sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
204f0d58f7053fcd1cfec0359921ff8de44df8dd7cb2c9fee88dc5a2edb0ceb8 | Shell | 585 | 27 | #!/bin/bash
#SBATCH -J inference
#SBATCH -t 00:10:00
#SBATCH --partition=volta-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 gc... |
16998156c3046dcf1baec37f9cd410f37f93d860e3750e4413c91b8d878c11ce | Shell | 586 | 21 | #!/bin/bash
# Usage: bash download_pdb_seqres.sh /path/to/download/directory
set -e
if [[ $# -eq 0 ]]; then
echo "Error: download directory must be provided as an input argument."
exit 1
fi
if ! command -v aria2c &> /dev/null ; then
echo "Error: aria2c could not be found. Please install aria2c (sudo apt i... |
496d4f7c34be707f28fc72b4af0dd1951b84eb5c1c39b4dab32ab886c20f7ac6 | Shell | 586 | 28 | #!/bin/bash
# Runs all experiments back-to-back
# Usage: ./run_all.sh <data_path>
# Example: ./run_all.sh ../data/processed/
set -e
data_path=$1
if [ -z "$data_path" ]
then
echo "Usage: ./run_all.sh <data_path>"
exit 1
fi
num_experiments=$(jq '. | length' experiments.json)
mkdir -p executed/
for i in $(se... |
83635eabc5b69312c916d150c304cc2d029a189f5a2939ec1fc02ee1abb034c5 | Shell | 587 | 23 | sbatch --wait << EOF
#!/bin/bash
#SBATCH -o logs/%j.job
#SBATCH -e logs/%j.job
#SBATCH -J DeepRAM-snakemake
#SBATCH --exclude=supergpu02pxe,supergpu03pxe,supergpu05,supergpu07,supergpu08
#SBATCH -p gpu_p
#SBATCH --gres=gpu:1
#SBATCH --qos=gpu
#SBATCH -c 4
#SBATCH --mem=15G
#SBATCH -t 24:00:00
#SBATCH --nice=10000
ech... |
0ea2bef3c102ca6fba85d94713f88a848670ec48db631cfb334227ab3e785cb4 | Shell | 590 | 23 | #!/usr/bin/env bash
COVER_PACKAGE=$1
TESTS_PATH=$2
EFS=/mnt/efs
mkdir -p ~/.mxnet/models
for f in $EFS/.mxnet/models/*.params; do
ln -s $f ~/.mxnet/models/$(basename "$f")
done
export MXNET_CUDNN_AUTOTUNE_DEFAULT=0
export MPLBACKEND=Agg
export KMP_DUPLICATE_LIB_OK=TRUE
if [[ $TESTS_PATH == *"auto"* ]]; then
... |
156d44478c02aba4927eb0c39eec9fe2709723349a1256394ecfda9d6829774a | Shell | 591 | 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=${DEEPSPEECH_PROD_MODEL//.pb/.tflite}
model_name=$(basename "${model_source}")
model_source_mmap=${DEEPSPEECH_PROD_MODEL_MMAP//.pb... |
6c5ba0198d1306287b1af36f34ab4a32711d6c127e3d0c155365d9270e5f23ec | Shell | 591 | 20 | #!/bin/bash
#Compile the IPEMToolboxManual tex files and create a PDF.
pdflatex -shell-escape -interaction=nonstopmode --src-specials IPEMToolboxManual.tex --enable-write18
#run bibtex on the aux file
bibtex IPEMToolboxManual.aux
#second iteration: include bibliography
pdflatex -shell-escape -interaction=nonstopmod... |
26444864f3c521a28d1453db7138442a37c5009998875e1abc4eb377ec05524f | Shell | 592 | 21 | #!/bin/bash
# Usage: bash download_small_bfd.sh /path/to/download/directory
set -e
if [[ $# -eq 0 ]]; then
echo "Error: download directory must be provided as an input argument."
exit 1
fi
if ! command -v aria2c &> /dev/null ; then
echo "Error: aria2c could not be found. Please install aria2c (sudo apt in... |
aab6e29d8b71a309d43b7c1b9607a569ec890d3cc1317dbbf49a0483bd300260 | Shell | 595 | 21 | #!/bin/bash
bowtie-build cel_cluster.fa cel_cluster
ec=`echo $?`
if [ $ec != 0 ];then
echo An error occured, exit code $ec
fi
mapper.pl reads.fa -c -j -k TCGTATGCCGTCTTCTGCTTGT -l 18 -m -p cel_cluster -s reads_collapsed.fa -t reads_collapsed_vs_genome.arf -v -n
ec=`echo $?`
if [ $ec != 0 ];then
echo An error occu... |
1ed106927a0eb9156d7c6faf43801a8fd45e46d614b4715692cd6f87c86a9687 | Shell | 596 | 21 | #!/bin/bash
# Usage: bash download_uniref90.sh /path/to/download/directory
set -e
if [[ $# -eq 0 ]]; then
echo "Error: download directory must be provided as an input argument."
exit 1
fi
if ! command -v aria2c &> /dev/null ; then
echo "Error: aria2c could not be found. Please install aria2c (sudo apt ins... |
c31a387183ea7f1679d7272ec90724a47a5af69b726401e81398ab0b39f2a179 | Shell | 603 | 41 | #!/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}"
download_data
node --version
npm --version
symlink_electron
export_node_bin_path
which electron
which node
if [ "${OS}" = "Linux" ]; then
... |
5ef321dbd43c16d15b58c4da18963699e45b31dda6485d349c01c6414e3c6886 | Shell | 605 | 17 | log_dir="reproduce_core"
mkdir -p log/$log_dir
init_model="model/helixdock.pdparams"
dataset_config="configs/dataset_configs/pdbbind_core.json"
model_config="configs/model_configs/helixdock_model.json"
train_config="configs/train_configs/lr8e-4_ema.json"
encoder_config="configs/model_configs/helixdock_encoder.json"
py... |
82fe679a0a70c6cbb59e6a7ed7474a0dbc0c61304978a54c8f5ee1eeebdd1c6f | Shell | 605 | 22 | #!/bin/bash
set -xe
source $(dirname "$0")/tc-tests-utils.sh
mkdir -p ${TASKCLUSTER_ARTIFACTS} || true
cp ${DS_DSDIR}/tensorflow/bazel*.log ${TASKCLUSTER_ARTIFACTS}/
package_native_client "native_client.tar.xz"
package_libdeepspeech_as_zip "libdeepspeech.zip"
if [ -d ${DS_DSDIR}/wheels ]; then
cp ${DS_DSDIR}... |
dbc5c10b370455036b5df085c5fcf9e75e23d5f868e46ed0c8ff26849036dbe8 | Shell | 605 | 30 | #!/bin/bash
if [ ! -d "data/superglue/" ] ; then
mkdir -p data
cd data
mkdir -p superglue
cd superglue
wget "https://dl.fbaipublicfiles.com/glue/superglue/data/v2/combined.zip"
unzip combined.zip
cd ../..
fi
if [ ! -d "data/fewglue/" ] ; then
mkdir -p data
cd data
git clone htt... |
53f9fb3e4e3fd9575d41bb2f298544a594b6ea108ff89c9b91267132aaa598da | Shell | 606 | 38 | NAMES=(detexam odexam powexam speelpenning traceless_scalar traceless_vector)
if [[ $# < 1 ]]; then
echo "usage: $0 config [arch]"
echo "where config is sparse|nosparse"
echo "and arch is optionally Win32 or x64"
echo "if ommitted arch defaults to Win32"
exit 0
fi
if [[ $# > 1 ]]; then
case $2 in
win32|Win32)... |
70564feb069195a4d47767c19e1c474e76f5f4d24b3b2d234c99273d71eebb49 | Shell | 607 | 20 | #!/bin/bash
#SBATCH -J TIL_correlations
#SBATCH -A MENON-SL3-CPU
#SBATCH -p icelake
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --time=00:30:00
#SBATCH --array=0-999
#SBATCH --mail-type=ALL
#SBATCH --mail-user=sb2406@cam.ac.uk
#SBATCH --output=/home/sb2406/CENTER-TBI_TIL/results/bootstrapping_results/hpc_logs/TIL_corr... |
8339b3e2d107ccaac55ca7712f0e2e1615ccc33dc0724bad548fcf06220c4dc5 | Shell | 607 | 17 | log_dir="reproduce_posebuster"
mkdir -p log/$log_dir
init_model="model/helixdock.pdparams"
dataset_config="configs/dataset_configs/poesbusters.json"
model_config="configs/model_configs/helixdock_model.json"
train_config="configs/train_configs/lr8e-4_ema.json"
encoder_config="configs/model_configs/helixdock_encoder.json... |
1167c3d498b872a0cdd468feb328fc667056597ecf14f8c68c9c6ace925482ed | Shell | 608 | 10 | #!/bin/bash
cd $(dirname $(realpath .))
wget 'https://storage.googleapis.com/gtex_analysis_v8/rna_seq_data/GTEx_Analysis_2017-06-05_v8_STARv2.5.3a_junctions.gct.gz'
wget 'https://storage.googleapis.com/gtex_analysis_v8/rna_seq_data/GTEx_Analysis_2017-06-05_v8_RNASeQCv1.1.9_gene_reads.gct.gz'
wget 'https://storage.googl... |
97cbbe04d1af1312d3a28628de9bda62e8355ec580052d39e915fe708bb5e648 | Shell | 608 | 33 | #!/bin/bash
# Script called by Travis to do a CPU-only build of and test Caffe.
set -e
MAKE="make --jobs=$NUM_THREADS --keep-going"
if $WITH_CMAKE; then
mkdir build
cd build
cmake -DBUILD_PYTHON=ON -DBUILD_EXAMPLES=ON -DCMAKE_BUILD_TYPE=Release -DCPU_ONLY=ON ..
$MAKE
if ! $WITH_CUDA; then
$MAKE runtest
... |
74668b9b31241cf0cbb4b148a7d0cec085a80ba658d3c80a8f3ea7bfd4ec7761 | Shell | 609 | 26 | #!/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 ${TASKCLUSTER_ARTIFACTS} || true
mkdir -p /tmp/train || true
mkdir -p /tmp/train_tflite || true
virtualenv_activate "${pyalias}" "deepspeech"
set -o pipefail
... |
e868fa408e9c054e6d9af4149c66332378f8b5675cdad7da13ce523e39f39bc1 | Shell | 609 | 26 | #!/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_ENV_FLAGS="TF_NEED_CUDA=1 ${TF_CUDA_FLAGS}"
BAZEL_BUILD_FLAGS="${BAZEL_CUDA_FLAGS} ${BAZEL_EXTRA_FLAGS} ${BAZEL_OPT_FLAG... |
136be0a9c0db05f2f2cdb3ab5930b8e631a28812198e513b7e696b5e9e6e900a | Shell | 610 | 18 | #!/bin/bash
#set -x
NAME="max query name length test"
BIN="ngmlr-"`grep -o "set( NGM_VERSION_MAJOR [0-9]* )" CMakeLists.txt | cut -d " " -f 3`"."`grep -o "set( NGM_VERSION_MINOR [0-9]* )" CMakeLists.txt | cut -d " " -f 3`"."`grep -o "set( NGM_VERSION_BUILD [^ ]* )" CMakeLists.txt | grep -v debug | cut -d " " -f 3`
PA... |
af5d0d590499fd51fb42524c192ceb20eafbcab4e9e932247fa33ddd7acb9760 | Shell | 610 | 21 | #!/usr/bin/env sh
# This script converts the mnist data into leveldb format.
EXAMPLES=./build/examples/siamese
DATA=./data/mnist
echo "Creating leveldb..."
rm -rf ./examples/siamese/mnist_siamese_train_leveldb
rm -rf ./examples/siamese/mnist_siamese_test_leveldb
$EXAMPLES/convert_mnist_siamese_data.bin \
$DATA/... |
0507ffa6f184569635d2120b3483e0b7ab55d580f3209b2d18239ebe16011d19 | Shell | 611 | 16 | ## Steps to obtain fast-evolving UCEs
# specifying species or clade in command line, (e.g. for i in `cat 93_avian_species.list`)
species=$1
cd {file_pathway}/$species
# get all.ACC.sc
cat $species.*.ACC.sc > $species.all.ACC.sc
cat $species.all.ACC.sc |grep "-"|sed 's/-//g' > all.ACC.sc
# calculate q value
R CMD BAT... |
270535ab7704afb4312bd74ae97644143fdfc98707d4e6e3b0918918dcc34ea6 | Shell | 611 | 24 | #!/usr/bin/env sh
GIST=$1
DIRNAME=${2:-./models}
if [ -z $GIST ]; then
echo "usage: download_model_from_gist.sh <gist_id> <dirname>"
exit
fi
GIST_DIR=$(echo $GIST | tr '/' '-')
MODEL_DIR="$DIRNAME/$GIST_DIR"
if [ -d $MODEL_DIR ]; then
echo "$MODEL_DIR already exists! Please make sure you're not overwriting ... |
218aa53ac22ff2d142ed18144e9320b32c2aef523e5607d07b443351989d83fb | Shell | 613 | 18 | #!/bin/bash
#SBATCH --mail-user=alanxu@usc.edu
#SBATCH --mail-type=ALL
#SBATCH --ntasks=1
#SBATCH --nodes=1
#SBATCH --cpus-per-task=20
#SBATCH --time=5:00:00
#SBATCH --mem=60GB
#SBATCH --account=bbenayou_34
#SBATCH --partition=epyc-64
# Summarizing at the gene level
WORKDIR=/scratch2/alanxu/2019_killi_rna_raw/bam_sor... |
497a15001d48fea3d02a454b6e67cc5c493ab34c75c5579e870435eb8e95f89f | Shell | 613 | 22 | #!/bin/bash -ve
#######################################################
## Run Trinity to Generate Transcriptome Assemblies ##
#######################################################
${TRINITY_HOME}/Trinity --seqType fq \
--max_memory 2G \
--left reads.left.fq.gz \
--right ... |
007abda47e8ace5af40d5eecd4020160475d2afc1b525d9ff2d3621a641e83e3 | Shell | 614 | 18 | #!/bin/bash
#SBATCH --mail-user=alanxu@usc.edu
#SBATCH --mail-type=ALL
#SBATCH --ntasks=1
#SBATCH --nodes=1
#SBATCH --cpus-per-task=20
#SBATCH --time=05:00:00
#SBATCH --mem=60GB
#SBATCH --account=bbenayou_34
#SBATCH --partition=epyc-64
# Summarizing at the gene level
WORKDIR=/scratch2/alanxu/2019_killi_rna_raw/bam_so... |
4a991291986a9b5476e1972f00d32463f8ec91783152d3154f8d577981f3e322 | Shell | 614 | 18 | #!/bin/bash
#SBATCH --mail-user=alanxu@usc.edu
#SBATCH --mail-type=ALL
#SBATCH --ntasks=1
#SBATCH --nodes=1
#SBATCH --cpus-per-task=20
#SBATCH --time=05:00:00
#SBATCH --mem=60GB
#SBATCH --account=bbenayou_34
#SBATCH --partition=epyc-64
# Summarizing at the exon level
WORKDIR=/scratch2/alanxu/2019_killi_rna_raw/bam_so... |
5a5e949b66e643c0b22b7d3348b0d987e829c47e77c3fcd1447b0e3f4e44000e | Shell | 614 | 23 | #!/bin/bash
source $HOME/.bashrc
echo "Creating conda env..."
conda create -n multirbp-cpu python==3.7
echo "Env created. Activating"
conda activate multirbp-cpu
conda config --add channels r
conda config --add channels bioconda
echo "Installing conda packages..."
mamba install pysam
mamba install -c conda-forge pa... |
66fdd38e4d6553a48fcfe752d0b384af4095510122f81c0b38a64f07e4de663b | Shell | 614 | 5 | #PBS -l walltime=72:00:00
#PBS -l select=1:ncpus=32:mem=124gb
module load anaconda3/personal
python2 RunRFMix.py PopPhased /rds/general/project/human-popgen-datasets/live/HGDP_1000g/X/HGDP_1000gNYC_3pop_target_ref_rfmix154_short_B_X.phased.alleles /rds/general/project/human-popgen-datasets/live/HGDP_1000g/RFMix/classe... |
978bc68eb61adfc45b05182eff356962523987026ce064e15993de4ff5115d40 | Shell | 614 | 23 | #!/bin/bash
set -xe
source $(dirname "$0")/all-vars.sh
source $(dirname "$0")/package-utils.sh
mkdir -p ${CI_ARTIFACTS_DIR} || true
cp ${DS_DSDIR}/tensorflow/bazel*.log ${CI_ARTIFACTS_DIR}/
package_native_client "native_client.tar.xz"
package_libdeepspeech_as_zip "libdeepspeech.zip"
if [ -d ${DS_DSDIR}/wheels ];... |
b82bab957b857bed543c791f994baa73ac581ab0693439c91089751ca077729b | Shell | 614 | 18 | #!/bin/bash
#SBATCH --mail-user=alanxu@usc.edu
#SBATCH --mail-type=ALL
#SBATCH --ntasks=1
#SBATCH --nodes=1
#SBATCH --cpus-per-task=20
#SBATCH --time=05:00:00
#SBATCH --mem=60GB
#SBATCH --account=bbenayou_34
#SBATCH --partition=epyc-64
# Summarizing at the exon level
WORKDIR=/scratch2/alanxu/2019_killi_rna_raw/bam_so... |
249ea4c28edeedddf1bba6f0e07f9929765d33402060e1fd0fb1e19ec169d38c | Shell | 615 | 16 | ## Steps to obtain fast-evolving UCEs
# specifying species or clade in command line, (e.g. for i in `cat 94_mammalian_species.list`)
species=$1
cd {file_pathway}/$species
# get all.ACC.sc
cat $species.*.ACC.sc > $species.all.ACC.sc
cat $species.all.ACC.sc |grep "-"|sed 's/-//g' > all.ACC.sc
# calculate q value
R CMD... |
5b904ed4fd8956b9fb3fd85c52b44a9e2770a8ece85e5db8a28d2e6e013e6f1a | Shell | 615 | 27 | #!/bin/bash
set -xe
source $(dirname "$0")/tc-tests-utils.sh
if [ -z "${GRADLE_USER_HOME}" ]; then
echo "Unable to generate cache without an emplacement"
exit 1
fi;
mkdir -p ${GRADLE_USER_HOME}
export ANDROID_HOME=${ANDROID_SDK_HOME}
# Gradle likes to play with us.
android_install_ndk
android_install_sdk
pus... |
125248e9d271e3309d13bf601e72242cdb0850c5d3a00e2b9fe124155c7b2a00 | Shell | 616 | 18 | #!/bin/bash
#SBATCH --mail-user=alanxu@usc.edu
#SBATCH --mail-type=ALL
#SBATCH --ntasks=1
#SBATCH --nodes=1
#SBATCH --cpus-per-task=20
#SBATCH --time=05:00:00
#SBATCH --mem=60GB
#SBATCH --account=bbenayou_34
#SBATCH --partition=epyc-64
# Summarizing at the exon level
WORKDIR=/scratch2/alanxu/2019_killi_rna_raw/bam_so... |
44a8214f38ac7c337fb1336adfd5b2ebd76b983ce85ce78dd749201d56db300b | Shell | 616 | 18 | #!/bin/bash
#SBATCH --mail-user=alanxu@usc.edu
#SBATCH --mail-type=ALL
#SBATCH --ntasks=1
#SBATCH --nodes=1
#SBATCH --cpus-per-task=20
#SBATCH --time=05:00:00
#SBATCH --mem=60GB
#SBATCH --account=bbenayou_34
#SBATCH --partition=epyc-64
# Summarizing at the exon level
WORKDIR=/scratch2/alanxu/2019_killi_rna_raw/bam_so... |
6db46dbde00097dae1dd513d2694e5140fc7c79f5e023d502942d6eaf174bb52 | Shell | 616 | 18 | #!/bin/bash
#SBATCH --mail-user=alanxu@usc.edu
#SBATCH --mail-type=ALL
#SBATCH --ntasks=1
#SBATCH --nodes=1
#SBATCH --cpus-per-task=20
#SBATCH --time=05:00:00
#SBATCH --mem=60GB
#SBATCH --account=bbenayou_34
#SBATCH --partition=epyc-64
# Summarizing at the gene level
WORKDIR=/scratch2/alanxu/2019_killi_rna_raw/bam_so... |
d8302ba03ef120a468b4ef449076ea4d1843db31bd5de184ed49feba586542b6 | Shell | 616 | 18 | #!/bin/bash
#SBATCH --mail-user=alanxu@usc.edu
#SBATCH --mail-type=ALL
#SBATCH --ntasks=1
#SBATCH --nodes=1
#SBATCH --cpus-per-task=20
#SBATCH --time=05:00:00
#SBATCH --mem=60GB
#SBATCH --account=bbenayou_34
#SBATCH --partition=epyc-64
# Summarizing at the gene level
WORKDIR=/scratch2/alanxu/2019_killi_rna_raw/bam_so... |
0ea1cf881e0c004f95a98d0f38f7655da6d5b3382f5bb1529ae07918d0ff88dd | Shell | 617 | 23 | #!/bin/bash
subj=$1
# containers
mriqc_con=/mnt/lustre/working/lab_lucac/shared/x_mriqc_containers/mriqc-0.16.1.simg
# paths
project_dir=/mnt/lustre/working/lab_lucac/lukeH/projects/OCDbaseline/
bids_dir=${project_dir}data/bids/
out_dir=${project_dir}data/derivatives/mriqc/
work_dir=${project_dir}data/scratch/mriqc/... |
ce56b30c4c6b147ff37e61a17161e14df28e7a78ceb1d232428198da01c654f5 | Shell | 618 | 21 | #!/bin/bash -ve
if [ -e reads.right.fq.gz ] && [ ! -e reads.right.fq ]; then
gunzip -c reads.right.fq.gz > reads.right.fq
fi
if [ -e reads.left.fq.gz ] && [ ! -e reads.left.fq ]; then
gunzip -c reads.left.fq.gz > reads.left.fq
fi
#######################################################
## Run Trinity to G... |
848f0919f11851a8bbfeff0cd439c2442c91f640c8499d483871c4ee263c498d | Shell | 619 | 19 | #!/bin/bash
#set -x
NAME="reads from stdin"
BIN="ngmlr-"`grep -o "set( NGM_VERSION_MAJOR [0-9]* )" CMakeLists.txt | cut -d " " -f 3`"."`grep -o "set( NGM_VERSION_MINOR [0-9]* )" CMakeLists.txt | cut -d " " -f 3`"."`grep -o "set( NGM_VERSION_BUILD [^ ]* )" CMakeLists.txt | grep -v debug | cut -d " " -f 3`
PARAMETER=" ... |
14e70acd779d36b0d175dd168e88df31c10bfdb98440218baacccfa43076a1ed | Shell | 621 | 16 | #Filter the elements with identity and coverage and merge the results to get the identity matrix of candidate UCEs in all species
species=$1 #specify species
#step1
python {file_pathway}/filter_blastn_out.py \
-i {file_pathway}/${species}.blastn.out \
-o {file_pathway}/${species}.blastn.filter.out
#step2
for i in {... |
44dec4837f6b9ac13e6ecfd6de2db7674ceeca4db017de06e857e492c1da1199 | Shell | 625 | 27 | #!/bin/bash
# dir=$1
# cd ./$1
ls *.zip > filelist.txt
ls *.zip -l | sed -e 's/\.zip$//' > subjectlist.txt
for i in $(cat filelist.txt) #unpack zipfiles in folder
do
echo "Unpacking $i"
tar -xvpf $i
done
for j in $(cat subjectlist.txt)
do
./dcm2niix $j/003_Sag_FSPGR_3D/
./dcm2niix $j/005_fMRI_de... |
9c47f2ac68501b99238d2c6452eec1bc2dfa01d61e2ed40c73792a25087154a4 | Shell | 625 | 15 | #!/bin/bash -ve
#######################################################
## Run Trinity to Generate Transcriptome Assemblies ##
#######################################################
cmd="../../Trinity --seqType fq --max_memory 2G --left reads.left.fq.gz --right reads.right.fq.gz --SS_lib_type RF --CPU 4 --grid_exec... |
f5301e2573045df9dd760f35d0ec5d5eae1e8ee9bf266c41b747d57300104559 | Shell | 625 | 17 | #!/bin/bash
BDIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
source ${BDIR}/emsdk_portable/emsdk_env.sh
DIR=${BDIR}/..
echo "Source dir=${DIR}"
cmake -DCMAKE_TOOLCHAIN_FILE=${DIR}/compiletools/Emscripten.cmake \
-DEigen3_DIR=${BDIR}/eigen3/share/eigen3/cmake \
-DCMAKE_CXX_FLAGS="-o0 -s WASM=1 -s... |
f489d36c0771a3c1487155becee58c18eff1a624e55064b69d3e6fad3c5021c9 | Shell | 626 | 16 | #!/bin/bash
#genome metadata
genome="adppg-mm10-apoe-chr-mapt-chr"
version="2021-A"
#paths
output_dir=/wynton/group/gladstone/biocore/projects/ADPPG/Huang/NicoleKoutsodendris-NK01-snRNAseq-pathology-mm10-oct-2021/analysis_hapoe_chr/parameters
#input files
fasta_custom="${output_dir}/adppg-mm10-apoe-chr-mapt-chr-2021... |
c6f771a9a42a15d5c48bab8b497caeb3d6d244d0e423d195450c73b8ba388185 | Shell | 627 | 21 | #!/usr/bin/env sh
# This script converts the mnist data into lmdb/leveldb format,
# depending on the value assigned to $BACKEND.
EXAMPLE=examples/mnist
DATA=data/mnist
BUILD=build/examples/mnist
BACKEND="lmdb"
echo "Creating ${BACKEND}..."
rm -rf $EXAMPLE/mnist_train_${BACKEND}
rm -rf $EXAMPLE/mnist_test_${BACKEND}... |
05fe0bde5172e12a75c951020fb27d3d4f894b0e1cb7c0b0d2016c5b30f53975 | Shell | 628 | 29 | #!/bin/bash
set -xe
source $(dirname "$0")/tc-tests-utils.sh
extract_python_versions "$1" "pyver" "pyver_pkg" "py_unicode_type" "pyconf" "pyalias"
ds=$2
frozen=$2
mkdir -p ${TASKCLUSTER_ARTIFACTS} || true
mkdir -p /tmp/train || true
mkdir -p /tmp/train_tflite || true
virtualenv_activate "${pyalias}" "deepspeech"
... |
6233865238fe2ed45212228075071b158f6c4f3951b85d18db0d5dca8263f921 | Shell | 630 | 29 | #!/bin/bash
#SBATCH --time=0-02:00:00 # 2 hours
#SBATCH --mem-per-cpu=16000 # 16000MB of memory
#SBATCH --array=0-5
#SBATCH --output=./slurm_logs/slurm-%A_%a.out
if [ -z "$MRI_DIR" ]
then
echo "MRI_DIR not set, exiting"
exit 1
fi
if [ -z "$SUBJECTS_DIR" ]
then
echo "SUBJECTS_DIR not set, exiting"
exit... |
c990fb28c05944c408dbec996053d41c8d70a4ed8d91819077b853ea4bc51efd | Shell | 630 | 14 | #!/bin/bash
# This script is called from Jupyter notebooks in the parent directory to convert
# produce Python scripts that can be called by torch.multiprocessing
nbname="${1:?Error: the notebook name must be specified}"
scriptname="converted/${nbname%.ipynb}"
jupyter nbconvert --to script --output "$scriptname" "$n... |
1429fc1e4256770053a5fbd253047b62c205307bd0ebcb8ca93d993de9c6562e | Shell | 632 | 18 | # NPC self-supervised learning example
python main.py --config config/self_supervised/npc_example.yml \
--njobs 32 \
--dev_njobs 4 \
--task self-learning\
--ckpdir ckpt/ \
--logdir log/ \
--seed 0
# Using NPC representation in ph... |
290abeaa3c31e4fb0b981844ac55f1abda9b265b7881d25ab5e21e6efd401f73 | Shell | 632 | 32 | #!/bin/bash
set -xe
arm_flavor=$1
api_level=$2
source $(dirname "$0")/tc-tests-utils.sh
# Android test code only supports 16kHz and hard-coded filename
ldc93s1_sample_filename='LDC93S1.wav'
model_source=${DEEPSPEECH_TEST_MODEL//.pb/.tflite}
model_name=$(basename "${model_source}")
download_data
force_java_apk_x8... |
73424500bb2c06f023a17231ca92b0963ea7795c0d6d7ab822379a87fa97def9 | Shell | 636 | 21 | _celery_completion() {
local IFS=$'
'
COMPREPLY=( $( env COMP_WORDS="${COMP_WORDS[*]}" \
COMP_CWORD=$COMP_CWORD \
_CELERY_COMPLETE=complete $1 ) )
return 0
}
_celery_completionetup() {
local COMPLETION_OPTIONS=""
local BASH_VERSION_ARR=(${BASH_VERSION//./ })
... |
b93bcace32ffab09955bc6ed58880b1ddf95bd302aeed2033e9314a140159b8c | Shell | 636 | 18 | #! /bin/bash
#$ -S /bin/bash -V
#$ -j y
#$ -cwd
#$ -o /mnt/yassamri/iEEG/sandra/analysis_pipeline_final/grid_outputs
#$ -pe openmp 15
#$ -p -2
#$ -l arch=linux-x64
#$ -l h='!Bane'
#$ -q yassa.q,shared.q
# This is an example job A002_extract_baseline_and_trials A003_condition_wise_spectral_analysis A003a_condition_wis... |
20ec3c3a1db607bcca159c2084ebe455bc07430cfbddac8857977a1ff2dc8ce7 | Shell | 638 | 30 | #!/bin/bash
# Generates all plots for the paper
# Usage: ./run_all.sh <data_path> <results_file>
# Example: ./run_all.sh ../data ../experiments/results.json
set -e
data_path=$1
results_file=$2
if [ -z "$data_path" ] || [ -z "$results_file" ]
then
echo "Usage: ./run_all.sh <data_path> <results_file>"
exit 1
... |
c1680f154d7f97fa7f5c070c8095d9111a0eabfa46fef9465d17641d815abf14 | Shell | 640 | 5 | #PBS -l walltime=72:00:00
#PBS -l select=1:ncpus=32:mem=62gb
module load anaconda3/personal
python2 RunRFMix.py PopPhased /rds/general/project/human-popgen-datasets/live/HGDP_1000g/X/HGDP_1000gNYC_3pop_target_ref_rfmix154_short_B_X_AFRAME.phased.alleles /rds/general/project/human-popgen-datasets/live/HGDP_1000g/RFMix/c... |
bdf0f46fe21869b1e3c00c60d365b76cbd255f5d2074c5c0a5a2538b86e8ffc3 | Shell | 641 | 15 | #!/bin/bash
#set -x
NAME="read name length"
BIN="ngmlr-"`grep -o "set( NGM_VERSION_MAJOR [0-9]* )" CMakeLists.txt | cut -d " " -f 3`"."`grep -o "set( NGM_VERSION_MINOR [0-9]* )" CMakeLists.txt | cut -d " " -f 3`"."`grep -o "set( NGM_VERSION_BUILD [^ ]* )" CMakeLists.txt | grep -v debug | cut -d " " -f 3`
PARAMETER=" ... |
21de8a9c1e06d20fe68fcdd9b99f0d9638b7bb5ae978403f9cd9fe0ef09b14e1 | Shell | 647 | 24 | #!/bin/bash
#SBATCH --ntasks=1
#SBATCH --nodes=1
#SBATCH --cpus-per-task=64
#SBATCH --time=3:00:00
#SBATCH --mem=60GB
#SBATCH --account=bbenayou_34
#SBATCH --partition=epyc-64
# Author: Alan Xu
# Software Used: fastp version 0.23.2
WORKDIR=/scratch2/alanxu/2019_killi_rna_raw/heart
cd $WORKDIR
for f in */
do
cd $f... |
bb98502246a51acf4e6f3c0ae576bc10171cdbb7507afaa24979386c28f03c31 | Shell | 648 | 24 | #!/bin/bash
#SBATCH --ntasks=1
#SBATCH --nodes=1
#SBATCH --cpus-per-task=64
#SBATCH --time=3:00:00
#SBATCH --mem=60GB
#SBATCH --account=bbenayou_34
#SBATCH --partition=epyc-64
# Author: Alan Xu
# Software Used: fastp version 0.23.2
WORKDIR=/scratch2/alanxu/2019_killi_rna_raw/spleen
cd $WORKDIR
for f in */
do
cd $... |
be3b81d5cee58a769f6ca21ea8a6745e3def9db414bcfddf5b648a69df2c53b1 | Shell | 648 | 24 | #!/bin/bash
#SBATCH --ntasks=1
#SBATCH --nodes=1
#SBATCH --cpus-per-task=64
#SBATCH --time=3:00:00
#SBATCH --mem=60GB
#SBATCH --account=bbenayou_34
#SBATCH --partition=epyc-64
# Author: Alan Xu
# Software Used: fastp version 0.23.2
WORKDIR=/scratch2/alanxu/2019_killi_rna_raw/muscle
cd $WORKDIR
for f in */
do
cd $... |
bfae773a3caf91ff047fecd7ac20fd05d80f785441b44c31f3999048563856e8 | Shell | 648 | 23 | #!/bin/bash -ve
if [ -e reads.right.fq.gz ] && [ ! -e reads.right.fq ]; then
gunzip -c reads.right.fq.gz > reads.right.fq
fi
if [ -e reads.left.fq.gz ] && [ ! -e reads.left.fq ]; then
gunzip -c reads.left.fq.gz > reads.left.fq
fi
#######################################################
## Run Trinity to G... |
cfb91b66287bca588755d6028a618a70fd0ae0f4d6fca61ff17159afabadd74f | Shell | 648 | 28 | #!/bin/bash
#SBATCH --mail-user=alanxu@usc.edu
#SBATCH --mail-type=ALL
#SBATCH --ntasks=1
#SBATCH --nodes=1
#SBATCH --cpus-per-task=12
#SBATCH --time=24:00:00
#SBATCH --mem=24GB
#SBATCH --account=bbenayou_34
#SBATCH --partition=oneweek
# Author: Alan Xu
# This script uses fastqc/0.11.9 to quality check the filtered re... |
e72f2821e1e49039b421f5bf842ade64813fcb8be006134bad5df7d2ec3e661b | Shell | 648 | 28 | #!/bin/bash
#SBATCH --mail-user=alanxu@usc.edu
#SBATCH --mail-type=ALL
#SBATCH --ntasks=1
#SBATCH --nodes=1
#SBATCH --cpus-per-task=12
#SBATCH --time=24:00:00
#SBATCH --mem=24GB
#SBATCH --account=bbenayou_34
#SBATCH --partition=oneweek
# Author: Alan Xu
# This script uses fastqc/0.11.9 to quality check the filtered re... |
f623d16c7a2dd52cdff0f1ede37d41dd3d6aa6bc796b9d520e31547d568e55d8 | Shell | 648 | 35 | #!/bin/bash
set -xe
runtime=$1
source $(dirname "$0")/tc-tests-utils.sh
source $(dirname "$0")/tf_tc-vars.sh
BAZEL_TARGETS="
//native_client:libdeepspeech.so
//native_client:generate_scorer_package
"
if [ "${runtime}" = "tflite" ]; then
BAZEL_BUILD_TFLITE="--define=runtime=tflite"
fi;
BAZEL_BUILD_FLAGS="${BAZEL... |
01a2efb2ce5cea40cf442f05def3aea4bc0ed7d894a7e74fb9b4b67553a80789 | Shell | 649 | 28 | #!/bin/bash
#SBATCH --mail-user=alanxu@usc.edu
#SBATCH --mail-type=ALL
#SBATCH --ntasks=1
#SBATCH --nodes=1
#SBATCH --cpus-per-task=12
#SBATCH --time=24:00:00
#SBATCH --mem=24GB
#SBATCH --account=bbenayou_34
#SBATCH --partition=oneweek
# Author: Alan Xu
# This script uses fastqc/0.11.9 to quality check the filtered re... |
66827365b6619a52c9f0c4bd29c6095c76fd0f482470cf8769fc61ed1b437408 | Shell | 649 | 26 | #!/bin/bash
set -xe
arch=$1
source $(dirname "$0")/tc-tests-utils.sh
mkdir -p ${TASKCLUSTER_ARTIFACTS} || true
cp ${DS_ROOT_TASK}/DeepSpeech/ds/tensorflow/bazel*.log ${TASKCLUSTER_ARTIFACTS}/
case $arch in
"--x86_64")
release_folder="Release-iphonesimulator"
artifact_name="deepspeech_ios.framework.x86_64.tar.... |
ae100e50b39419ced4b89c92b2abcdc67b3405976145a3a3be4e1324c21fd7c6 | Shell | 649 | 28 | #!/bin/bash
#SBATCH --mail-user=alanxu@usc.edu
#SBATCH --mail-type=ALL
#SBATCH --ntasks=1
#SBATCH --nodes=1
#SBATCH --cpus-per-task=12
#SBATCH --time=24:00:00
#SBATCH --mem=24GB
#SBATCH --account=bbenayou_34
#SBATCH --partition=oneweek
# Author: Alan Xu
# This script uses fastqc/0.11.9 to quality check the filtered re... |
05d11f1301cf54536d79905d159c23830b373b669c0d0dab135be54ac192bd8f | Shell | 651 | 24 | sbatch --wait << EOF
#!/bin/bash
#SBATCH -o logs/%j.job
#SBATCH -e logs/%j.job
#SBATCH -J pred-BERT-RBP-snakemake
#SBATCH -p cpu_p
#SBATCH -c 4
#SBATCH --mem=8G
#SBATCH -t 03:00:00
#SBATCH --nice=10000
source $HOME/.bashrc
conda activate bert-rbp
mkdir tmp.workdir
cp $1 tmp.workdir/dev.tsv
cp $2/* tmp.workdir/
pyth... |
2c273b4a37aafafc160ace13c6bfbe50e5b3b3199e26179aac6452e95493f280 | Shell | 651 | 23 | #!/bin/bash
ORIGIN=/ethoscope_data/results
NASMNT=/mnt/nas/auto_generated_data/ethoscope_results/
INDEXFILE=$NASMNT/index.txt
#generate a list of the files to be synced
rsync -arv $ORIGIN/* $NASMNT --dry-run | grep "\.db" > /tmp/synced_files.txt
#generate a temporary addition to the index file
echo "" > /tmp/tmp_inde... |
89cec3d888f2cef2547a9322a5001c4c6790330f4cccad49cf709e576c706ec2 | Shell | 652 | 30 | #!/bin/bash
target=$1
temp=$2
ulimit -s unlimited
export CRFALIGN_HOME=/gpfs/deepfold/project/crfalign.sangjin
export PATH=$CRFALIGN_HOME/bin:$PATH
export LD_LIBRARY_PATH=$CRFALIGN_HOME/lib:$LD_LIBRARY_PATH
export PYTHONPATH=$CRFALIGN_HOME/lib:$PYTHONPATH
export HHLIB=/gpfs/deepfold/programs/build/hhsuite-2.0.13
... |
ba27c06df88e51a7d81b3bb21fdccdc05d47a5e59f14f8a4cb64cda88444e230 | Shell | 652 | 24 | #!/bin/bash
# Usage: bash download_uniref90.sh /path/to/download/directory
set -e
if [[ $# -eq 0 ]]; then
echo "Error: download directory must be provided as an input argument."
exit 1
fi
if ! command -v aria2c &> /dev/null ; then
echo "Error: aria2c could not be found. Please install aria2c (sudo apt ins... |
eeaeba424bc19f16f8be803eed09699af5088c5269a82c98de856fcecbca1679 | Shell | 652 | 24 | sbatch --wait << EOF
#!/bin/bash
#SBATCH -o logs/%j.job
#SBATCH -e logs/%j.job
#SBATCH -J pred-BERT-RBP-snakemake
#SBATCH -p cpu_p
#SBATCH -c 4
#SBATCH --mem=12G
#SBATCH -t 14:00:00
#SBATCH --nice=10000
source $HOME/.bashrc
conda activate bert-rbp
mkdir tmp.workdir
cp $1 tmp.workdir/dev.tsv
cp $2/* tmp.workdir/
pyt... |
fe6e9b2dc51137da607543656a3df32ca06be25f1b2111b400725323a8ab03b2 | Shell | 652 | 27 | #!/bin/bash
#SBATCH -p gpu_4l
#SBATCH -c 28
#SBATCH -N 1
#SBATCH -J LJS_TEST
#SBATCH --gres=gpu:4
#SBATCH -o corigami.%j.out
#SBATCH -e corigami.%j.err
#SBATCH -A tangfuchou_g1
#SBATCH --qos=Tangfuchoug4c
set -euo pipefail
SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
REPO_ROOT="$(cd "${SCRIPT_DIR}/../..... |
9e02706ca31957eed22e638a9e4214f19e490fb6a93286c9da4519dfb022cfe2 | Shell | 655 | 33 | #!/bin/bash
set -xe
bitrate=$1
package_option=$2
source $(dirname "$0")/tc-tests-utils.sh
bitrate=$1
set_ldc_sample_filename "${bitrate}"
if [ "${package_option}" = "cuda" ]; then
PROJECT_NAME="DeepSpeech-GPU"
elif [ "${package_option}" = "--tflite" ]; then
PROJECT_NAME="DeepSpeech-TFLite"
model_source... |
68fcfb95364dd923154918f182a20e16d234054ce66c33fd2d47d52b5117eb7a | Shell | 656 | 35 | #!/bin/bash
#SBATCH --time=0-00:30:00
#SBATCH --mem-per-cpu=4000
#SBATCH --output=./slurm_logs/slurm-%A.out
INPUT_DIR=/scratch/n/tbi/er_data_new
OUTPUT_DIR=/scratch/n/tbi-meg/v/processed
echo "INPUT_DIR set as $INPUT_DIR"
echo "OUTPUT_DIR set as $OUTPUT_DIR"
SUBJECT=$1
ml purge
module load teflon
ml anaconda3
sourc... |
7b4312c69d159294c8b5d825b7a62e3c90844be04ff9488f7963b91439450bec | Shell | 656 | 15 | #!/usr/bin/env bash
source activate opencv_pyqt5
cd ..
pyuic5 -x score_window_ui.ui -o score_window_ui.py
pyuic5 -x ObjectSpace/trial_dialog_ui.ui -o ObjectSpace/trial_dialog_ui.py
pyrcc5 video_in_icons.qrc -o video_in_icons_rc.py
pyuic5 video_control_ui.ui -o video_control_ui.py
pyuic5 tracking_controller/tracker_co... |
5c723cd6fdc04bce927fa83270f7b3d1f14484fcd562945af91de613dfc7974d | Shell | 657 | 9 | #!/usr/bin/env bash
source new_venv/bin/activate
for mode in 'bioseq2seq' 'EDC' 'start';
do
for arch in 'LFNet' 'CNN-Transformer';
do
CUDA_LAUNCH_BLOCKING=1 python bioseq2seq/bin/hyperparam_search.py --train_src $BIOHOME/data/mammalian_200-1200_train_RNA_balanced.fa --train_tgt $BIOHOME/data/mammalian_200-1... |
972bcfeacefcdbad08a5e483e37acc3add5dd43d890daf0e21144b5c3139f873 | Shell | 657 | 14 | # Run ft_postfreesurferscript to prepare Freesurfer surfaces for MNE source reconstruction.
#
# Must have the HCP toolbox added to PATH to run (https://www.humanconnectome.org/software/).
#
# The script ft_postfreesurferscript is part of FieldTrip and found in fieldtrip/bin/ft_postfreesurferscript
export HCPPIPEDIR=~/... |
1b0fd761a61fc8685483be4c4fd21fc7bbbfd16315dd0315debc12f947d7fbdd | Shell | 658 | 29 | #!/bin/bash
set -xe
source $(dirname "$0")/tc-tests-utils.sh
extract_python_versions "$1" "pyver" "pyver_pkg" "py_unicode_type" "pyconf" "pyalias"
ds=$2
mkdir -p ${TASKCLUSTER_ARTIFACTS} || true
mkdir -p /tmp/train || true
mkdir -p /tmp/train_tflite || true
virtualenv_activate "${pyalias}" "deepspeech"
set -o pi... |
48bd80fb993e64071a121005b7311e627614759e2ea91c11c5d0d3d7946b53d5 | Shell | 658 | 21 | # 修改此处数据集路径
path='./datasets/SEN1-2/20%_train/ROIs1158_spring_20%_train'
# path='./datasets/SAR2Opt'
# 修改此处
name='re-SEN1-2_20%_spring'
# 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... |
4919a81549251082279fc6c9dd355d350f28f4a0e0dc00a0671e9b0f8db42d8a | Shell | 658 | 17 | ##annova annotation (here, use human reference as example for mUCE annotation)
#step1
gtfToGenePred -genePredExt {file_pathway}/hg38.chr.gtf human_refGene.txt
#step2
perl {file_pathway}/retrieve_seq_from_fasta.pl \
--format refGene \
--seqfile {file_pathway}/hg38_chr.fa human_refGene.txt \
-out human_refGeneMna.fa
... |
fa2099cea2564b65982bd5acca15cb07118f2eec753ba89827d737e7767b02c4 | Shell | 660 | 21 | #!/bin/bash
set -e
echo "Starting entrypoint script..."
echo "Waiting for database to start..."
sleep 5
echo "Preparing database..."
cd /carbonserver
echo "Current directory: $(pwd)"
echo "Listing files in /carbonserver:"
ls -la
echo "Running alembic upgrade head..."
python3 -m alembic -c carbonserver/database/alembic.... |
082f380c5b809a9c40aee894beb0794f903834d8301dee5983b9738d68f9a2fd | Shell | 661 | 18 | #!/bin/bash
mpirun -np 20 MMPBSA.py.MPI -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat -cp combine.prmtop -rp VSD.prmtop -lp TOX.prmtop -y *.mdcrd > o.log
mkdir withmem
mv _MMPBSA_* withmem
mv FINAL_RESULTS_MMPBSA.dat withmem
cp z-energies-process-awk-PBSA.sh withmem
cd withmem
bash z-energies-process-awk-PBSA.sh
cd ..
... |
3ef79ad81d285011fbbfbe42fc517eb0b359f470e6243b6c1a4ca20e56e49f33 | Shell | 662 | 23 | #!/bin/bash
set -x
tf_git_version=$(grep "STABLE_TF_GIT_VERSION" "bazel-out/stable-status.txt" | cut -d' ' -f2)
ds_version=$(grep "STABLE_DS_VERSION" "bazel-out/stable-status.txt" | cut -d' ' -f2)
ds_git_version=$(grep "STABLE_DS_GIT_VERSION" "bazel-out/stable-status.txt" | cut -d' ' -f2)
ds_graph_version=$(grep "STA... |
f6d1b542e99de47bfad23c4c965ba036833a496d23df07d2cfd465075b6cb0a7 | Shell | 662 | 24 | #!/bin/bash
# Usage: bash download_uniref90.sh /path/to/download/directory
set -e
if [[ $# -eq 0 ]]; then
echo "Error: download directory must be provided as an input argument."
exit 1
fi
if ! command -v aria2c &> /dev/null ; then
echo "Error: aria2c could not be found. Please install aria2c (sudo apt ins... |
c81b43c289978c7983dd85a129ec3733cd486c1b89d5799f80d8e4b42bdf2d9e | Shell | 663 | 26 | #!/bin/sh
if [ -z "${REPO_URL}" ]; then
echo "REPO_URL environment variable is not set. Unable to initialize the git server."
exit 1
fi
GIT_PROJECT=$(basename "$REPO_URL" .git)
if [ ! -d "${GIT_PROJECT}.git" ]; then
echo "Cloning repository..."
git clone --bare "${REPO_URL}" "${GIT_PROJECT}.git"
fi
... |
7f3d1b5bee182a620cbae146449913d1f0aaaa3fe3abe47d43e6ddf154939b96 | Shell | 665 | 20 | # 修改此处数据集路径
path='./datasets/SEN1-2/10%_train/ROIs1158_spring_10%_train'
# 参数中需要修改的：
# （1）--name：实验结果存储路径
# （2）--data_length：数据集长度
# 10%: spring: 1948 summer: 1220 fall: 2028 winter: 1012
# 20%: spring: 3898 summer: 2440 fall: 4058 winter: 2025
# 30%: spring: 9746 summer: 6102 fall: 101... |
688fafd162dd2bde89e36075e214d40a6853b616126d9df88f295d807a5f965e | Shell | 668 | 28 | #!/bin/bash
# Copyright (c) Jupyter Development Team.
# Distributed under the terms of the Modified BSD License.
set -e
# Syncing DAFi scripts and notebooks from Github repo
cd /var/DAFi-gating
git pull
cd $HOME
if [ -d "work" ]; then
cp /var/DAFi-gating/Notebooks/*.ipynb ~/work
else
cp /var/DAFi-gati... |
d27a9d076199ce6ad0ce0f8880d4b3fc451826e787868379e192ec67252de11a | Shell | 668 | 18 | #!/bin/bash
# Modify the following parameter values according to your experiment
# Do not modify the parameter names or remove parameters
# Do not add spaces around the equal (=) sign
# Global parameters
NCPUS=10 # Number of CPUs to use for analyses (int, 1+)
# Genome indexing
SKIP_GENOME_INDEXING... |
67f16dfd4e0737e150849ce9cfbedf041e5ead44929ce1f2c943cad5c89c7bbb | Shell | 670 | 26 | #!/bin/bash -ve
if [ -e reads.right.fq.gz ] && [ ! -e reads.right.fq ]; then
gunzip -c reads.right.fq.gz > reads.right.fq
fi
if [ -e reads.left.fq.gz ] && [ ! -e reads.left.fq ]; then
gunzip -c reads.left.fq.gz > reads.left.fq
fi
#######################################################
## Run Trinity to G... |
efecc673b3e698d3c53eb4c7783224ad4a63842acde0751ca5918f494d764308 | Shell | 671 | 25 | #!/bin/bash
declare -i i=0
seed_file="ensemble_seeds.txt"
while IFS= read -r line
do
stringarray=($line)
rseed=${stringarray[0]}
np_seed=${stringarray[1]}
tf_seed=${stringarray[2]}
i+=1
DePTH predict --test_file data/Zheng_2021/zheng_2021_HLA_I_pairs.csv \
--hla_class HLA_I \
... |
f44a950aa0c9e1f10e6d4192bf19666e81ff481dcc89fa0d5c1a1ae1c3e1b474 | Shell | 672 | 22 | #$ -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/template.$JOB_ID.stdout
#$ -e /cbica/projects/pnc_fixel_cs/scripts/MRtrix_recon/script_output/template.$JOB_ID.stderr
#!/bin/bash
project=/cbica/projects/pnc_fix... |
0d0de9e217bdda2e4adc625731e1760da095296688dcdedb8632bda7d56ac70f | Shell | 673 | 21 | #!/bin/bash
set -e
# D100 - Missing docstring in public module.
# D2XX - Whitespace issues.
# D3XX - Quoting issues.
# D401 - First line should be in imperative mood
# D403 - First word of the first line should be properly capitalized
args="--ignore=D --select=D100,D201,D202,D206,D207,D208,D209,D211,D3,D403"
# If t... |
cca9e3f512e6ce74fd8c576e525e61307bf0e4dc5da1bb27be450d46cb33b149 | Shell | 676 | 13 | #!/bin/bash
NAME="simple read length test"
BIN="ngmlr-"`grep -o "set( NGM_VERSION_MAJOR [0-9]* )" CMakeLists.txt | cut -d " " -f 3`"."`grep -o "set( NGM_VERSION_MINOR [0-9]* )" CMakeLists.txt | cut -d " " -f 3`"."`grep -o "set( NGM_VERSION_BUILD [^ ]* )" CMakeLists.txt | grep -v debug | cut -d " " -f 3`
PARAMETER=" --... |
edaeddaf9c9068fbb6a82d006a7443d3d9acc11fb70b2269daeba2ec5221285a | Shell | 679 | 20 | #!/usr/bin/env bash
##############################################################################
#
# wrapper script for stopping the GenePattern Server
# Usage:
# nohup ./stop-genepattern.sh &
#
# # optionally set server customization environment
# nohup ./stop-genepattern.sh -c server-env-custom.sh &
#
... |
f179e91a0d6dc873bf6517d41d8d6c779e57f4fb7e85c1f5e3678354859e36ff | Shell | 681 | 12 | #Step1. calcuate the wMISi for all nodes in networks
perl get_MIS.pl 1M_input/1M_mean.csv 1M_input/AD1M_r.0.05.0.4.csv AD AD1M_MIS.xls
perl get_MIS.pl 2M_input/2M_mean.csv 2M_input/AD2M_r.0.05.0.4.csv AD AD2M_MIS.xls
perl get_MIS.pl 3M_input/3M_mean.csv 3M_input/AD3M_r.0.05.0.4.csv AD AD3M_MIS.xls
perl get_MIS.pl 6M_i... |
431b7daa5bbd4db9af12ac70d6f7397eb52873ab7e933b52a3dff6d62a811253 | Shell | 682 | 25 | #!/bin/bash
declare -i i=0
seed_file="ensemble_seeds.txt"
while IFS= read -r line
do
stringarray=($line)
rseed=${stringarray[0]}
np_seed=${stringarray[1]}
tf_seed=${stringarray[2]}
i+=1
DePTH predict --test_file data/Szeto_2020/HLA_I_szeto_2020_compatible_pairs.csv \
--hla_class HLA_I ... |
bd23943049bfd0d8e76428a84a5e2eb64ec9f6282d2fad10f4707c26d2258cb7 | Shell | 682 | 21 | #!/bin/bash
BISMAKEJ="-j8"
IDIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
BDIR="$( cd ${IDIR}/../build && pwd )"
SRCDIR="$( cd ${BDIR}/.. && pwd )"
echo "-----------------------------------------------------------------------"
echo "SRCDIR=${SRCDIR}, BDIR=${BDIR}"
echo "------------------------------------... |
cbcf8b583a336da957dec37f70ebea01fe1c3add824647d5f91858c4f6660b00 | Shell | 682 | 24 | #!/bin/bash
# Usage: bash download_small_bfd.sh /path/to/download/directory
set -e
if [[ $# -eq 0 ]]; then
echo "Error: download directory must be provided as an input argument."
exit 1
fi
if ! command -v aria2c &> /dev/null ; then
echo "Error: aria2c could not be found. Please install aria2c (sudo apt in... |
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