sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 17k | content stringlengths 1 200k |
|---|---|---|---|---|
edac8d6ca4ed88ecd6578b781f7d4a04a26a5de65bad4044118e9bad8c9dfb79 | Shell | 864 | 31 | #!/bin/bash
#
# reproducible script to install gmx_MMPBSA on Ubuntu 24.04.3 LTS
# might also work on some other Linux distributions
ENV=gmx_MMPBSA
# conda env and python
conda create -n $ENV "python=3.12" -y -q
conda activate $ENV
set -u
#set -x
# packages which are not available through pip
# (too bad, or we could... |
4171e9a32b27004ef9688ffb68231e6875908f4e6e262b36af243ec163e755d8 | Shell | 874 | 33 | #!/bin/sh
# script for execution of deployed applications
#
# Sets up the MATLAB Runtime environment for the current $ARCH and executes
# the specified command.
#
exe_name=$0
exe_dir=`dirname "$0"`
echo "------------------------------------------"
if [ "x$1" = "x" ]; then
echo Usage:
echo $0 \<deployedMCRroot\>... |
2f28321d849b938373e7f711a9915426232f24cab739769fd99b5225a0c35cf3 | Shell | 875 | 33 | #!/bin/sh
# script for execution of deployed applications
#
# Sets up the MATLAB Runtime environment for the current $ARCH and executes
# the specified command.
#
exe_name=$0
exe_dir=`dirname "$0"`
echo "------------------------------------------"
if [ "x$1" = "x" ]; then
echo Usage:
echo $0 \<deployedMCRroot\>... |
a7b1900694161f7f57ae777261e98c38135268f1bc141e12a0b4cf6d7b98a8f1 | Shell | 875 | 24 | #!/bin/bash
#
# CBIG_replace_old_with_new_function_name.sh $old_function_name $new_function_name
# Wrapper function to search for all instances of old function name
# inside a predefined set of directories and replace them by the new function name,
# if prompted
# Input can be the function name, a file name, or full p... |
b1ed95abb9ead926a8216503365ed923b803fb4cd396a0b6c0c58d6adb327143 | Shell | 875 | 33 | #!/bin/sh
# script for execution of deployed applications
#
# Sets up the MATLAB Runtime environment for the current $ARCH and executes
# the specified command.
#
exe_name=$0
exe_dir=`dirname "$0"`
echo "------------------------------------------"
if [ "x$1" = "x" ]; then
echo Usage:
echo $0 \<deployedMCRroot\>... |
771a57beca00b51720239cc57785bae7f97b7cd6ce1b72e561487b52fced161b | Shell | 876 | 33 | #!/bin/sh
# script for execution of deployed applications
#
# Sets up the MATLAB Runtime environment for the current $ARCH and executes
# the specified command.
#
exe_name=$0
exe_dir=`dirname "$0"`
echo "------------------------------------------"
if [ "x$1" = "x" ]; then
echo Usage:
echo $0 \<deployedMCRroot\>... |
7efb47eb9467d414e363e52aea87b915bf7ac8397229578ce1e722350f0fbe15 | Shell | 876 | 32 | #!/bin/bash
set -e # Stop on error
SH_SCRIPT_DIR=$(cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd)
CONDA_ENV_PY3=encode-atac-seq-pipeline
SRC_DIR=${SH_SCRIPT_DIR}/../src
conda --version # check if conda exists
CONDA_PREFIX_PY3=$(conda env list | grep -P "\b${CONDA_ENV_PY3}\s" | awk '{if (NF==3) print $3; else print... |
abae86b6182fe8ee7f798490c09d0eb11072a8641afab2f060524007e1171d87 | Shell | 877 | 33 | #!/bin/sh
# script for execution of deployed applications
#
# Sets up the MATLAB Runtime environment for the current $ARCH and executes
# the specified command.
#
exe_name=$0
exe_dir=`dirname "$0"`
echo "------------------------------------------"
if [ "x$1" = "x" ]; then
echo Usage:
echo $0 \<deployedMCRroot\>... |
91e4c4c1b879325e9c16bf7d1ea57a53415bc5368c9a2754a9ee994368afbe7d | Shell | 878 | 33 | #!/bin/sh
# script for execution of deployed applications
#
# Sets up the MATLAB Runtime environment for the current $ARCH and executes
# the specified command.
#
exe_name=$0
exe_dir=`dirname "$0"`
echo "------------------------------------------"
if [ "x$1" = "x" ]; then
echo Usage:
echo $0 \<deployedMCRroot\>... |
fd43af4cd2ee1d8ffb85e1c27d8503e921b7901c59397ab697a6348f50181fda | Shell | 880 | 24 | #!/bin/sh
# Written by Xiuming Zhang and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
queue=circ-spool
# BET on baseline scans in 11 batches
# Each batch uses a different set of BET parameters/procedure
outDir=~/storage/forPNASRelease/outputs/VBM_bl/brains/
for i in {1..11}; do... |
3fe0ce07cbf269d53d2a857c9f37055e9ff4aa34a0f486d17b019ba0f5eabdba | Shell | 882 | 33 | #!/bin/sh
# script for execution of deployed applications
#
# Sets up the MATLAB Runtime environment for the current $ARCH and executes
# the specified command.
#
exe_name=$0
exe_dir=`dirname "$0"`
echo "------------------------------------------"
if [ "x$1" = "x" ]; then
echo Usage:
echo $0 \<deployedMCRroot\>... |
47bbfc9759a242b4c3bd690eff909f81eb82a2d5cda623e992a100d9b4aa29e4 | Shell | 882 | 30 | #!/bin/bash -xve
SPNG=/usr/src/spng/spng
MINIZ=/usr/src/miniz
compile_options=(
-O2
-I$MINIZ -DMINIZ_NO_STDIO=1
$MINIZ/miniz_zip.c $MINIZ/miniz_tinfl.c $MINIZ/miniz_tdef.c $MINIZ/miniz.c
# spng defaults to zlib if we don't force miniz
# it also prints a warning about SIMD if we don't disable SIMD
... |
8ba6e8d3a8c7ff801d33daca96274412e7680779dcd732316eb4f8a757677337 | Shell | 883 | 33 | #!/bin/sh
# script for execution of deployed applications
#
# Sets up the MATLAB Runtime environment for the current $ARCH and executes
# the specified command.
#
exe_name=$0
exe_dir=`dirname "$0"`
echo "------------------------------------------"
if [ "x$1" = "x" ]; then
echo Usage:
echo $0 \<deployedMCRroot\>... |
21d1335a4033e1aecdb7d52a904f28cca84d0c97521b0d57c2f7c98e2e8ea468 | Shell | 885 | 25 | H5AD_REMOTE_PATHS=(\
"https://ftp.cngb.org/pub/SciRAID/stomics/STDS0000062/stomics/FP200000498TL_D2_stereoseq.h5ad"\
"https://ftp.cngb.org/pub/SciRAID/stomics/STDS0000062/stomics/FP200000498TL_E4_stereoseq.h5ad"\
"https://ftp.cngb.org/pub/SciRAID/stomics/STDS0000062/stomics/FP200000498TL_E5_stereoseq.h5ad"\... |
86db8fa15907a871d285cd1318e28007656f05a70bf8942f3d1626fb0db709b3 | Shell | 886 | 30 | #!/bin/bash
# prepare a new data directory of HMM word output
. ./path.sh
set -eu
out_dir= # same as in train.sh
dec_lmparam= # LM hyperparameters (e.g., 7.0.0)
dec_exp=tri3b # what HMM stage to decode (e.g., tri3b)
dec_suffix=word
dec_splits="train valid"
dec_data_dir=$out_dir/dec_data_word # where to write H... |
d722ad66a062f3bf7b882eed895c021578dede74d2a002bda29346855d659c8c | Shell | 886 | 28 | #!/bin/bash
# Stop on error
set -e
CONDA_ENV=encode-atac-seq-pipeline
CONDA_ENV_PY3=encode-atac-seq-pipeline-python3
if which conda; then
echo "=== Found Conda ($(conda --version))."
else
echo "=== Conda does not exist on your system. Please install Conda first."
echo "https://conda.io/docs/user-guide/install/i... |
46c55a0080881fcbf12f8c47eca1a0261a7bd0cb4960dc8547dc43cc24883a6c | Shell | 890 | 37 | #!/bin/bash
sil_prob=0.5
num_sil_states=3
num_nonsil_states=1
. ./cmd.sh
. ./path.sh
. parse_options.sh
set -eux
dict=$1
data_dir=$2
dict_dir=$data_dir/local/dict
tmplm_dir=$data_dir/local/lang_tmp
lm_dir=$data_dir/lang
mkdir -p $dict_dir $tmplm_dir $lm_dir
# prepare dict
echo "SIL" > $dict_dir/silence_phones.tx... |
0f3b67e92dfd327fb6648864743d9ef30b7cc4c90319e184d4c19d22583aa86c | Shell | 892 | 25 | #!/bin/bash
#
# CBIG_check_format_and_license_in_all_functions.sh
# Wrapper function to check format and license of all functions inside a predefined set of directories
DIRECTORY_NAMES=("utilities" "stable_projects" "setup" "data")
EXTENSIONS_TO_CHECK=("m" "sh" "csh" "c" "cpp" "py" "r")
for name in "${DIRECTORY_NAME... |
48e76d19e3226ce03b2f33e6c036d6e52fb7882752c433bf311bad99cb7450e1 | Shell | 893 | 23 | # Path of the folder containing all data
dir="/root/dir"
# List of subjects
declare -a sub=("sub-SPAIN01" "sub-SPAIN02" "sub-SPAIN04" "sub-SPAIN06" "sub-SPAIN07" "sub-SPAIN08" "sub-SPAIN11" "sub-SPAIN13" "sub-SPAIN15" "sub-SPAIN16" "sub-SPAIN19" "sub-SPAIN20" "sub-SPAIN21" "sub-SPAIN24" "sub-SPAIN25" "sub-SPAIN26" "su... |
affb3ab0b493967fd6f7130d15345cac614b60a439d536763291134cf8e33f76 | Shell | 893 | 23 |
#!/bin/bash
#databases path
ALPHAFOLD_DB=/path/to/alphafold_db
#singularity sif
ALPHAFOLD_SIF=/path/to/tcrmodel2.sif
#output directory
OUTPUT_DIR=/path/to/output_directory
# run tcrmodel singularity
singularity run --nv -B $ALPHAFOLD_DB $ALPHAFOLD_SIF \
--job_id=test_clsI_6kzw \
--output_dir=$OUTPUT_DIR \... |
133fca63003248478d5816e625da5744580ebb124b8d4992ca2aa3c18b2b16c1 | Shell | 897 | 25 | #!/usr/bin/env zsh
dir="$1"
cp="$dir/checkpoints/checkpoint_last.pt"
echo "dir: $dir"
declare -A tasks
tasks[cola]="/fsx-wav2vec/abaevski/data/nlp/GLUE/CoLA-bin"
tasks[qnli]="/fsx-wav2vec/abaevski/data/nlp/GLUE/QNLI-bin"
tasks[mrpc]="/fsx-wav2vec/abaevski/data/nlp/GLUE/MRPC-bin"
tasks[rte]="/fsx-wav2vec/abaevski/dat... |
a70cf8f40676060e2c55826a5c7ed6068930c5d6122fafa9562f4c67b9532779 | Shell | 898 | 15 | # you can change cmd.sh depending on what type of queue you are using.
# If you have no queueing system and want to run on a local machine, you
# can change all instances 'queue.pl' to run.pl (but be careful and run
# commands one by one: most recipes will exhaust the memory on your
# machine). queue.pl works with Gri... |
8d017b1c502aa5d9c4b6a01b48f52aadfa9e030d50944879ef0921b46997586b | Shell | 899 | 21 | #!/usr/bin/env zsh
job_id=$1
task_id=$2
dir="$3"
cp="$dir/$task_id/checkpoints/checkpoint_last.pt"
echo "job_id: $job_id, task_id: $task_id, dir: $dir"
declare -A tasks
tasks[cola]="/private/home/jgu/data/GLUE/CoLA-bin"
tasks[qnli]="/private/home/jgu/data/GLUE/QNLI-bin"
tasks[mrpc]="/private/home/jgu/data/GLUE/MRPC-... |
48b78f15e4f500d69067011db06b7ffae78f2b2be91e84f0317e15c5ba54bac0 | Shell | 907 | 38 | #!/bin/bash
### Script handling creation of data binaries
### for model training within fairseq
fairseq_root="."
data_root=$1
train_prefix="${data_root}/train"
valid_prefix="${data_root}/eval"
test_prefix="${data_root}/test"
dest_dir="$data_root/"
#echo "src dict: $src_dict" > "$dest_dir/src_dict.txt"
#echo "trg ... |
62fa5840252a23091510302073ec3ee738436a91288654a5fee273f3edc00978 | Shell | 907 | 17 | #!/usr/bin/env bash
#SBATCH --job-name=cdna_alignment_orf_to_genome_orf
#SBATCH --output=cdna_alignment_orf_to_genome_orf.out
#SBATCH --time=0-2:0
#SBATCH -n 1
#SBATCH -N 1
# module apptainer
# apptainer exec -e -B="/scratch/nxu/SFARI:/scratch/nxu/SFARI" ~/tools/transdecoder.v5.7.1.simg /usr/local/bin/util/cdna_alignm... |
002b739cda9b2043354b0528011e937cf9e3ec11c0706fd19700b820abf28efd | Shell | 912 | 28 | #!/usr/bin/env bash
set -euo pipefail
# Repro for issue #697: --stdout should emit merged reads in merge mode.
python - <<'PY' > /tmp/fp_repro_697.interleaved.fq
seq='AATGTCCCCCAATGGGAAGTTCATCTGGCACTGCCCACAGGTGAGGAGGTCATGATCCCCTTCTGGAGC'
comp=str.maketrans('ACGTN','TGCAN')
rc=seq.translate(comp)[::-1]
qual='I'*len(se... |
d9ab49f4afad47ae621d630659f351be7ce2637ee948326b2d88917cf4834e6c | Shell | 912 | 30 | #!/bin/usr/env sh
# Copyright (c) 2018-present, Facebook, Inc.
# All rights reserved.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
set -e
URL=$1
FILENAME=$(basename --suffix=".warc.wet.gz" "${URL}")
echo "Processing ${FILENAME}."
wget... |
c21d56c301d5902a555c6c372ad888ba6787673915f40153ce745e440d06f179 | Shell | 916 | 21 | #!/usr/bin/env zsh
dir="$1"
cp="$dir/checkpoints/checkpoint_last.pt"
echo "dir: $dir"
declare -A tasks
tasks[cola]="/fsx-wav2vec/abaevski/data/nlp/GLUE/CoLA-bin"
tasks[qnli]="/fsx-wav2vec/abaevski/data/nlp/GLUE/QNLI-bin"
tasks[mrpc]="/fsx-wav2vec/abaevski/data/nlp/GLUE/MRPC-bin"
tasks[rte]="/fsx-wav2vec/abaevski/dat... |
3f05b4a3913dab7b3ad6d298018928a16a511538b42e32a24e49d5eaadd139e5 | Shell | 922 | 22 | #!/bin/bash
cfg_templ=optimize.e1.template.cfg
for i_hsq in $(seq 0 2); do
for i_coding in $(seq 0 2); do
for i_noncoding in $(seq 0 2); do
for i_s2coding in $(seq 0 2); do
for i_repeat in $(seq 10); do
cfg_f=optimize.e1.hsq_${i_hsq}.coding_${i_coding}.nonco... |
2098fa20c6a814d7eb2974c20f1cc7bde0f107cb26362b1a37593f0f2cded04e | Shell | 924 | 27 | #!/usr/bin/env bash
# slurm_submit.sh — Step 2 of the SLURM sweep workflow.
#
# Prerequisites:
# jobs.sh must exist (created by sweep_creator.py).
# slurm.sh must exist and contain your #SBATCH directives.
#
# What this script does:
# 1. Snapshots jobs.sh to jobs_<timestamp>.sh so that late-running array
# t... |
b36d591d0fa11596daf4c407e9c04da9c5e5885f53de70c7952a777dc1a4929d | Shell | 929 | 52 | #! /bin/bash
WHAT=$1
DIR=$2
MINIC=$3
MAXIC=$4
MINOC=$5
MAXOC=$6
prefix=$8
meanstatsfilename=$2/mean.html
WORK_DIR=tmp
mkdir $WORK_DIR
DATA_FILE=`find $DIR -name "*.dat" | grep _${WHAT}`
if [ -n "$DATA_FILE" ]; then
echo ""
echo "$1..."
for FILE in $DATA_FILE
do
##echo hello world
##echo... |
c3329d364a0c951889fa97af8b8e20c8773b30345f0501a1ab72c7a04a6c4e39 | Shell | 930 | 23 | #!/bin/bash
echo "Downloading the data to ./examples/ ..."
wget -c -O ./examples/data.tar.gz https://zenodo.org/record/7995778/files/data.tar.gz?download=1 && cd examples && tar -xzvf data.tar.gz && cd .. && echo "Done"
echo "Downloading the model weights ..."
wget -c -O models.tar.gz https://zenodo.org/record/79957... |
5362b5a197cb6fa44b4c3af16d0c37d8773cfc9f4a0fc78d6cf801d495b47cca | Shell | 931 | 18 | # assumes you are in the nnunet repo!
# prepare raw datasets
python nnunetv2/dataset_conversion/datasets_for_integration_tests/Dataset999_IntegrationTest_Hippocampus.py
python nnunetv2/dataset_conversion/datasets_for_integration_tests/Dataset998_IntegrationTest_Hippocampus_ignore.py
python nnunetv2/dataset_conversion/... |
023a5e94e0074d82f00f369cbf64c835e6b41d4d149056bd98c45c592af9baaa | Shell | 933 | 26 | #!/usr/bin/env zsh
dir="$1"
cp="$dir/checkpoints/checkpoint_last.pt"
echo "dir: $dir"
declare -A tasks
tasks[cola]="/fsx-wav2vec/abaevski/data/nlp/GLUE/CoLA-bin"
tasks[qnli]="/fsx-wav2vec/abaevski/data/nlp/GLUE/QNLI-bin"
tasks[mrpc]="/fsx-wav2vec/abaevski/data/nlp/GLUE/MRPC-bin"
tasks[rte]="/fsx-wav2vec/abaevski/dat... |
fa407e4ec0e5f7f17f21ac851bb295be928dd4843e044b4e71bfe82f193fa7a1 | Shell | 934 | 21 | #!/usr/bin/env zsh
job_id=$1
task_id=$2
dir="$3"
cp="$dir/checkpoints/checkpoint_last.pt"
echo "job_id: $job_id, task_id: $task_id, dir: $dir"
declare -A tasks
tasks[cola]="/fsx-wav2vec/abaevski/data/nlp/GLUE/CoLA-bin"
tasks[qnli]="/fsx-wav2vec/abaevski/data/nlp/GLUE/QNLI-bin"
tasks[mrpc]="/fsx-wav2vec/abaevski/data... |
92a83075a0fef1d9772e7ea1dfda2132d0627508707f5a111d34ddff36cc9f24 | Shell | 936 | 31 | #!/bin/bash
# Setup directories
export data_folder=/data/elevchenko/MovieProject2/bids_data
# Extract subject IDs dynamically from the bids_data folder
subjects=$(ls -d $data_folder/sub-* | awk -F'/' '{print $NF}' | sed 's/sub-//')
# Run
for subj_id in $subjects; do
if [[ $subj_id -eq "10" ]]; then
# U... |
ccef49ce2703597320146ea864d1d78a3ebd95f42511b55f4b14e6b63d3c7187 | Shell | 942 | 27 | # Compile all the individual TWAS files into a single large table for significance filtering
for dz in $(ls -d $HOME/TWAS_data/*/)
do
for direc in $(ls -d ${dz}* | head -n 1)
do
tissue=${direc##*/}
dzn=${dz##*_data/}
dznm=${dzn%/}
for NIDP in $(ls $direc | head -n 1); ... |
6a1645bee2c63998ba01d2df8430ff7cd6923dde0bd24489b1902ac610671eef | Shell | 948 | 63 | #!/bin/bash
git clone git@github.com:boostorg/boost.git || exit 1
pushd boost/libs && git submodule init callable_traits \
algorithm \
align \
any \
array \
array \
assert \
atomic \
bind \
concept_check \
config \
container \
container_hash \
core \
detail \
exception \
filesystem \
... |
aa205576964385a06f2501ebc44c5201df420fb7188e535273ed333ccecedb53 | Shell | 949 | 21 | #!/usr/bin/env zsh
dir="$1"
cp="$dir/checkpoints/checkpoint_last.pt"
echo "dir: $dir"
declare -A tasks
tasks[cola]="/fsx-wav2vec/abaevski/data/nlp/GLUE/CoLA-bin"
tasks[qnli]="/fsx-wav2vec/abaevski/data/nlp/GLUE/QNLI-bin"
tasks[mrpc]="/fsx-wav2vec/abaevski/data/nlp/GLUE/MRPC-bin"
tasks[rte]="/fsx-wav2vec/abaevski/dat... |
24bb2216e7a331cd07a425c5c5c7980db553fad4adf02b1f6a51b626aee95fbd | Shell | 956 | 37 | #!/bin/bash
split="dev_other"
ref_txt="" # ground truth transcript path
psd_txt="" # pseudo transcript path
get_best_wer=true
dec_name="decode"
graph_name="graph"
kenlm_path=/checkpoint/abaevski/data/speech/libri/librispeech_lm_novox.phnc_o6.bin
. ./cmd.sh
. ./path.sh
. parse_options.sh
exp_root=$1
unsup_args=""
i... |
59a642cf8f1b9cae35af0e0557db2fb50623c87386ad9177963db8531693c5dc | Shell | 957 | 15 | #!/bin/bash
# Written by Siyi Tang and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
cd ~/storage
rsync -a --exclude .git CBIG/* Standalone_Tang2020_ASDFactors
# remove useless stable projects
rm -r Standalone_Tang2020_ASDFactors/stable_projects/brain_parcellation/Kong2019_MSHBM
r... |
95de8a8c8709e72124d4d024ebcb0d0d891611aa7a609e7898dc6cd8962ca451 | Shell | 961 | 37 | #!/bin/bash
if [ $# -ne 5 ]; then
echo "usage: $0 [dataset=wmt14/full] [langpair=en-de] [databin] [bpecode] [model]"
exit
fi
DATASET=$1
LANGPAIR=$2
DATABIN=$3
BPECODE=$4
MODEL=$5
SRCLANG=$(echo $LANGPAIR | cut -d '-' -f 1)
TGTLANG=$(echo $LANGPAIR | cut -d '-' -f 2)
BPEROOT=examples/backtranslation/subwor... |
1574977fc4548136efceb8e3bb60686b06a91b2b09c3dd7b0a4fb52896b17546 | Shell | 963 | 42 | #!/bin/bash
# TReNDS Nov 2023
# Main script to convert ADNI DICOM to BIDS
# format before GIFT processing
# Downloaded FBB pet from ADNI were according
# with subject ID in
# 04_ADNI_Downloaded_DCM_FBB.txt file
# to /root/data_fbb/ADNI_FBB directory
# Downloaded T1 from ADNI were according
# with image... |
566db9d73b7cb0c7b4091af5d172ee3e6919991c857bbbda2f3a916cafe1c0e7 | Shell | 964 | 30 | #!/bin/bash
# Copyright (c) Facebook, Inc. and its affiliates.
# All rights reserved.
#
# This source code is licensed under the license found in the
# LICENSE file in the root directory of this source tree.
if [ -z $WORKDIR_ROOT ] ;
then
echo "please specify your working directory root in environment variable... |
bcab55cd40c6db61b44a041870c51966230f862d35e06423e9a3257b26f89502 | Shell | 965 | 32 | #!/bin/bash
#SBATCH -p gpu
#SBATCH --mem=32g
#SBATCH --gres=gpu:rtx2080:1
#SBATCH -c 2
#SBATCH --output=example_2.out
source activate mlfold
folder_with_pdbs="../PDB_complexes/pdbs/"
output_dir="../PDB_complexes/example_2_outputs"
if [ ! -d $output_dir ]
then
mkdir -p $output_dir
fi
path_for_parsed_chains=$out... |
2778fac3061d2026044861e072f42ed748b8b97ddf783526f8879f67586b786c | Shell | 974 | 16 | #!/bin/sh
# Written by CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
cd ~/storage
rsync -a --exclude .git CBIG/* Standalone_Yan2023_homotopic
# remove useless stable projects
rm -r Standalone_Yan2023_homotopic/stable_projects/brain_parcellation/Yeo2011_fcMRI_clustering
rm -r Stand... |
deee440d7d125046c6ef08111166874a8b54df88fa22c7c80c74b3824cee9c10 | Shell | 984 | 35 | #!/bin/bash
split="dev_other"
ref_txt="" # ground truth transcript path
psd_txt="" # pseudo transcript path
get_best_wer=true
dec_name="decode"
graph_name="graph"
kenlm_path=/checkpoint/abaevski/data/speech/libri/librispeech_lm_novox.phnc_o6.bin
phonemize_lexicon=""
. ./cmd.sh
. ./path.sh
. parse_options.sh
. /priv... |
f7947cef8ae71e513567d00125562ec32b2c1c5bba62e77d27f33cb33d686b38 | Shell | 989 | 33 | #!/bin/bash
#SBATCH -p gpu
#SBATCH --mem=32g
#SBATCH --gres=gpu:rtx2080:1
#SBATCH -c 3
#SBATCH --output=example_6.out
source activate mlfold
folder_with_pdbs="../PDB_homooligomers/pdbs/"
output_dir="../PDB_homooligomers/example_6_outputs"
if [ ! -d $output_dir ]
then
mkdir -p $output_dir
fi
path_for_parsed_cha... |
82e0f10267757f338aa0dd099540b7463d4cbff98f56b50d4c5c89a7d740105d | Shell | 996 | 23 | pip install gdown
cd data
mkdir -p Split_Dataset/Data
mkdir -p Split_Dataset/Ground_truth
cd Split_Dataset/Data/
# Pre-annotation apporaches
gdown https://drive.google.com/uc?id=1p7noO4lOgf942FXBVwd40OrmFO5Go0Hn -O test_annotated.npy
gdown https://drive.google.com/uc?id=1u089d0apWGPCsoRu7NR8ubbBfxWNvrvi -O train_ann... |
a6db0ff810ce8280e816cf23a32025171fa98785a881d8bbd145f96bb432e0e6 | Shell | 998 | 34 | #!/bin/bash
# Stop on error
set -e
CONDA_ENV=encode-atac-seq-pipeline
SH_SCRIPT_DIR=$(cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd)
if which conda; then
echo "=== Found Conda ($(conda --version))."
else
echo "=== Conda does not exist on your system. Please install Conda first."
echo "=== https://conda.io/docs/... |
89679250bac0577d7eea4af6beadfa4b4eb355e8cd3d65c70b729e10680ca613 | Shell | 1,004 | 22 | #!/bin/bash
# Run the whole pipeline from the bids conversion to the very end (lots of comp resources are needed)
# The pipeline was executed in a step-by-step manner
# conversion to bids, freesurfer, sswarper and suma
sudo nohup bash analysis/01_convert_to_bids.sh > analysis/logs/01_convert_to_bids.out &
nohup bash ... |
fb97186a8f95f7215ecc7d5ee5410f9056c493b9ecdc44f9915f9ed61e5f3a4d | Shell | 1,006 | 24 | #!/bin/sh
# This script builds the liblsl.so for linux machines without bigger quirks
# and no recent CMake version, i.e. ARM boards and PCs with old distributions.
# For development, install a recent CMake version, either via pip
# (pip install cmake) or as binary download from cmake.org
set -e -x
# Try to read LSLG... |
c6fb3ac6d7dd808cefc7954dae37c3ba8fe08892986cd66076b1a9ec9732430d | Shell | 1,008 | 16 | #!/bin/bash
cd /home/david/atual/new-methods
source /home/david/ambientes/alignn/bin/activate 2>/dev/null
PROD_LOG=data/perovskites/batio3_casestudy/siesta_production.log
# 1. esperar produção terminar
until grep -q "DONE:" "$PROD_LOG" 2>/dev/null || ! pgrep -f run_siesta_production >/dev/null; do sleep 60; done
echo "... |
4e4fe5fc66326e984b4be5a5ad9aa778f402a2c310049b68e5b0080e5aa31b94 | Shell | 1,009 | 31 | #!/bin/bash
# Base directory
export deriv_root="/egor2/egor/MovieProject2/bids_data/derivatives"
# Create a temporary list of tSNR files
tsnr_list="tsnr_group_inputs.txt"
rm -f $tsnr_list
# Loop over subjects and append valid tSNR paths
for subj_dir in "${deriv_root}"/sub-*/backtothefuture/sub-*.results.*; do
ts... |
35922bccad6c1b9987cb114f4b52778225fc4f6a9ddfcf12aa13524b51bc462a | Shell | 1,015 | 33 | #!/bin/bash
# decode into phones (and prepare a new data directory for HMM outputs)
. ./path.sh
set -eu
out_dir= # same as in train.sh
dec_lmparam= # LM hyperparameters (e.g., 7.0.0)
dec_exp=
dec_script=
dec_splits="train valid"
dec_data_dir=$out_dir/dec_data # where to write HMM output
data_dir=${out_dir}/data... |
a50d970b93b1acfc9e6205fad235182089e31cf2ea89605aa9d6ba4f0870fdb0 | Shell | 1,015 | 35 | #!/bin/bash
# Stop on error
set -e
CONDA_ENV=encode-atac-seq-pipeline
SH_SCRIPT_DIR=$(cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd)
if which conda; then
echo "=== Found Conda ($(conda --version))."
else
echo "=== Conda does not exist on your system. Please install Conda first."
echo "=== https://conda.io/docs/... |
dfc5fe82ae9ee6b5048a9f878bcc16cfc94c083c7ef9857cbffd1e74416c00cc | Shell | 1,016 | 45 | #!/bin/bash
black='\E[30m'
red='\E[31m'
green='\E[32m'
yellow='\E[33m'
blue='\E[34m'
magenta='\E[35m'
cyan='\E[36m'
white='\E[37m'
if [ -f $2 ]; then
data=$2
if [ -f $1.summ ]; then rm $1.summ; fi
if [ -f $1.snap ]; then rm $1.snap; fi
else
data=$1
fi
if ! ./$1 < $data > /dev/null 2> .runtest.log ; then
ec... |
2053c5d7d920a9b8aca7cb7554979962f4a43dbff9b23ae03d9557c5895e3078 | Shell | 1,018 | 36 | set -xe
device_id=0 # which device to run the program, for multi-gpus, set params like device_id=0,2,5,7. [Note that] the device index in python refers to 0,1,2,3 respectively.
# params
data_dir=./data/
data_name=gse133344_k562gi_oe_pert227_84986_19264_withtotalcount
split=simulation
result_dir=./results
seed=1
epoc... |
ef7dee81cdf271df959db8147073a9f67d280c8bca387fba33da6bc589d32abb | Shell | 1,018 | 24 | #!/bin/sh
# This script builds the liblsl.so for linux machines without bigger quirks
# and no recent CMake version, i.e. ARM boards and PCs with old distributions.
# For development, install a recent CMake version, either via pip
# (pip install cmake) or as binary download from cmake.org
set -e -x
# Try to read LSLG... |
322e4c5bd6ab08f518caf7b2cb1fe309de3a07afd29d43829d56b28fd632aa89 | Shell | 1,023 | 27 | # Path of the folder containing all data
dir="/root/dir"
# List of subjects
declare -a sub=("sub-SPAIN01" "sub-SPAIN02" "sub-SPAIN04" "sub-SPAIN06" "sub-SPAIN07" "sub-SPAIN08" "sub-SPAIN11" "sub-SPAIN13" "sub-SPAIN15" "sub-SPAIN16" "sub-SPAIN19" "sub-SPAIN20" "sub-SPAIN21" "sub-SPAIN24" "sub-SPAIN25" "sub-SPAIN26" "su... |
3e28d1d18e2ec14da0997d94944cdaa0d222de987e5d856d5a355f424374dc71 | Shell | 1,023 | 24 | #! /bin/sh
# Last successfully run on May 2nd 2017
# DO NOT CHANGE: This clears old freesurfer variables if they previously exists
if [ -n "$FREESURFER_HOME" ]; then
$FREESURFER_HOME/bin/clear_fs_env.csh
fi
# PLEASE CHANGE: Please specify location of CBIG repository
export CBIG_CODE_DIR=/data/users/xzhang/storag... |
09bef3258ddb5ebe72382987a6a6a9765d6ee819fd2142fccb9a840170278847 | Shell | 1,025 | 35 | #!/bin/bash
# Copyright (c) Facebook, Inc. and its affiliates.
# All rights reserved.
#
# This source code is licensed under the license found in the
# LICENSE file in the root directory of this source tree.
if [ -z $WORKDIR_ROOT ] ;
then
echo "please specify your working directory root in environment variabl... |
028dd2f3e9f07b0d99b5157bea75d08765312ea0f4ac70407147306223e4adf5 | Shell | 1,032 | 38 | #!/usr/bin/env bash
#
# copyright (c) 2017-present, facebook, inc.
# all rights reserved.
#
# this source code is licensed under the MIT license found in the
# license file in the root directory of this source tree.
#
# script for SVO
DIR=data/SVO-tensor-dataset
FASTTEXTDIR=../../
# compile
pushd $FASTTEXTDIR
make opt... |
e566f7f9687204f1829f0d144b5054052746c216b243340d34112fb3f02c9f97 | Shell | 1,035 | 26 | # Path of the folder containing all data
dir="/root/dir"
# List of subjects
declare -a sub=("sub-SPAIN01" "sub-SPAIN02" "sub-SPAIN04" "sub-SPAIN06" "sub-SPAIN07" "sub-SPAIN08" "sub-SPAIN11" "sub-SPAIN13" "sub-SPAIN15" "sub-SPAIN16" "sub-SPAIN19" "sub-SPAIN20" "sub-SPAIN21" "sub-SPAIN24" "sub-SPAIN25" "sub-SPAIN26" "su... |
5441f0ccd5fff74566f8cb943efb8ecbbf6f5e6c80591d58418cad451707d75b | Shell | 1,040 | 23 | #!/usr/bin/env zsh
job_id=$1
task_id=$2
dir="$3"
cp="$dir/checkpoints/checkpoint_last.pt"
echo "job_id: $job_id, task_id: $task_id, dir: $dir"
declare -A tasks
tasks[cola]="/fsx-wav2vec/abaevski/data/nlp/GLUE/CoLA-bin"
tasks[qnli]="/fsx-wav2vec/abaevski/data/nlp/GLUE/QNLI-bin"
tasks[mrpc]="/fsx-wav2vec/abaevski/data... |
ec2adc3ce7e1096cd6df8b2b4f4e61d21d0044d472bb2027abdba8de2e8e97f0 | Shell | 1,041 | 36 | #!/bin/bash
#
# Wrapper script to run polarLDA estimate on bootstrapped samples
#
# Written by Siyi Tang and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
# Take input variables
input_dir=$1 # absolute directory where the docs are saved
out_dir=$2
K=$3 # number of factors
N=$4 ... |
29d66f586fb8c4d7b5250e02e5a040da214a7bfbcf2bf0f1e198c96e6a793a0f | Shell | 1,044 | 37 | set -xe
device_id=7 # which device to run the program, for multi-gpus, set params like device_id=0,2,5,7. [Note that] the device index in python refers to 0,1,2,3 respectively.
# params
data_dir=./data/
data_name=gse90063_k562_ko_tf20_37160_19264
split=simulation
result_dir=./results
seed=1
epochs=15
batch_size=32 #3... |
a3c057cc4b1377631e44668f00879381deef21f2fe456fccaa77dac8ca74f033 | Shell | 1,044 | 21 | # Path of the folder containing all data
dir="/root/dir"
sct_dir="/sct/dir/6.5"
# List of subjects
declare -a sub=("sub-SPAIN01" "sub-SPAIN02" "sub-SPAIN04" "sub-SPAIN06" "sub-SPAIN07" "sub-SPAIN08" "sub-SPAIN11" "sub-SPAIN13" "sub-SPAIN15" "sub-SPAIN16" "sub-SPAIN19" "sub-SPAIN20" "sub-SPAIN21" "sub-SPAIN24" "sub-SPA... |
3d1ae44623a18f5314c3d2d5b3715f8b95aea1880cc7e73d4688b4f85ee9563c | Shell | 1,047 | 37 | set -xe
device_id=6 # which device to run the program, for multi-gpus, set params like device_id=0,2,5,7. [Note that] the device index in python refers to 0,1,2,3 respectively.
# params
data_dir=./data/
data_name=gse90546_k562_63587_19264_10k_log1p
split=simulation
result_dir=./results
seed=1
epochs=15
batch_size=30 ... |
48872b398ff8e31482b7de83cbb2ba1fc0d52587aa0c607b5c29a6b39e7421ad | Shell | 1,047 | 21 | # Path of the folder containing all data
dir="/root/dir"
sct_dir="/sct/dir/6.5"
# List of subjects
declare -a sub=("sub-SPAIN01" "sub-SPAIN02" "sub-SPAIN04" "sub-SPAIN06" "sub-SPAIN07" "sub-SPAIN08" "sub-SPAIN11" "sub-SPAIN13" "sub-SPAIN15" "sub-SPAIN16" "sub-SPAIN19" "sub-SPAIN20" "sub-SPAIN21" "sub-SPAIN24" "sub-SPA... |
f882d5301f787fe3a433e6f2d2a2959f9381fcaf6473dca99cdc4b056b49dc51 | Shell | 1,049 | 28 | #!/bin/bash
# Run it from retinotopy/ folder
export fs_folder=/egor2/egor/MovieProject2/bids_data/derivatives/freesurfer
# Define list of subjects
# subjects=$(ls -d $fs_folder/sub-* | awk -F'/' '{print $NF}' | sed 's/sub-//' | sort -n)
# subjects=("sub-01" "sub-02" "sub-03" "sub-04" "sub-05" "sub-06") # DONE
# subje... |
6508516d776622fc5e2fdca0a4e3318b27516aa9767d847289c5e56aa547d28b | Shell | 1,051 | 40 | #!/usr/bin/env bash
set -e
# This script documents how to build the singularity container
# from the Dockerfile
if [[ $(/usr/bin/id -u) -ne 0 ]]; then
echo "Must run script with sudo or as root"
exit
fi
# exit on errors
trap 'exit' ERR
# docker registry server to host docker image locally
# do nothing if ru... |
8be9c1b9efdc58a5437ac9b45ba9c247791a01737d0551646d66d295457c44ba | Shell | 1,056 | 16 |
## get embedding embedding already in the data folder
# CUDA_VISIBLE_DEVICES=0 python run_pytorch_embedding.py --ckpt_path ../0.1B-trans-pGAU-shuffle5-autobin100-mask0.3-bts1024-0226-bin100-k8s-lr1e-4-resume/models/model_step=35999.ckpt --ckpt_name 50M-0.1B-res
# ## Embedding
CUDA_VISIBLE_DEVICES=0 python run_DeepCDR... |
a43c1bd35e5c1acf446be9df66ea382f66c2cbe8f1c139f61a290c91a1f0e284 | Shell | 1,058 | 33 | #!/bin/bash
# Florian Bénitière 16/03/2025
# This script downloads and indexes AlphaMissense annotation files for VEP.
# It creates a dedicated directory for resources, fetches the necessary data
# for GRCh38 (hg38) assembly (command lines commented for GRCh37 (hg19)), and indexes them using tabix.
# Ensure that 'tab... |
421189f7e57cfc241f96c9c14a30b0d1cb45bef8b68746e79c490b510fd99baa | Shell | 1,059 | 27 | # Paths
dir="/root/dir"
# List of subjects
declare -a sub=("sub-SPAIN01" "sub-SPAIN02" "sub-SPAIN04" "sub-SPAIN06" "sub-SPAIN07" "sub-SPAIN08" "sub-SPAIN11" "sub-SPAIN13" "sub-SPAIN15" "sub-SPAIN16" "sub-SPAIN19" "sub-SPAIN20" "sub-SPAIN21" "sub-SPAIN24" "sub-SPAIN25" "sub-SPAIN26" "sub-SPAIN27" "sub-SPAIN28" "sub-SPA... |
27e6206a6134d3e7fd4c1941b3056566e93ff6c9b3919adfee442f03c7287c90 | Shell | 1,070 | 48 | #!/usr/bin/env bash
# Usage check
if [ $# -ne 2 ]; then
echo "Usage: $0 <fasta_file> <entries_per_file>"
exit 1
fi
# Input arguments
input_file="$1"
x="$2"
# Remove trailing .fasta if it exists to get a base name
# (If your file doesn’t end with .fasta, basename without the second argument
# will just remove th... |
141322e1eddfc158b6fd32724cfa9db004f797821d17476c0fd0f47cb9174b64 | Shell | 1,071 | 25 | # Path of the folder containing all data
dir="/root/dir"
# List of subjects
declare -a sub=("sub-SPAIN01" "sub-SPAIN02" "sub-SPAIN04" "sub-SPAIN06" "sub-SPAIN07" "sub-SPAIN08" "sub-SPAIN11" "sub-SPAIN13" "sub-SPAIN15" "sub-SPAIN16" "sub-SPAIN19" "sub-SPAIN20" "sub-SPAIN21" "sub-SPAIN24" "sub-SPAIN25" "sub-SPAIN26" "su... |
f0eddec2ac8832a0c0bcfab54d352134997a62e2a5f808a57daee04a91f55ea8 | Shell | 1,088 | 45 | #!/bin/bash
FAIRSEQ= # Setup your fairseq directory
config_dir=${FAIRSEQ}/examples/mr_hubert/config
config_name=mr_hubert_base_librispeech
# Prepared Data Directory
data_dir=librispeech
# -- data_dir
# -- train.tsv
# -- valid.tsv
label_dir=labels
# -- label_dir
# -- train.km
# -- valid.km
# -- dict.... |
c701d2153ab390a1c4cd8c68149cad3502b128958954784456c5a8242edc9fe4 | Shell | 1,090 | 21 | token=biomap ## change to yours
### Cell embedding
taskname=Baron_demo
tgthighres=a5
mkdir -p ./demo/${taskname}/${tgthighres}
python ./client.py --input_type singlecell --output_type cell --pool_type all --pre_normalized F --version 0.2 --tgthighres $tgthighres --data_path ./data/baron_human_samp_19264_fromsaver_dem... |
83a9581725c8a53461402c10830d7a9e10fc757b8969136d02680acc8da58e96 | Shell | 1,096 | 39 | #!/bin/bash
# Clean pdbs
dir=$(pwd)
reduce_exe=$dir/pdb_parser_scripts/reduce/reduce_src/reduce
pdb_dir=$1
pdb=$2
# Create data directories
mkdir -p $pdb_dir/cleaned
mkdir -p $pdb_dir/parsed
python $dir/pdb_parser_scripts/clean_pdb.py --pdb_file_in $pdb_dir/raw/$pdb.pdb \
... |
e8c4a78ad077327237b28b2e12f7936a67df148f565d75616213a07de3dc20b1 | Shell | 1,096 | 28 | #!/usr/bin/env zsh
dir="$1"
cp="$dir/checkpoints/checkpoint_last.pt"
echo "dir: $dir"
declare -A tasks
tasks[cola]="/fsx-wav2vec/abaevski/data/nlp/GLUE/CoLA-bin"
tasks[qnli]="/fsx-wav2vec/abaevski/data/nlp/GLUE/QNLI-bin"
tasks[mrpc]="/fsx-wav2vec/abaevski/data/nlp/GLUE/MRPC-bin"
tasks[rte]="/fsx-wav2vec/abaevski/dat... |
5979118a8564dad3f344f4caf0b7e4224f246261c1b039b207a6c029319b63c1 | Shell | 1,104 | 25 | # Path of the folder containing all data
dir="/root/dir"
# List of cervical spine images
declare -a sub=("sub-SPAIN01" "sub-SPAIN02" "sub-SPAIN04" "sub-SPAIN06" "sub-SPAIN07" "sub-SPAIN08" "sub-SPAIN11" "sub-SPAIN13" "sub-SPAIN15" "sub-SPAIN16" "sub-SPAIN19" "sub-SPAIN20" "sub-SPAIN21" "sub-SPAIN24" "sub-SPAIN25" "sub... |
72685c3ef67d23166966ec69caab89abb8d1032d97b6300c522fa2280c261301 | Shell | 1,105 | 33 | #!/usr/bin/env bash
# usage: bash binarize_manifest <dest_dir> <train_split> <valid_split>
DEST_DIR=$1
TRAIN_SPLIT=$2
VALID_SPLIT=$3
FAIRSEQ_ROOT=$4
mkdir -p $DEST_DIR
# split file path and lengths into separate files
cut -f1 $TRAIN_SPLIT.tsv > $DEST_DIR/train_fnames.txt
cut -f1 $VALID_SPLIT.tsv > $DEST_DIR/valid_f... |
1e9994ba884d3e6c4734a0e95f960207b020c75330fb0813b71c89b199c9ef46 | Shell | 1,114 | 41 | #!/bin/bash
# Written by Xiuming Zhang and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
###########################################
# Usage and Reading in Parameters
###########################################
# Usage
usage() { echo "
Usage: $0 <brainDir>
- brainDir Dire... |
b33fc23b856e2f2cf80ba612efd1f3230ad52f3568a479bbf097d5bc39bcdab6 | Shell | 1,115 | 33 | #!/bin/bash
# ---------------------------------------------------------------------
# SLURM script to run FunBurd Association Test Across Traits and Genelists
# ---------------------------------------------------------------------
#
#SBATCH --job-name=FunBurd
#SBATCH --time=02:00:00
#SBATCH --ntasks=4
#SBATCH --cpus... |
d71e42b1ce44a960e09e268af0cad6633a9cc2f14b48587453e8e54e39def3c5 | Shell | 1,121 | 48 | #!/usr/bin/env bash
set -euo pipefail
apt-get update && apt-get install -y --no-install-recommends apt-utils
apt-get update && apt-get install -y --no-install-recommends ca-certificates && \
update-ca-certificates
# (!) Keep the list below sorted (!)
# Use available packages from the Ubuntu release selected in Doc... |
398ceab3d825e91237a6062e8e7aa7e4f1f9d5f39c8d79d387396b68e390d802 | Shell | 1,125 | 33 | #!/bin/bash
# Submit Exp D transformer jobs to Slurm cluster
# Usage: conda activate kattn-sim && bash submit_expD_cluster.sh
LUSTRE=/lustre/grp/gglab/liut/K-attention/K-attention/Kattn-sim-dev
SIMDIR=$LUSTRE/src/simulation
mkdir -p /lustre/grp/gglab/liut/logs
# Override paths so new kattn is used (not old editable i... |
54e595cc4b1d75d3ebda04eb71df514bf041c96a275cfd5bb0895a8d47a00488 | Shell | 1,130 | 25 | #! /bin/sh
# Last successfully run on May 2nd 2017
# Written by [xxx] and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
# DO NOT CHANGE: This clears old freesurfer variables if they previously exists
if [ -n "$FREESURFER_HOME" ]; then
$FREESURFER_HOME/bin/clear_fs_env.csh
fi
... |
9ba0992a8b8baa324349ca30f53075518338dc6be3100ac2bc3a35722af85665 | Shell | 1,130 | 25 | #! /bin/sh
# Written by [xxx] and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
# Last successfully run on May 2nd 2017
# DO NOT CHANGE: This clears old freesurfer variables if they previously exists
if [ -n "$FREESURFER_HOME" ]; then
$FREESURFER_HOME/bin/clear_fs_env.csh
fi
... |
48f5845f861e2f04627965310f037125fa8badbf6778d03b9db17d3e281179cd | Shell | 1,131 | 27 | # Path of the folder containing all data
dir="/root/dir"
# List of subjects
declare -a sub=("sub-SPAIN01" "sub-SPAIN02" "sub-SPAIN04" "sub-SPAIN06" "sub-SPAIN07" "sub-SPAIN08" "sub-SPAIN11" "sub-SPAIN13" "sub-SPAIN15" "sub-SPAIN16" "sub-SPAIN19" "sub-SPAIN20" "sub-SPAIN21" "sub-SPAIN24" "sub-SPAIN25" "sub-SPAIN26" "su... |
60ec72391129b748300363dad4bba512fa11a2b69dd259a6af0b4a50bdebd768 | Shell | 1,137 | 46 | #!/bin/bash
if [ $# -ne 5 ]; then
echo "usage: $0 [dataset=wmt14/full] [langpair=en-de] [databin] [bpecode] [model]"
exit
fi
DATASET=$1
LANGPAIR=$2
DATABIN=$3
BPECODE=$4
MODEL=$5
SRCLANG=$(echo $LANGPAIR | cut -d '-' -f 1)
TGTLANG=$(echo $LANGPAIR | cut -d '-' -f 2)
BPEROOT=examples/backtranslation/subwor... |
112468a3e4a20c0c24786af50be595db7471656b2e8546c2668319f338cb3d08 | Shell | 1,142 | 29 | #!/bin/bash
# echo "If this is your first time installing Anaconda, you will need to run 'conda init bash' before running this script."
# echo "Run this command and then *restart the shell* for changes to take effect. Then run this script. Thank you!"
# read -p "Press Enter to continue..."
set -ex # abandon script on... |
f81a6bb4103194345a3bad2f4d1a5b223ed959ad8642f78d75f08c2cd9cee9ef | Shell | 1,147 | 37 | #!/bin/bash
#SBATCH --account=nn9114k
#SBATCH --time=24:00:00 --cpus-per-task 16 --mem-per-cpu=3936M
trait_id=$1
i_repeat=$2
CFG_FILE="optimize.e1_real.template.${trait_id}.${i_repeat}.cfg"
LOG_FILE="cmm_${SLURM_JOBID}.optimize.log"
CFG_FILE_WITH_ID="cmm_${SLURM_JOBID}.${CFG_FILE}"
#SBATCH --job-name=optimize_${JOB_ID... |
73a293135c2321b7b30b2e7968df7a05fb3efc4c48a9393e15cfff83c7a51445 | Shell | 1,148 | 39 | #!/bin/bash
# One-time setup script for installing Miniconda and dependencies for the Rest+TAU project
# ==== CONFIGURATION ====
ROOTDIR=/MyWorkingDirectory
cd ${ROOTDIR}/code
# ==== DOWNLOAD AND INSTALL MINICONDA ====
wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
chmod +x Miniconda3-lat... |
f78cdd368051616c2f84f260dec8f82e253a68f8622537b38d5544c478c2ac46 | Shell | 1,150 | 44 | #!/bin/bash
# converts 2d nii file into csv file
# Cyrus Eierud, TReNDS 112325
# Init variables
DIR_PREV=$(pwd)
mkdir /out/tmp_dir
# find project prefix
S_PREFIX_AND_FILE=$(echo /out/*_group_loading_coeff_.nii)
S_PREFIX="${S_PREFIX_AND_FILE##*/}" # strip path
S_PREFIX="${S_PREFIX%_group_loading_coeff_.nii}"
# E... |
8438bfc8e99572f13add6a709d8f7348077175517b668df1e4e6da5393c89de2 | Shell | 1,151 | 44 |
#!/bin/bash
# Usage: ./process_batch.sh list_sample_to_process.txt input_file_gvcf_path fasta_ref cpus
# set -euo pipefail
# Arguments
list_sample_to_process="$1"
input_file_gvcf_path="$2"
fasta_ref="$3"
cpus="$4"
batch_id=$(basename "${list_sample_to_process}")
mkdir -p data/processed/gvcf_per_sample/${batch_id}/... |
508fba9520eb20a64874ad73fa4b4e417646227608fb61d5e771e8d9634023a8 | Shell | 1,164 | 40 | #!/bin/bash
# Setup freesurfer and directories
export FREESURFER_HOME=/tools/freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.sh
export SUBJECTS_DIR=/data/elevchenko/MovieProject2/bids_data/derivatives/freesurfer/
export data_folder=/data/elevchenko/MovieProject2/bids_data
# Extract subject IDs dynamically from t... |
b1ba954ce46dd6c54e6ab9ec8b41eda7fc1688474da7c66fc106994fcf73fd35 | Shell | 1,170 | 34 | #!/bin/bash
#
# CBIG_prepend_prefix_to_function_name_wrapper.sh $file_path
# Wrapper function to search for all instances of a function name (without prefix)
# inside a predefined set of directories and replace them by the new function name
# with the prefix prepended, if prompted
# Input can be the function name, a f... |
ea5669d87aa704e61a89727b18751d02e4a9ed72dc45ed71f8c8078ec38acd5b | Shell | 1,179 | 39 | #!/usr/bin/env bash
#
# Copyright (c) 2016-present, Facebook, Inc.
# All rights reserved.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
#
RESULTDIR=result
DATADIR=data
mkdir -p "${RESULTDIR}"
mkdir -p "${DATADIR}"
if [ ! -f "${DATADIR}/f... |
0c494cc576ef770ef80a365b57d83eb5ad8c386c65e3a2177d99e4a12c33c9ee | Shell | 1,181 | 43 | #!/usr/bin/env bash
#
# Copyright (c) 2016-present, Facebook, Inc.
# All rights reserved.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
#
# This script applies quantization to the models from Table 1 in:
# Bag of Tricks for Efficient Text ... |
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