sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
15de19c21f9ded5e31e0679061c69a37342b69cf9e0bc97896f3d8f9f265a004 | Shell | 465 | 25 | #! /bin/bash
nRep=10 #10
methodAll=("ss")
pctAll=("0.9" "0.7" "0.5" "0.3")
cd /group/qtlchenggrp/tianjing/singlestep_nnlmm/pig_n3534_p10000
for pct in "${pctAll[@]}"
do
cd "$pct"
for method in "${methodAll[@]}"
do
cd run_"$method"
for rep in $( eval echo {1..$nRep} ) #rep1,...,rep20
do
sbatch ... |
474ce572d5f5078f07c3dd33b5fa6ed943460d89e1031ba8b3c2d81bf241eae2 | Shell | 466 | 21 | #$ -pe threaded 8-12
#$ -l h_vmem=64G
#$ -M josiane.i.bourque@gmail.com
#$ -m e
#$ -m a
#$ -o /cbica/projects/pnc_fixel_cs/scripts/MRtrix_recon/script_output/smooth.$JOB_ID.stdout
#$ -e /cbica/projects/pnc_fixel_cs/scripts/MRtrix_recon/script_output/smooth.$JOB_ID.stderr
#!/bin/bash
project=/cbica/projects/pnc_fixel_c... |
55b692e4c5211492ec932dfd57a4e0c544c0c17219f1c1f1e36a2f6faf093229 | Shell | 467 | 23 | #!/bin/bash
set -xe
source $(dirname "$0")/all-vars.sh
source $(dirname "$0")/all-utils.sh
source $(dirname "$0")/asserts.sh
bitrate=$1
set_ldc_sample_filename "${bitrate}"
model_source=${DEEPSPEECH_TEST_MODEL//.pb/.tflite}
model_name=$(basename "${model_source}")
model_name_mmap=$(basename "${model_source}")
expor... |
739c51ce12f1061520b68863abb2ac7892991df4d9088279643bbdee59e2db38 | Shell | 467 | 26 | sbatch --wait << EOF
#!/bin/bash
#SBATCH -o logs/%j.job
#SBATCH -e logs/%j.job
#SBATCH -J jupyter
##SBATCH -p gpu_p
##SBATCH --gres=gpu:1
##SBATCH --qos=gpu
#SBATCH -p cpu_p
#SBATCH -c 48
##SBATCH -c 4
#SBATCH --mem=200G
##SBATCH --mem=40G
#SBATCH -t 48:00:00
#SBATCH --nice=10000
source $HOME/.bashrc
conda activate ... |
3169a96117f8a79354df07d886f55981d60526b05d013362a074cb0f49aa3ee3 | Shell | 469 | 28 | sbatch --wait << EOF
#!/bin/bash
#SBATCH -o logs/%j.job
#SBATCH -e logs/%j.job
#SBATCH -J jupyter
##SBATCH -p gpu_p
##SBATCH --gres=gpu:1
##SBATCH --qos=gpu
#SBATCH -p cpu_p
#SBATCH -c 48
##SBATCH -c 4
#SBATCH --mem=200G
##SBATCH --mem=40G
#SBATCH -t 48:00:00
#SBATCH --nice=10000
source $HOME/.bashrc
conda activate ... |
4a5222a327336376cd88f6384ec338dbe87338e030e87e04f983442a899ed903 | Shell | 469 | 9 | CUDA_VISIBLE_DEVICES=2
spec='python3 driver.py --dataset tc_full_kinase --cross_validation
--max_iter 42 --evaluate_freq 3 --patience 3 --model tf_regression
--prot_desc_path davis_data/prot_desc.csv --no_concord
--prot_desc_path metz_data/prot_desc.csv --prot_desc_path KIBA_data/prot_desc.csv
--prot_desc_path... |
73ca47f227f1ac6fe65dd7cb4c16e1b985764fd9499166b878092ab2cb10def4 | Shell | 469 | 22 | #!/bin/bash -ve
#######################################################
## Run Trinity to Generate Transcriptome Assemblies ##
#######################################################
## use jellyfish
../../Trinity \
--seqType fq \
--max_memory 2G \
--left reads.left.fq.gz \
--right reads.right.fq.gz ... |
c225801167911f02fbec19a4f46e208abd2fe3e6e0ebc8843decc49397392990 | Shell | 474 | 27 | #!/bin/bash
set -xe
runtime=$1
source $(dirname "$0")/tc-tests-utils.sh
source $(dirname "$0")/tf_tc-vars.sh
BAZEL_TARGETS="
//native_client:libdeepspeech.so
"
if [ "${runtime}" = "tflite" ]; then
BAZEL_BUILD_TFLITE="--define=runtime=tflite"
fi;
BAZEL_BUILD_FLAGS="${BAZEL_BUILD_TFLITE} ${BAZEL_OPT_FLAGS} ${BAZ... |
5ec30b8cdd4fe09bdaf1f2bc2b10aa6e21dc571434bafc48ca2bdaed057bcf0d | Shell | 475 | 17 | #! /usr/bin/bash
#SBATCH -o /cellar/users/dlaub/projects/ML4GLand/EUGENe_paper/scripts/out/%A_%a_%x.out
#SBATCH -e /cellar/users/dlaub/projects/ML4GLand/EUGENe_paper/scripts/err/%A_%a_%x.err
#SBATCH -p carter-compute
#SBATCH -J rechunk
#SBATCH -a 0-37%8
#SBATCH -c 2
#SBATCH --mem 48G
wdir=/cellar/users/dlaub/project... |
3303fa60ab810f5db37f7edefa4f90b665ea5557c53fa50cb732e99edb56b673 | Shell | 476 | 14 | #!/usr/bin/env bash
set -euo pipefail
SCRIPT_DIR="$(cd -- "$(dirname -- "${BASH_SOURCE[0]}")" && pwd)"
# Get all release hashes from git tags and write them to a file
# The first tag to include is the v3.0.4 because it is the first
# that uses hatchling.build as the build backend.
git tag --list --sort=v:refname \
|... |
54a7c440fdba71d8e337f3df52e8560cc876b0e8a2bda59952eadbc90186d339 | Shell | 478 | 13 | PROJDIR=/projects/pfenninggroup/singleCell/McLean_chronic_opioid_monkey_snRNA-seq
PROJDIR2=/projects/pfenninggroup/singleCell/Logan_BU_Striatum_snRNA-seq
rsync -Pav ${PROJDIR2}/code/final_code/HeKleyman2021_macaque_striatum_data_processing \
${PROJDIR}/code/final_code
rsync -Pav ${PROJDIR2}/data/tidy_data/HeKleyman20... |
8d531ae900ae2fb94d71caa647dac3361a27a6529308a0879fb47a3a00eaa3f0 | Shell | 478 | 19 | #!/bin/bash
# This sample script runs a Hopfield network simulation. Additional flags can
# be provided at the command line and are appended to the end of the command.
if [[ $# -lt 1 ]]; then
echo "Usage: ./2a_hopfield.sh fileroot [-flag value ...]"
exit 1
fi
src/search.o \
-fileroot "out/$1" \
-X_dir "out/p... |
4f17617a469f29ca1327f1853e71aca6db7daec37c8856cdd6cd2050fed5da25 | Shell | 479 | 8 | python train_alpha_pose.py --dataset coco \
--model alpha_pose_resnet101_v1b --mode hybrid --num-joints 17 \
--lr 0.001 --wd 0.0 --lr-mode step --lr-decay-epoch 30,60 \
--num-epochs 90 --batch-size 32 --num-gpus 4 -j 60 \
--dtype float32 --warmup-epochs 0 --use-pretrained-base \
--save-dir params_al... |
6bb15121935015b171d88fa28e5bf88305e30a641ef9ffcff96fb00b634188fe | Shell | 481 | 4 | python neuron_to_tensor.py --root=/home/luketaylor/PycharmProjects/NeuralPred --dataset=multi_pvc1 --split=train --ntau=25
python neuron_to_tensor.py --root=/home/luketaylor/PycharmProjects/NeuralPred --dataset=multi_pvc1 --split=test --ntau=25
python neuron_to_tensor.py --root=/home/luketaylor/PycharmProjects/NeuralPr... |
63d4748613e150239acbde2794262ac690de038c6c0fe10397eb381ddeb244db | Shell | 482 | 23 | #!/bin/bash
# command-line arguments:
# 1: trial id
# 2: run type (1,2,...)
# 3: run id (e.g., run-001)
TRIAL=$1
RUN=$2
RUN_ID=$3
# output directory
OUT_DIR="$HOME/projects/dynamic-engrams/simulations/sim_rc_p11/$RUN_ID"
# source directory
SOURCE="src"
DIR=$OUT_DIR/$SOURCE
$DIR/run-burn_in.sh $TRIAL $RUN $RUN_ID
$... |
c8642ee491143e709150d958e5b9d3b5b606edaf95e82775031a2122a2a3c3ce | Shell | 482 | 29 | #!/bin/bash
set -xe
source $(dirname "$0")/all-vars.sh
source $(dirname "$0")/all-utils.sh
source $(dirname "$0")/asserts.sh
bitrate=$1
set_ldc_sample_filename "${bitrate}"
model_source=${DEEPSPEECH_TEST_MODEL//.pb/.tflite}
model_name=$(basename "${model_source}")
model_name_mmap=$(basename "${model_source}")
down... |
271c7d6cc1271177258a2d709eb92c1c5baab1dcda351e10cb2ca742fe167530 | Shell | 484 | 15 | #!/bin/bash
set -e -u
# Build the installer for MacOS.
# This script needs to be run from the root of the repository.
# Prerequisites: wheel has been build, e.g. using build_wheel.sh
rm -rf dist_pyinstaller build_pyinstaller
WHL_NAME=$(cd dist && ls ./*.whl && cd ..)
pip install "dist/${WHL_NAME}[stable,structurema... |
7f9d869641ed18458495d61ea4b819d0e8e7b892fb0a5691d20728b8ebab52d5 | Shell | 485 | 27 | #!/bin/bash
set -xe
arm_flavor=$1
api_level=$2
source $(dirname "$0")/tc-tests-utils.sh
bitrate=$3
set_ldc_sample_filename "${bitrate}"
model_source=${DEEPSPEECH_TEST_MODEL//.pb/.tflite}
model_name=$(basename "${model_source}")
export DATA_TMP_DIR=${ANDROID_TMP_DIR}/ds
download_material "${TASKCLUSTER_TMP_DIR}/ds... |
6a9cb821734436d42761e8bbcb286c906bfce69e877c7ac9473ccecd992ec4b4 | Shell | 487 | 18 | #!/bin/bash
module load singularity/3.7.0
singularity exec \
--env WORKING_DIRECTORY=/home/pymc/src/paper/experiments \
--env PYTHONPATH=/home/pymc/src \
--env PYCOX_DATA_DIR=/tmp/.pycox \
--env MPLCONFIGDIR=/tmp/.matplotlib \
--env PYTENSOR_FLAGS="base_compiledir=/tmp/.pytensor" \
--env NUMBA... |
0dc9c90eb15c9ed57fcc66cb2da0792c59ef0f7b960abfa71bd411990a6eafec | Shell | 488 | 26 | #!/bin/bash
set -xe
source $(dirname "$0")/all-vars.sh
source $(dirname "$0")/all-utils.sh
source $(dirname "$0")/asserts.sh
bitrate=$1
set_ldc_sample_filename "${bitrate}"
model_source=${DEEPSPEECH_PROD_MODEL}
model_name=$(basename "${model_source}")
model_source_mmap=${DEEPSPEECH_PROD_MODEL_MMAP}
model_name_mmap... |
8b288b82d2addc6dde01b703fe9bb2eb1b4fd5349812c926cfb793afc399035b | Shell | 491 | 7 | #!/usr/bin/env bash
source venv/bin/activate
python experiments/preprocessing/parse_refseq.py
python experiments/preprocessing/build_datasets.py 1200
# additional BLAST+NEEDLE filtering
python experiments/analysis/parse_blast.py blast data/mammalian_200-1200_train_PROTEIN_balanced.fa data/mammalian_200-1200_test_RNA_no... |
f9ad9d2fe01757c77b18be92a2ae7d7aedc280464c307602ded49fb19abe98dd | Shell | 493 | 20 | #!/bin/bash -ve
#######################################################
## Run Trinity to Generate Transcriptome Assemblies ##
#######################################################
## use jellyfish
../../Trinity --seqType fq --max_memory 2G --left reads.left.fq.gz,reads2.left.fq.gz --right reads.right.fq.gz,read... |
ce5328ad0515435a5a2bbc1bbd8d3dc7fe2f270d057e4d7350e602da4d32f2f1 | Shell | 494 | 15 | #Aligning all reads from different genomes to the ancestor genome, separately
species=$1 #specify species genome
#step1
bowtie2 -p 4 \
-x {file_pathway}/ancestor.fa \
-f {file_pathway}/${species}_50bp_reads.fa \
--no-unal \
-S {file_pathway}/${species}_50bp_reads.sam
#step2
samtools view -bS {file_pathway}/${spec... |
78b4f451d6d8cfbe1f08c08bfb25b3e4f945e4555bb0e1c7a6710d389eb0ff51 | Shell | 496 | 34 | #!/bin/bash
# make a brain mask using bet
usage() {
echo "$0 <nifti_file> <mask_file> [bet_flags]"
}
# validate args
if [ ! "$2" ]; then
usage
exit 0;
fi
infile="$1"
shift;
maskfile="$1"
shift;
if [ ! "$1" ]; then
betflags="-f 0.5 -g 0 -n -m";
else
betflags="$@";
fi
# setup the environment
if ... |
e51f24c835e6f7fca0089c4e5f0ee2c80199dd0e3f22045adabc32068e0af310 | Shell | 496 | 22 | #!/bin/sh
#
# Script for generating key-cert pairs
#
if [[ $# -ne 2 ]]; then
echo "Usage: ${0##*/} KEY CERT"
exit
fi
KEY=$1
CERT=$2
PSWD=test
read -s -p "Enter Password: " $PSWD
openssl genrsa -des3 -passout pass:$PSWD -out $KEY.key 1024
openssl req -new -key $KEY.key -out $KEY.csr -passin pass:$PSWD
cp $KEY.ke... |
574e880219b6a2f2caf6edc07515d540b2239c6edb8158500db8080eab49a46d | Shell | 498 | 16 | FILE=$1
echo "Note: available models are edges2shoes, edges2handbags, night2day, maps, and facades"
echo "downloading [$FILE]"
MODEL_DIR=./pretrained_models/${FILE}
mkdir -p ${MODEL_DIR}
MODEL_FILE_G=${MODEL_DIR}/latest_net_G.pth
URL_G=http://efrosgans.eecs.berkeley.edu/BicycleGAN//models/${FILE}_net_G.pth
wget -N $... |
31940ccc84e042ad349282f8fe0cb13513ee7299b3659d31ea34feacb3177e5a | Shell | 499 | 21 | #!/bin/bash
#SBATCH --mail-user=kieran.d.nehil-puleo@vanderbilt.edu
#SBATCH --mail-type=end
#SBATCH --error=MEGNN_%J.err
#SBATCH --output=%J.out
#SBATCH --job-name=megnn
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --time=04:00:00
#SBATCH --gres=gpu:1
#SBATCH --partition=day-long-tesla
#SBATCH --exclude=node7,node9,nod... |
8c29b8caeb2694c34d9a5b94a932d471852cb0771426f1a6fd16e5f0ab276a07 | Shell | 504 | 27 | #!/bin/bash
set -xe
source $(dirname "$0")/tc-tests-utils.sh
bitrate=$1
set_ldc_sample_filename "${bitrate}"
model_source=${DEEPSPEECH_TEST_MODEL//.pb/.tflite}
model_name=$(basename "${model_source}")
model_name_mmap=$(basename "${model_source}")
export DATA_TMP_DIR=${TASKCLUSTER_TMP_DIR}
download_material "${TASK... |
dcba3a4f4c5830fe1636e6723f401c27f43e260a58a0e1a63870a19451a905c7 | Shell | 504 | 15 | #!/bin/bash -ve
#######################################################
## Run Trinity to Generate Transcriptome Assemblies ##
#######################################################
docker run --rm -v `pwd`:`pwd` trinityrnaseq/trinityrnaseq \
Trinity --seqType fq --max_memory 2G \
--lef... |
31f0dc31b258ac2af47cab5b72f1beaffa67db541ad56203983c8d7e8d88f602 | Shell | 505 | 25 | #!/bin/bash
set -xe
source $(dirname "$0")/all-vars.sh
source $(dirname "$0")/all-utils.sh
source $(dirname "$0")/asserts.sh
bitrate=$1
set_ldc_sample_filename "${bitrate}"
model_source=${DEEPSPEECH_PROD_MODEL//.pb/.tflite}
model_name=$(basename "${model_source}")
model_name_mmap=$(basename "${model_source}")
model... |
c6378867ab00502a362dd32612883f13e4aa6539f47c30364e29532f1b2d32ea | Shell | 507 | 22 | #!/bin/bash -l
#SBATCH -J first_projinv
#SBATCH --array=0-779 # jobs
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=6
#SBATCH --mem-per-cpu=6G
#SBATCH -t 00:20:00
#SBATCH --mail-type=ALL
#SBATCH --mail-user=${USER}.edu
#SBATCH -p msismall,amdsmall
#SBATCH -o batch_logs/%x_%A_%a.out
#SBATCH -e bat... |
08511562ea5a10d082d18f8f570cb8681abc802327c618d155de692635cca114 | Shell | 508 | 16 | #!/usr/bin/env sh
TOOLS=./build/tools
$TOOLS/caffe train \
--solver=examples/cifar10/cifar10_full_solver.prototxt
# reduce learning rate by factor of 10
$TOOLS/caffe train \
--solver=examples/cifar10/cifar10_full_solver_lr1.prototxt \
--snapshot=examples/cifar10/cifar10_full_iter_60000.solverstate
# red... |
d3bd5689af1f9575302e523642b74db89879ab891f90033f690350edaca97339 | Shell | 508 | 18 | #!/bin/bash
#SBATCH --partition=carter-compute
#SBATCH --cpus-per-task=16
#SBATCH --mem=64G
#SBATCH --time=14-00:00:00
#SBATCH -o ./%x.%A.%a.out
#SBATCH -e ./%x.%A.%a.err
#SBATCH --array=1-2%2
# Usage: sbatch --job-name=ray13_evaluation ray13_evaluation.sh
# Define the model to run
models=(setA ST MT Kipoi)
model=${mo... |
45949959d274fcd8781b5c84492a5b07eadfbb1db01dbfa48f601fbdb04740de | Shell | 509 | 11 | #!/bin/bash
set -e -u
release="$(curl -fsSL https://api.github.com/repos/sylabs/singularity/releases/latest | jq -r .tag_name)"
[ "${release}x" = "x" ] && echo "Failed to get latest singularity release name" && exit 1 || true
codename="$(lsb_release -cs)"
arch="$(dpkg --print-architecture)"
wget -q -O /tmp/singularit... |
9f8d67fecb3724f85bb675e096366d8b0f01d32f643717ebecc507cde4a159ee | Shell | 511 | 22 | #!/bin/bash
set -xe
source $(dirname "$0")/tc-tests-utils.sh
bitrate=$1
set_ldc_sample_filename "${bitrate}"
model_source=${DEEPSPEECH_PROD_MODEL//.pb/.tflite}
model_name=$(basename "${model_source}")
model_name_mmap=$(basename "${model_source}")
model_source_mmap=${DEEPSPEECH_PROD_MODEL_MMAP//.pbmm/.tflite}
export... |
09217db9aa2c65f2a8bf0ff4968cedbbbe2cad35234d7340645768760e8b0e1e | Shell | 513 | 20 | sbatch --wait << EOF
#!/bin/bash
#SBATCH -o logs/%j.job
#SBATCH -e logs/%j.job
#SBATCH -J pred-DeepRAM-snakemake
#SBATCH -p cpu_p
#SBATCH -c 4
#SBATCH --mem=8G
#SBATCH -t 14:00:00
#SBATCH --nice=10000
echo $HOSTNAME
source $HOME/.bashrc
conda activate deepram
python deepRAM/deepRAM.py --data_type DNA --train False ... |
f8b190c55a9f42867cdf3b989d3a8c614cff6c55cbf9985d9c9c11b00bdac583 | Shell | 514 | 10 | #!/bin/bash
gtf="modified_gencode.vM23.primary_assembly.annotation.gtf"
bedfile="mouse.modified_gencode.vM23.bed"
geneUp2kfile="mmouse.modified.genecode.vM23.gene.up2k.bed"
awk 'BEGIN{FS=OFS="\t"}($3=="gene"){split($9,a,"\""); print $1,$4-1,$5,a[6],$6,$7}' ${gtf}\
| sort -k1,1 -k2,2n > ${bedfile}
awk 'BEGIN{FS=O... |
6a77906224faa89ef7168368e205b5069e183c6fbe9f254a170cb163e368bdcb | Shell | 515 | 24 | QSUB_CMD="qsub -l h_rt=1:00:00 -l h_vmem=2.9G -l tmem=2.9G -l s_stack=128M -j y -S /bin/sh -b y -cwd -V -o job_output -e job_error"
# $1: folder containing the original mask
# $2: folder containing the dilated mask
# $3: pixel to dilate
# if [ ! -d job_output ]
# then mkdir job_output
# fi
# if [ ! -d job_error ]
# t... |
890620872cd70d4cc8b07ceef898cc100c9355ec549c535af63b54c8fcb0dac2 | Shell | 518 | 23 | #!/bin/bash
isort --check --sl -c gradient_accumulator
if ! [ $? -eq 0 ]
then
echo "Please run \"sh shell/format.sh\" to format the code."
exit 1
fi
echo "no issues with isort"
flake8 gradient_accumulator
if ! [ $? -eq 0 ]
then
echo "Please fix the code style issue."
exit 1
fi
echo "no issues with flake8"
black... |
117eb87a5002e0fed99a6f9fd10d5e0a2eb4301d723fff6cde6de24c11b7ab9b | Shell | 519 | 12 | #!/usr/bin/env bash
#export dir="/home/bb/valejose/valejose/revisions/bioseq2seq"
export dir="/nfs/stak/users/valejose/hpc-share/bioseq2seq"
export scripts="${dir}/experiments/scripts"
source $scripts/templates.sh
suffix=${1}
# verified validation set attributions
bash $scripts/run.sh $dir/txt/mdig_val_verified_${suff... |
2ce72834bba3f833664680d0ce02e26af876c7deafd52596c5565e2223bab9ab | Shell | 519 | 26 | #!/bin/bash
set -xe
OS=$(uname)
if [ "${OS}" != "Darwin" ]; then
echo "This should only run on OSX."
exit 1
fi;
flavor=$1
source $(dirname "$0")/tc-tests-utils.sh
if [ -z "${TASKCLUSTER_TASK_DIR}" ]; then
echo "No TASKCLUSTER_TASK_DIR, aborting."
exit 1
fi
if [ "${flavor}" = "--builds" ]; then
cd ${... |
d832b0cf24e3a713484c2e49cd512eb43cb57dae97a6d1c809076177fd3be741 | Shell | 520 | 28 | #!/bin/bash
set -xe
source $(dirname "$0")/tc-tests-utils.sh
source $(dirname "$0")/tf_tc-vars.sh
BAZEL_TARGETS="
//native_client:libdeepspeech.so
//native_client:generate_scorer_package
"
BAZEL_BUILD_FLAGS="${BAZEL_ARM_FLAGS} ${BAZEL_EXTRA_FLAGS}"
BAZEL_ENV_FLAGS="TF_NEED_CUDA=0"
SYSTEM_TARGET=rpi3
SYSTEM_RASPBIA... |
4eecb6d56be6fc15fd6f1d432db2aea1b5a9f33dd28cffbe19cacefde2c7fcd2 | Shell | 523 | 18 | #!/usr/bin/env bash
set -euo pipefail
commit="$(git rev-parse HEAD 2>/dev/null || true)"
remote="$(git config --get remote.origin.url 2>/dev/null || true)"
dirty="0"
if ! git diff --quiet 2>/dev/null || ! git diff --cached --quiet 2>/dev/null; then
dirty="1"
fi
if [[ -n "$commit" ]]; then
printf 'STABLE_BUILD_SCM... |
68e8893fb8f60ae3d56c16cc832781fb06019f2a0f344646df27c3aa5d06d747 | Shell | 523 | 29 | #!/bin/bash
SUBJECTS_DIR=/scratch/n/tbi/mri_recons
OUTPUT_DIR=/scratch/n/tbi-meg/v/processed
echo "SUBJECTS_DIR set as $SUBJECTS_DIR"
echo "OUTPUT_DIR set as $OUTPUT_DIR"
ml anaconda3
conda init bash >/dev/null 2>&1
source ~/.bashrc
conda activate mne
cd $SUBJECTS_DIR || exit 1
dirnames=(*/)
COHORTS=$1
TASK=EC
f... |
6cc50b3af6cc4e0b57d9486dbd46e30abe5b55baa98d557ba47dd0b3c8b8f174 | Shell | 523 | 22 | QSUB_CMD="qsub -l h_rt=1:00:00 -l h_vmem=2.9G -l tmem=2.9G -l s_stack=128M -j y -S /bin/sh -b y -cwd -V -o job_output -e job_error"
# $1: folder containing the original mask
# $2: folder containing the dilated mask
# $3: pixel to dilate
if [ ! -d job_output ]
then mkdir job_output
fi
if [ ! -d job_error ]
then mkdir j... |
9bc7bbf8d5425aa6615a62071ec95cb0728d5eeb400f84dd114c8772a520905a | Shell | 523 | 22 | #!/usr/bin/env bash
#
# Wrapper script for <java> command line module.
#
# Alternate implementations:
# 1) Skip this script and use a substitution,
# java=<run-with-env> -u Java java
#
# 2) directly call run-with-env.sh
# "${script_dir}/run-with-env.sh" -u Java java "${@}"
function run_java() {
local __di... |
db81cd13fd5695a45c7bfc9a9c011a4b41f90123a7af20c7f08437b285c0e92e | Shell | 524 | 28 | #!/bin/bash
set -xe
source $(dirname "$0")/all-vars.sh
source $(dirname "$0")/all-utils.sh
source $(dirname "$0")/asserts.sh
bitrate=$1
set_ldc_sample_filename "${bitrate}"
model_source=${DEEPSPEECH_PROD_MODEL}
model_name=$(basename "${model_source}")
model_source_mmap=${DEEPSPEECH_PROD_MODEL_MMAP}
model_name_mmap... |
9d0acc7d53a7f5e3c3b5c3f89b2c2a0db7ce9bcc8743b9bfa9e412341447604d | Shell | 527 | 19 | #!/usr/bin/env bash
data=($1)
echo 'Filter out single-copy annotations'
for i in `echo $data|awk '{print $1}'`; do
perl /EDTA/util/output_by_list.pl \
1 \
<(perl -nle 's/#.*//; print $_' $i.mod.EDTA.TElib.novel.fa) \
1 \
<(perl /EDTA/util/find_flTE.pl $i.mod.out | \
awk '{print $10}'| \
s... |
be379d098dafa464e55225abb4f278f73a21e71e87841c460274853a34742324 | Shell | 528 | 19 | #!/bin/bash -ve
#######################################################
## Run Trinity to Generate Transcriptome Assemblies ##
#######################################################
if [ -z ${TRINITY_HOME} ]; then
echo "Must set env var TRINITY_HOME"
exit 1
fi
${TRINITY_HOME}/Trinity --seqType fq --max_me... |
117a697e4219c36952f679d7e010273bfa27f8ee73cf6c2ae49807887f5a0af5 | Shell | 529 | 28 | #!/bin/bash
set -xe
source $(dirname "$0")/tc-tests-utils.sh
source $(dirname "$0")/tf_tc-vars.sh
BAZEL_TARGETS="
//native_client:libdeepspeech.so
//native_client:generate_scorer_package
"
BAZEL_BUILD_FLAGS="${BAZEL_ARM64_FLAGS} ${BAZEL_EXTRA_FLAGS}"
BAZEL_ENV_FLAGS="TF_NEED_CUDA=0"
SYSTEM_TARGET=rpi3-armv8
SYSTEM... |
5684253d8c90c6a155a71daeee9ee98620239cb5ea9b625712e3ff87b2141187 | Shell | 529 | 9 | CUDA_VISIBLE_DEVICES=1
spec='python driver.py --dataset tc_full_kinase --hyper_param_search
--max_iter 42 --evaluate_freq 3 --patience 3 --model tf_regression
--early_stopping --prot_desc_path davis_data/prot_desc.csv --no_concord
--prot_desc_path metz_data/prot_desc.csv --prot_desc_path KIBA_data/prot_desc.csv ... |
9fb0487974882ec363a8f75c24930927ef7e5eb6e74b795848e40219bb73bc07 | Shell | 530 | 16 | FILE=$1
if [[ $FILE != "cityscapes" && $FILE != "night2day" && $FILE != "edges2handbags" && $FILE != "edges2shoes" && $FILE != "facades" && $FILE != "maps" ]]; then
echo "Available datasets are cityscapes, night2day, edges2handbags, edges2shoes, facades, maps"
exit 1
fi
echo "Specified [$FILE]"
URL=http://efros... |
1456f6278a9a871cec33813726f7f01720f43ce6c7a9c73be71684ac2300b7d6 | Shell | 531 | 28 | #!/bin/bash
set -xe
libs="
/opt/fsl/lib/libfsl-newimage.so
/opt/fsl/lib/libfsl-miscmaths.so
/opt/fsl/lib/libfsl-NewNifti.so
/opt/fsl/lib/liblapack.so.3
/opt/fsl/lib/libblas.so.3
/opt/fsl/lib/libstdc++.so.6
/opt/fsl/lib/libgcc_s.so.1
/opt/fsl/lib/libfsl-utils.so
/opt/fsl/lib/libfsl-cprob.so
/opt/fsl/lib/libfsl-znz.so
... |
b692ce4ac9ea3b7e8f0328eb99256f430f7ed428c5742ce81d20c3bae16bb858 | Shell | 531 | 30 | #!/bin/bash
#SBATCH -o job_out/job.%j.out
#SBATCH -J helixfold_dcu
#SBATCH -p normal
#SBATCH --cpus-per-task=32
#SBATCH --ntasks-per-node=1
#SBATCH -N 1
#SBATCH -t 1000:00:00
#SBATCH --gres=dcu:4
module rm compiler/rocm/2.9
module load compiler/rocm/4.0.1
echo $SLURM_JOB_NODELIST
allhost=''
for i in `scontrol show h... |
be677953893cc44edd9b254738303469ffead607e546c168d5bb2831011b5a6d | Shell | 531 | 9 | #!/bin/bash
# build all containers
docker build -t camera_node -f models/camera/Dockerfile models/camera
docker build -t classifier_node -f models/scene_classification/Dockerfile models/scene_classification
docker build -t saccade_node -f models/saccade_generation/Dockerfile models/saccade_generation
docker build -t s... |
c17022df4747762c6ead4a4be6bad46ea22551d14a7ea2f0adfed717f3baa11b | Shell | 531 | 11 | #!/bin/bash
set -ex -o pipefail
release="$(curl -fsSL https://api.github.com/repos/sylabs/singularity/releases/latest | jq -r .tag_name)"
codename="$(lsb_release -cs)"
arch="$(dpkg --print-architecture)"
wget -O /tmp/singularity-ce.deb "https://github.com/sylabs/singularity/releases/download/$release/singularity-ce_${... |
e3d620323395e435717c1dd7c51b213b99560d41f2345a0c4742d590a16fd566 | Shell | 532 | 14 | #!/bin/bash
sum_dir="/Users/szu/git-recipes/mouseBrainAtlas/CEMBA2/04.cCREgene/sa2.cicero/out/sa2pdcsum"
all_pdc_file="${sum_dir}/mba.whole.sa2subclass.merge.pdc.all"
distal_peak_nm="${sum_dir}/mba.whole.sa2subclass.all.distal.peaks.from.pdc.all.txt"
distal_peak_bed="${sum_dir}/mba.whole.sa2subclass.all.distal.peaks.f... |
7d3d80ed64439f62e1948018f2f07a5249c929ca5a04b36f16979032790526ca | Shell | 535 | 22 | #!/bin/bash
set -xe
source $(dirname "$0")/tc-tests-utils.sh
source $(dirname "$0")/tf_tc-vars.sh
BAZEL_TARGETS="
//native_client:libdeepspeech.so
"
BAZEL_ENV_FLAGS="TF_NEED_CUDA=1 ${TF_CUDA_FLAGS}"
BAZEL_BUILD_FLAGS="${BAZEL_CUDA_FLAGS} ${BAZEL_EXTRA_FLAGS} ${BAZEL_OPT_FLAGS}"
SYSTEM_TARGET=host
EXTRA_LOCAL_CFLAG... |
c5263812ab4fc14b5763c143343e3dca1bd6cb955e232620b4996380ecb0deff | Shell | 535 | 21 | # $1: folder containing the original images
# $2: folder containing the brain masks
# $3: folder to put the extracted brain images
# export QSUB_CMD="qsub -l h_rt=1:00:00 -pe smp 1 -R y -l h_vmem=1G -l tmem=1G -j y -S /bin/sh -b y -cwd -V -o job_output -e job_error" # -l s_stack=128M
if [ ! -d job_output ]
then mkdi... |
ba944a648e07b204f793855bb8409c22e70b8eab7bf0caa656fd5d1028a88187 | Shell | 536 | 18 | #!/bin/bash
# Helper script because it is way too painful to deal with Windows' CMD.exe
# ways of escaping things when pushing JSON
set -xe
TC_EXPIRE=$1
TC_INSTANCE=$2
TC_INDEX=$3
source $(dirname "$0")/tc-tests-utils.sh
if [ ! -z "${TC_EXPIRE}" -a ! -z "${TC_INSTANCE}" -a ! -z "${TC_INDEX}" ]; then
curl -sSL -... |
7ff3e64ab91659f87e80b9f3df579803835973ef1c3afa5c10f927ba3d49abae | Shell | 538 | 28 | #!/bin/bash
set -xe
runtime=$1
source $(dirname "$0")/all-vars.sh
source $(dirname "$0")/all-utils.sh
source $(dirname "$0")/build-utils.sh
source $(dirname "$0")/tf-vars.sh
BAZEL_TARGETS="
//native_client:libdeepspeech.so
//native_client:generate_scorer_package
"
if [ "${runtime}" = "tflite" ]; then
BAZEL_BUIL... |
92643e28a3e4269ece01dec8474dde1b1082091f5610823607e993037c31fe95 | Shell | 538 | 22 | # 修改此处数据集路径
path='/workspace/Image_translation_codes/ASGIT/datasets/SAR2Opt'
# path='./datasets/SAR2Opt'
# 修改此处
name='SAR2Opt'
# name='SAR2Opt'
for ((i=1; i<=5; i++));
do
echo "Processing"$i"th epoch..."
python /workspace/Image_translation_codes/ASGIT/test.py \
--netG resnet_9blocks \
... |
26bd5ebaab0c82a4ad89d404a414ae8abcbe9418b456e2bc73ae3e07020d4476 | Shell | 540 | 30 | #!/bin/bash
#SBATCH -o job.%j.out
#SBATCH -J helixfold_dcu
#SBATCH -p normal
#SBATCH --cpus-per-task=32
#SBATCH --ntasks-per-node=1
#SBATCH -N 1
#SBATCH -t 1000:00:00
#SBATCH --gres=dcu:4
#SBATCH --no-requeue
module rm compiler/rocm/2.9
module load compiler/rocm/4.0.1
echo $SLURM_JOB_NODELIST
allhost=''
for i in `sc... |
feba68954a76ee6892e4f57124226b771ed24d7eb852af7fc7cafb7704113254 | Shell | 541 | 29 | #!/bin/bash
set -xe
source $(dirname "$0")/all-vars.sh
source $(dirname "$0")/all-utils.sh
source $(dirname "$0")/asserts.sh
bitrate=$1
set_ldc_sample_filename "${bitrate}"
model_source=${DEEPSPEECH_TEST_MODEL//.pb/.tflite}
model_name=$(basename "${model_source}")
model_name_mmap=$(basename "${model_source}")
expor... |
1f1b0d09a1c61c11f47f88df498c265ca1fde068447ef6ddacd3c76528a2b3d3 | Shell | 544 | 32 | #!/bin/bash
#list=$1
export HHLIB=/gpfs/deepfold/programs/build/hhsuite-2.0.13
# use intel compiler
module purge
module load intel/compiler/latest
module load intel/compiler-rt/latest
module load intel/mpi/latest
module load python/3.9
#path=/share/protein/casp10/TS/server/TSWIR
#cd $path/
#list=list_select
#... |
6e7e005e9018589f3cd0e0d9efdf86bbd550dc816df299905b4fe9371a901a56 | Shell | 547 | 30 |
ROOT="."
ROOT+="/lsfm"
COLORS=(calb sst)
WAVELENGTHS=(488 561)
for c in 0
do
COLOR="${COLORS[$c]}"
WAVELENGTH="${WAVELENGTHS[$c]}"
for i in {08..23}
do
MOV="$ROOT/init_oct/${COLOR}_${WAVELENGTH}/down_9.9um/${COLOR}.${i}.nii.gz"
FIX="$ROOT/init_oct/neun_638/down_9.9um/neun.${i}.nii.gz"
OUT="$ROOT/align_channels/${C... |
85687ceb7f0392cfdc7b0c8f77bb44fc3e2991b84e6a1e9d1b2d741267f8e101 | Shell | 552 | 17 | #!/bin/bash
if [[ $# -ne 1 ]]; then
echo "Error: one argument required (e.g. ./compile.sh search.c)"
exit 1
fi
args=" -DMKL_ILP64 -m64 -I\"${MKLROOT}/include\""
if [[ $(uname -s) == "Darwin" ]]
then
args+=" -L${MKLROOT}/lib -Wl,-rpath,${MKLROOT}/lib -lmkl_intel_ilp64 -lmkl_sequential -lmkl_core -lpthread -lm -l... |
c1c12f3c3bbf568e6712c0d7709c95cd3674bba9e9949ad6a2a9a6b10ab838cf | Shell | 552 | 24 | #!/bin/bash
pwd
ls
ls src/rpy2
flake8 \
--max-line-length 90 \
src/rpy2/ipython/ \
src/rpy2/robjects/c*.py \
src/rpy2/robjects/environments.py \
src/rpy2/robjects/functions.py \
src/rpy2/robjects/help.py \
src/rpy2/robjects/language.py \
src/rpy2/robjects/lib \
src/rpy2/robjects/... |
2c9ac9ed9a181977941c7e94fd83a130909f9d34090aa58f5bda5485aa167f9d | Shell | 553 | 22 | #$ -pe threaded 8-12
#$ -l h_vmem=32G
#$ -M josiane.i.bourque@gmail.com
#$ -m e
#$ -m a
#$ -o /cbica/projects/pnc_fixel_cs/scripts/MRtrix_recon/script_output/fdc.$JOB_ID.stdout
#$ -e /cbica/projects/pnc_fixel_cs/scripts/MRtrix_recon/script_output/fdc.$JOB_ID.stderr
#!/bin/bash
project=/cbica/projects/pnc_fixel_cs
SIF=... |
e5376791067181cb3f4bb00d7ad34d603da9ed348d613c06f6c4f6e280aa950f | Shell | 553 | 12 | #!/bin/bash
PROJDIR=/projects/pfenninggroup/singleCell/Logan_BU_Striatum_snRNA-seq
cd $PROJDIR
mkdir ${PROJDIR}/data/raw_data/BU_snRNAseq_Pilot ${PROJDIR}/data/raw_data/BU_snRNAseq_Run1 ${PROJDIR}/data/raw_data/BU_snRNAseq_Run2
### download BCL files
bs download run -i 215462301 -o ${PROJDIR}/data/raw_data/BU_snRN... |
68260809fead58bc8093b0d238434b51681a222ecce61fb0cbdd94aa5ac69a3c | Shell | 554 | 16 | #! /bin/bash
filepath=/Users/wang/Desktop/Research_projects/BBSC/Functional/T1_analysis/
cd $filepath
ls | grep -i sub- >$filepath/subjList.txt # command grep is trying to filter the input with 'sub-'. -i ignore the high or low cases
for sub in $(cat $filepath/subjList.txt); do
export FREESURFER_HOME=/Applicatio... |
9c601c021434f5edfc35009e3f12aca663177eae97c0b1375065af244cf28090 | Shell | 554 | 25 | #! /bin/bash
# @author: Pieter Barkema
# A bash script executed on the server side to start modelling.
#
# Variables:
# 1 = path to the project dir
# 2 = model name
# 3 = data type dir
# 4 = session id
# 5 = model directory
# 6 = user email address
PROJECTDIR=$1
SCRIPTDIR=`dirname $0`
PYTHON_ENV=$7
# Activate our virt... |
f168e98421681c43a2f3dd5009cc087778f2c83a502507cba53968530b2d6791 | Shell | 556 | 30 | #!/bin/bash
set -xe
source $(dirname "$0")/all-vars.sh
source $(dirname "$0")/all-utils.sh
source $(dirname "$0")/asserts.sh
bitrate=$1
set_ldc_sample_filename "${bitrate}"
model_source=${DEEPSPEECH_PROD_MODEL}
model_name=$(basename "${model_source}")
model_source_mmap=${DEEPSPEECH_PROD_MODEL_MMAP}
model_name_mmap=... |
5a48706ab0042d10b5fd9c7bfe58862e15311c9e097aad6e0421016b17232f9b | Shell | 557 | 29 | #!/bin/bash
set -xe
kind=$1
source $(dirname "$0")/tc-tests-utils.sh
set_ldc_sample_filename "16k"
model_source=${DEEPSPEECH_TEST_MODEL//.pb/.tflite}
model_name=$(basename "${model_source}")
model_name_mmap=$(basename "${model_source}")
download_material "${TASKCLUSTER_TMP_DIR}/ds"
mkdir -p ${TASKCLUSTER_ARTIFAC... |
eabb24f491ec4caa19096c91b99835ba6b2f9d2919e408340a02d1ba9a2c6592 | Shell | 559 | 34 | IPIPATH=<COMPLETE i-pi path>
lmp=<COMPLETE lammps path>
HOST=$(hostname)
NTIME=36000
echo {"init",$( date -u)} >>LIST
grep '<step>' RESTART >> LIST
######### CHECK RESTART FILE ###############
if [ ! -f "RESTART" ]
then
cp input.xml RESTART
fi
######### CHECK RESTART FILE ###############
# Run the program:... |
235b29fc7c34f0612ec23602036f75094fff7f6a1ac5917fe5002aa3e28e5f9e | Shell | 562 | 29 | #!/bin/bash
#SBATCH -p normal
#SBATCH --cpus-per-task=8
##SBATCH --gres-flags=enforce-binding
echo "$fasta run"
log=./logs/log_$fasta
rm -rf $log
touch $log
conda activate unifold
data_dir=database
if [ -f "$output_path/$fasta/features.pkl" ]; then
echo "$output_path/features.pkl exist."
else
/usr/bin/tim... |
22bddfd898abe0122c336e8dcf6572c0d12444cb29e54fabb25ed439e0d7391d | Shell | 563 | 20 | export QSUB_CMD="qsub -l h_rt=1:00:00 -pe smp 1 -R y -l h_vmem=1G -l tmem=1G -j y -S /bin/sh -b y -cwd -V -o job_output -e job_error" # -l s_stack=128M
# $1: folder containing the original images
# $2: folder containing the brain masks
# $3: folder to put the extracted brain images
if [ ! -d job_output ]
then mkdir j... |
5ff09610bc6d1cc413d22e88c9cc1a64f057afabcbd146bdbb8c1f5b8c78537b | Shell | 563 | 23 | #!/bin/bash
ROOT="."
nitorch reslice \
$ROOT/oct/oct.nii \
-il $ROOT/mri2oct/affine/affine.lta \
-il $ROOT/mri/transforms/recon2samseg.lta \
-o $ROOT/warp2surf/oct.2samseg.nii.gz
nitorch reslice \
$ROOT/oct/vessels.manual.nii.gz \
-il $ROOT/mri2oct/affine/affine.lta \
-il $ROOT/mri/transforms/recon2samseg.lta... |
20f7c52173988e409103e07752d7ab99016c19ffad6727e3138521e3bdaab216 | Shell | 565 | 19 | # 修改此处数据集路径
path='./datasets/SAR2Opt'
# 修改此处
name='SAR2Opt'
# 修改此处测试集样本数量(test.py无需修改)
# 10%: spring: 488 summer: 1220 fall: 2028 winter: 1012
# 20%: spring: 3898 summer: 2440 fall: 4058 winter: 2025
# 50%: spring: 9746 summer: 6102 fall: 10145 winter: 5064
# data_length=1220
python test.py --netG... |
a1b14fa38467dd02fcb02fb8458a94072546e99b07b6ae708555bab5d7698606 | Shell | 565 | 19 | #!/usr/bin/env bash
TAG=${TAG:-"master"}
set -xe
if [ ! -d SimpleITK ]; then
git clone https://github.com/SimpleITK/SimpleITK.git &&
(cd SimpleITK && git checkout ${TAG})
fi
mkdir SimpleITK-build && \
cd SimpleITK-build && \
cmake -G Ninja\
-DBUILD_DOXYGEN=ON\
-DWRAP_DEFAULT=OF... |
f5fa6c571b47abf5282a47567ccb8ecf72494d00fb26b22855e83cc046f4e0e1 | Shell | 566 | 27 | #!/bin/bash -l
# Request ten minutes of wallclock time (format hours:minutes:seconds).
#$ -l h_rt=20:0:0
# Request 1 gigabyte of RAM per process.
#$ -l mem=10G
# Request scratch space.
#$ -l tmpfs=15G
# Set the name of the job.
#$ -N download_prots
# Set the working directory
#$ -wd /lustre/home/ucfaata/Scratch/lf... |
ded70eef1a3953c4437a40a94bb058d712192f97ff3f3cabafbec6abefda3b03 | Shell | 568 | 15 | set -eux
# The following two lines are only necessary if you are using sumrep. The second line checks if the sumrep dependencies are available.
git submodule update --init --recursive
SUMREP_PATH=$(git submodule | grep sumrep | cut -d ' ' -f3); /opt/conda/bin/conda run -n vampire R --vanilla --slave -e "library(devtoo... |
3b68d4de4a5f376361aff6d7cafade643e87549de63294f834d5cb8a2b8cdbd1 | Shell | 569 | 17 | #!/bin/bash
#SBATCH --job-name=l2_p3_regression
#SBATCH --output=./output/net_word%A_%a.out
#SBATCH --error=./output/net_word%A_%a.err
#SBATCH --gres=gpu:GEFORCEGTX1080TI:1
#SBATCH --mem=8000
#SBATCH --time=03:30:00
#SBATCH --cpus-per-task=2
module add openmind/cuda/9.1
module add openmind/cudnn/9.1-7.0.5
source acti... |
5ba7ce5c675f9176459426bcddacc0ad77c3813fee06dbb62d555a48b4a60f11 | Shell | 569 | 26 | #!/bin/bash
set -xe
source $(dirname "$0")/all-vars.sh
source $(dirname "$0")/all-utils.sh
source $(dirname "$0")/asserts.sh
bitrate=$1
set_ldc_sample_filename "${bitrate}"
model_source=${DEEPSPEECH_PROD_MODEL//.pb/.tflite}
model_name=$(basename "${model_source}")
model_name_mmap=$(basename "${model_source}")
model... |
ae48e381de76fca9bd4de6a4adc7a3079055713e459a127b3c8a8fc935d24e9f | Shell | 570 | 10 |
# check the quality of the data
docker run -it --rm -v /Users/wang/Desktop/Research_projects/BBSC/Functional/Data/Reorganized/All:/data:ro \
-v /Users/wang/Desktop/Research_projects/BBSC/Functional/QC/Report_all:/out \
nipreps/mriqc:23.1.0 /data /out participant
docker run -it... |
eb468bdf6bfa2e24c285b886bc051a5dfc66d0f6440b59302d249841e947c186 | Shell | 571 | 13 | export QSUB_CMD="qsub -l h_rt=5:00:00 -pe smp 4 -R y -l h_vmem=1G -l tmem=1G -j y -S /bin/sh -b y -cwd -V -o job_output -e job_error"
export QSUB_SEG_MATH="qsub -l h_rt=1:00:00 -pe smp 1 -R y -l h_vmem=8G -l tmem=8G -j y -S /bin/sh -b y -cwd -V -o job_output -e job_error"
export PARCELLATION_NNR="-ln 3 -lp 3 -sx 0.4"... |
1b7db9aad2d12c05217cac3048edbbd941c5b4118b006c28977177b65fae8d5c | Shell | 572 | 10 | PROJDIR=/projects/pfenninggroup/singleCell/Logan_BU_Striatum_snRNA-seq
DATADIR=$PROJDIR/data/tidy_data/HeKleyman2021_macaque_striatum_data_processing
mkdir -p $DATADIR/rdas
cd $DATADIR/rdas
wget https://ftp.ncbi.nlm.nih.gov/geo/series/GSE167nnn/GSE167920/suppl/GSE167920%5FResults%5FMSNs%5Fprocessed%5Ffinal%2Erds%2Egz
... |
1eb8c22f4a945c92743841f91d77abbfd68816a633220f2e8f6d59fbf867aaa4 | Shell | 572 | 31 | #!/bin/bash
#SBATCH -J inference
#SBATCH -p normal
#SBATCH -o logs/inference.out
#SBATCH --gres=gpu:1
#SBATCH --gres-flags=enforce-binding
echo "inference run"
log=./logs/inference
rm -rf $log
touch $log
conda activate unifold
/usr/bin/time -o $log --append \
python run_from_pkl.py \
--pickle_paths $pickle... |
a0fd38d1e2999c62b77fff46db75d7d8574d5848e2594547830e359d78e65d3f | Shell | 572 | 13 | export QSUB_CMD="qsub -l h_rt=5:00:00 -pe smp 4 -R y -l h_vmem=1G -l tmem=1G -j y -S /bin/sh -b y -cwd -V -o job_output -e job_error"
export QSUB_SEG_MATH="qsub -l h_rt=1:00:00 -pe smp 1 -R y -l h_vmem=8G -l tmem=8G -j y -S /bin/sh -b y -cwd -V -o job_output -e job_error"
export PARCELLATION_NNR="-ln 4 -lp 4 -sx 0.6"... |
181364622e56203fdb2ca051fe14b1d1f6d86e4cc29b959fe8bd7026002bd3bf | Shell | 573 | 28 | #!/bin/bash -l
# Request wallclock time (format hours:minutes:seconds).
#$ -l h_rt=5:0:0
# Request RAM.
#$ -l mem=10G
# Request TMPDIR space (default is 10 GB).
#$ -l tmpfs=10G
# Select the number of threads.
#$ -pe mpi 1
# Set the name of the task.
#$ -N BUSCO_LF
# Set working directory
#$ -wd /home/btaylor/LF_a... |
7c219b1307c3f70a33b20f5e6e5138baaff4466cb2c9290b1d4d4d45e31f8a44 | Shell | 573 | 13 | export QSUB_CMD="qsub -l h_rt=5:00:00 -pe smp 4 -R y -l h_vmem=1G -l tmem=1G -j y -S /bin/sh -b y -cwd -V -o job_output -e job_error"
export QSUB_SEG_MATH="qsub -l h_rt=1:00:00 -pe smp 1 -R y -l h_vmem=12G -l tmem=12G -j y -S /bin/sh -b y -cwd -V -o job_output -e job_error"
export PARCELLATION_NNR="-ln 3 -lp 3 -sx 0.... |
3003cb53b6c7269d57e01247cf037c43be0ca4c351a830963d3f530c1f05139e | Shell | 574 | 13 | export QSUB_CMD="qsub -l h_rt=5:00:00 -pe smp 4 -R y -l h_vmem=1G -l tmem=1G -j y -S /bin/sh -b y -cwd -V -o job_output -e job_error"
export QSUB_SEG_MATH="qsub -l h_rt=1:00:00 -pe smp 1 -R y -l h_vmem=12G -l tmem=12G -j y -S /bin/sh -b y -cwd -V -o job_output -e job_error"
export PARCELLATION_NNR="-ln 4 -lp 4 -sx 0.... |
5483541713e10e30fa6b829cddd5f7ddd91af3f7f41ad8f9a79561f98ba0c7bc | Shell | 574 | 19 | #!/bin/bash
#SBATCH --mail-user=alanxu@usc.edu
#SBATCH --mail-type=ALL
#SBATCH --ntasks=1
#SBATCH --nodes=1
#SBATCH --cpus-per-task=10
#SBATCH --time=2:00:00
#SBATCH --mem=60GB
#SBATCH --account=bbenayou_34
# Author: Alan Xu
# This script uses star/2.7.0e to generate genome index
module purge
module load gcc/8.3.0
mo... |
71aa1ece971254a1c534eaae0b31d896270ef770948f5480e675475157925966 | Shell | 574 | 15 | #!/bin/bash
set -xe
arm_flavor=$1
source $(dirname "$0")/tc-tests-utils.sh
mkdir -p ${TASKCLUSTER_ARTIFACTS} || true
cp ${DS_ROOT_TASK}/DeepSpeech/ds/tensorflow/bazel*.log ${TASKCLUSTER_ARTIFACTS}/
cp ${DS_ROOT_TASK}/DeepSpeech/ds/native_client/java/app/build/outputs/apk/release/app*.apk ${TASKCLUSTER_ARTIFACTS}/... |
9a6f0a643a999681a9c14f686ba3a5919276ca5ce559972f3f022d8dacf5575e | Shell | 574 | 22 | #$ -pe threaded 8-12
#$ -l h_vmem=32G
#$ -M josiane.i.bourque@gmail.com
#$ -m e
#$ -m a
#$ -o /cbica/projects/pnc_fixel_cs/scripts/MRtrix_recon/script_output/fixel_mask.$JOB_ID.stdout
#$ -e /cbica/projects/pnc_fixel_cs/scripts/MRtrix_recon/script_output/fixel_mask.$JOB_ID.stderr
#!/bin/bash
project=/cbica/projects/pnc... |
b12206b8cf3fb4bd6423ce3995445e6a841d16ca8972f5797f05e138535b9820 | Shell | 576 | 22 | #$ -pe threaded 8-12
#$ -l h_vmem=64G
#$ -M josiane.i.bourque@gmail.com
#$ -m e
#$ -m a
#$ -o /cbica/projects/pnc_fixel_cs/scripts/MRtrix_recon/script_output/tracks.$JOB_ID.stdout
#$ -e /cbica/projects/pnc_fixel_cs/scripts/MRtrix_recon/script_output/tracks.$JOB_ID.stderr
#!/bin/bash
project=/cbica/projects/pnc_fixel_c... |
c3225e0f62fbf34c70f2e4c4318e90727077ac3d6f3d07fdbfe9747258233ab6 | Shell | 578 | 19 | #!/bin/bash
###########################################
######## transfer from Lane to SCC ########
LANEDIR=bnphan@lanec1.compbio.cs.cmu.edu:/projects/pfenninggroup/singleCell/Logan_BU_Striatum_snRNA-seq
BU_DIR=/restricted/projectnb/singlecell-rl/Logan_BU_Striatum_snRNA-seq
mkdir -p $BU_DIR/data/raw_data
rsync -Pavh... |
eb4d1b7770dec576cde7c6d83dc6748cdedffbcb20ffaf426a2d367f3835eed8 | Shell | 579 | 21 | #!/bin/bash
TYPE=$1
if [ -z $TYPE ]; then
echo "No type detected. Choices: cpu, gpu"
exit 1
fi;
if [ $TYPE == cpu ] || [ $TYPE == CPU ]; then
docker build --no-cache -f Dockerfile.cpu -t gluon-cv-1:cpu-latest .
docker tag gluon-cv-1:cpu-latest $AWS_ECR_REPO:cpu-latest
docker push $AWS_ECR_REPO:cpu-latest
elif [... |
18f1854dc377d7aedc0cc11c815694dd4615f5d63649836214abf14d37bf49a7 | Shell | 580 | 19 | #!/bin/bash
work=/cbica/projects/pnc_fixel_cs
#Average response function from template subjects
responsemean \
${work}/data/MRtrix_recon/template/sub-*/sub-*_response_wm.txt \
${work}/data/MRtrix_recon/template/av_wm_response_new.txt \
-force
responsemean \
${work}/data/MRtrix_recon/template/sub-*/sub-*_r... |
608a564a36c4f21deceb2e8440aeece704b0c89d5bf3c6dc610f956fe7b81fb6 | Shell | 584 | 30 | #!/bin/bash
SUBJECTS_DIR=/scratch/n/tbi/mri_recons
OUTPUT_DIR=/scratch/n/tbi-meg/v/processed
AVERAGES_DIR=/scratch/n/tbi-meg/v/averages/camcan
echo "SUBJECTS_DIR set as $SUBJECTS_DIR"
echo "OUTPUT_DIR set as $OUTPUT_DIR"
ml anaconda3
conda init bash >/dev/null 2>&1
source ~/.bashrc
conda activate mne
cd $SUBJECTS_D... |
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