sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 17k | content stringlengths 1 200k |
|---|---|---|---|---|
49169bb1e89ae8be1c56ad2cf8c49c0b18772581a25034fcad4e11007c4188b3 | Shell | 556 | 10 | #!/bin/bash
# this function is the wrapper to run the `CBIG_pMFM_step1_generate_permutation_order_schaefer.m`
# Written by Kong Xiaolu and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
cd ../../../../part2_pMFM_control_analysis/STDFCD_permutation_Schaefer100/scripts
matlab -nospla... |
032433fc48b2cf192938afb73dda432146c3cfd24eed711fca6b3d1b264da623 | Shell | 558 | 23 | #!/bin/bash
work_path=$(dirname $0)
p=HEK293_RBP_HL_bind_matrix_total
p2=$p
la=10
# part=Test
mkdir $work_path/out
mkdir $work_path/out/models
mkdir $work_path/out/log
train_data='data/halflife/'$p'.train.npz'
test_data='data/halflife/'$p'.test.npz'
pred_data='data/halflife/'${p2}'.test.npz'
# CUDA_VISIBLE_DEVICE="0... |
9a2bc2dcaa17477b2cb61de607ea7ecac7e9e2afc13da518c9012d37cfff1d6c | Shell | 559 | 10 | #!/bin/bash
# this function is the wrapper to run the `CBIG_pMFM_step2_STDFCD_permutation_correlation_desikan.m`
# Written by Kong Xiaolu and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
cd ../../../../part2_pMFM_control_analysis/STDFCD_permutation_Desikan/scripts
matlab -nosplas... |
5a67536836d69769e5ec0edb7451e7e36e84b68405ef2914efc7a37717d0e990 | Shell | 563 | 23 | #!/bin/sh
# Written by Nanbo Sun and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
progressFile=${1}
fullList=${2}
# Do not return until all jobs are finished
if [ -z ${fullList} ]; then
noJobs=1
else
noJobs=`grep -c "^" ${fullList}`
fi
noJobsDone=0
noJobsDonePrev=-1
wh... |
5d65e5c2862bbd21c9961bf1560326b5666874501b8800b06f219c44cac107a7 | Shell | 564 | 25 | #!/bin/bash
#SBATCH --job-name=novae
#SBATCH --output=/gpfs/workdir/blampeyq/.jobs_outputs/%j
#SBATCH --time=00:30:00
#SBATCH --partition=gpu
#SBATCH --mem=32gb
#SBATCH --cpus-per-task=8
#SBATCH --gres=gpu:1
module purge
module load anaconda3/2023.09-0/none-none
source activate novae
cd /gpfs/workdir/blampeyq/novae/s... |
2063c443860d05d132d33826bb793e6e96f820d079ed83966e17c6e2697df210 | Shell | 565 | 18 | #!/bin/bash
#SBATCH --job-name=plot_power
#SBATCH --mail-type=END,FAIL
#SBATCH --mail-user=YOUR_EMAIL
#SBATCH --output=/path/to/logs/plot_power_%A.out
#SBATCH --error=/path/to/logs/plot_power_%A.err
#SBATCH --time=00:30:00
#SBATCH --cpus-per-task=1
#SBATCH --mem=1G
# Load the required Python environment.
module load Y... |
82b40a8d8e6d680e56f02d820bc591963d93553c77ffc1a6c082a63ec8fedd86 | Shell | 569 | 10 | #!/bin/bash
# this function is the wrapper to run the `CBIG_pMFM_step2_STDFCD_permutation_correlation_schaefer.m`
# Written by Kong Xiaolu and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
cd ../../../../part2_pMFM_control_analysis/STDFCD_permutation_Schaefer100/scripts
matlab -no... |
6e47108dcd55ac86961ad5d84e3c268a543090378e323e131483b860a014138b | Shell | 570 | 9 | #! /bin/bash
set -e
lcov --directory bin.v2 --capture --no-external --directory $(pwd) --output-file coverage.info > /dev/null 2>&1
lcov --extract coverage.info $(pwd)'/boost/beast/*' --output-file coverage.info > /dev/null
lcov --remove coverage.info $(pwd)'/boost/beast/_experimental/*' --output-file coverage.info > /... |
9233af6c103a87a8b52d637ad17ba469111c713fc2d78fd1048247e986417790 | Shell | 573 | 25 | #!/bin/bash
VERSION="v0.02"
NO_CACHE=""
# Parse command line options
while [[ "$#" -gt 0 ]]; do
case "$1" in
--no-cache)
NO_CACHE="--no-cache"
shift
;;
*)
echo "Unknown option: $1"
exit 1
;;
esac
done
docker build $NO_CACHE -t doduo1.umcn.nl/nnunet_for_pathology/sol2:... |
cc38e68d46aa4fd314842de34b4f55bf5daa274d11c76e2a6ff95c13fd15872e | Shell | 573 | 22 | #!/bin/sh
QUERY=$1
INDEX_DIR=$2
OUTPUT_DIR=$3
MAX_PARTITION_SIZE=200000
total_num=`wc -l ${INDEX_DIR}/${QUERY}.idx | awk '{ print $1 }'`
total_partition=$(($total_num / $MAX_PARTITION_SIZE))
# echo $total_num
# echo $total_partition"
for i in $(seq 0 $total_partition)
do
echo "downloading partition ${i}/${total_... |
d2ba72f65a231c2bb60864092fd4e19d6d3d4af2d205eb69e89fe7890c64b781 | Shell | 579 | 25 | #!/bin/bash
#SBATCH --job-name=novae
#SBATCH --output=/gpfs/workdir/blampeyq/.jobs_outputs/%j
#SBATCH --time=4:00:00
#SBATCH --partition=gpu
#SBATCH --mem=10G
#SBATCH --tmp=20G
#SBATCH --cpus-per-task=1
#SBATCH --gres=gpu:1
module purge
module load anaconda3/2023.09-0/none-none
module load gcc/15.1.0/gcc-15.1.0
modul... |
57f2f083c5c83777003e579f4049a2144a21505b409872064695369b160dab68 | Shell | 582 | 29 | #!/bin/sh
datadir="/media/sf_Projects"
datadir="/media/sf_MRI-Data/Projects"
project=${1}
datadir=${datadir}/${project}
#/${vnum}/${hum_num}
#bids=${vnum}_${hum_num}
#echo ${datadir}
search_dir=/the/path/to/base/dir
for entry in $(ls $datadir)
do
vnum="$entry"
echo $vnum
for entry in $(ls $datadir/$vnum)
do
... |
8d372309aa97494d09eee92f4a4dd483f4366c548ff9e112ebce21e5ada8e2a8 | Shell | 582 | 22 | #!/bin/bash
#SBATCH --job-name=novae
#SBATCH --output=/gpfs/workdir/blampeyq/.jobs_outputs/%j
#SBATCH --time=4:00:00
#SBATCH --partition=gpua100
#SBATCH --mem=10G
#SBATCH --tmp=20G
#SBATCH --cpus-per-task=1
#SBATCH --gres=gpu:1
module purge
module load anaconda3/2023.09-0/none-none
module load gcc/15.1.0/gcc-15.1.0
m... |
0ac5ca642d2c2254aae976bfbdd7ca875d4d5e4ce4503585d5e79bc82d7039d6 | Shell | 583 | 15 | #!/bin/bash
#$ -cwd
#$ -l bluejay,mf=10G,h_vmem=10G,h_fsize=100G,h_stack=256M
#$ -N download_reads
#$ -o ./logs/download.reads.$TASK_ID.txt
#$ -e ./logs/download.reads.$TASK_ID.txt
#$ -t 2-103
# https://www.ncbi.nlm.nih.gov/sra?term=SRP199498
FILELIST=/dcs04/lieber/lcolladotor/with10x_LIBD001/HumanPilot/Analysis/he_la... |
246cd6408d557eb9424af2f77b229346b48d46f3da9fe4cae7416bba88cab91f | Shell | 584 | 13 | #!/bin/bash
alignment_file="test/strap/ZACN.Homo_sapiens.filter2.fasta"
trait_file="test/strap/BodyMass_kg_permulation.cfg"
simulated_traits_file="test/strap/phylorest.tab"
output_file_unfiltered="test/strap/unfiltered.boot"
output_file_filtered="test/strap/filtered.boot"
alignment_format="phylip-relaxed"
python ct... |
53fd40d2604def967154827e4d867bdc15bd3852fa01ff121dd40a87d29f370a | Shell | 584 | 4 | cat $MONQ/medline/2014/baseline/medline14n0001.xml | sh preprocessMEDLINE.sh | gzip > $MONQ/medline/2014/baseline_annotated/medline14n0001.xml.gz
cat $MONQ/medline/2014/baseline/medline14n0002.xml | sh preprocessMEDLINE.sh | gzip > $MONQ/medline/2014/baseline_annotated/medline14n0002.xml.gz
cat $MONQ/medline/2014/basel... |
04ecb214478ab9eb275b336b636522e5405f71470ac934bcef6322bf3be644e9 | Shell | 589 | 15 | #!/bin/bash
#$ -cwd
#$ -l bluejay,mf=10G,h_vmem=10G,h_fsize=100G,h_stack=256M
#$ -N download_reads
#$ -o ./logs/download.reads.$TASK_ID.txt
#$ -e ./logs/download.reads.$TASK_ID.txt
#$ -t 2-13
# https://www.ncbi.nlm.nih.gov/sra?term=SRP199498
FILELIST=/dcs04/lieber/lcolladotor/with10x_LIBD001/HumanPilot/Analysis/hafner... |
c198e5092b2d56c0ee613529292e1ec76014c84a00c354fe52c2eec67abbd3fc | Shell | 593 | 17 | #!/bin/sh
#PBS -l walltime=01:00:0
#PBS -l mem=6gb
# Will come into play only if this script is qsub'ed
# Written by Xiuming Zhang and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
fast -R 0.3 -H 0.1 -o ${outDir}${filename} ${brain}
# Generate the partial GM list for template c... |
9079ca41ac6efc912410ec7b6e56eab6b03e26a84f55cc9827a0ef1f9c01f992 | Shell | 594 | 14 | #!/bin/bash
# Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
OUTDIR=data/CommonsenseQA
mkdir -p $OUTDIR
wget -O $OUTDIR/train.jsonl https://s3.amazonaws.com/commensenseqa/train_rand_split.j... |
a7aecc6adffdb7e25a247e82c66866bd74692f9fde997dfbcb0e610d8a5ed084 | Shell | 594 | 15 | #!/bin/bash
# Written by Nanbo Sun and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
./CBIG_MMLDA_infer_new_subjects.sh \
-i ${CBIG_CODE_DIR}/stable_projects/disorder_subtypes/\
Sun2019_ADJointFactors/infer_new_subjects/input/T1_list.txt \
-d ${CBIG_CODE_DIR}/stable_projects/diso... |
cbe49a478c465edef87bd5cf3d40f1bf9d020a7246ec6afa165be42bbeb49686 | Shell | 596 | 31 | #!/bin/bash
#SBATCH --time=8:00:00
#SBATCH --cpus-per-task=8
#SBATCH --array=1-9
#SBATCH --mem=96G
#SBATCH --qos=nopreemption
#SBATCH -p cpu
QUERY_PATH="path/to/query.txt"
query_name=$(sed -n "${SLURM_ARRAY_TASK_ID}p" $QUERY_PATH)
DATA_PATH="path/to/data/${query_name}"
OUTPUT_PATH="path/to/output/${query_name}"
VO... |
6678e88acbecf467eefa615d2c904aebd1a57ec22ee1f869432dc46713189995 | Shell | 597 | 20 | #!/bin/bash
if [[ "${transitional}" == "false" ]]
then
antsaffine.sh 3 ${anat} ${pet} pet2anat_
ln -s *Affine.txt ${participant}${suffix.pet2anat}
else
transitionalPet="${transitional}/tmp/*tmp-estimate.nii.gz"
#transitionalAff="${transitional}/transform/*${suffix.pet2anat}"
antsaffine.sh 3 \${... |
109da1975f4131802924f49433892f5b7989f6dc116a3f4b1cfc3dac440bf31f | Shell | 601 | 10 | #!/usr/bin/env bash
#SBATCH --job-name=hmmsearch_predict
#SBATCH --output=slurm_logs/hmmsearch_predict.out
#SBATCH --time=0-12:0
#SBATCH -n 1
#SBATCH -N 1
module apptainer
apptainer exec -e -B="/scratch/nxu/SFARI:/scratch/nxu/SFARI" ~/tools/transdecoder.v5.7.1.simg hmmsearch --cpu 40 -E 1e-10 --domtblout pfam.domtblou... |
b539a38cb407839c82ceb389696169622cc565c8a03f79b3dbc9cb40b19bd426 | Shell | 607 | 22 | #!/bin/sh
export LC_COLLATE=C
echo "// string constants"
echo ' "<unknown-field>",'
cat $1 | sort -f | uniq | sed 's/^/ \"/; s/$/\",/'
echo
echo "enum class field : unsigned short"
echo "{"
echo " unknown = 0,"
echo
#cat $1 | uniq | sort -f | sed 's/./\L&/g; s/^/\t/; s/$/,/'
cat $1 | sort -f... |
84723c9301d8775e2af0d2bc2e9e24433ebdfb2a84e91fb8df7425e2b61be839 | Shell | 609 | 23 | #!/usr/bin/env bash
#aws s3 cp s3://imlab-open/Data/MetaXcan/1000G-WB/ . --recursive
if [[ ! -d "data" ]] ; then
mkdir data
fi
if [ ! -f data/DGN-WB_0.5.db ]; then
wget https://s3.amazonaws.com/imlab-open/Data/MetaXcan/1000G-WB/data/DGN-WB_0.5.db -O data/DGN-WB_0.5.db
fi
if [[ ! -d intermediate ]] ; then
... |
9636908e1b9064d63cd8f68a27cd16cb276391f2e1dca6466d9efaff1691384d | Shell | 609 | 11 | #!/bin/sh
# Written by Jingwei Li and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
curr_SUBJECTS_DIR=$SUBJECTS_DIR
export SUBJECTS_DIR=$CBIG_CODE_DIR/data/templates/volume
cmd="mri_vol2vol --mov $CBIG_CODE_DIR/data/templates/volume/FSL_MNI152_FS4.5.0/mri/aparc+aseg.mgz --s FSL_M... |
09012fe320b52f36a5325d2fdaee7a75c7ad10715c9f11dfd79bdf17a53f3769 | Shell | 611 | 15 | # the absolute path to the extracted boost source archive (https://www.boost.org/users/download/)
set -e
set -x
BOOSTPATH=/tmp/boost_1_78_0
TMPPATH=/tmp/lslboost
# copy all needed boost files and rename all mentions of boost to lslboost
mkdir -p $TMPPATH
bcp --unix-lines --boost=$BOOSTPATH --namespace=lslboost --scan ... |
892366209392e72651cf51e8dfc984d383776040d4e6556e97f541ede0ea3e77 | Shell | 613 | 11 | #!/bin/bash
# Written by Nanbo Sun and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
cd ~/storage
rsync -a --exclude .git CBIG/* Standalone_Sun2019_ADJointFactors
# remove useless stable projects
rm -r Standalone_Sun2019_ADJointFactors/stable_projects/brain_parcellation
rm -r Stan... |
b4d5304b54ff1de1edc1a09d0de14146b38324851609587ea7a884fc5db2bc05 | Shell | 618 | 28 | #!/bin/bash
if (($# < 2)); then
echo "Usage: $0 compilerlist.txt benchfile.cpp"
else
compilerlist=$1
benchfile=$2
g=0
source $compilerlist
# for each compiler, compile benchfile and run the benchmark
for (( i=0 ; i<g ; ++i )) ; do
# check the compiler exists
compiler=`echo ${CLIST[$i]} | cut -d " " -f 1`
... |
e5bbfc244a6d8b30726b852a7d4ebc9a6d0cde04cd33adb09372df41ae21c35a | Shell | 621 | 13 | #!/bin/bash
docker run -ti --rm \
-v /tmp:/tmp \
-v /var/tmp:/var/tmp \
-v /home/cyrus/ext4max/fromSsd/Documents/trends/work/2023/jeremy/keater/docker111925/spect_bids/:/data \
-v /home/cyrus/ext4max/fromSsd/Documents/trends/work/2023/jeremy/keater/docker111925/spect_bids/derivatives/05/:/out \
-v /home/cyru... |
ef045a43b9a95d97a1ee98b76c8086111563ee90b223036d4ddaccbeaa393568 | Shell | 630 | 27 | #!/usr/bin/env bash
export PYTHONPATH=/home/rowanz/code/fakenewslm
max_seq_length=1024
num_tpu_cores=8
batch_size_per_core=2
model_type=$1
input_file=""
OUTPUT_DIR=""
init_checkpoint=""
model_type=""
let batch_size="$batch_size_per_core * $num_tpu_cores"
python validate.py \
--config_file=configs/${model_type}... |
82078de0f178b7a56bff7c71e0c55945efc2869250af00e20c91280f7b4b4133 | Shell | 631 | 38 | #!/bin/bash
set -u
val_sets="dev_other"
graph_name=graph
decode_suffix=""
decode_script="steps/decode_fmllr.sh"
decode_args=""
nj=60
. ./cmd.sh
. ./path.sh
. parse_options.sh
set -x
exp_dir=$1
data_root=$2
lang_test=$3
graph=$exp_dir/$graph_name
if [ ! -d $graph ]; then
utils/mkgraph.sh $lang_test $exp_dir $gra... |
6b1583f9dd17e77c1ed82daeb991d01f841353ba739d5df91ba9b32872746718 | Shell | 640 | 5 | bash down.sh GSM4653863_HC1 GSM4653863_HC1/barcodes.tsv.gz https://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4653nnn/GSM4653863/suppl/GSM4653863%5FHC1%5Fbarcodes.tsv.gz
bash down.sh GSM4653863_HC1 GSM4653863_HC1/features.tsv.gz https://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4653nnn/GSM4653863/suppl/GSM4653863%5FHC1%5Ffeatures.t... |
2af277554a6b84bbb69801b91252ce511fdca93b25d8633fd2ff54271d7774c4 | Shell | 641 | 15 | pip install gdown
cd data
mkdir -p Split_Dataset/Data
mkdir -p Split_Dataset/Ground_truth
cd Split_Dataset/Data/
gdown https://drive.google.com/uc?id=1IgxzmajC09aUTz_awABPD_iEJ2s1VR0E -O test.npy
gdown https://drive.google.com/uc?id=1xCoXFl0GTc5VbW7L-7joAL9ViudD0Nbh -O train.npy
gdown https://drive.google.com/uc?id... |
1062e01a1d626913c557dc7bf6bf57d24cab9cefde402f2ac9d5a478f5d99390 | Shell | 642 | 5 | # Stringtie needs ts tag from minimap2 to be able to detect splice junctions. merged.bam does not contain ts tags
# minimap2 does not accept PacBio Bam format, convert BAM to fastq first
sbatch -J bamtofastq -t 0-2:0 -N 1 -n 1 -o slurm_logs/bamtofastq.out --wrap="/home/s/shreejoy/nxu/miniforge3/envs/SQANTI3.env/bin/bed... |
1c07a94ef38e8925b0b9a6becc01a14d92715e11b01e0280bf7f611d336a6658 | Shell | 646 | 15 | sudo pip install gdown
cd data
mkdir -p Split_Dataset/Data
mkdir -p Split_Dataset/Ground_truth
cd Split_Dataset/Data/
gdown https://drive.google.com/uc?id=1IgxzmajC09aUTz_awABPD_iEJ2s1VR0E -O test.npy
gdown https://drive.google.com/uc?id=1xCoXFl0GTc5VbW7L-7joAL9ViudD0Nbh -O train.npy
gdown https://drive.google.com/... |
3dd9af8a30cead7c325232a5ffa1f2a86a72a8526a56f25069160eb80766248a | Shell | 651 | 15 | ## Script copies basic freesurfer files
##Written by Alexander Schaefer and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
for i in fsaverage fsaverage5 fsaverage6;
do mkdir ../FreeSurfer/$i/label/
mkdir ../FreeSurfer/$i/surf/
rsync -az $FREESURFER_HOME/subjects/${i}/label/*cortex.... |
716a0d66b7aa40e122d32da91a0fc6a01cc276050d51cc905f4f50652ce3cd6f | Shell | 651 | 41 | #!/bin/bash
set -eu
scriptdir=$(dirname "$0")
target=matlab
if (($# > 0))
then
case "$1" in
(--octave)
target=octave
;;
(--matlab)
target=matlab
;;
(*)
echo "recognized options are --octave or --matlab, default is matlab" 1>&2
... |
bc54b0847b2c2d5ddebd6ce5849834aaaa208d4dac8bbda0f64cac307c3120ec | Shell | 651 | 41 | #!/bin/bash
set -eu
scriptdir=$(dirname "$0")
target=matlab
if (($# > 0))
then
case "$1" in
(--octave)
target=octave
;;
(--matlab)
target=matlab
;;
(*)
echo "recognized options are --octave or --matlab, default is matlab" 1>&2
... |
e009b94615deeb248b2fde1a562094b48e3e0cd5c09a849365680e3a4afc432d | Shell | 651 | 20 | #!/bin/bash
# Florian Bénitière 16/03/2025
# It downloads the required indexed cache files for both GRCh38 GRCh38 (hg38) assembly (command lines commented for GRCh37 (hg19)).
ORIG_DIR=$(pwd)
path_project=resources/vep_cache/
mkdir -p $path_project
cd $path_project
# Download cache assembly data for vep
curl -O https... |
5787442dc809ecc986c47c984009d81608af241cfc63a2e8cdcf229bff6b1ee8 | Shell | 657 | 21 | #!/bin/bash
# --- HPC cluster specific SLURM settings ------------------------
# add your settings here.
#SBATCH --job-name="symmnet sweep"
#SBATCH --time=<xx:xx:xx>
#SBATCH ...
# ----------------------------------------------------------------
# --- HPC cluster specific setup:---------------------------------
# e.g. ... |
0fc76bbe70b2d00beee242a4b77b1f149a71ea05dcd6cfb5835e093882395695 | Shell | 662 | 26 | #!/bin/bash
source ../scripts/config.py
test -d ./output || mkdir ./output
n=1000
# for bedpe in ./hg19.*${n}.bedpe; do
for bedpe in ../data/hg19.*${n}_per_group.bedpe.gz; do
echo $bedpe
bn=`basename $bedpe .bedpe.gz`
../scripts/fetch_attention_bedpe.py \
$bedpe \
-m $SPLICEBERT \
... |
b3940575557af71d2380b46f743908d528a4abfa59b3a53b83d560dc637432ae | Shell | 664 | 30 | #!/bin/bash
# Nov 2023 TReNDS
# Simple HMC processing head motion correction
# SLURM array across 191 subject
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --mem=20g
#SBATCH -p qTRD
#SBATCH -t 1440
#SBATCH -J <SLURM-HMC-PET>
#SBATCH -e error%A.err
#SBATCH -o out%A.out
#SBATCH -A trends53c17
#SBATCH --mail-type=ALL
#SBATCH --mai... |
2a24803cab4d2906e7eee08e04375189096959e2a1ed5dfe7df4f90c90585354 | Shell | 667 | 23 | #!/bin/sh
mamba activate SQANTI3.env
cpat \
-x "data/Human_Hexamer.tsv" \
-d "data/Human_logitModel.RData" \
-g "full_nt.fasta" \
--min-orf=50 \
--top-orf=50 \
-o SFARI \
1> SFARI_cpat.output \
2> SFARI_cpat.error
scripts/orf_calling.py \
--orf_coord "SFARI.ORF_prob.tsv" \
--orf_fasta "SFARI.ORF_s... |
2e1d678d9f0db3c195627c9fbab3bb354214bfcf1625285eb8888ec6653bf7c3 | Shell | 668 | 26 | #!/bin/sh
export BIOLIB_LOG="debug"
if [[ "$(hostname)" == nia* ]]; then
echo "We are on Niagara"
mamba deactivate
module load NiaEnv/2019b python/3.11.5
source .virtualenvs/DeepTMHMM/bin/activate
else
echo "We are on narval"
module load python/3.11.5
source .virtualenvs/DeepTMHMM/bin/activate
fi
DIREC... |
75d5209d318365fdbc3a572ef8a1129d0c813b9f1be2e270463fec7cd422b0d1 | Shell | 668 | 27 | #!/bin/bash
#SBATCH -p gpu
#SBATCH --mem=32g
#SBATCH --gres=gpu:rtx2080:1
#SBATCH -c 2
#SBATCH --output=example_1.out
source activate mlfold
folder_with_pdbs="../PDB_monomers/pdbs/"
output_dir="../PDB_monomers/example_1_outputs"
if [ ! -d $output_dir ]
then
mkdir -p $output_dir
fi
path_for_parsed_chains=$output... |
d7bc2933f61aada5b882290167d8ae83f03be13e0e5fdd12155f9247ca98938a | Shell | 671 | 3 | #!/bin/bash
lang="$1"
PYTHONPATH=. PREFIX=INFER HYDRA_FULL_ERROR=1 python examples/speech_recognition/new/infer.py -m --config-dir examples/mms/asr/config/ --config-name infer_common decoding.type=viterbi dataset.max_tokens=4000000 distributed_training.distributed_world_size=1 "common_eval.path='/fsx-wav2vec/androstj/e... |
ed460904dd347e65b3717d9704e5ab2062bf508224d7234f9080a0adf8f6a7aa | Shell | 671 | 23 | #!/bin/bash
#SBATCH --job-name=submit_percolator
#SBATCH --output=slurm_logs/submit_percolator.out
#SBATCH --time=0-1:0
#SBATCH --nodes=1
#SBATCH --ntasks=1
ls data/tc-1154/*.pin | xargs -I {} tail -n +2 {} > pooled.pin
echo "$(head -1 data/tc-1154/tc_1154_F1A_JM10561.pin)" | cat - pooled.pin > temp && mv -f temp poo... |
64551d17d2e048a30de0a639257ed2e85455a58a8ceaa52887239eb2cdfac984 | Shell | 672 | 15 | #!/bin/bash
#SBATCH --job-name=sqanti3_qc
#SBATCH --output=slurm_logs/sqanti3_qc.out
#SBATCH --time=0-6:0
#SBATCH --nodes=1
#SBATCH --ntasks=1
mamba activate SQANTI3.env
python /home/s/shreejoy/nxu/tools/SQANTI3/sqanti3_qc.py \
-t 40 \
--skipORF \
--output SQANTI3_qc \
--CAGE_peak "${GENOMIC_DATA_DIR}"... |
f4d1c4c12137943f02dc2ab581ec78480c36e86f5f89e54b2183734b47227b62 | Shell | 675 | 23 | #!/bin/bash
#SBATCH --job-name=submit_percolator_2
#SBATCH --output=slurm_logs/submit_percolator_2.out
#SBATCH --time=0-1:0
#SBATCH --nodes=1
#SBATCH --ntasks=1
ls data/tc-1154/*.pin | xargs -I {} tail -n +2 {} > pooled_2.pin
echo "$(head -1 data/tc-1154/tc_1154_F1A_JM10561.pin)" | cat - pooled_2.pin > temp && mv -f ... |
1038caae91a5bf865b601ead257f81a7a4700ccb619c26b2aed825b51313161e | Shell | 690 | 35 | #!/usr/bin/env bash
langdir=""
lmdir=""
. ./cmd.sh
. ./path.sh
. parse_options.sh
arpa_lm=$1
data=$2
if [ -z $langdir ]; then
langdir=$data/lang
fi
if [ -z $lmdir ]; then
lmdir=$data/lang_test
fi
if [ ! -d $langdir ]; then
echo "$langdir not found. run local/prepare_lang.sh first" && exit 1
fi
mkdir -p $lmd... |
442edfb978239093d8f1a7447a485d4ba5e84233012ef17f72ad8c49f4d21c70 | Shell | 691 | 23 | #!/bin/sh
#PBS -l walltime=960:00:0
#PBS -l mem=500mb
# Written by CBIG/Xiuming Zhang under under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
# Print settings for future recall
date
echo Documents: ${docs}
echo K = ${noTopics}
echo Inference settings are:
cat ${curDir}CBIG_LDA_infSetting... |
e739e9834e9c00e62d3500bea28dc4c3d74406e6a33fe9268afc385e1a842204 | Shell | 694 | 23 | #!/bin/bash
BUCKET_NAME="vz-ffpe-showcase"
OUTPUT_DIR="./merscope"
for BUCKET_DIR in $(gsutil ls -d gs://$BUCKET_NAME/*); do
DATASET_NAME=$(basename $BUCKET_DIR)
OUTPUT_DATASET_DIR=$OUTPUT_DIR/$DATASET_NAME
mkdir -p $OUTPUT_DATASET_DIR
for BUCKET_FILE in ${BUCKET_DIR}{cell_by_gene,cell_metadata}.csv... |
4dcb3376aaf08d918bc8acfa1b1b9606bdd52a9bfd3bb649d32968e9c889aaa1 | Shell | 696 | 4 | cat /home/whatizit/monq/medline/2016/baseline/medline16n0001.xml | sh preprocessMEDLINE.sh | gzip > /home/whatizit/monq/medline/2016/baseline_annotated/medline16n0001.xml.gz
cat /home/whatizit/monq/medline/2016/baseline/medline16n0002.xml | sh preprocessMEDLINE.sh | gzip > /home/whatizit/monq/medline/2016/baseline_anno... |
1cea4e9f72742f3114aff58abe61408013f023e3f08e1ff901030d51af09e2a9 | Shell | 698 | 13 | #!/bin/sh
# Written by CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
cd ~/storage
rsync -a --exclude .git CBIG/* Standalone_Kong2019_MSHBM
# remove useless stable projects
rm -r Standalone_Kong2019_MSHBM/stable_projects/brain_parcellation/Schaefer2018_LocalGlobal
rm -r Standalone_... |
344192949b98cb2ab319ce685e1a215bf86ee4b812ef65012f066c46222b25a0 | Shell | 699 | 15 | #!/bin/bash
# LD_LIBRARY_PATH explicito: o binario acha libscalapack/libmpi por ele, nao por RPATH,
# e com ambiente limpo o SIESTA morre em milissegundos sem que o laco perceba.
export LD_LIBRARY_PATH=/usr/lib64/mpi/gcc/openmpi5/lib64:$LD_LIBRARY_PATH
export OMP_NUM_THREADS=8
unset OMP_PROC_BIND OMP_PLACES # OMP_P... |
03cfe50d5d6cd1a2f1ff7d309b45ef6845993677537fed9186868b947f9c6d15 | Shell | 702 | 11 | # (optional) create a new directory
mkdir Xenium_Prime_Human_Lung_Cancer_FFPE_outs
cd Xenium_Prime_Human_Lung_Cancer_FFPE_outs
# download H&E/alignment files
curl -O https://cf.10xgenomics.com/samples/xenium/3.0.0/Xenium_Prime_Human_Lung_Cancer_FFPE/Xenium_Prime_Human_Lung_Cancer_FFPE_he_image.ome.tif
curl -O https://... |
ec6a651b80c015767671f08341aa621849cd72b5dafc561d1d4f08d03aaa9596 | Shell | 706 | 20 | #!/bin/bash
#SBATCH --qos=high
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=16
#SBATCH --gpus-per-task=1
#SBATCH --mem=32G
#SBATCH --time=04:00:00
#SBATCH --job-name=interactive_nnunetv2
#SBATCH --output=/home/<username>/logs/slurm-%j.out
# First runs install of the latest verison available on our cluster, feel free to... |
356baed4de53130d8aa69e1de4f924a96ba557db87f79c7ab5fc1e1483af34e3 | Shell | 708 | 13 | #!/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_Kong2019_MSHBM
# remove useless stable projects
rm -r Standalone_Kong2019_MSHBM/stable_projects/brain_parcellation/Schaefer2018_LocalGlobal
rm -r Standalone_... |
5d12cc8c77135587ce85e4123b6b95ed07d318fe1211f4614a1802dd7cddbdb9 | Shell | 709 | 30 | #!/bin/bash
#SBATCH --job-name=novae
#SBATCH --output=/gpfs/workdir/blampeyq/.jobs_outputs/%j
#SBATCH --time=24:00:00
#SBATCH --partition=gpu
#SBATCH --mem=300G
#SBATCH --cpus-per-task=8
#SBATCH --gres=gpu:1
module purge
module load anaconda3/2023.09-0/none-none
module load gcc/15.1.0/gcc-15.1.0
module load cmake/3.31... |
77d63e4270c2dddecc1af3a6ea61322b4d1bbb8c355ce463f2100f1c7d20abea | Shell | 709 | 28 | # created by DebarpanB
# date 1st September, 2022
stage=0
# annotationdir='annotations/LABELS/'
#audiodir='/data1/srikanthr/Coswara/data_preparation/Coswara-Data-Extracted'
# pathfile='path_files/wav.scp'
# metadata_file='metadata_files/combined_data.csv'
audiocategory='counting-normal'
datadir_name='data'
#datadir=... |
c64642803354eff9202066cb397680f09b01cee896f786fb8b777366f356e391 | Shell | 722 | 30 | #!/bin/bash
#SBATCH --job-name=novae
#SBATCH --output=/gpfs/workdir/blampeyq/.jobs_outputs/%j
#SBATCH --time=24:00:00
#SBATCH --partition=gpu
#SBATCH --mem=300G
#SBATCH --cpus-per-task=8
#SBATCH --gres=gpu:1
module purge
module load anaconda3/2023.09-0/none-none
module load gcc/15.1.0/gcc-15.1.0
module load cmake/3.31... |
0f18248d693f02521bcad828fd337d3b63b1183e07bcd7675bdb35de79f1eb97 | Shell | 724 | 25 | #Compile all data independently of significance
for fil in $(ls $HOME/TWAS_data/*/*_exc_allpvals.txt | head -n 1)
do
head $fil -n 1 > $HOME/TWAS_data/all_exc_assocs_PGCancestryTWAS.txt
done
for fil in $(ls $HOME/TWAS_data/*/*_exc_allpvals.txt)
do
echo $fil
tail $fil -n +2 >> $HOME/TWAS_data/a... |
49de50bbf8ddb28e4188f5aaef73ab3e18412c5bb6cafd5dd943a48757d06cb2 | Shell | 726 | 19 | #!/bin/bash
#SBATCH --job-name=<job_name>
#SBATCH --mail-type=END,FAIL
#SBATCH --mail-user=<email_address>
#SBATCH --output=<log_dir>/<job_name>%A_%a.out
#SBATCH --error=<log_dir>/<job_name>%A_%a.err
#SBATCH --time=1:00:00
#SBATCH --cpus-per-task=8
#SBATCH --mem=1G
#SBATCH --array=0-<njobs-1>%<n_parallel_jobs> # explan... |
075ce68ccf3dadda06ec35c3cbb6f1f70d4eaff129f4dc00e32b8473913dbe88 | Shell | 728 | 13 | #!/bin/sh
#PBS -l walltime=3:00:0
# Will come into play only if this script is qsub'ed
# Written by Xiuming Zhang and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
fsl_reg ${GM} ${nonlinTmp} ${outDir}${filename}_GMToNonlinTmp -fnirt "--config=GM_2_MNI152GM_2mm.cnf --jout=${outDi... |
3376a2587aafcbf1b7f691a904af6e6c5c700eb62faf5e01edf463e9e35fdb25 | Shell | 728 | 25 | #!/bin/bash
# Setup directories
export FREESURFER_HOME=/tools/freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.sh
export data_folder=/data/elevchenko/MovieProject2/bids_data
# Extract subject IDs dynamically from the bids_data folder
subjects=$(ls -d $data_folder/derivatives/freesurfer/sub-* | awk -F'/' '{print $... |
fcfac796ffde5f3b2402a15416a34761b8c9493f3ef6af6a57148025964ca2b6 | Shell | 739 | 20 | #!/usr/bin/env zsh
dir="$1"
cp="$dir/checkpoints/checkpoint_last.pt"
echo "dir: $dir"
declare -A tasks
tasks[qnli]="/private/home/jgu/data/GLUE/QNLI-bin"
tasks[sst_2]="/private/home/jgu/data/GLUE/SST-2-bin"
lrs="5e-6 1e-5 2e-5 5e-5 1e-4 2e-4 5e-4 1e-3"
for task data_path in ${(kv)tasks}; do
for lr in $(echo "$lr... |
9ca5af833d810e20261076ed549bf2b68a80f28b978447e14e90f2baf9934701 | Shell | 741 | 17 | #!/bin/bash
# this function runs replication of all results in our paper
#
# Written by Kong Xiaolu and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
root_dir=`dirname "$(readlink -f "$0")"`
cd root_dir/part1_pMFM_main/scripts
bash CBIG_pMFM_step1_training_main_wrapper.sh
bash CB... |
f46235351ea4f72c1ca1651dea2020300bbb5387aa22238edcf64880b0c5c7d0 | Shell | 747 | 25 | #!/bin/bash
#SBATCH --account=nn9114k
#SBATCH --time=24:00:00 --cpus-per-task 16 --mem-per-cpu=3936M
CFG_FILE="makeinput.e1_real.cfg"
LOG_FILE="cmm_${SLURM_JOBID}.makeinput.log"
CFG_FILE_WITH_ID="cmm_${SLURM_JOBID}.${CFG_FILE}"
#SBATCH --job-name=makeinput_${JOB_ID}
source /cluster/bin/jobsetup
module purge # clear ... |
f30232762c03058f4f198eee80b96942f8caff46cee5a20603c81112b21014fa | Shell | 748 | 13 | #!/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_Kong2022_ArealMSHBM
# remove useless stable projects
rm -r Standalone_Kong2022_ArealMSHBM/stable_projects/brain_parcellation/Schaefer2018_LocalGlobal
rm -r S... |
706e1c2ce938571df679cf2d9bfde5dbe1da561bfc9ea79d80a78f06c00ac62d | Shell | 758 | 27 | #!/usr/bin/env sh
# Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
#
# Please follow the instructions here http://alt.qcri.org/tools/arabic-normalizer/
# to install tools needed for Arabic
ec... |
0d732a2c367c0ad3c45466fa4e1133b50909e2629e9991b0d06ff62707ed4236 | Shell | 765 | 14 | #!/bin/sh
# Written by Kong Xiaolu and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
cd ~/storage
rsync -a --exclude .git CBIG/* Standalone_Kong2021_pMFM
# remove useless stable projects
rm -r Standalone_Kong2021_pMFM/stable_projects/fMRI_dynamics/Liegeois2017_Surrogates
rm -r Sta... |
209fb7680fb1de7b68fb76419f8bb9e1cb4b3c60111ef052a5106510388edbfb | Shell | 766 | 19 | #!/usr/bin/env zsh
dir="$1"
cp="$dir/checkpoints/checkpoint_last.pt"
echo "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-bin"
tasks[rte]="/private/home/jgu/data/GLUE/RTE-bin"
tasks[sst_2]... |
f95cedbeb2d5931a65baf1079acbafa75b307d04c3af4a01e310a66dc3e5e525 | Shell | 773 | 20 | #!/bin/bash
# Written by Xiuming Zhang and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
cd ../lib/
smoothingSigma=4.246
queue=circ-spool
# VBM from scratch on 810 ADNI-1 baseline scans
brainList=/data/users/xzhang/storage/forPNASRelease/outputs/VBM_bl/brainList.txt
outDir=~/st... |
8173a880bb6d1d7f9ef48c503000f697636e89a91e0095b9f0c8e447b354fedd | Shell | 777 | 42 | #!/usr/bin/env bash
project=$1
log_path="./log/${project}/"
[[ -d $log_path ]] || mkdir -p $log_path
_LOG_INFO() {
echo -e "$(date "+[%Y-%m-%d %H:%M:%S]")\tINFO\t$2\t$1" >>./log/${project}/info.log
}
_LOG_ERROR() {
echo -e "$(date "+[%Y-%m-%d %H:%M:%S]")\tERROR\t$2\t$1" >>./log/${project}/error.log
exit $2
}
li... |
bcec597708ede8ec67fc02c7c5dad38518aa77f959d1b7515e8a64fd79604646 | Shell | 782 | 33 | #!/bin/bash
# Nov 2023 TReNDS
# PETPrep was run on 190 subjects successfully using SLURM array
# Some subjects did not complete unless memory was increased to 30GB
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --mem=20g
#SBATCH -p qTRD
#SBATCH -t 1440
#SBATCH -J <PETPrep>
#SBATCH -e error%A.err
#SBATCH -o out%A.out
#SBATCH -A tr... |
c430e1063532c8a6d5fbb69f140f8077383aa04be2529f1947de6332bce7092a | Shell | 782 | 11 | #!/bin/sh
# commands to update the document pages from homepage
lynx -dont_wrap_pre -dump "http://iso2mesh.sourceforge.net/cgi-bin/index.cgi?keywords=Download&embed=1" > Download_and_License.txt
lynx -dont_wrap_pre -dump "http://iso2mesh.sourceforge.net/cgi-bin/index.cgi?keywords=Doc/Installation&embed=1" > INSTALL.t... |
d849fa7d1e8d8edcc5b9fdf70cbbc0238b4b19c5fc9e72f0006d33760231bf39 | Shell | 784 | 28 | # created by DebarpanB
# date 1st September, 2022
stage=0
annotationdir='annotations/LABELS/'
#audiodir='/data1/srikanthr/Coswara/data_preparation/Coswara-Data-Extracted'
pathfile='path_files/wav.scp'
audiocategory='breathing-deep,breathing-shallow,cough-heavy,cough-shallow,vowel-a,vowel-e,vowel-o,counting-normal,cou... |
16ac2327c7a652ed5c56754a81a06a516af942714288b97ab1fa7fde4a8634a9 | Shell | 787 | 19 | # the absolute path to the extracted boost source archive (https://www.boost.org/users/download/)
set -e
set -x
BOOSTPATH=/tmp/boost_1_69_0
TMPPATH=/tmp/lslboost
# copy all needed boost files and rename all mentions of boost to lslboost
mkdir -p $TMPPATH
bcp --unix-lines --boost=$BOOSTPATH --namespace=lslboost --scan ... |
ae29207c80fe80f64fc5fc35778f3dcbb8c7ef82f20f352980abd09ece70b1e2 | Shell | 790 | 26 | #!/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.
lang_pairs="en-fr,en-cs,fr-en,cs-en"
path_2_data=$1 # <path to data>
lang_list=$2 # <path to a file which conta... |
6ef04412e1d9a25fbdbd9b43761185eebb64c2b26dff73308705508e41d20f23 | Shell | 798 | 17 | pip install gdown
cd data
mkdir -p Split_Dataset/Data
mkdir -p Split_Dataset/Ground_truth
cd Split_Dataset/Data/
gdown https://drive.google.com/uc?id=1L-4spewLWN7jMzA5uTiBNTHhPl926j64 -O relish_documents.tsv
gdown https://drive.google.com/file/uc?id=1-c-00aJd_ybSL17Jqs22nEKMPd1lz4TZ -O input_train_text_data.tsv
gdow... |
2053dbbb28eed9602c7eef322c311aef4ef14e1e0b2767402d7f10d0cac373f2 | Shell | 801 | 14 | #!/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_Schaefer2018_LocalGlobal
# remove useless stable projects
rm -r Standalone_Schaefer2018_LocalGlobal/stable_projects/brain_parcellation/Kong2019_MSHBM
rm -r S... |
fd5bc04a546e7e44a0b16bc1da0a9856e6822ce20c6a1fd1256b16feb15d928d | Shell | 801 | 19 | #!/usr/bin/env bash
# Example: train a NEMO bimodal embedding on a C4-format dataset and evaluate
# k-NN classification on a held-out labelled set.
#
# Prerequisites:
# - Install the NEMO package: pip install -e comparison_methods/nemo
# - C4 H5 datasets available locally (set NEMO_DATASETS_DIR or place files
# ... |
3fd88e1e9b90342f0d3695bae4ff78d5397426c6020ad14bb54101babd8ab5f8 | Shell | 806 | 29 | #!/bin/bash
output_file_unfiltered="test/strap/unfiltered.boot"
output_file_filtered="test/strap/filtered.boot"
# Step 1. Select a species to be modified
species="Tarsius_wallacei" # Now this is Tarxius_wallacei
# Step 2. Select the cycles where this species appears LIST 1
cat test/strap/phy... |
771bd34bc29076b588d1e11a3c2ed467b93faefc4151f302abd6ada31f1ab876 | Shell | 810 | 19 | #!/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... |
5d76ea92df2561b1e9b473d21c50c1d6b604aa808f8fc464bdf3bd9b4c36a145 | Shell | 824 | 19 | #!/bin/bash
CHR_IDS="21 22";
ANNOT_F="../annot.test"
SUMSTATS_F="../sumstats.tets"
for i in ${CHR_IDS}; do
head chr${i}.bim | cut -f2 > chr${i}.snps.test;
plink --make-bed --bfile chr${i} --extract chr${i}.snps.test --out ../chr${i}.test;
plink --bfile ../chr${i}.test --freq --out ../chr${i}.test;
pli... |
d959a95eda2b2072a395776015b71016f0c96c0f4ba2da25af6a84bb69966c44 | Shell | 824 | 27 | #!/bin/bash
# Copyright (c) Facebook, Inc. and its affiliates.
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
set -eu
train_json=$1
sr=$2
nbins=$3
out_dir=$4
out_prefix=$5
f0_dir="$out_dir/f0"
python examples/textless_nlp/pgslm/preprocess... |
b883115548d067fca1aaba828870ffdbbfde1026965afb3a6d7fd3fb069026f6 | Shell | 826 | 35 | #!/bin/bash
num_sil_states=3
num_nonsil_states=1
. ./cmd.sh
. ./path.sh
. parse_options.sh
set -eux
dict=$1
data_dir=$2
lexicon=$3
dict_dir=$data_dir/local/dict_word
tmplm_dir=$data_dir/local/lang_tmp_word
lm_dir=$data_dir/lang_word
mkdir -p $dict_dir $tmplm_dir $lm_dir
# prepare dict
echo "SIL" > $dict_dir/sile... |
a4ae1ff2503b2fa98e0501a05c56d116f2a5cdd0dcf55dac21afe448b3ce5f90 | Shell | 827 | 33 | #!/bin/bash
# Adapted from https://github.com/facebookresearch/MIXER/blob/master/prepareData.sh
URLS=(
"https://s3.amazonaws.com/research.metamind.io/wikitext/wikitext-103-v1.zip"
)
FILES=(
"wikitext-103-v1.zip"
)
for ((i=0;i<${#URLS[@]};++i)); do
file=${FILES[i]}
if [ -f $file ]; then
echo "$... |
aada08a8d0189826ccb1f8e829f50755a1e68620f8916032029e8f934ac4bedf | Shell | 836 | 23 | #!/bin/sh
# create MNI 1mm mask
mask_MNI1mm=GM_Mask_MNI1mm
mri_binarize --i ${CBIG_CODE_DIR}/data/templates/volume/FSL_MNI152_FS4.5.0/mri/aparc+aseg.mgz --match 2 41 77 251 252 253 254 255 7 46 4 5 14 43 44 15 72 31 63 0 24 --inv --o $mask_MNI1mm.nii.gz
# downsample MNI 1mm mask to MNI 2mm mask
input=${mask_MNI1mm... |
9eb8b1e9cb1fa620cfbc126de0c921abf015148f3ae45d7c9e5c0ff2a4e846d9 | Shell | 838 | 14 | #!/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_Xue2021_IndCerebellum
# remove useless stable projects
rm -r Standalone_Xue2021_IndCerebellum/stable_projects/brain_parcellation/Schaefer2018_LocalGlobal
rm ... |
7c2147277a5d0ff4e348782342a8fb37acbf150c31b3ab57b161e97c986aa02a | Shell | 840 | 44 | #!/bin/bash
work_path=$(dirname $0)
name=$(basename $work_path)
da=clip_data
if [ ! -d $work_path/out ];then
mkdir $work_path/out
mkdir $work_path/out/log
fi
# N threads according to your GPU
SEND_THREAD_NUM=2
###########################
tmp_fifofile="/tmp/$$.fifo"
mkfifo "$tmp_fifofile"
exec 6<>"$tmp_fifofi... |
daf9d113cee8cff3444c5e0752f2f9dcc0de67d5bf5be34592c01582258e3923 | Shell | 840 | 25 | #!/usr/bin/env bash
set -euo pipefail
# Run IsoQuant for Nanopore long-read cDNA-seq data from mouse cerebellar GCP samples.
# Run this script from the repository root after placing input/reference files in the paths below.
REFERENCE_FASTA="reference/Mus_musculus.GRCm39.dna.primary_assembly.fa"
ANNOTATION_GTF="refere... |
58001111390590d1449e4af1699f4623b45b3f6ceb51437c72398af9bf8a3118 | Shell | 841 | 48 | #! /bin/bash
WHAT=$1
DIR=$2
MINIC=$3
MAXIC=$4
MINOC=$5
MAXOC=$6
meanstatsfilename=$2/mean.html
WORK_DIR=tmp
mkdir $WORK_DIR
DATA_FILE=`find $DIR -name "*.dat" | grep _${WHAT}`
echo ""
echo "$1..."
for FILE in $DATA_FILE
do
##echo hello world
##echo "mk_mean_script1" ${FILE}
BASE=${FILE##*/} ; BASE=$... |
07896e3280706a3d8228035b340068900ec3dfedc21c63d15e698ac8978c30e1 | Shell | 845 | 26 | export MODEL_PATH=/home/zhihan/6
# for cp in $(ls $MODEL_PATH)
# do
# cd $MODEL_PATH/$cp
# mv checkpoin* checkpoint-0
# done
for model in $(ls $MODEL_PATH | head -345)
do
export MODEL="$model"
export CHECKPOINT=$(ls $MODEL_PATH/$MODEL)
CUDA_VISIBLE_DEVICES=0 python run_finetune.py \
--mode... |
f5708d9fb3e4c9f69d04e38e36d87027f64f3a6f8e5cf0c68e570ea4017b3447 | Shell | 846 | 27 | #!/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... |
5706da6b6550d8624291c24221ada35ac3393c13ede4b2bb62fb1fdc5a55610f | Shell | 848 | 16 | #!/bin/bash
# work3: so os 12 pontos SOC, em spin-orbit+onsite (o offsite com projetores lj infla o SOC do Pb em 31 % no atomo isolado com o conjunto stringent)
# LD_LIBRARY_PATH explicito: o binario acha libscalapack/libmpi por ele, nao por RPATH,
# e com ambiente limpo o SIESTA morre em milissegundos sem que o laco p... |
a21cc9fd716744d9ed5932d236c892456b6ab861f68373243d74203514ae23ef | Shell | 851 | 32 | #!/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\>... |
94cc7e72d86b1fe9f206fb968b0cd269ee55af2f6677cdb7fe6f289ca80e510c | Shell | 853 | 31 | #!/bin/bash
# Load MRIQC module (adjust based on your HPC environment)
module load mriqc
# Set cohort and timepoint
Cohort='Cohort1' # adjust as needed
Timepoint='T1' # adjust as needed
# Define root directory
ROOTDIR=/MyWorkingDirectory
# Clean up and reorganize individual MRIQC outputs
for s i... |
d16f336686120dcef8f0d8f2b52b350cba065214b5fa1e8ed488e48042255df4 | Shell | 862 | 16 | #!/bin/bash
# roda cada script em sem_copias/ (SEM_COPIAS=1) e em controle_completo/ (SEM_COPIAS=0)
source /home/david/ambientes/alignn/bin/activate
export OMP_NUM_THREADS=16 PYTHONWARNINGS=ignore MPLBACKEND=Agg
BASE=/home/david/atual/new-methods/submissions/oce-jpcc-perovskites/REVISAO_R1/calculos
LISTA="r1_eta2_e_neg... |
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