sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
fab1655ab66e3377f44d61a3660357ad30829e314744bd0becb122196eca803c | Shell | 399 | 13 | #Mapping the candidate UCEs to each species genome
species=$1 #specify species genome
#step1
makeblastdb -in {file_pathway}/${species}.fa \
-dbtype nucl \
-out {file_pathway}/${species}_db
#step2
blastn -query {file_pathway}/candidate_UCEs.fa \
-db {file_pathway}/${species}_db \
-out {file_pathway}/${species}.bla... |
ae5d54ee37404b73a28c94726aeff56bcc409bd329ba74a0d3a49c1279feb369 | Shell | 400 | 14 | #!/bin/bash
set -e
mv Makefile.config.example Makefile.config
if $WITH_CUDA; then
# Remove default gencode set; only generate compute_50.
sed -i 's/-gencode arch=.*\\//' Makefile.config
sed -i 's/CUDA_ARCH :=//' Makefile.config
GENCODE="-gencode arch=compute_50,code=sm_50"
GENCODE="$GENCODE -gencode arch=c... |
f7fd503da509d808d234db9c8b092bd5d69369f4d17678f25ea2fdfb928af961 | Shell | 400 | 7 | python train_simple_pose.py \
--model simple_pose_resnet50_v1b --mode hybrid --num-joints 17 \
--lr 0.001 --wd 0.0 --lr-mode step --lr-decay-epoch 90,120 \
--num-epochs 140 --batch-size 32 --num-gpus 8 -j 60 \
--dtype float32 --warmup-epochs 0 --use-pretrained-base \
--save-dir params_simple_pose_re... |
8dbcdf31285af5d1534be43fd65a1d55181a2a52c4ac0bcdc2602b0aef3e6953 | Shell | 401 | 10 | PROJDIR=/projects/pfenninggroup/singleCell/Logan_BU_Striatum_snRNA-seq
DATADIR=$PROJDIR/data/tidy_data/SynGO_bulk_download_release_20210225
mkdir -p $DATADIR/tables
cd $DATADIR/tables
wget -O SynGO_bulk_download_release_20210225.zip https://www.syngoportal.org/data/SynGO_bulk_download_release_20210225.zip
unzip SynG... |
d2943151ddba31e3a7591112fda5db970a8f55caaa421905cbd55265ad810032 | Shell | 402 | 8 | CUDA_VISIBLE_DEVICES=5
spec='python driver.py --dataset davis --hyper_param_search
--max_iter 41 --evaluate_freq 3 --patience 3 --model graphconvreg
--early_stopping --prot_desc_path davis_data/prot_desc.csv
--no_concord --no_r2 --log_file GPhypersearch_temp_davis_updated.log
--model_dir ./model_dir/model_dir_... |
d15cf97732070c53fc91f9bb69abbc296f65611932f18b80614f4805a4b31359 | Shell | 403 | 17 | #!/bin/sh
DIR=`pwd`
for SEED in 123; do
for TAU in 600; do
for LAMBDA in 0 1; do
for PHI in 0 1; do
echo "cd $DIR; ./run_snn_augmented_grad.sh $LAMBDA $PHI $TAU $SEED"
echo "cd $DIR; ./run_snn.sh $LAMBDA $PHI $TAU $SEED"
echo "cd $DIR; ./run_snn_fixed_inh.sh $LAMBDA $PHI $TAU $SEED"
echo "cd ... |
a1607cbe78b1c38799eef36141e5ee7b6a50223f086bebbe333a57bb3b028930 | Shell | 404 | 7 | #! /bin/bash
set -eu
for PACKAGE in alakazam ape argparse cowplot CollessLike data.table devtools dplyr entropy HDMD hexbin jsonlite latex2exp magrittr Peptides pROC RecordLinkage shazam seqinr stringdist stringr svglite testthat textmineR yaml
do
R --vanilla --slave -e "if(!require($PACKAGE)){install.packages('$P... |
c50add5521daf554ec12d80a245830dec1a10b33c690c263e081ed1872900631 | Shell | 404 | 15 | #!/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 --SS_lib_type RF --CPU 2... |
f0242cc65604bbd27fef8717eca04d611e5dc5de98fda627a7370de621049ed2 | Shell | 404 | 18 | #!/usr/bin/env bash
set -e # stop if any error happens
GIT_REPO="/home/quentin/comput/ethoscope-git/"
SERVER_SCRIPT="../../../scripts/device_server.py"
#config_file=test_generic_config.json
#config_file="test_sleep_monit_arena.json"
for config_file in test_*.json
do
echo "TESTING $config_file"
time python $SERVER_... |
4210681a7087ef82a0e9393493f60ddfcde51df7314e13e20739d46bba35fe5a | Shell | 406 | 8 | #!/bin/bash -x
acdc-nn seq Q104H tests/profiles/2ocjA.prof.gz
acdc-nn struct Q104H tests/profiles/2ocjA.prof.gz tests/structures/2ocj.pdb.gz A
acdc-nn struct V51I tests/profiles/1bsaA.prof.gz tests/structures/1bsa.pdb.gz A
acdc-nn istruct V51I tests/profiles/1bsaA.prof.gz tests/structures/1bsa.pdb.gz A I51V tests/prof... |
9d91f38ea76510811a805f1934ab1b55b2f0537ecd1f65ab9809caa9b7271451 | Shell | 406 | 18 | sbatch --wait << EOF
#!/bin/bash
#SBATCH -o logs/%j.job
#SBATCH -e logs/%j.job
#SBATCH -J DeepCLIP-snakemake
#SBATCH -p cpu_p
#SBATCH -c 5
#SBATCH --mem=16G
#SBATCH -t 30:00:00
#SBATCH --nice=10000
source $HOME/.bashrc
conda activate deepclip
python deepclip/DeepCLIP.py --runmode train --data_split 0.90 0.09 0.01 -n... |
877fe4536c8e2be2ce9f860a988a3880b333b696ac267c3ccbcf70434a162dac | Shell | 407 | 27 | #!/usr/bin/env bash
DOCKER_HOME=$(pwd)
DOCKER_BUILD_DIR=${DOCKER_HOME}/build
echo ${DOCKER_BUILD_DIR}
cd ..
rm dist/*
python setup.py sdist
python setup.py bdist_wheel
cd ${DOCKER_BUILD_DIR}
rm -f *.whl
cp ../../dist/*.whl .
WHEEL_FILE=$(ls *.whl)
sed "s/WHEEL_FILE/${WHEEL_FILE}/" Dockerfile.in > Dockerfile
do... |
3c6b337cb3a362a89ea313ff6ffe8076116aa7a0300b88a4fe4eb27289f763df | Shell | 408 | 23 | 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 --mem=200G
#SBATCH -t 12:00:00
#SBATCH --nice=10000
source $HOME/.bashrc
conda activate multirbp-cpu
#conda activate mult... |
892d553fcedd1bc2f7ab634348b7160c032110ab170680cb185457ad8ae22d00 | Shell | 408 | 16 | #!/bin/bash
# module add openmind/miniconda/4.0.5-python3
module add openmind/miniconda/2020-01-29-py3.7
# module add nklab/pytorch/1.1.0_cuda10.0.130
module add openmind/cudnn/9.1-7.0.5
module add openmind/cuda/9.1
export CONDA_ENVS_PATH=~/my-envs:/om4/group/mcdermott/user/jfeather/conda_envs_files
source activate... |
fb5558d603c7dee48b2987686801646e975d39fbf2a0dbe92eb8fdddac3d51d7 | Shell | 408 | 14 | #!/bin/bash
mkdir -p ~/.ssh
if [ ! -f ~/.ssh/id_rsa ]; then
# Generate a new SSH key, that the user should copy to the submission host of qsub.
ssh-keygen -t rsa -N "" -C "PCNportal" -f ~/.ssh/id_rsa
echo "copy the following content to ~/.ssh/authorized_keys"
cat ~/.ssh/id_rsa.pub
fi
env > /tmp/env.txt
chmod... |
1bfe60f473571ba679ba22b6bc79802e9d52f0c239176cdd7c939157118e0610 | Shell | 409 | 23 | sbatch --wait << EOF
#!/bin/bash
#SBATCH -o logs/%j.job
#SBATCH -e logs/%j.job
#SBATCH -J deepripe
#SBATCH -p cpu_p
## SBATCH -p gpu_p
## SBATCH --gres=gpu:1
## SBATCH --qos=gpu
#SBATCH -c 48
#SBATCH --mem=32G
#SBATCH -t 12:00:00
#SBATCH --nice=10000
source $HOME/.bashrc
conda activate multiresbind-2
python script... |
7a8bd2fdccf066dac6fea0eceb87c2c144cbb967f7c9666092b7936295201718 | Shell | 409 | 18 | sbatch --wait << EOF
#!/bin/bash
#SBATCH -o logs/%j.job
#SBATCH -e logs/%j.job
#SBATCH -J DeepCLIP-snakemake
#SBATCH -p cpu_p
#SBATCH -c 4
#SBATCH --mem=16G
#SBATCH -t 30:00:00
#SBATCH --nice=10000
source $HOME/.bashrc
conda activate deepclip
python deepclip/DeepCLIP.py --runmode train --data_split 0.90 0.09 0.01 -n... |
892959e228f3dbdbc02be334a1906beee4244bababbb53f2f546b37e0d5b3d16 | Shell | 410 | 14 | #!/bin/bash
set -e
cd $1
echo "moving to $(pwd)"
TMP_FILE=chunks.tmp
echo "Merging $(ls *.h264 | wc -l) h264 chunks in tmp file"
cat *.h264 > $TMP_FILE
fps=$(ls *.h264 | head -n 1 | cut -d _ -f 5 | cut -d @ -f 2)
prefix="whole_$(ls *.h264 | head -n 1 | cut -d . -f 1)"
echo "Using ffmpeg to create $(pwd)/$prefix.mp4"... |
81d11c2f83f874f6bf5fc4623a94f2627589aa9807bdae4eebc35de1c1983921 | Shell | 411 | 8 | CUDA_VISIBLE_DEVICES=4
spec='python driver.py --dataset kiba --hyper_param_search
--max_iter 41 --evaluate_freq 3 --patience 3 --model graphconvreg
--early_stopping --prot_desc_path KIBA_data/prot_desc.csv
--no_concord --no_r2 --log_file GPhypersearch_temp_kiba.log
--model_dir ./model_dir/model_dir_sch_kiba --... |
a1425bd2f133f3f75074ea9ddc6f4f0a134fe0659ceafe1c67429909994affc5 | Shell | 411 | 8 | CUDA_VISIBLE_DEVICES=1
spec='python driver.py --dataset kiba --hyper_param_search
--max_iter 42 --evaluate_freq 3 --patience 3 --model tf_regression
--early_stopping --no_concord --filter_threshold 6
--prot_desc_path KIBA_data/prot_desc.csv --no_r2
--log_file GPhypersearch_t4_kiba.log --model_dir ./model_dir/m... |
2a3d47a01d544adf8fff6028ba6f9e9e9007a6c46b3cc55beac61135b1c29a9a | Shell | 413 | 21 | #!/usr/bin/env bash
set -e # stop if any error happens
GIT_REPO="/home/quentin/comput/ethoscope-git/"
SERVER_SCRIPT="../../../scripts/device_server.py"
#config_file=test_generic_config.json
#config_file="test_sleep_monit_arena.json"
for config_file in $(ls test_*.json)
do
echo "TESTING $config_file"
time python $S... |
3221f7d8971adc09dd35edc9956a3b25d3dfc1714f9a449eca2b40c6eb7afec8 | Shell | 414 | 14 | #!/bin/bash
#step1 get biallelic SNVs and calculate frequency
vcftools --gzvcf {file_pathway}/GRCg6a.sample928.SNP.vcf.gz \
--remove-indels \
--max-alleles 2 \
--min-alleles 2 \
--freq \
--out {file_pathway}/GRCg6a.sample928.SNP.vcf.freq
#step2
echo -e "CHROM\tPOS\tID\tref\talt\tN_ALLELES\tN_CHR\tref_freq\talt_f... |
54daed01911c616253da0256e7f38bf83daad23e2144654aa8f5a486f00a6a23 | Shell | 414 | 9 | #!/bin/sh
wget http://yann.lecun.com/exdb/mnist/train-images-idx3-ubyte.gz
gunzip -f train-images-idx3-ubyte.gz
wget http://yann.lecun.com/exdb/mnist/train-labels-idx1-ubyte.gz
gunzip -f train-labels-idx1-ubyte.gz
wget http://yann.lecun.com/exdb/mnist/t10k-images-idx3-ubyte.gz
gunzip -f t10k-images-idx3-ubyte.gz
wget h... |
89247d18dec181f7f75a3b7034c8da6a67ce37863c2a2b614249375db4df5fe4 | Shell | 414 | 7 | CUDA_VISIBLE_DEVICES=2
spec='python driver.py --dataset nci60 --prot_desc_path davis_data/prot_desc.csv
--model tf_regression --prot_desc_path full_toxcast/prot_desc.csv
--prot_desc_path metz_data/prot_desc.csv --prot_desc_path KIBA_data/prot_desc.csv
--model_dir ./model_dir/model_dir4_tc_w --arithmetic_mean --a... |
e19c1629f524e5f8f6857ae0fb18182e465bfabe4724ac06d626dbe856cc5b08 | Shell | 414 | 4 | #!/bin/bash
samtools view $1 | awk 'BEGIN {FS="\t"; OFS="\t"} {name1=$1; str1=and($2,16); chr1=substr($3, 4); pos1=$4; mapq1=$5; getline; name2=$1; str2=and($2,16); chr2=substr($3, 4); pos2=$4; mapq2=$5; if(name1==name2) { if (chr1>chr2){print name1, str2, chr2, pos2,1, str1, chr1, pos1, 0, mapq2, mapq1} else {print na... |
007e4d2609f14e8ee621fabe96d6293c270a59331d0e15a5ed51a4c63e454d37 | Shell | 415 | 21 | #! /bin/bash
nRep=10
pctAll=("0.9" "0.7" "0.5" "0.3")
method="centerzg_fixvar_noy"
cd /group/qtlchenggrp/tianjing/singlestep_nnlmm/pig_n3534_p10000
for pct in "${pctAll[@]}"
do
cd "$pct"
cd run_"$method"
for rep in $( eval echo {1..$nRep} ) #rep1,...,rep20
do
sbatch /group/qtlchenggrp/tianjing/singles... |
505ea9e530d9dd53b030b728064d62a8fe211113ff1320840495b0a5d02dc694 | Shell | 416 | 24 | #!/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... |
6242ec53c12af8cbf4b7266e497b6120310fbd88a4e3cd416c95181d7591c66c | Shell | 416 | 17 | #!/bin/bash
echo "## Checking plugin installations:"
echo
if [ -e "trinity-plugins/slclust/bin/slclust" ]
then
echo "slclust: has been Installed Properly"
else
echo "slclust Installation appears to have FAILED"
fi
if [ -e "trinity-plugins/COLLECTL/collectl/collectl" ]
then
echo "collectl: ... |
7fcbc534658366acf8d8f09c7f59a21053dbb1cbcd9542f185750cd454fec2ea | Shell | 416 | 24 | #!/bin/bash
OUTPUT_DIR=/scratch/n/tbi-meg/v/processed
echo "OUTPUT_DIR set as $OUTPUT_DIR"
ml anaconda3
conda init bash >/dev/null 2>&1
source ~/.bashrc
conda activate mne
cd "$OUTPUT_DIR" || exit 1
dirnames=(*/)
for d in "${dirnames[@]}"
do
sub=${d%?}
if [ -n "$sub" ]
then
echo "${sub}"
srun python... |
da870f692ef0c949ed6ba50857da15b5495a89a53779a043b2a0401aabc3d3b6 | Shell | 416 | 23 | #!/bin/bash
set -xe
source $(dirname "$0")/all-vars.sh
source $(dirname "$0")/all-utils.sh
source $(dirname "$0")/build-utils.sh
source $(dirname "$0")/tf-vars.sh
BAZEL_TARGETS="
//native_client:libdeepspeech.so
//native_client:generate_scorer_package
"
BAZEL_BUILD_FLAGS="${BAZEL_ARM_FLAGS} ${BAZEL_EXTRA_FLAGS}"
B... |
82d4b968b9080d64abb47a6bd039cfb8d0cf0a969d37d7b32d9e174174dbe56b | Shell | 417 | 7 | CUDA_VISIBLE_DEVICES=1
spec='python driver.py --dataset nci60 --prot_desc_path davis_data/prot_desc.csv
--model graphconvreg --prot_desc_path full_toxcast/prot_desc.csv
--prot_desc_path metz_data/prot_desc.csv --prot_desc_path KIBA_data/prot_desc.csv
--model_dir ./model_dir/model_dir_tc_w --arithmetic_mean --agg... |
ac27e1688c037bdda28b9e371e08bcb6d1d73f7a8728c9f28472210c027af5c6 | Shell | 417 | 7 | #!/bin/bash
#Author: Yang Li <yal054@health.ucsd.edu>
#File: run.sh
#Create Date: Sat Feb 26 10:26:52 PST 2022
snakemake -p --rerun-incomplete -k -j 128 --cluster "qsub -l {cluster.ppn} -l {cluster.time} -N {params.jobname} -q {cluster.queue} -o pbslog/{params.jobname}.pbs.out -e pbslog/{params.jobname}.pbs.err" --jo... |
1bc065ccbfbc980457d8b98c8a4632aa087092ce1712e0e28f29c3ebf24bacfa | Shell | 418 | 13 | #evaluate ultraconservation using 12 vertebrate genomes
species=$1
#step1 make blastdb
makeblastdb -in {file_pathway}/$species.fna \
-dbtype nucl \
-parse_seqids -out {file_pathway}/$species.index/
#step2 blastn
blastn -query {file_pathway}/AnceSeq_len200_{mUCEs_or_aUCEs}.fa \
-db {file_pathway}/$species \
-out {... |
4da84bc8a7d432009ef7b1b072df74050c42d65f45888f3f551475dee8beedba | Shell | 418 | 23 | #!/bin/bash
set -xe
source $(dirname "$0")/tc-tests-utils.sh
source $(dirname "$0")/tf_tc-vars.sh
BAZEL_TARGETS="
//native_client:libdeepspeech.so
"
BAZEL_BUILD_FLAGS="${BAZEL_ARM_FLAGS} ${BAZEL_EXTRA_FLAGS}"
BAZEL_ENV_FLAGS="TF_NEED_CUDA=0"
SYSTEM_TARGET=rpi3
SYSTEM_RASPBIAN=/tmp/multistrap-raspbian-buster
maybe... |
6b0a3ddeeecf2e68a9bfa0cccd8f8e28d59c237ac0bbbce993a8154724e3507f | Shell | 418 | 25 | #!/bin/bash
set -xe
kind=$1
source $(dirname "$0")/tc-tests-utils.sh
set_ldc_sample_filename "16k"
download_material "${TASKCLUSTER_TMP_DIR}/ds"
mkdir -p ${TASKCLUSTER_ARTIFACTS} || true
export PATH=${TASKCLUSTER_TMP_DIR}/ds/:$PATH
if [ "${kind}" = "--basic" ]; then
run_valgrind_basic
run_valgrind_stream
fi... |
7db49c281fec0401fc093e92526c8217f381d21d36775f4af541b93abf7866d4 | Shell | 418 | 23 | #!/bin/bash
set -xe
source $(dirname "$0")/all-vars.sh
source $(dirname "$0")/all-utils.sh
source $(dirname "$0")/build-utils.sh
source $(dirname "$0")/tf-vars.sh
BAZEL_TARGETS="
//native_client:libdeepspeech.so
//native_client:generate_scorer_package
"
BAZEL_BUILD_FLAGS="${BAZEL_ARM64_FLAGS} ${BAZEL_EXTRA_FLAGS}"... |
000b6e94b710e904b2777527ba7fae9fb074727a738968531ae9fe9e6e67d3ff | Shell | 420 | 23 | #!/usr/bin/env bash
apt-get update
apt-get -y install \
apt-transport-https \
ca-certificates \
curl \
software-properties-common
curl -fsSL https://download.docker.com/linux/ubuntu/gpg | apt-key add -
add-apt-repository \
"deb [arch=amd64] https://download.docker.com/linux/ubuntu \
$(lsb_rele... |
5ebea479a58460a388c6f45dafb950cfa2f37ea9923024adb08425358319b0a8 | Shell | 420 | 17 | #!/bin/bash
#
# Copy this file in the emsdk-portable directory
#
echo "Copy this file in the emsdk-portable directory"
./emsdk update
./emsdk install clang-e1.38.31-64bit
./emsdk activate clang-e1.38.31-64bit
./emsdk install node-8.9.1-64bit
./emsdk activate node-8.9.1-64bit
./emsdk install emscripten-1.38.31
./emsd... |
202a11e32883104121a4eed0eae541e881640b97e091a1363d4a7fab3ed141fe | Shell | 421 | 10 | #!/bin/bash -ve
#######################################################
## Run Trinity to Generate Transcriptome Assemblies ##
#######################################################
## use jellyfish
../../Trinity --seqType fq --max_memory 2G --left reads.left.fq.gz --right reads.right.fq.gz --SS_lib_type RF --CPU 4... |
963a4e16ff7ecdefb18ac62a1ecfcadbd737bdc4a0aebc9c7c71f42ff9ce440f | Shell | 421 | 9 | PROJDIR=/projects/pfenninggroup/singleCell/Logan_BU_Striatum_snRNA-seq
CODEDIR=$PROJDIR/code/final_code/compare_to_Glud1tg_microarray
DATADIR=$PROJDIR/data/tidy_data/compare_to_Glud1tg_microarray
mkdir -p $CODEDIR $DATADIR/sra
cd $DATADIR/sra
tar -xvf GSE11419_RAW.tar # https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?... |
9b131654a02d10c02e735b1f406823ffaf589e10d92363570cb16d547755f0ad | Shell | 421 | 22 | sbatch --wait << EOF
#!/bin/bash
#SBATCH -o logs/%j.job
#SBATCH -e logs/%j.job
#SBATCH -J pred-iDeepS-snakemake
#SBATCH -p cpu_p
#SBATCH -c 4
#SBATCH --mem=16G
#SBATCH -t 24:00:00
#SBATCH --nice=10000
source $HOME/.bashrc
conda activate ideeps
cp $1 sequences.fa.gz
cp $2 model.pkl
python iDeepS/ideeps.py --predict=... |
9c3411c10f7bdd18ddf161fe834be229e2ce77925fdd40bf53d12a9047bcab6a | Shell | 424 | 16 | #!/bin/sh
set -e
python -m pip install --upgrade pip cibuildwheel twine
export CIBW_BUILD="cp310-* cp311-* cp312-* cp313-* cp314-*"
export CIBW_ENVIRONMENT="VERSION=\"${VERSION}\""
export CIBW_TEST_REQUIRES="pytest"
export CIBW_TEST_COMMAND="pytest {project}/python/tests"
python -m cibuildwheel --output-dir wheelhou... |
bc9706a3fc84d3cf339c7eae8b8221b074a314f60e29e8ef8b3bfa5fba76e1e3 | Shell | 424 | 7 | set -e
mkdir -p built/
cp scripts/build.sh built/
docker run -t -i --rm -v `pwd`/built:/io \
centos:centos6 \
bash -c "yum install -y git curl wget && wget http://people.centos.org/tru/devtools-2/devtools-2.repo -O /etc/yum.repos.d/devtools-2.repo && yum install -y devtoolset-2-gcc devtoolset-2-binutils devtool... |
d5ee4f67f9b000c221066e2f8f3c35d227436282072421329455690cf427e113 | Shell | 424 | 13 | if ! bazel version; then
arch=$(uname -m)
if [ "$arch" == "aarch64" ]; then
arch="arm64"
fi
echo "Installing wget and downloading $arch Bazel binary from GitHub releases."
yum install -y wget
wget "https://github.com/bazelbuild/bazel/releases/download/5.2.0/bazel-5.2.0-linux-$arch" -O /usr/local/bin/baz... |
32043083409e77f91f5f429347b57d019183620a5a541dfdec7ec732b97edd4d | Shell | 425 | 25 | echo "Choose one of the following options:"
echo ""
echo " 1) install venv from yml"
echo " 2) activate venv"
echo ""
read OPTION
echo ""
if [[ OPTION -eq 1 ]]
then
conda deactivate
conda env create -f environment.yml
conda activate asos
earthengine authenticate
fi
if [[ OPTION -eq 2 ]]
then
cond... |
823888fe9a24e7df2a5d4805682fa7ef2626c4fbcba59a7502511ace7c109fc9 | Shell | 425 | 12 | #! /bin/bash
export SUBJECTS_DIR=/Users/wang/Desktop/Research_projects/BBSC/Functional/T1_analysis/sub-3
export FREESURFER_HOME=/Applications/freesurfer/7.2.0
source $FREESURFER_HOME/SetUpFreeSurfer.sh
cd $SUBJECTS_DIR
ls -d */ | grep -i ses- >$SUBJECTS_DIR/sesList.txt #list files with 'ses-' in sub directories to se... |
cb54e22f37c7656ec89d013e31ee22bdc9f1db04f0d5da5b48436ac6338d0e04 | Shell | 425 | 8 | CUDA_VISIBLE_DEVICES=4
spec='python driver.py --dataset davis --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 --no_r2
--log_file GPhypersearch_t4_davis.log --... |
01d9dfa267bdef88ae2964a902797d3302bc943e89c5516f8681bb208a9ab2fa | Shell | 427 | 17 | #! /bin/bash
NAME="model_name"
DATA_DIR="../data"
out_root=output/$NAME
mkdir output
mkdir "$out_root"
LOG_FILE="$out_root/version_0".log
LOG_FILE=$LOG_FILE python train_model.py \
--name $NAME \
--config=configs/xcat.yml \
--data.img_dir="$DATA_DIR/annotated" \
--data.mask_dirs=["$DATA_DIR/masks/ten... |
7e34341c86b22b9f632266a3af2cad223c17793f21f6b15cf1ddf3cace009981 | Shell | 427 | 8 | #!/bin/sh
# Install Couchbase's GPG key
sudo wget -O - http://packages.couchbase.com/ubuntu/couchbase.key | sudo apt-key add -
# Adding Ubuntu 18.04 repo to apt/sources.list of 19.10 or 19.04
echo "deb http://packages.couchbase.com/ubuntu bionic bionic/main" | sudo tee /etc/apt/sources.list.d/couchbase.list
# To instal... |
87f03e2dc7b37fb87d506f4f3faa73e8e1ac2163ae021d13162dbc29534f67db | Shell | 427 | 23 | #!/bin/bash
set -xe
source $(dirname "$0")/tc-tests-utils.sh
source $(dirname "$0")/tf_tc-vars.sh
BAZEL_TARGETS="
//native_client:libdeepspeech.so
"
BAZEL_BUILD_FLAGS="${BAZEL_ARM64_FLAGS} ${BAZEL_EXTRA_FLAGS}"
BAZEL_ENV_FLAGS="TF_NEED_CUDA=0"
SYSTEM_TARGET=rpi3-armv8
SYSTEM_RASPBIAN=/tmp/multistrap-armbian64-bust... |
a5a775a4cf4d6f92e1583577ef0691c294f814ab805d37478d89763be2b0236d | Shell | 428 | 13 | #!/bin/bash -ve
#######################################################
## Run Trinity to Generate Transcriptome Assemblies ##
#######################################################
../../Trinity --seqType fq --max_memory 2G \
--left reads.left.fq.gz \
--right reads.right.fq.gz \
... |
c5bcd3e286449b99012f7ffcb90eb43139156650d53f8a9147e90d31dec6527c | Shell | 428 | 22 | #!/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 "${model_source}")
export DATA_TMP_DIR=${CI_TMP_DIR}
download_materia... |
1d004e735fa3bf274d123893cafe8c2313d7aba72c01c09c5b83dff72685c80e | Shell | 429 | 13 | #!/bin/bash
export MRTRIX_NTHREADS=$2
bblid=$1
#Estimate response function
dwi2response dhollander \
/work/data/MRtrix_recon/sub-${bblid}/ses-PNC1/dwi/sub-${bblid}_ses-PNC1.mif \
/work/data/MRtrix_recon/template/sub-${bblid}/sub-${bblid}_response_wm.txt \
/work/data/MRtrix_recon/template/sub-${bblid}/sub-${bblid}_... |
a755310b2126b9184563106c1a7b567929d6e255f5b7db3a9cc757aaf1f7c1b6 | Shell | 429 | 14 | #!/bin/bash
BDIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
DIR=${BDIR}/..
echo "Source dir=${DIR}"
cmake -DBIS_A_EMSCRIPTEN=OFF -DPYTHON_EXECUTABLE=`which python3` \
-DEigen3_DIR=${BDIR}/eigen3/share/eigen3/cmake \
-DCMAKE_VERBOSE_MAKEFILE=ON \
-DBIS_A_MATLAB=ON \
-DBIS_USEGPL=ON -D... |
af9b796227d81de7e75d6b277628be925be6d5f7e9e75bc37adb6e5f31d6d927 | Shell | 429 | 18 | #! /bin/bash
#$ -S /bin/bash -V
#$ -j y
#$ -cwd
#$ -o /tmp/yassamri/iEEG/sandra/analysis_pipeline_final/grid_outputs
#$ -pe openmp 15
#$ -p -2
#$ -l arch=linux-x64
#$ -q yassa.q,shared.q
# This is an example job
# -pe openmp 3 is the number of CPUs
# -o is the where the standard output will go
echo "$HOSTNAME"
pwd
... |
04cd2f11e11b63131f89d6f566a0d9263707e01921c2408b20efb6d2636602f7 | Shell | 431 | 18 | #!/usr/bin/env sh
# This script converts the cifar data into leveldb format.
EXAMPLE=examples/cifar10
DATA=data/cifar10
echo "Creating leveldb..."
rm -rf $EXAMPLE/cifar10_train_leveldb $EXAMPLE/cifar10_test_leveldb
./build/examples/cifar10/convert_cifar_data.bin $DATA $EXAMPLE
echo "Computing image mean..."
./bui... |
1a4faf002cfabe520b2e38cd9b25f764cb7527fb981a31f96e3f8c12eab91a8d | Shell | 434 | 12 | for i in `seq 0 31`;
do
gmx grompp -f dir-$i/nvt.mdp -c dir-$i/mtd0.gro -p topol.top -o dir-$i/mtd1.tpr -maxwarn 666
rm mdout.mdp
done
mpirun -n 32 mdrun -ntomp 1 -deffnm mtd1 -multidir \
dir-0 dir-1 dir-2 dir-3 dir-4 dir-5 dir-6 dir-7 dir-8 dir-9 \
dir-10 dir-11 dir-12 dir-13 dir-14 dir-15 dir-16 dir-17 dir-18 dir-... |
ee43e3e49fedf2bf52b750e9ecbc4fd1a5019859f4f4becf022f88ea64a9a586 | Shell | 434 | 13 | #!/bin/sh
cd "$(dirname "$0")"/..
xsd_path="lib/galaxy/tools/xsd/galaxy.xsd"
# Lint the XSD
xmllint --noout "$xsd_path"
test_tools_path='test/functional/tools'
# test all test tools except upload.xml which uses a non-standard conditional
# (without param) which does not survive xsd validation
tool_files_list=$(ls "$... |
30bb1eac4974695406b1a7063b28e3e575986da5ab0e98ab0af0f4e115193bf7 | Shell | 435 | 21 | #! /bin/bash
nRep=10
pctAll=("0.9" "0.7" "0.5" "0.3") #"0.9" "0.7" "0.5" "0.3"
method="centerzg_fixvar"
cd /group/qtlchenggrp/tianjing/singlestep_nnlmm/pig_n3534_p10000
for pct in "${pctAll[@]}"
do
cd "$pct"
cd run_"$method"
for rep in $( eval echo {1..$nRep} ) #rep1,...,rep20
do
sbatch /group/qtlcheng... |
32a43f641e30304cb31e548eaf3e1856bb43d4169f25a01bba540cedc7edf832 | Shell | 436 | 19 | #!/bin/bash
set -xe
source $(dirname "$0")/tc-tests-utils.sh
extract_python_versions "$1" "pyver" "pyver_pkg" "py_unicode_type" "pyconf" "pyalias"
mkdir -p ${TASKCLUSTER_ARTIFACTS} || true
virtualenv_activate "${pyalias}" "deepspeech"
set -o pipefail
pip install --upgrade pip==19.3.1 setuptools==45.0.0 wheel==0.3... |
3c9ffc212963076219cfbe9955320b84d4e1982843a46724b9aa5a659dc781ec | Shell | 436 | 7 | 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 90,120 \
--num-epochs 140 --batch-size 32 --num-gpus 4 -j 60 \
--dtype float32 --warmup-epochs 0 --use-pretrained-base \
--save-dir params_... |
3465c58214ee3ec5034749d78cb4007db33f16c2cc82feb556f54676a73d7546 | Shell | 437 | 24 | sbatch --wait << EOF
#!/bin/bash
#SBATCH -o logs/%j.job
#SBATCH -e logs/%j.job
#SBATCH -J multiresbind
#SBATCH -p cpu_p
#SBATCH -c 48
##SBATCH -p gpu_p
##SBATCH --gres=gpu:1
##SBATCH --qos=gpu
##SBATCH -c 4
#SBATCH --mem=48G
#SBATCH -t 2-00:00:00
#SBATCH --nice=10000
source $HOME/.bashrc
conda activate multiresbind... |
91ce16502664825438417add3f1e2b4db61f9827021c102a690ec63c5d3e3b43 | Shell | 437 | 23 | #!/bin/bash
#SBATCH -J train
#SBATCH -t 2-00:00:00
#SBATCH --partition=gpu
#SBATCH --cpus-per-task=8
#SBATCH --mem=32G
#SBATCH --gres=gpu:1
#SBATCH --output=jobs/R-%x.%j.out
#SBATCH --error=jobs/R-%x.%j.err
#SBATCH --gres=gpu:1
#SBATCH --qos=gpu_access
source ~/.bashrc
conda activate thermoMPNN
module load gcc
module... |
b3eba4e89a2b5a194562354fed9c736517664ba7f3d67a69548ff189a9ed67fc | Shell | 437 | 24 | sbatch --wait << EOF
#!/bin/bash
#SBATCH -o logs/%j.job
#SBATCH -e logs/%j.job
#SBATCH -J multiresbind
#SBATCH -p cpu_p
#SBATCH -c 60
##SBATCH -p gpu_p
##SBATCH --gres=gpu:1
##SBATCH --qos=gpu
##SBATCH -c 4
#SBATCH --mem=32G
#SBATCH -t 2-00:00:00
#SBATCH --nice=10000
source $HOME/.bashrc
conda activate multiresbind... |
5f1ca74fd978dff856d55ef2321f96b16344b712f5acf1329cd26ef90da0b083 | Shell | 439 | 11 | epochs=20000;
lr=1e-4;
logfile=out.log
#for N in 8 16 32 64 80 100 105 110 128 150 200 256 512 1024 2048 4096 8192 16384 32768 65536 131072; do
#for N in 512 1024 2048 4096 8192 16384 32768 65536 131072; do
for N in 200 350; do
for gpu in {0..7}; do i=$(($gpu+1234));echo $i;CUDA_VISIBLE_DEVICES=${gpu} python hvd_hval... |
73a9bf741c71f2b7b14fccde402310cf3a94a9511342e2bd344cdb023e655b96 | Shell | 440 | 22 | #!/bin/bash
set -xe
source $(dirname "$0")/tc-tests-utils.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=$(basename "${model_source_mmap}")
download_material "${TASKCL... |
82986355a17db81a690db086f1538b574050fbd2b71fc1534d5e6c4cfe7ba23e | Shell | 440 | 25 | #!/bin/bash
#
# Author: Jue Ruan
#
REF=$1
CTG=$2
# change this path to your mummer
MUM=/public/software/mummer-323-intel
if [ -z $REF ] || [ -z $CTG ]; then
echo "Usage: $0 <ref> <ctg>"
exit
fi
echo "REF:$REF"
echo "CTG:$REF"
$MUM/nucmer --mumreference -l 100 -c 1000 -d 10 --banded -D 5 $REF $CTG
$MUM/delta-filte... |
dd00221f4ce0a4e955ba8c78ccb9ab2bd0aa37ec55ac4dc0fb9ecae11cb0c4d7 | Shell | 441 | 13 | #!/usr/bin/env bash
#export dir="/nfs/stak/users/valejose/hpc-share/bioseq2seq"
export dir="/home/bb/valejose/valejose/revisions/bioseq2seq/"
export scripts="${dir}/experiments/scripts"
source $scripts/templates.sh
suffix=${1}
# class-only
#bash $scripts/run.sh txt/pred_class_${suffix}.txt
# with protein
bash $scrip... |
513fd78ccf070f7be7427d1278a6f176b6eba384253fc657111f0501e4285880 | Shell | 442 | 15 | #!/bin/bash
#SBATCH --job-name=inhouse-20230531
#SBATCH --time=15:00:00
#SBACTH --ntasks=1
#SBATCH --output="out/inhouse-20230531-%j.out"
#SBATCH --mem=2G
#SBATCH -p evlab
source /mindhive/mcdermott/u/gretatu/anaconda/etc/profile.d/conda.sh
conda activate auditory_brain_dnn
set -x
cd /mindhive/mcdermott/u/gretatu/au... |
738f8a4d4c3900a7196cd146bde068d59a02e9c0a6924c14ddf19692aab6313d | Shell | 442 | 15 | #!/bin/bash -ve
#######################################################
## Run Trinity to Generate Transcriptome Assemblies ##
#######################################################
${TRINITY_HOME}/Trinity --seqType fq --max_memory 2G \
--left reads.left.fq.gz \
--right reads.right.fq.gz... |
004b7f2515e038c979916ef294d973ab766d94343ab1a1ce01e4a7378e1998e3 | Shell | 443 | 9 | CUDA_VISIBLE_DEVICES=3
spec='python3 driver.py --dataset tc_kinase --hyper_param_search
--max_iter 42 --evaluate_freq 3 --patience 3 --no_concord
--early_stopping --prot_desc_path davis_data/prot_desc.csv
--prot_desc_path metz_data/prot_desc.csv --prot_desc_path KIBA_data/prot_desc.csv
--prot_desc_path toxcast... |
d1a00809638482ae20122623a0874adeeec12b6fa0e0936be8323121d8af2a05 | Shell | 445 | 15 | #!/bin/bash -ve
#######################################################
## Run Trinity to Generate Transcriptome Assemblies ##
#######################################################
${TRINITY_HOME}/Trinity --seqType fq --max_memory 2G \
--left reads.left.fq.gz \
--right reads.right.fq.gz... |
32c2efda4ac6f65b5cc4afeaa04093495ebc1f247b6484fa910eab557c290f75 | Shell | 446 | 15 | #!/bin/csh
#$ -M ganantha@nd.edu # Email address for job notification
#$ -m abe # Send mail when job begins, ends and aborts
#$ -q gpu # Specify queue
#$ -l gpu_card=1
#$ -N lr5_100e_weights # Specify job name
#$ -pe smp 4 # Specify parallel environment and legal core size
setenv OMP_NUM_T... |
6b0e7e099510a324a347b6bf2c492d216e0e8f062f2a7dbe17b1127fdaa52999 | Shell | 447 | 26 | #!/bin/bash
#SBATCH -J align
#SBATCH -p normal
#SBATCH -o logs/align.out
#SBATCH --gres-flags=enforce-binding
echo "alignments run"
log=./logs/align_log
rm -rf $log
touch $log
conda activate unifold
data_dir=database
/usr/bin/time -o $log --append \
python generate_pkl_features.py \
--fasta_dir ./example_... |
bd3a0d361070b89d2e800d360da1332d010c0e8cf02f330bc0c8486266a04af8 | Shell | 448 | 21 | #!/bin/sh
## step 1: evaluation and save results
# output: results/evaluation
# line evaluation
python evaluation/Eval_line_global.py
python evaluation/Eval_line_local.py
# color evaluation
python evaluation/Eval_color_illusion_vs_control.py
## step 2: perform statistical test and visualization
# output: results/p... |
2e477b7cb5a6210db58466c43ac9d21b47c4ac9047a955830e487ce3fb3b5c08 | Shell | 449 | 24 | #!/bin/bash
INPUT_DIR=/scratch/n/tbi/meg
OUTPUT_DIR=/scratch/n/tbi-meg/v/processed
echo "INPUT_DIR set as $INPUT_DIR"
echo "OUTPUT_DIR set as $OUTPUT_DIR"
AR_TYPE=$1
if [ -z "$AR_TYPE" ]
then
echo "Artifact type argument [ecg,eog] is required"
exit 1
fi
ml purge
module load teflon
ml anaconda3
conda init bash... |
78ab68421ca309891903150dc8297177957a0493d032b5cac67991b19c4b1b0f | Shell | 451 | 14 | #!/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 test set attributions
bash $scripts/run.sh $dir/txt/ism_test_verified_${suffix}.t... |
e8f3db25218e925fc05d9bb69aa4c6f57824084c281a1c73dae660556782cf32 | Shell | 451 | 15 | #!/bin/bash
##########################################################
# Code to downsample image using ImageMagick (if required)
##########################################################
# show details about image file, including size (width x height) in pixels
identify filename.jpg
# downsample image (where '-res... |
baff6c831e61336b5063cee1d90be9e3b34adc063c202dbe06bab859fb67c264 | Shell | 452 | 24 | #!/bin/bash
INPUT_DIR=/scratch/n/tbi/meg
OUTPUT_DIR=/scratch/n/tbi-meg/v/processed
echo "INPUT_DIR set as $INPUT_DIR"
echo "OUTPUT_DIR set as $OUTPUT_DIR"
AR_TYPE=$1
if [ -z "$AR_TYPE" ]
then
echo "Artifact type argument [ecg,eog] is required"
exit 1
fi
FNAME=no_${AR_TYPE}_matches.txt
ml purge
module load te... |
2b64112304bd15a4d5df192b4192cb6dfb1c0ddaf197b6dfd1df406d3646c783 | Shell | 453 | 15 | #!/bin/csh
#$ -M ganantha@nd.edu # Email address for job notification
#$ -m abe # Send mail when job begins, ends and aborts
#$ -q gpu # Specify queue
#$ -l gpu_card=1
#$ -N lr4_200e_weights # Specify job name
#$ -pe smp 4 # Specify parallel environment and legal core size
setenv OMP_NUM_T... |
3aeee7c8b69a65595447ac6726ca4ff4efafd300ea0d4d2e4670d1fc85286e08 | Shell | 453 | 9 | PROJDIR=/projects/pfenninggroup/singleCell/Logan_BU_Striatum_snRNA-seq
DATADIR=$PROJDIR/data/tidy_data/Seney2021_OUDvsCTL_bulk_DLPFC_NAc_tables
mkdir -p $DATADIR/tables
cd $DATADIR/tables
wget -O Seney2021_OUD_RNA-seq_DEGs.Data_File_S2.DLFPC.xlsx https://ars.els-cdn.com/content/image/1-s2.0-S000632232101369X-mmc4.xl... |
5361ed7676597a45395a7b7c61fde42ec755800c3b3bb76d35c80c67bc85a336 | Shell | 453 | 19 | #! /bin/bash
#$ -S /bin/bash -V
#$ -j y
#$ -cwd
#$ -o /tmp/yassamri/iEEG/sandra/analysis_pipeline_final/grid_outputs
#$ -pe openmp 3
#$ -p -2
#$ -l arch=linux-x64
#$ -l h='!Revan&!Bane'
#$ -q yassa.q
# This is an example job
# -pe openmp 3 is the number of CPUs
# -o is the where the standard output will go
# ,shared.q... |
630e7a72390fd1d9c87c57571b0a85b2e608ac09b72d85721248588a3dc23faf | Shell | 453 | 8 | #!/bin/bash
find /sys/class/powercap/intel-rapl/* -name energy_uj -exec bash -c "echo {} && cat {}" \;
# cat /sys/class/powercap/intel-rapl/intel-rapl:1/energy_uj
# cat /sys/class/powercap/intel-rapl/intel-rapl:0/energy_uj
python full_cpu.py
find /sys/class/powercap/intel-rapl/* -name energy_uj -exec bash -c "echo {} &... |
70cdcefd67a36425be3d5350916aa7b5eef346998d294be3884115987cca6cbc | Shell | 453 | 15 | #!/bin/csh
#$ -M ganantha@nd.edu # Email address for job notification
#$ -m abe # Send mail when job begins, ends and aborts
#$ -q gpu # Specify queue
#$ -l gpu_card=1
#$ -N lr9_200e_weights # Specify job name
#$ -pe smp 4 # Specify parallel environment and legal core size
setenv OMP_NUM_T... |
b6fff6f273f930ffaeac72ddcf001402906d3acfac43d95fb5a3cc4feaad1768 | Shell | 453 | 15 | #!/bin/csh
#$ -M ganantha@nd.edu # Email address for job notification
#$ -m abe # Send mail when job begins, ends and aborts
#$ -q gpu # Specify queue
#$ -l gpu_card=1
#$ -N lr8_200e_weights # Specify job name
#$ -pe smp 4 # Specify parallel environment and legal core size
setenv OMP_NUM_T... |
ce7b0750a598b06c11c947d02156c1abdfdf25278f6ee60238e281c8c8bcfa95 | Shell | 455 | 12 | for i in `seq 0 31`;
do
gmx grompp -f dir-$i/nvt.mdp -c dir-$i/mtd0.gro -p topol.top -o dir-$i/mtd1.tpr -maxwarn 666
rm mdout.mdp
done
mpirun -n 32 mdrun -ntomp 1 -deffnm mtd1 -plumed plumedpt.dat -multidir \
dir-0 dir-1 dir-2 dir-3 dir-4 dir-5 dir-6 dir-7 dir-8 dir-9 \
dir-10 dir-11 dir-12 dir-13 dir-14 dir-15 dir-... |
d2ab7b32a13ccc48f4751e9dfb31ad9a9db56cee1c0353b6447021e4413f7cda | Shell | 455 | 17 | #!/bin/bash
#SBATCH --array=0-50
#SBATCH --job-name=tunl1d_analysis
#SBATCH --output=analysis-%A_%a.out
#SBATCH --error=analysis-%A_%a.err
#SBATCH --partition=long
#SBATCH --gres=gpu:1
#SBATCH --cpus-per-task=6
#SBATCH --mem=20G
#SBATCH --mail-type=END,FAIL
module load python/3.7 python/3.7/cuda/11.0/cudnn/8.0/pytorch... |
4744f46c7b7e6f0465a611b395f82f7a5fbbdeed47260afa6ba67fb812bb9c44 | Shell | 456 | 23 | #!/bin/sh
set -o errexit
DIR=`mktemp -d`
trap "rm -rf $DIR" 0 2
OS=`uname -s | tr '[A-Z]' '[a-z]'`
if [ "$OS" = darwin ] ; then
OS=macos
STANDALONE=FALSE
else
STANDALONE=TRUE
fi
VER=empi-`git describe --tags --exact-match`-$OS
mkdir -p $DIR/$VER
cp README.md LICENCE $DIR/$VER
cmake -DSTANDALONE=$STANDALONE -DWI... |
c4187fbec5431c8b8873efcf5f425987f765896bf45c1a4957716dea968a5a66 | Shell | 456 | 19 | # Structural Parcellation shell script (SGE)
# Author: Ma Da (d.ma.11@ucl.ac.uk)
# Version 0.8_2013.10.19 to be modified ...
#!/bin/bash
# echo "Bash version ${BASH_VERSION}..."
# $1: folder include all the images to be masked
# $2: atlas folder
# $3: parcellation parameter file (if exist)
#!/bin/bash
DILATE=4
ATLAS=$... |
dfc07665b2a10cf12e72355150d64a5dff7b06c34b628cd423806ec6110c95b8 | Shell | 456 | 8 | #!/usr/bin/env bash
# https://github.com/cmdcolin/jbrowse-plugin-mafviewer/blob/master/bin/convert.sh
# maf2bed modified to work right as a python script by ross lazarus in desperation
# MAF file must contain the species name and chromosome name
# e.g. hg38.chr1 in the sequence identifiers with hg38 passed in as $2
p... |
0efcd8a30f5f250c843e56b6eadcec9cf8e4d927bc9793f51baee649c9b43084 | Shell | 457 | 10 | # clone the DTox git repository and change `code/dtox.py` and
# `code/dtox_learning.py` to allow selection of random seeds
git clone https://github.com/EpistasisLab/DTox.git
git -C DTox checkout -b dtox-robustness 10c909b
git -C DTox apply ../patch_seeds.diff
# setup conda environment
conda env create --name dtox_env ... |
2692bea457b7e4463bd65b1c360a78a4dd314c6ceaa70bf922625f2a72b7b3c0 | Shell | 458 | 10 | #get BED file containing GC-AT and AT-GC sbustitution positions
species=$1
cd {file_pathway}/${species}
less {file_pathway}/${species}/${species}_GC-AT |awk -F ":" '{print $1"\t"$2}' |awk -F "-" '{print $1"\t"$2}' |awk '{print $1"\t"$2+$4-1"\t"$2+$4}' > ${species}_GC-AT.bed
less {file_pathway}/${species}/${species}... |
3852b583036ef579f2b0d10d35f86533c84b234b0afeabb1826b481197f80bea | Shell | 458 | 17 | #!/bin/bash
# Run once to intialize repository and prepare for usage
# Download controlled access data
# Note - currently requires synapse login and dbGAP controlled access
bash scripts/initialize/download_data.sh
# Install correct R package versions
Rscript --vanilla scripts/install.R
# Process RNAseq and Mutation... |
5daf92657d5acca81bfcbc95c25586e0342d12e5d0a4fc617a4d8aaabc205d0b | Shell | 458 | 23 | sbatch --wait <<- EOF
#!/bin/bash
#SBATCH -o logs/%j.job
#SBATCH -e logs/%j.job
#SBATCH -J snakemake
#SBATCH -p gpu_p
#SBATCH --exclude=supergpu05,supergpu07,supergpu08
#SBATCH --gres=gpu:1
#SBATCH --qos=gpu
#SBATCH -c 4
#SBATCH --mem=16G
#SBATCH -t 06:00:00
#SBATCH --nice=10000
mkdir logs
source $HOME/.bashrc
conda... |
8d470350ad69504f47735282bbe1b2dbd79fdaa9d063fc13f982da03d6496057 | Shell | 458 | 17 | #!/bin/bash
sudo apt-get install mysql-server
#sudo mysql_secure_installation
#sudo mysql -u root -p
# Database restore
sudo mysql -u root -e "create database BiopolisDB;"
sudo mysql -u root BiopolisDB < ./Dump20210521.sql
# Root password configure
sudo mysql -u root -e "ALTER USER 'root'@'localhost' IDENTIFIED WITH... |
f166d7171c43928165fce64af9a203cd5a5746441eeab711e5c9653c3348911c | Shell | 460 | 30 | #!/bin/bash
function split() {
arr=("$@")
for i in ${arr[@]};
do
A=$(cut -d'_' -f1 <<<$i)
A=${A#”}
echo $A
done
}
val="$@"
timepoints=$(split ${val[@]})
#get unique
timepointsU=($(printf "%s\n" "${timepoints[@]}" | sort | uniq -c | sort -rnk1 | awk '{ print $2 }'))
#echo each unique t... |
22b71df6026d29929da36cb45d0c9d26d1a5559378cac7c18bba615effc16055 | Shell | 461 | 9 | CUDA_VISIBLE_DEVICES=2
spec='python3 driver.py --dataset tc_full_kinase
--max_iter 42 --evaluate_freq 3 --patience 3 --model graphconvreg
--prot_desc_path davis_data/prot_desc.csv --arithmetic_mean
--prot_desc_path metz_data/prot_desc.csv --prot_desc_path KIBA_data/prot_desc.csv
--prot_desc_path full_toxcast/p... |
bdf0ca2fa66f27bf5b2e867fb4e22d331a1a892cf7b0cb5408dba9790040d38b | Shell | 461 | 14 | cd /home/mikkel/PD_long/data_share/textfiles
dest='/home/mikkel/PD_long/data_share/BIDS_data'
# Copy
cp CHANGES $dest
cp README $dest
cp participants.json $dest
cp dataset_description.json $dest
cp ./derivatives/warpimg/dataset_description.json $dest/derivatives/warpimg/dataset_description.json
cp ./derivatives/warpi... |
ca703f328c0ec89b8a62ac1877563fabdf3d07ab8aa261f2ea33c73350bdbad9 | Shell | 461 | 17 | cd /data/users/jared/ENS/preprocessing/scripts
#cd ./preprocessing/scripts
#Downloads necessary files for index building
Rscript get_velo_files_mm10_10xv2.R > get_velo_files_mm10_10xv2.log 2>&1
#Builds index
bash index_build.sh > index_build.log 2>&1
#run kallisto pseudoalignment
jobid=$(sbatch --parsable run_kalli... |
5759857a1ff26d21b4d301adff00ee6ae46d4b83f2c31807a0bc19cb5319b933 | Shell | 464 | 23 | #!/bin/bash
# You Only Run Once!
find_in_conda_env(){
conda env list | grep "${@}" >/dev/null 2>/dev/null
}
conda init bash
if find_in_conda_env ".*deepopt.*" ; then
conda activate deepopt
conda env update --file deepopt.yml --prune
else
conda env create -f deepopt.yml
fi
wget -qO- https://raw.githu... |
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