell | 407 | 16 | #!/bin/bash
#SBATCH --job-name=cebra_train
#SBATCH --partition=gpu
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --gres=gpu
#SBATCH --output=./outputs/cebra_train.o%j
#SBATCH --error=./error/cebra_train.e%j
source /etc/profile.d/conda.sh
eval "$(/opt/conda/bin/conda shell.bash hook)"
conda activate cebra_cuda
python ~... |
ffd9e4f7401fcc7f31ff6f3b93e0589ee51ede9843b8b23ae1b902f3267cc62c | Shell | 408 | 13 | #!/bin/bash
# Create File List
#echo file videos/shocker_rafa_sebastian_LV_iter_0.mp4 > mylist.txt
#echo file videos/shocker_rafa_sebastian_LV_iter_1.mp4 >> mylist.txt
#echo file videos/shocker_rafa_sebastian_LV_iter_2.mp4 >> mylist.txt
#echo file videos/shocker_rafa_sebastian_LV_iter_3.mp4 >> mylist.txt
# Concatena... |
6ad57e8b5629237111fbc32d43fc500ee997eb521cbde336afab653bd62d4b9b | Shell | 410 | 23 | #!/bin/bash
# Set FSL environment variables
FSLDIR=/usr/local/fsl
PATH=${FSLDIR}/bin:${PATH}
FSLOUTPUTTYPE=NIFTI_GZ
# Source the FSL configuration script
source ${FSLDIR}/etc/fslconf/fsl.sh
case "$1" in
terminal)
bash
;;
*)
eval python3 /app/Pipeline.py "$@"
cmd_exit="$?"
... |
08674a244d311f17e67d3857c4e3e6f286d7e941ee1c9c02cca578eb6e729755 | Shell | 414 | 13 | #!/bin/bash
echo $LSB_JOBINDEX
echo $1
line=$(head -n $LSB_JOBINDEX $1 | tail -n1)
echo $line
sampleid=$(echo $line | awk {'print $1'})
folder=$(echo $line | awk {'print $2'})
TPATH=refgenomes/cellranger/refdata-cellranger-GRCh38-3.0.0
/software/kilpinen/cellranger-3.1.0/cellranger count --id=${sampleid} --fastqs=$... |
09a277a01e3bd44c02ba0b1f103e641a10b4789f77b7e00d2012716d7e4b02cc | Shell | 415 | 14 | #!/bin/sh
# This script takes the release notes for the most recent release
# and reformats them for use in GitHub.
# In GitHub PR and release descriptions, a single line break is
# equivalent to <br>, so we pipe the text through pandoc to unwrap all lines.
set -eu
repo_root="$(dirname "$0")/.."
awk '/^## / { hn +... |
40c290357b40e2eaf4e483671bfe3db714e5e4699400a0fd127aca755ff39f5f | Shell | 415 | 14 | #!/bin/bash
. /gonzo/conda/etc/profile.d/conda.sh
if [[ -n "$CONDA_DEFAULT_ENV" ]]; then
CURRENT_ENV=$CONDA_DEFAULT_ENV
conda deactivate
else
CURRENT_ENV=gonzo
fi
export FASTSURFER_HOME=/gonzo/FastSurfer
source $FREESURFER_HOME/SetUpFreeSurfer.sh
conda activate $CURRENT_ENV
export PATH="$CURRENT_ENV/bin:$PATH"
ex... |
a86be7e60c0cdb66706b0cafa949e1a14e7d76910cf499b406c02270951ac3dc | Shell | 416 | 18 | #!/bin/zs
echo "convert nii to gii"
palm -i /data/MFC_left.shape.gii \
-s /data/hemi-left_midthickness.5k.surf.gii \
-i /data/MFC_right.shape.gii \
-s /data/hemi-right_midthickness.5k.surf.gii \
-d /data/designmatrix_test.mat \
-t /data/contrasts_test.con \
-o /result/MFC \
-n 5000 ... |
eeb4051a271c75c581fb382d9fdda33bb79e9ebad224a1250d17b3b661c8b92e | Shell | 416 | 16 | #!/bin/bash
#SBATCH --job-name=oscill
#SBATCH --partition=gpu
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --gres=gpu
#SBATCH --output=./outputs/cebra_train.o%j
#SBATCH --error=./error/cebra_train.e%j
source /etc/profile.d/conda.sh
eval "$(/opt/conda/bin/conda shell.bash hook)"
conda activate cebra_cuda
python ~/CEBR... |
f6087ba1348625771c41b5d321ca65cf4ebf82a53226ad862d0a631e6ce4cb9f | Shell | 418 | 14 | #!/bin/bash
echo $(date +"%Y-%m-%d %H:%M:%S")
for dataset in cifar100 imagenet
do
for model in snn_resnet18 snn_resnet50 snn_vgg16
do
for batchSize in 16 32 64 128
do
out_file="fps/"${dataset}_${model}_${batchSize}_framerate
echo "start to get "$out_file
python train.py -device 0 -datasets $dataset -ne... |
ab45f0164707cc068d0f83b02e236b9a3b0b4f68260cabaab20509d7c4eeca3d | Shell | 419 | 8 | #!/bin/bash
# Now only downloads server-pymeshlab'd FINISHED mesh to local for emailing to participant
read -p "Enter subj num to download with no leading 0s: " SUBJ_NUM
printf -v SUBJ_NUM_4D '%04d' $SUBJ_NUM
read -p "Enter path to download folder (abs or rel from curr local dir): " LOCAL_DL_FOLDER
scp ecco:/archival... |
5349df1d9537aa650f7c22587fba99ba823c1675c7176231ffbdb76499bd5536 | Shell | 421 | 11 | #!/bin/sh
BW=$1
REGIONS=$2
cat $REGIONS | while read chr start end n; do \
echo $chr $start $end $n mean `bigWigSummary -type=mean $BW $chr $start $end $n`;
echo $chr $start $end $n min `bigWigSummary -type=min $BW $chr $start $end $n`;
echo $chr $start $end $n max `bigWigSummary -type=max $BW $chr $start... |
aab08c1d0daaa271c2ac36b2781788e09ba0b765c8c175b9d6d402a9550606c8 | Shell | 421 | 20 | #!/bin/sh
set -eu
TESTDIR=$(dirname $0)
SHOVILL="$TESTDIR/../bin/shovill"
OUTDIR="$TESTDIR/testout"
echo "TESTDIR = $TESTDIR"
echo "OUTDIR = $OUTDIR"
echo "SHOVILL = $SHOVILL"
$SHOVILL --version
$SHOVILL --check
$SHOVILL --help
! $SHOVILL --doesnotexist
rm -frv "$OUTDIR"
$SHOVILL --outdir "$OUTDIR" --R1 "$TESTDIR/R... |
76843f2ad700aed43ef83336faa557e19b8f931ed33a8a8f31f17f30cec844e0 | Shell | 425 | 3 | python train.py --num_layers=6 --data_path='mixed_set_psf_5' --num_train_data=1200 --num_val_data=100 --num_test_data=100 --psf_size=5 --initial_lr=0.0001 --batch_size=1 --epochs=200 --num_frames=20 --im_dim=256
python train.py --num_layers=6 --data_path='mixed_set_psf_6' --num_train_data=1200 --num_val_data=100 --num... |
057e469264f04dc4436be017c2a0e23138dd7e0b08fc69b9bc4fb695ba43e179 | Shell | 426 | 20 | mypython=$1
$mypython $MARINE/marine.py \
--bam_filepath \
$MARINE/tests/strandedness_tests/bams/F1R2_pair.bam \
--annotation_bedfile_path \
$MARINE/annotations/hg38_gencode.v35.annotation.genes.bed \
--output_folder \
$MARINE/tests/strandedness_tests/F1R2_pair_test \
--min_dist_from_end \
0 \
--min_base_quality \
0 \... |
8acc7fcf2e3822b2ecab3e0e71e6022ccad9913e69ae2f56e5deec1df5f6262a | Shell | 426 | 19 | #!/bin/bash
set -euo pipefail
HOST="$1"
CONTROL_PATH="$2"
REMOTE_RUN_DIR="$3"
LOCAL_RUN_DIR="$4"
INTERVAL_S="$5"
LOG_PATH="$6"
mkdir -p "${LOCAL_RUN_DIR}"
while true; do
rsync -az --delete \
-e "ssh -o BatchMode=yes -o ControlMaster=auto -o ControlPath=${CONTROL_PATH} -o ControlPersist=yes" \
"${HOST}:${REM... |
0cba5d358883a57256b2186d01561c9e3b464d54a4affa6de2b98854f0bfa052 | Shell | 427 | 14 | #!/usr/bin/env bash
# Runs tests of executables
set -Eeuo pipefail
echo "=== Executing modcc test ======================================"
modcc python/example/cat/dummy.mod
test -f "dummy.hpp"
echo "executable modcc: OK."
echo "=== Executing a-b-c test ======================================"
arbor-build-catalogue --... |
9caf74935c8f6a0ab33b4de7ed23fa8bc753123afc7fb751a430ead15766a923 | Shell | 427 | 18 | #! /bin/sh
cd tests
. ./compat.sh
sort -k2,2 > ${pref}.md5sum <<EOF
7f78bc16dedc972fc253bf1378e01561 ${pref}.histo
EOF
echo "Counting 22-mers on ${nCPUS} CPU" && \
$JF count --matrix seq10m_matrix_22 -m 22 -t $nCPUs -o $pref \
-s 10000000 --timing ${pref}.timing --min-quality 3 seq10m.fq && \
$JF histo -... |
695cb0d427a316c66acce09bd924e959abff0ba8c08bd57dfeb8cc7104fef0a4 | Shell | 428 | 21 | #!/bin/bash
#SBATCH --time=5:00:00
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --job-name=gnn_ddd_boot
#SBATCH --output=logs/gnn_ddd_boot-%j.log
#SBATCH --mem=4GB
#SBATCH --partition=regular
lambda=${1}
mu=${2}
cap=${3}
ntips=${4}
family_name=${5}
tree_name=${6}
path=${7}
ml R
Rscript ../S... |
ca39cc1413b38865204f175be0ef61b028aea28c11f1dadfe212a20ad55983c5 | Shell | 432 | 21 | #!/bin/bash
#Change PROT to match your system
PROT=cTEMPPROT
function combine(){
local fname=$1
inp1=pc1_pc2_pc3/${fname}_1.xvg
inp2=pc1_pc2_pc3/${fname}_2.xvg
#Removes xmgrace headers from the .xvg files
tail -n +18 $inp1 > tmp1
tail -n +18 $inp2 > tmp2
echo " Processing $inp1 $inp2 ..."
pyth... |
df7aa691f849f9e31af200ad7f1c15f25df75e3bdf0e69d1c4e4f8cb74b97991 | Shell | 432 | 15 | #!/bin/bash
if [ -d "./.env" ]; then
echo "Running from virtualenv -> if you encounter problems delete .env-Folder and retry"
source ./.env/bin/activate
which python
python3 -u src/tms_app.py
else
echo "Initializing! Setting up python virtual env for tmsExplorer!"
python3 -m venv .env
sourc... |
cc5b16941562939bd300bc71bf6adcabd69db40a2fb0076811a414a4227596d7 | Shell | 435 | 17 | #!/bin/bash
WORKDIR=""
#mkdir temp_annot # make a temporary directory to host the intermediate files
Data_File="$WORKDIR/AUX/g1000_eur"
Annot_File="$WORKDIR/AUX/annotation_file.genes.annot"
SNP_Pval_File="$WORKDIR/sumstats/snp_pval.txt"
Output_Prefix="adult_midbrain"
./magma \
--bfile $Data_File \
--gene-annot $An... |
d02642e33aff19e3ccec61f4913788d58516b26e0b29d579b4cc8c31b3d0b683 | Shell | 437 | 5 | wget https://www.cms.gov/Medicare/Coding/ICD10/Downloads/2017-ICD10-Code-Tables-Index.zip
wget https://www.cms.gov/Medicare/Coding/ICD10/Downloads/2017-ICD10-Code-Descriptions.zip
wget https://www.cms.gov/Medicare/Coding/ICD10/Downloads/2017-PCS-Long-Abbrev-Titles.zip
wget https://www.cms.gov/Medicare/Coding/ICD10/Down... |
fb9c375200869319922d3f8b5a7725e8d6c5387cd5f5f10f2c0329d538abe28e | Shell | 437 | 10 | if [ -n "$CUDA_FOUND" ]; then
EIKONAL_SOURCE_FILES="eikonal_solver.c cuda_fim.cu cuda_fim_kernel.cu"
EIKONAL_HEADER_FILES="eikonal_solver.h common_def.h cuda_fim.h cuda_fim_kernel.h"
EIKONAL_EXTRA_LIB_PATH=$CUDA_LIBRARY_PATH
EIKONAL_DYNAMIC_LIBS="c cudart"
COMPILE_SHARED_LIB "eikonal_solver" "$EIK... |
2308553d33c140d5821b575d6ece8e19974be51e877d99eda7f2f44a0372fb52 | Shell | 441 | 14 | source /$1/bin/activate
which python3
ls -l
source /root/.thalamusrc
source /etc/profile.d/VimbaUSBTL_64bit.sh
env | sort
echo $PATH
python3 setup.py bdist_wheel --generator Ninja
PLATFORM_TAG=`ldd --version | awk '/ldd/ {print "manylinux_" $NF}' | sed "s/\\./_/"`
LINUX_NAME=`ls dist`
MANYLINUX_NAME=`echo $LINUX_NAME |... |
82c67a8d57ec347f12f702778f9b8938f6effcbe15688c394e9570db42cee5d3 | Shell | 441 | 17 | #!/bin/bash
#SBATCH -o %j_predict.out
#SBATCH -e %j_predict.err
#SBATCH -D ./
#SBATCH -J predict
#SBATCH --partition=CPU
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=20
#SBATCH --time=0-05:00:00
#SBATCH --mem=0
source activate PpaPred
python -u predict.py -p ${1} -id $SLURM_JOB_ID
mv $SLURM_J... |
9163c72a87cb1ae37b72225433a59e8578905349ede56a84bac6ff28ae43c116 | Shell | 443 | 18 | #!/bin/bash
#SBATCH --job-name=cebra_train
#SBATCH --partition=gpu
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --gres=gpu
#SBATCH --mem=64G
#SBATCH --mail-type=FAIL
#SBATCH --output=./outputs/cebra_train.o%j
#SBATCH --error=./error/cebra_train.e%j
source /etc/profile.d/conda.sh
#eval "$(/opt/conda/bin/conda shell.bas... |
e877aec0a8c9be16da0b7feec4e923aba41aa3e7b949c1ca9ef946efc5cc7a12 | Shell | 443 | 19 | #! /bin/sh
cd tests
. ./compat.sh
[ -z "$ENABLE_RUBY_BINDING" ] && exit 77
LOADPATH="$BUILDDIR/swig/ruby/.libs"
K=$($RUBY -e 'print(rand(15) + 6)')
I=$($RUBY -e 'print(rand(5))')
$JF count -m $K -s 10M -t $nCPUs -C -o ${pref}.jf seq1m_$I.fa
$JF dump -c ${pref}.jf > ${pref}.dump
$JF histo ${pref}.jf > ${pref}.histo
... |
011d4a29789287dc67a8145e83c1a96726709d3c75915b5ed3aee31fab65fa96 | Shell | 444 | 17 | #!/bin/bash
#SBATCH --job-name=gene_denoise_v1
#SBATCH --partition=256GBv1
#SBATCH --nodes=8
#SBATCH --ntasks=200
#SBATCH --time=24:00:00
#SBATCH --output=mutiTaskJob.%j.out
#SBATCH --error=mutiTaskJob.%j.time
#SBATCH --mail-user=chen.tang@utsouthwestern.edu
#SBATCH --mail-type=ALL
module add python/3.8.x-anaconda
mod... |
6639d87cb250e6ca69cb942e671c1206b979c9d9f50dce53b3cab5550374fc4e | Shell | 447 | 7 | # FCN
wget -nc "https://raw.githubusercontent.com/longjon/caffe/6e3916766c6b63bff07e2cfadf210ee5e46af807/src/caffe/proto/caffe.proto" --output-document=./caffe_6e3916.proto
protoc ./caffe_6e3916.proto --python_out=./
# b590f1d (ResNet)
wget -nc "https://raw.githubusercontent.com/BVLC/caffe/b590f1d27eb5cbd9bc7b9157d447... |
8ca620b5efab17760c254668561e3a2f0c86c5f896389e54403f465523536b65 | Shell | 448 | 17 | mypython=$1
$mypython $MARINE/marine.py \
--bam_filepath \
$MARINE/tests/singlecell_tests/bams/9_3000526_only_5_cells.bam \
--annotation_bedfile_path \
$MARINE/annotations/cellranger-mm10-3.0.0.annotation.genes.bed \
--output_folder \
$MARINE/tests/singlecell_tests/only_5_cells_bulk_mode_test \
--min_dist_from_end \
0... |
06a3c882d535d4727fd6e610b7074869a0a776e5ef7cf511bd04edc56819afea | Shell | 454 | 20 | mypython=$1
$mypython $MARINE/marine.py \
--bam_filepath \
$MARINE/tests/strandedness_tests/bams/tax1bp3_chr17_3665556.bam \
--annotation_bedfile_path \
$MARINE/annotations/hg38_gencode.v35.annotation.genes.bed \
--output_folder \
$MARINE/tests/strandedness_tests/tax1bp3_chr17_3665556_test \
--min_dist_from_end \
0 \
... |
002eb6f25aa03d14dcf645e79f44c0ba76438b9cb0c365b14211de6dc54a9b7a | Shell | 458 | 7 | # Paths
smk_dir="/path/to/NovaScope" # Path to the NovaScope pipeline repo.
job_dir="$smk_dir/testrun/minimal_test_run" # Path to your Job directory, which should have a config_job.yaml file and will be used to save the log files.
Ncores=8 # Number of... |
14008c7468207fcdfb42d3dff915ac6d1b98f01c3e8d5a4d22e7a1038fb34835 | Shell | 458 | 20 | mypython=$1
$mypython $MARINE/marine.py \
--bam_filepath \
$MARINE/tests/strandedness_tests/bams/F2R1_end_second_in_pair.bam \
--annotation_bedfile_path \
$MARINE/annotations/hg38_gencode.v35.annotation.genes.bed \
--output_folder \
$MARINE/tests/strandedness_tests/F2R1_end_second_in_pair_test \
--min_dist_from_end \
... |
0106d449219a7853d5b3ef5c6df268729685304c1556b3396caf16c27b9fe489 | Shell | 459 | 14 | #added another A so it wouldn't trim my synthetic A-tail 2022-03-07
input_folder=$1
sample=$2
output_folder=$3
#had to tweak some modules for centos7, not sure if these will work, but trying out
module load python/3.7.7
module load cutadapt/1.18
module load trim_galore/0.6.5
echo Trimming sample: $sample
trim_gal... |
1216aabff02f624ed80f37ae7cae914bf833244f9bf8529f4017c436cd4cb740 | Shell | 459 | 25 | #!/bin/bash
#SBATCH --account=def-rfm
#SBATCH --gres=gpu:1
#SBATCH --cpus-per-task=16
#SBATCH --mem=12G
module load python/3.8.2 blender/3.6.0 scipy-stack
#source $SLURM_LIBDIR/env/bin/activate
# export IMAGEDIR=$SLURM_TMPDIR/images
# mkdir $IMAGEDIR
# export IMAGEDIR=`mktemp -d -p .`
mkdir $SLURM_TMPDIR/images
exp... |
2b15a5c25b569698e7a4fba4a72595356862762b12406520a1ff17fb0429b74a | Shell | 459 | 18 | mypython=$1
$mypython $MARINE/marine.py \
--bam_filepath \
$MARINE/tests/singlecell_tests/bams/9_3000526_only_5_cells.bam \
--annotation_bedfile_path \
$MARINE/annotations/cellranger-mm10-3.0.0.annotation.genes.bed \
--output_folder \
$MARINE/tests/singlecell_tests/only_5_cells_test \
--min_dist_from_end \
0 \
--min_b... |
4122c7cd702d386d27a0e03f09673f6cfeafd314ae0b974fc52db52752e4bcec | Shell | 459 | 15 | #!/bin/bash
#
# anat_brain-extract_using-inv2.sh <anat> <anat_mp2rage_inv2>
#
# - brain extraction of anatomy (MP2RAGE UNI or processed) by running
# bet on inv2 from the same acquisition and applying the resulting mask
anat=$1
anat_mp2rage_inv2=$2
bet $anat_mp2rage_inv2 $(basename $(remove_ext $anat_mp2rage_inv2))... |
b1f6bfed1c72a913d62948c118dd73901a8db7dd4b184174fe684639b4fd13d6 | Shell | 459 | 19 | mypython=$1
$mypython $MARINE/marine.py \
--bam_filepath \
$MARINE/tests/strandedness_tests/bams/citrine435.bam \
--annotation_bedfile_path \
$MARINE/annotations/hg38_gencode.v35.annotation.genes.bed \
--output_folder \
$MARINE/tests/strandedness_tests/unstranded_pair_test \
--min_dist_from_end \
0 \
--min_base_qualit... |
6d4cefc99b28d62f4c78a6da762e46e75875e9b8dc43f58d0fb985dc3a179117 | Shell | 460 | 7 | # Paths
smk_dir="/path/to/NovaScope" # Path to the NovaScope pipeline repo.
job_dir="$smk_dir/testrun/deep_liver_section" # Path to your Job directory, which should have a config_job.yaml file and will be used to save the log files.
Ncores=8 # Number ... |
dfa6e19a0e2893aed38bf745fa2644a421d43f8dbf1fc4b166ac81ac87ae3414 | Shell | 462 | 18 | #!/bin/bash
#SBATCH -J make_ds
#SBATCH -o make_ds.o%j
#SBATCH -t 20:00:00
#SBATCH -N 1 -n 8
#SBATCH --mem=128G
source activate Ali
python examples/makeDS.py \
--INPUT_DIR=/home/lhuang37/datasets/50_plex/S1/final \
--OUTPUT_DIR=/home/lhuang37/repos/VisQ-Search-Engine/examples/data/myelo_panel_all \
--BBXS_FILE=/hom... |
58407d452cd08c6283e9b7cfed1ff0e54dd15d434df3583da036255367bd0a24 | Shell | 463 | 7 | # Paths
smk_dir="/path/to/NovaScope" # Path to the NovaScope pipeline repo.
job_dir="$smk_dir/testrun/shallow_liver_section" # Path to your Job directory, which should have a config_job.yaml file and will be used to save the log files.
Ncores=8 # Numb... |
742cc4ea5d35d39c863ba6413463aa692e92fe03cce18c495615d578a29d710f | Shell | 463 | 18 | vcf_path=$1 #where WGS VCF files are located
script_dir="$(dirname "${BASH_SOURCE[0]}")"
log_dir=$script_dir/../../logs/gen_fasta_consensus
job_script=$script_dir/prep_VCF_for_fasta_consensus_job_script.sh
job_name=CreateSNPOnlyVCFBCF
log_dir=$log_dir/gen_fasta_consensus
#create directory for stderr and stdout
if [ ... |
ce2ac7128458a5aaf7dfef01139abaadca049bce93e37d2914a78c6e2c53a422 | Shell | 463 | 23 | #!/bin/csh
# this script produces 2D projections from a processed nmrpipe spectrum file in pipe format
if( $# < 1 ) then
echo "Use: $0 <spectrum type> "
exit 1
endif
set proc_out=test%03d.dat
cat $1 | pipe2xyz -out ft/${proc_out} -x -verb -ov
proj3D.tcl -in ft/${proc_out}
rm -r ft
if( $1:e == 'P3') then
f... |
427e260a8b54efc24c1b1309e971363d540ce83563883641cb35488d9602e310 | Shell | 464 | 14 | for i in `ls ./nobackup/output/filtered_sam/*.sam`; do samtools view -c $i >> tmp1; done
echo "part 1 of 3 done"
wc -l tmp1
for i in `ls ./nobackup/output/rmdup_sam/*.sam`; do samtools view -c $i >> tmp2; done
echo "part 2 of 3 done"
wc -l tmp2
for i in `ls ./nobackup/output/rmdup_sam_2/*.sam`; do samtools view -c $i >... |
ffcf113becc78fe3cb4d1073b4ce63b2611bb1335869b41cbbdfb9985ff18523 | Shell | 464 | 20 | mypython=$1
$mypython $MARINE/marine.py \
--bam_filepath \
$MARINE/tests/strandedness_tests/bams/tax1bp3_chr17_3665556_read.bam \
--annotation_bedfile_path \
$MARINE/annotations/hg38_gencode.v35.annotation.genes.bed \
--output_folder \
$MARINE/tests/strandedness_tests/tax1bp3_chr17_3665556_read_test \
--min_dist_from_... |
041eeffd7f63e55a33aba45c6dbce8bb97349889fb04a4385e0c7543baf91053 | Shell | 465 | 20 | mypython=$1
$mypython $MARINE/marine.py \
--bam_filepath \
$MARINE/tests/strandedness_tests/bams/same_pos_dif_reads.bam \
--annotation_bedfile_path \
$MARINE/annotations/hg38_gencode.v35.annotation.genes.bed \
--output_folder \
$MARINE/tests/strandedness_tests/same_pos_dif_reads_test \
--min_dist_from_end \
0 \
--min_... |
1d4f4263269082b4265bb2e9e5983c547e3327c470954e8c1b2ab6db1815bc52 | Shell | 466 | 16 | #!/bin/bash
for contrast in "motor" "ffa" "vwfa" "shape1" "shape3" "all_shapes"; do
./03c_stich_surfaces.sh adults category $contrast &
./03c_stich_surfaces.sh kids category $contrast &
done
for contrast in "geom_theory" "geom_behavior_online" "geom_behavior_scanner"; do
./03c_stich_surfaces.sh adults geometry ... |
f5eb5cdf3376119aa67747067a6e49e7bcd8ff032f618d93b5ba9f4c770b039d | Shell | 466 | 20 | mypython=$1
$mypython $MARINE/marine.py \
--bam_filepath \
$MARINE/tests/strandedness_tests/bams/same_pos_dif_reads.bam \
--annotation_bedfile_path \
$MARINE/annotations/hg38_gencode.v35.annotation.genes.bed \
--output_folder \
$MARINE/tests/strandedness_tests/no_edits_edge_case_test \
--min_dist_from_end \
0 \
--min_... |
0c58effdb3afe57836dd8b52d1dc3d55559236d5d2d986479b1489024bc618b0 | Shell | 467 | 17 | #! /bin/sh
cd tests
. ./compat.sh
[ -z "$ENABLE_PERL_BINDING" ] && exit 77
LOADPATH="$BUILDDIR/swig/perl5"
K=$($PERL -e 'print(int(rand(16)) + 6)')
I=$($PERL -e 'print(int(rand(5)))')
$JF count -m $K -s 10M -t $nCPUs -C -o ${pref}.jf seq1m_$I.fa
$JF dump -c ${pref}.jf > ${pref}.dump
$JF histo ${pref}.jf > ${pref}.his... |
0ef6f571312d3c6d19231696e231e09884e0cfe4d73ee750e8ec83a275c69226 | Shell | 468 | 12 | #!/bin/bash
NUMOFFILE=$(($(ls -1 output_neighbors-00000-*.json | wc -l)-1))
tmpfile="tmplist"
for i in $(seq -f %05.f 0 $NUMOFFILE); do
echo $i: $(
for f in output_neighbors-*-$i.json; do
cat $f | sed -r -e 's/\s*[0-9]*: \[[^[]*\] \[([^[]*)\]/\1/' -e 's/\([ 0-9]{3}\)//g' | tr ' ' '\n' | sort -gu | tr '\n' ' '
... |
1c00247622e3dd5fdf7d1712b24c6f6b5d93a309ded8397cd35d5e9dcfbc546c | Shell | 472 | 18 | #!/bin/bash
IFS=$'\n' read -r -d '' -a columns < <(sed -n '2,$p' $1/timing-00000.dat | cut -f1 -d" ") # && printf '\0' )
echo "#Name Calls Average Min Max"
for c in ${columns[@]}; do
echo $c $(grep "$c " $1/timing-00000.dat | awk '{print $3}') $(grep $c $1/* | awk '{print $5}' | awk '
{
if(min=="") {
m... |
62fa9fadedda02b5e59c5418f24d9b58540530a6c22e138118a8da220ee13124 | Shell | 472 | 20 | mypython=$1
echo "Python is $mypython"
$mypython $MARINE/marine.py \
--bam_filepath \
$MARINE/tests/strandedness_tests/bams/F1R2_pair.bam \
--annotation_bedfile_path \
$MARINE/annotations/hg38_gencode.v35.annotation.genes.bed \
--output_folder \
$MARINE/tests/strandedness_tests/F1R2_pair_test-single_end_mode_sailor \
... |
97d7c8a296be9af4f68588ff1ed60a4aa2f46157b38a9b2a0dca08826312fe62 | Shell | 473 | 21 | #!/bin/bash
#
# select_runs_add-ext.sh <runlist_file> <ext> <idx1> <idx2> ...
#
# - returns a selected list of files from runlist_file with added extension ext
# - e.g. when file contains only basename and nulle/nonnulled needs to be added
# - lines idx1, idx2, ... are selected
runlistFile=$1
ext=$2
fileIdcs=${@:3}
f... |
26401ad8f686569d5566173c00364c77a8fd3b60f0d2c49f115c9b052b3597a4 | Shell | 476 | 20 | #!/bin/bash
set -e
# get data
resource_url="https://github.com/gagneurlab/drop_demo_data/archive/refs/heads/main.zip"
tmpdir="$(dirname "$(mktemp)")"
wget -nc -P $tmpdir $resource_url
# if the directory Data does not exist
if [ ! -d "Data" ]; then
unzip "$tmpdir/main.zip"
mv drop_demo_data-main/Data Data
rm -rf d... |
5b3ca9ce400b0f87532bdf8ba265fe19538ced7c6372f6808e5055afcdeccf31 | Shell | 476 | 20 | mypython=$1
$mypython $MARINE/marine.py \
--bam_filepath \
$MARINE/examples/data/LR_single_cell.md.subset.filtered.sorted.bam \
--annotation_bedfile_path \
$MARINE/annotations/cellranger-mm10-3.0.0.annotation.genes.bed \
--output_folder \
$MARINE/examples/sc_long_read_test \
--min_dist_from_end \
0 \
--min_base_qualit... |
98efc9bb520f5408920ea09edc0e03173e00cef42fa403eb36eb2c41f8e5cab8 | Shell | 478 | 7 |
slamdunk all -r slamdunk/test/data/ref.fa -b slamdunk/test/data/actb.bed -o slamdunk/test/data/output -rl 100 -mbq 27 -5 0 slamdunk/test/data/reads.fq
grep -v "^#" slamdunk/test/data/output/count/reads_slamdunk_mapped_filtered_tcount.tsv > slamdunk/test/data/output/count/reads_slamdunk_mapped_filtered_tcount_noheader... |
b28e34fb895e34cb7ef6318a2db1663132c72893e687c314b60851047181d402 | Shell | 478 | 25 | #!/bin/bash -l
#
#SBATCH --nodes=1
#SBATCH --gres=gpu:a100:1
#SBATCH --partition=a100
#SBATCH --constraint=a100_80
#SBATCH --job-name=zsssl
#SBATCH --time=23:59:59
#SBATCH --mail-user=zhengguo.tan@fau.de
#SBATCH --mail-type=ALL
#SBATCH --output=%x.%j.out
#
# do not export environment variables
#SBATCH --export=NONE
un... |
c15b8821827f2b51b86c046f17f56808366fd85552c9a5dfcb267b680e87b330 | Shell | 481 | 16 | #!/bin/bash
# PediatricOpenTargets 2021
set -e
set -o pipefail
# This script should always run as if it were being called from
# the directory it lives in.
# copied from https://github.com/AlexsLemonade/OpenPBTA-analysis/blob/master/scripts/run_in_ci.sh
script_directory="$(perl -e 'use File::Basename;
use Cwd "abs_p... |
08d67694d1f4f2eabf5c50a30716d7d4226a6c5b9561186876a75050b093ea75 | Shell | 482 | 20 | mypython=$1
echo "Python is $mypython"
$mypython $MARINE/marine.py \
--bam_filepath \
$MARINE/tests/strandedness_tests/bams/F1R2_pair.bam \
--annotation_bedfile_path \
$MARINE/annotations/hg38_gencode.v35.annotation.genes.bed \
--output_folder \
$MARINE/tests/strandedness_tests/F1R2_pair_test-single_end_mode \
--min_d... |
8ee2f36dd24dddb6d70ffbe47289c205b18c570cee479b4e9ef404ba774f8405 | Shell | 482 | 16 | #!/bin/sh
##
# push.sh
#
# Run this from the $BOWTIE2_HOME/doc/website subdirectory.
#
# Copies the files that comprise the website at
# http://bowtie-bio.sourceforge.net/bowtie2 to sourceforge. You must
# have the right sourceforge privileges to do this. The SF_USER
# environment variable must be set appropriately.... |
a25a2ac0977d947b595cddc824959253d7d9416853a4d728114c28fdb3452b20 | Shell | 482 | 13 | if [ -n "$CUDA_FOUND" ]; then
EXTRA_CUDA_LIBS="cudart cublas cusparse"
if [ -n "$AMGX_FOUND" ]; then
EXTRA_CUDA_LIBS="$EXTRA_CUDA_LIBS $AMGX_LIBRARY"
fi
fi
CHECK_CUSTOM_FILE
COMPILE_SHARED_LIB "default_linear_system_solver" "linear_system_solver.c ${CUSTOM_FILE}" "gpu_solvers_cublas_12.c gpu_so... |
4e7154a571f6b45d8174e4ee2c25496bb991e320da651dd01d8a6106024e6fc3 | Shell | 483 | 22 | #!/bin/bash
#SBATCH --time=00:10:00
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --job-name=gnn_sim_qt_start
#SBATCH --output=logs/gnn_sim_qt_start-%j.log
#SBATCH --mem=1GB
#SBATCH --partition=short
ml R
Rscript -e "devtools::install_github('EvoLandEco/eve')"
name=${1}
nrep=${2}
for (( param_set = 1; param_set <= 2... |
880528732a4655c9acb8728fb4ef76492fdcf9d333607b605f166171687cea23 | Shell | 483 | 11 | #!/bin/bash
######################
# run python script
######################
source /cbica/projects/luo_wm_dev/miniconda3/etc/profile.d/conda.sh
conda activate luo_wm_dev
python ./identify_variants.py "PNC" "/cbica/projects/luo_wm_dev/two_axes/code/config/config_PNC.json"
python ./identify_variants.py "HCPD" "/cbi... |
21048f89375c7ac7d776f1444210d910ca72e3c434946e6f970ff65d5bfbe8ad | Shell | 484 | 23 | #!/bin/bash -l
#
#SBATCH --nodes=1
#SBATCH --gres=gpu:a100:1
#SBATCH --partition=a100
#SBATCH --job-name=vae
#SBATCH --time=04:59:59
#SBATCH --mail-user=zgtan@med.umich.edu
#SBATCH --mail-type=ALL
#SBATCH --output=%x.%j.out
#
# do not export environment variables
#SBATCH --export=NONE
unset SLURM_EXPORT_ENV
module lo... |
347199b278c69948ff9f035811dc62f05e915d5031be532f9828dd61eb124e6a | Shell | 484 | 21 | mypython=$1
$mypython $MARINE/marine.py \
--bam_filepath \
$MARINE/tests/strandedness_tests/bams/pair_example_18_49488551_49590000.sorted.bam \
--annotation_bedfile_path \
$MARINE/annotations/cellranger-GRCh38-3.0.0.annotation.genes.bed \
--output_folder \
$MARINE/tests/strandedness_tests/pair_test \
--min_dist_from_e... |
70958ffae28aadc394c537d3146ba0f629cb2916856117fb663ae113c7736549 | Shell | 484 | 16 | #!/bin/bash
#SBATCH -J test_reID
#SBATCH -o test.o%j
#SBATCH -t 26:00:00
#SBATCH -N 1 -n 8
#SBATCH --gpus=1
#SBATCH --mem=256G
source activate Ali
CUDA_VISIBLE_DEVICES=7
python examples/RWM_testUnet.py \
-d brain -a unet --resume /home/lhuang37/repos/VisQ-Search-Engine/examples/logs/single_subtypew0/model_best.pt... |
5a630760a60bb387253833a0cbe9979325cbbf77926ab45bc48dbd6f709d76e3 | Shell | 485 | 7 | #!/bin/bash
# generate llvm report
# llvm-cov-9 show ./nastja unittest/unittest -instr-profile=coverage.profdata -format=html -output-dir=cov_html -ignore-filename-regex="/external/" --Xdemangler=c++filt
# generate lcov report
llvm-cov-9 export ./unittest/unittest -object ./nastja -instr-profile=coverage.profdata --fo... |
38eb8f2f3b036bd73c5be3669b70a3178f55cebd160bc18e1b75995b584cf551 | Shell | 487 | 21 | #!bin/bash
./gcta/gcta64 --mlma-loco \
--bfile merged_plink_qc \
--grm merged_plink_qc_grm \
--pheno pheno_iwrd_residuals.txt \
--out gwas_output/iwrd \
--thread-num 10
./gcta/gcta64 --mlma-loco \
--bfile merged_plink_qc \
--grm merged_plink_qc_grm \
--pheno pheno_pics_residuals.txt \
--out gwas_output/pics \
--thread... |
2853c741cd426ac26acf64463320d74b72ed296a41a4c8b58e5bcc3c7a761a62 | Shell | 489 | 22 | #!/usr/bin/env bash
set -e
input_image=$1
output_image=$2
output_bias_field=$3
if [[ $# -ne 3 ]]; then
echo "Usage: $0 <input_image> <output_image> <output_bias_field>"
exit 1
fi
N4BiasFieldCorrection -d 3 \
-v 1 \
-s 4 \
-b [180] \
... |
dea7e1c20b222bbaf91477f8ea91b6fc270412a6640c6886514bfad0a10d4520 | Shell | 489 | 17 | #!/bin/sh
# Provide the last residue number
end=11
# Provide the file name (filename="relaxed_200_0.pdb")
filename="output_300_3.pdb"
# You can change this value if want to use more cpus
increment=10
# Change this value if you do not want to start from residue 1
start=1
int_end=$increment
while [ $start -le $end ]; do... |
480b2c0a049a32ad9502a960f102ef1bec2beecbf82d993ab3669580688fe9db | Shell | 492 | 8 | # Allow the test S3 server through Smokescreen's SSRF protection.
#
# CVAT sources this init script in the server and import/export/chunk workers.
# Moto runs on a private Docker network, so resolve its address and allow it
# explicitly. This lets cloud storage tests use the proxy without disabling
# its protection for... |
91d5d3c244bf58f0595daa7e7642424c38c1c2e68231a61b22a004fe5e8627d0 | Shell | 492 | 18 | #!/bin/bash
#SBATCH --time=1-00:00:00
#SBATCH --gres=gpu:1
#SBATCH --constraint=v100
#SBATCH --partition=gpu
#SBATCH -n 1
#SBATCH --mem 100G
#SBATCH --mail-type=FAIL
#SBATCH --mail-user=<EMAIL>
# Example SLURM script for running the Sei framework code
# on variants in the input VCF file
vcf_filepath="${1:-}" # path ... |
eacdb814deb8774f7e680483a56853d7f9b95d079bc2a4ba0a227cc35cb43ca2 | Shell | 492 | 26 | #!/bin/bash -l
#
#SBATCH --nodes=1
#SBATCH --gres=gpu:a100:1
#SBATCH --partition=a100
#SBATCH --constraint=a100_80
#SBATCH --job-name=zsssl
#SBATCH --time=23:59:59
#SBATCH --mail-user=zgtan@med.umich.edu
#SBATCH --mail-type=ALL
#SBATCH --output=%x.%j.out
#
# do not export environment variables
#SBATCH --export=NONE
un... |
166a0b33cb9927395cfe0d4a8ed18ee7515c7be55278241a99e2891da671c9dc | Shell | 494 | 34 | #! /bin/bash
# aponteeduardo@gmail.com
# Copyright (C) 2017
set -e
DEBUGM=0
for i in "$@"
do
case $i in
-d|--debug)
DEBUGM=1
shift # past argument=value
;;
#-s=*|--searchpath=*)
#SEARCHPATH="${i#*=}"
#shift # past argument=value
#;;
esac
done
... |
9b1fc1682898ddbd98b252a33c994ac6c1e721e023ed207654d2dc41feb00145 | Shell | 494 | 10 |
#!/bin/bash
cp ~/two_axes/code/run_babs_qsirecon/qsirecon_json_files/noddi.json ~/input/HCPD/derivatives/babs_noddi/analysis/code
cp ~/two_axes/code/run_babs_qsirecon/qsirecon_json_files/mapmri.json ~/input/HCPD/derivatives/babs_mapmri/analysis/code
cp ~/two_axes/code/run_babs_qsirecon/qsirecon_json_files/noddi.... |
0634cc5f96d990d2c3ec0fcc315e5568555ed36658b6a042e1d36714ed4b8a43 | Shell | 495 | 16 | #!/bin/bash
#
# Krutika Gaonkar D3b
#
# Integrate molecular subtyping results
set -e
set -o pipefail
# Set the working directory to the directory of this file
cd "$(dirname "${BASH_SOURCE[0]}")"
# Add molecular_subtype, integrated_diagnosis, short_histology,
# broad_histology and Notes from `compiled_molecular_subt... |
ed234ab6a1233918d7256a61a44962ea01e86033101d0025d5a02f050fd5f75f | Shell | 495 | 2 | echo COMMAND ./b2 cxxflags="$1" linkflags="$2" --stagedir=stage-$3 --with-filesystem --with-date_time --with-system --with-program_options --with-log --with-json --with-container link=static cxxstd=20 $3
./b2 toolset=$4 cxxflags="$1" cflags="$1" linkflags="$2" --stagedir=stage-$3 --with-atomic --with-chrono --with-thre... |
0927b9904a0df833bfc408969bed4f1bfe3a2366eca834d2d75b495900d1ce23 | Shell | 497 | 8 | #!/bin/bash
in=$1
hcppath=$2
yourpath=$3
wb_command -volume-to-surface-mapping ${yourpath}/inputs_query_new/${in}_2.nii.gz ${hcppath}/100307/MNINonLinear/fsaverage_LR32k/100307.L.midthickness_MSMAll.32k_fs_LR.surf.gii ${yourpath}/surf_query/$in.L.func.gii -trilinear
wb_command -volume-to-surface-mapping ${yourpath}... |
37ae9a34b7bd6178bf1f4e9e8f1609450684ab8e62974dc8329c776de17d6942 | Shell | 497 | 8 | #!/usr/bin/env bash
echo "Create desktop file for macular and macularTemplateEngine"
sed -i "s,%PREFIX%,$PREFIX,g" $PREFIX/share/macular/macular.desktop
sed -i "s,%PREFIX%,$PREFIX,g" $PREFIX/share/macular/macular-template-engine.desktop
mkdir -p $HOME/.local/share/applications
ln -sf $PREFIX/share/macular/macular.desk... |
3ed87289d3475faa3c471e25a21d8c229ea206312a1ddc6a311828ff4296038a | Shell | 497 | 11 |
#pull docker image with necessary R packages
#docker site: https://hub.docker.com/r/audreycluo/r-packages-for-cubic/tags
#tag: https://hub.docker.com/layers/audreycluo/r-packages-for-cubic/0.0.7/images/sha256-7064f5c09ef83f442986d51061e963951f9499cdfe92717a883e6cc4010516f3
# pull the docker image onto cubic clust... |
52a00962dae4c5b42f2bc6d72d3f17a446355402476f20e1f57fc1d95d112e5e | Shell | 498 | 17 | #!/bin/bash
#Change PROT below to match your system
#Change clusters and max_cluster below to match your number of clusters
xtc=../../raw_traj/s1cPROT/s1cPROT_all.xtc
gro=../../prot.gro
ndx=cluster.ndx
clusters=( 1 2 3 4 5 6 7 )
max_cluster=7
##############################################
for c in ${clusters[@]}; ... |
921297cbf805e6272d0986801539e2ae7054ed0a30a0fbf3bbf165c512c0fe04 | Shell | 500 | 16 | #run using python3 (tried on python 3.6)
#pysam matching with samtools 1.7+
#accepts .sam/.bam/.fastq or .fastq.gz for fastq1 and fastq2 variables below
fastq1=
fastq2=
bwa_index=
outdir=
prefix=
mapq=
length_cutoff=
threads=8
memory_per_thread="20G"
per_chr=1 # set this to one if you don't want per chromosome output ... |
4529e7bb72970da523c1c143e01f370626b34f96765e32bf1fdcf642fece1e6c | Shell | 503 | 5 | antsRegistration --dimensionality 3 --float 1 --output [ANTs/registeredMoment,ANTs/registeredWarpedMoment.nii.gz] --interpolation Linear --winsorize-image-intensities [0.005,0.995] --use-histogram-matching 0 --initial-moving-transform [oasis_157_image.nii.gz,oasis_157_image_rotated.nii.gz,1] --transform Rigid[0.1] \
-... |
5f9201ec3d24ce720c075663abf3e9d3295f3b5c1fdced0865e6f7f1bb3c3746 | Shell | 503 | 12 | GPU_UTILS_SOURCE_FILES="gpu_utils.c"
GPU_UTILS_HEADER_FILES="gpu_utils.h"
if [ -n "$CUDA_FOUND" ]; then
GPU_UTILS_EXTRA_LIB_PATH=$CUDA_LIBRARY_PATH
GPU_UTILS_DYNAMIC_LIBS="c cudart"
GPU_UTILS_SOURCE_FILES="$GPU_UTILS_SOURCE_FILES gpu_utils.cu"
fi
COMPILE_SHARED_LIB "gpu_utils" "$GPU_UTILS_SOURCE_FILES" "... |
2875ea051128fb78bdbd116d0b58c7c9c58cb413fb9e625edd84ab85a3295021 | Shell | 508 | 11 | rm -r obj/
rm -r out/*
dotnet build ./RawConverterDotnetCore.csproj
rm -r ./out/RawConverterDotNetCoreWindows;
rm -r ./out/RawConverterDotNetCoreLinux;
dotnet publish -c Release --self-contained true -r win10-x64 -o ./out/RawConverterDotNetCoreWindows/;
dotnet publish -r linux-x64 -o ./out/RawConverterDotNetCoreLinux... |
47043fb518d5b5913636156d04d83e5a66a6c7f07716952cc51b2eb04014ed51 | Shell | 509 | 17 | #!/bin/bash
set -e
set -o pipefail
# This script should always run as if it were being called from
# the directory it lives in.
script_directory="$(perl -e 'use File::Basename;
use Cwd "abs_path";
print dirname(abs_path(@ARGV[0]));' -- "$0")"
cd "$script_directory" || exit
# This determines whether the analysis ... |
50760902863f53357704dcec7147547ae814d839caa79fa862290adcff64e28c | Shell | 509 | 23 | #!/bin/bash
set -e
# Start container
echo "Starting container..."
docker compose -f docker-compose.yml up -d
# Wait for container to be ready
echo "Waiting for container..."
sleep 5
# Get the container ID from docker compose
CONTAINER_NAME=$(docker compose -f docker-compose.yml ps -q surface_morphometrics)
# Enter... |
17e879df0bb2dbe072a47855fb63fc63176958d721d672c79a6fcc8a1acd517c | Shell | 510 | 13 | echo CLANG
echo QQQQQQ $1 $2 $3 $4
PATH=/c/Program\ Files/LLVM/bin:$PATH
echo PATH=$PATH
$1 --target-os=win64 --arch=x86_64 --cc=clang --enable-static --disable-shared --extra-cflags="$3" $4 --prefix=$2 | tee ffmpeg_config.log
sed -i s/LIBPREF=lib/LIBPREF=/ ffbuild/config.mak
sed -i s/LIBSUF=.a/LIBSUF=.lib/ ffbuild/... |
40e40f5912034368e2da35f5b12cc7640b47220b0ff12ce32bc51a52d4d4ed6c | Shell | 510 | 13 |
cd ..
device=0
for b in batchnorm none
do
for lr in 0.02 0.01 0.005 0.002 0.001
do
python offline_main.py --model_type RLIF --nb_epochs 100 --nb_hiddens 1024 --normalization $b --momentum 0.99 --lr $lr --lr_step_size 5 --devices "$device" --new_exp_folder bptt-batch-lr --nb_layers 3
python offline_main.py --mo... |
f65107bf09264aa8dc6532542decbd3dd2fee8b2df5202053589b6907215f545 | Shell | 510 | 29 | eval "$(/pollard/home/sdrusinsky/miniforge3/bin/conda shell.bash hook)"
source /pollard/home/sdrusinsky/miniforge3/bin/activate enformer_ft
conda update --all
conda \
install -y \
-c pytorch \
-c nvidia \
pytorch=2.3.1 \
pytorch-cuda=12.1
conda \
install -y \
-c conda-forge \
cython \
ipyt... |
2dbfacf8f95095d6c602cfa30cee79268b12b9c1043cf2735465683266f2747d | Shell | 511 | 18 | #!/bin/bash
# Author: Abhishek Choudhary
set -euo pipefail
IFS=$'\n\t'
input_bam=$1
prefix=$2
threads=$3
suffix=Aligned.toTranscriptome_noIDS.out.bam
output_bam=$prefix.$suffix
samtools view $input_bam -@ $threads | awk '{print $1}' | sort | uniq > readids_all
samtools view $input_bam -@ $threads | awk '$6 ~ "I|D|S... |
75e262a2c6574dee5e81a0bb490fa792747e3d11a411d7bbfb4688f4e9ae5eb5 | Shell | 512 | 15 | #!/bin/bash
set -eu
#emulate fsl_sub output capturing while running locally
#use exec so the command gets the same pid as the log files use
#note, exec doesn't understand env variables like "OMP_NUM_THREADS=1 wb_command ..."
#so, you need to run "OMP_NUM_THREADS=1 captureoutput.sh wb_command ..." instead
#remove path... |
930a83257e373d8b3262fd6871382e994d54a654786b0aea5d3775f7f5594ecf | Shell | 512 | 11 | #!/bin/bash
# this script takes the array ID that's going into sbatch_fmriprep as a positional argument
read -p "Enter subj num to fmriprep with no leading 0s: " SUBJ_NUM
SCRIPT_DIR=/home/data/eccolab/SPLaT_fMRI/code/shell
SBATCH_OUT_FMRIPREP=$(sbatch --array=$SUBJ_NUM $SCRIPT_DIR/sbatch_fmriprep.sh)
JOB_ID=${SBATCH_... |
e058ea5c7088ff05f3926d35000e62e11411ad7dd0f2e2242c57ccc64a0ec939 | Shell | 513 | 24 | #!/bin/bash -l
#
#SBATCH --nodes=1
#SBATCH --gres=gpu:a100:1
#SBATCH --partition=a100
#SBATCH --constraint=a100_80
#SBATCH --job-name=llr
#SBATCH --time=05:59:59
#SBATCH --mail-user=zgtan@med.umich.edu
#SBATCH --mail-type=ALL
#SBATCH --output=%x.%j.out
#
# do not export environment variables
#SBATCH --export=NONE
unse... |
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