sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
d03639a5098eea3c25e47964613c4da03eff33e65789e551ea702ef32b2b22e1 | Shell | 951 | 33 | #!/bin/bash
##################################### Quality control for the CNV and plot difference in the CN detection #####################
if [ -v $1 ]
then
echo 'to run this script you need R with the following packages: argparse, ggplot2, grid, gridExtra'
echo 'this script should be run like this:'
echo './Cnv_D... |
66cb3e86e24d292b06d5cc01af8df1ff3d427e0f22dc5ace0aa3a4b957554f00 | Shell | 953 | 36 | #!/bin/bash
#SBATCH --partition=gpu4_medium
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --mem=30G
#SBATCH --job-name=04_Add_Header
#SBATCH --output=rq_04_Add_Header_%A_%a.out
#SBATCH --error=rq_04_Add_Header_%A_%a.err
module load pathganplus/3.6
python3 ./utilities/h5_handling/nc_create_metadata_h5.py ... |
daebbed4db5e20947f287e950eaa105392d65b84bd0b7a2829458a17ade0d27c | Shell | 955 | 20 | #!/bin/bash
#SBATCH --account=def-lpenacas
#SBATCH --time=00:02:00
#SBATCH --mem=1G
module load bedtools
bash odb_labels.sh -d ../../operons/data_odb -t 224308 -n old_locus_tag=
# bash odb_labels.sh -d ../../operons/data_odb -t 196627 -n locus_tag=
bash odb_labels.sh -d ../../operons/data_odb -t 511145 -n locus_tag=... |
165307c8837f51cce898985de271aafb0445b5154a5cda5c3793400c950d1fdb | Shell | 957 | 23 | export OUTPUT_PATH=outputs/experiment/perturb/synthetic_data/sage
export WANDB_API_KEY=YOUR_WANDB_KEY
DATASET_NAME=nonlinear_additive
DATA_SIZE=100000
FEATURE_DIM=1000
python perturb_synthetic_data.py nonlinear-additive-sage-inverse-loss \
--pert.perturbation-num 5 \
--pert.sage.n-permutations 256000 \
--p... |
106066c1576261a3a5337506d490046cadeaad3cd2b8560d4b2430c10bcd0fd7 | Shell | 959 | 23 | export OUTPUT_PATH=outputs/experiment/perturb/synthetic_data/lime
export WANDB_API_KEY=YOUR_WANDB_KEY
DATASET_NAME=orange_skin_additive
DATA_SIZE=10000
FEATURE_DIM=100
python perturb_synthetic_data.py orange-skin-additive-lime-inverse-loss \
--pert.perturbation-num 3 \
--pert.sage.n-permutations 256000 \
-... |
4907ff165181a1b5d09dff8e9dc05254838889dfeeff3ee52f924269d5a6f428 | Shell | 959 | 23 | export OUTPUT_PATH=outputs/experiment/perturb/synthetic_data/sage
export WANDB_API_KEY=YOUR_WANDB_KEY
DATASET_NAME=orange_skin_additive
DATA_SIZE=10000
FEATURE_DIM=100
python perturb_synthetic_data.py orange-skin-additive-sage-inverse-loss \
--pert.perturbation-num 3 \
--pert.sage.n-permutations 256000 \
-... |
cef37c69c3826529dd9828d2a37dcbfe17f609c28dc05bba3af9707c9994a1f8 | Shell | 959 | 19 | python train.py --model.dim 64 \
--model.input-dim 334 \
--trainer.starting_cell_type HSC_2 \
--trainer.deep_velo_model_dim 334 \
--trainer.cell_type_ratio_keys DCs Precursors \
--trainer.train-batch-size 64 \
--trainer.train-num-steps 3000 \
--trainer.save-and-sample-every 500 \
--train... |
1120fe4421c9b4dba0a6c71670960d71aa34a22d9faafe338c9470fb30bd4f60 | Shell | 961 | 23 | export OUTPUT_PATH=outputs/experiment/perturb/synthetic_data/fimap
export WANDB_API_KEY=YOUR_WANDB_KEY
DATASET_NAME=orange_skin_additive
DATA_SIZE=10000
FEATURE_DIM=100
python perturb_synthetic_data.py orange-skin-additive-fimap-inverse-loss \
--pert.perturbation-num 3 \
--pert.sage.n-permutations 256000 \
... |
b2320fdd2b133092d55bba3137eeaf35c076a6bc0e5bb4d4585369c84d91c089 | Shell | 965 | 33 | #!/bin/bash
##################################### Quality control for the CNV and plot difference in the CN detection #####################
if [ -v $1 ]
then
echo 'to run this script you need R with the following packages: argparse, ggplot2, grid, gridExtra'
echo 'this script should be run like this:'
echo './Cnv_D... |
cdfcd33041314208e1b6ae2571bff6e94415554472b3ef443ca6f90c610b07dd | Shell | 965 | 23 | export OUTPUT_PATH=outputs/experiment/perturb/synthetic_data/cxplain
export WANDB_API_KEY=YOUR_WANDB_KEY
DATASET_NAME=orange_skin_additive
DATA_SIZE=10000
FEATURE_DIM=100
python perturb_synthetic_data.py orange-skin-additive-cxplain-inverse-loss \
--pert.perturbation-num 3 \
--pert.sage.n-permutations 256000 \... |
3cb171eda64763c8ef371528344d6730bf875c82be1f88385dfac5a61dee65e7 | Shell | 967 | 23 | export OUTPUT_PATH=outputs/experiment/perturb/synthetic_data/saliency
export WANDB_API_KEY=YOUR_WANDB_KEY
DATASET_NAME=orange_skin_additive
DATA_SIZE=10000
FEATURE_DIM=100
python perturb_synthetic_data.py orange-skin-additive-saliency-inverse-loss \
--pert.perturbation-num 3 \
--pert.sage.n-permutations 256000... |
8535b3e43d4af2ab3b4fc819f871412d508073ec50bd919fc30a343e3402ed7a | Shell | 971 | 25 | #!/bin/bash
##################################### Match sample base on genotype and create new annotation file for the merging #####################
if [ -v $1 ]
then
echo 'to run this script you need R with the following packages installed: argparse, circlize, ComplexHeatmap, RColorBrewer, doParallel'
echo 'this sc... |
9b6b1aeb49214d5b96cc775c4b9d80b0a5f647a60f06f893b584ef0571c870cb | Shell | 973 | 23 | export OUTPUT_PATH=outputs/experiment/perturb/synthetic_data/permutation
export WANDB_API_KEY=YOUR_WANDB_KEY
DATASET_NAME=orange_skin_additive
DATA_SIZE=10000
FEATURE_DIM=100
python perturb_synthetic_data.py orange-skin-additive-permutation-inverse-loss \
--pert.perturbation-num 3 \
--pert.sage.n-permutations ... |
5fff76758308d3b8312433eb70483594ba842f152a3b48ba150d201d2f8a10cb | Shell | 981 | 23 | export OUTPUT_PATH=outputs/experiment/perturb/synthetic_data/smooth_saliency
export WANDB_API_KEY=YOUR_WANDB_KEY
DATASET_NAME=orange_skin_additive
DATA_SIZE=10000
FEATURE_DIM=100
python perturb_synthetic_data.py orange-skin-additive-smooth_saliency-inverse-loss \
--pert.perturbation-num 3 \
--pert.sage.n-permu... |
75bb5e0f7dc46dbfb1a1165c18b12deb95d14496505ffe7215cee6c8984780b1 | Shell | 981 | 23 | export OUTPUT_PATH=outputs/experiment/perturb/synthetic_data/mean_importance
export WANDB_API_KEY=YOUR_WANDB_KEY
DATASET_NAME=orange_skin_additive
DATA_SIZE=10000
FEATURE_DIM=100
python perturb_synthetic_data.py orange-skin-additive-mean_importance-inverse-loss \
--pert.perturbation-num 3 \
--pert.sage.n-permu... |
31bfde6adbfab91d39376cacd62a9ca62d3e6a7fc1be9e73739848bb1c0eee7b | Shell | 982 | 29 | #!/bin/sh
SCRIPTSDIR=$(cd "$(dirname "$0")"; pwd)
BASEDIR="$(dirname "$SCRIPTSDIR")"
cd "$BASEDIR"
CMP_BUILD_DATE="$(date -u +"%Y-%m-%dT%H:%M:%SZ")"
echo "$CMP_BUILD_DATE"
VERSION="v$(python get_version.py)"
echo "$VERSION"
VCS_REF="$(git rev-parse --verify HEAD)"
echo "$VCS_REF"
MAIN_DOCKER="sebastientourbier/mial... |
5dd9952028032e061dddb32b713489ea0b0b1f1bc7b495c8de031c9278b854e9 | Shell | 983 | 23 | export OUTPUT_PATH=outputs/experiment/perturb/synthetic_data/feature_ablation
export WANDB_API_KEY=YOUR_WANDB_KEY
DATASET_NAME=orange_skin_additive
DATA_SIZE=10000
FEATURE_DIM=100
python perturb_synthetic_data.py orange-skin-additive-feature_ablation-inverse-loss \
--pert.perturbation-num 3 \
--pert.sage.n-per... |
e48dec4df7dbb850f20192aebd3256d28c2f88ffefda3dd42313baa8e665eda6 | Shell | 983 | 23 | export OUTPUT_PATH=outputs/experiment/perturb/synthetic_data/permutation_test
export WANDB_API_KEY=YOUR_WANDB_KEY
DATASET_NAME=orange_skin_additive
DATA_SIZE=10000
FEATURE_DIM=100
python perturb_synthetic_data.py orange-skin-additive-permutation_test-inverse-loss \
--pert.perturbation-num 3 \
--pert.sage.n-per... |
6e1461247df61e67deae4e5d11898f08eb5ab0f416107ab69d9ebe7d058e52d9 | Shell | 1,009 | 43 | #!/bin/bash
##################################### Plot LRR and BAF with detected CN #####################
if [ -v $1 ]
then
echo 'to run this script you need R with the following packages installed: ggplot2, argparse, grid, gridExtra'
echo 'this script should be run like this:'
echo './Cnv_Plot_LRR-BAF.sh <path Rscr... |
cad6b1ed415ca969ece84ef09a353473a3772432bbcd7666eb883674c9218317 | Shell | 1,009 | 36 | #!/bin/bash
Help()
{
# Display Help
echo "SynDIR: scriptTemplate [-r|d|l]"
echo "options:"
echo "r RNA-seq access codes separated by ','."
echo "d Directory"
echo "l Layout, P for Paired or S for Single."
}
while getopts r:d:l: flag
do
case "${flag}" in
d) DIR=${OPTARG};;
... |
14329117825ddb367644cf9fde7c5dcfaefe44922f5b8a4970ae31deb02224fb | Shell | 1,025 | 21 | #!/usr/bin/env bash
# VisA (all 12 categories): matched ResNet18-GLASS baseline, 100 epochs.
# Same data/schedule/config as the proposed model; ONLY the backbone differs.
# Faithful GLASS light backbone: layer2 (/8) + layer3, NO gate -> --downsampling 8.
datapath=/content/VisA
augpath=/content/dtd/images
python main... |
b9936d6bb434d380fd51b96bcc5c22efad42813201346ae01ed88b0ff2768d51 | Shell | 1,025 | 46 | #!/usr/bin/env bash
### Parse HCVC segmentations (simple)
## Extract voxel num for each label and calculate complete HV/CSF
## Labels:
## 11 - L-HC
## 12 - L-CSF
## 21 - R-HC
## 22 - R-CSF
set -x
IN_DIR=$1
OUT_FILE=$2
LHC=${3:-11}
RHC=${4:-21}
LCSF=${5:-12}
RCSF=${6:-22}
[ ! -d $IN_DIR ] && exit 1
[ -f $OUT_FILE ]... |
94dd805831ff0e29e6887f084453c34628251d5bdf2af79857c73e3cb1bb21c8 | Shell | 1,029 | 33 | #!/bin/bash
#SBATCH --partition=fn_medium
#SBATCH --time=72:00:00
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --mem=50G
unset PYTHONPATH
x=$(printf %.2f $1)
echo $x
module load singularity/3.9.8
singularity shell --bind /gpfs/data/osmanlab/Processing/HPL/HPL_test_github/case_study:/mnt docker://gcfntnu/scan... |
ac991a3983af25e38df8dd7a412ee46e4cf90745401d2121faa70d1e6edbd9bd | Shell | 1,036 | 22 | #!/usr/bin/env bash
# Matched ResNet18-GLASS baseline on additional dataset: pill.
# Same split/schedule/config as the proposed model; ONLY the backbone differs.
# Faithful GLASS light backbone: layer2 (/8) + layer3, NO gate.
# Maskless dataset: fg=0, forced distribution 3, image-level metrics only.
# NOTE: layer2 is /... |
00d01d8d6998a0b890033c9bc24b8fc4d0b6f0197e3b147b5ad76e3419279010 | Shell | 1,039 | 29 | # This script will be run in the root directory.
### 1. GCNII ######################
for SEED in {0..3}; do
python main.py --cfg configs/GCNII/peptides-func-GCNII.yaml device cuda:$SEED seed $SEED wandb.project lrgb-gcnii-8l name_tag GCNII-peptides-func &
done
wait
for SEED in {0..3}; do
python main.py --cfg... |
286f392a8314f8880c3fb08c9a1d3a8d34e7ac251e3be2dda2cd62dbfce4f93f | Shell | 1,043 | 30 | #!/bin/bash
# SPDX-FileCopyrightText: Copyright (c) 2025-2026, NVIDIA CORPORATION.
# SPDX-License-Identifier: Apache-2.0
# Support invoking test script outside the script directory
cd "$(dirname "$(realpath "${BASH_SOURCE[0]}")")"/../ || exit 1
export DEPENDENCY_FILE_KEY=test_python_accel_sklearn
source ./ci/test_pyt... |
8b8579201dd3e5c46642faa47bf9fd9622215172feaebc0b5b3a480717a2d5e9 | Shell | 1,043 | 45 | plink --bfile ../135inds_auto_SNPs --indep-pairwise 50 10 0.2 --out 135inds_auto_LD50_10_0.2.indsort
plink --bfile ../135inds_auto_SNPs --extract 135inds_auto_LD50_10_0.2.indsort.prune.in --make-bed --out 135inds_auto_LD50_10_0.2
#!/bin/bash
INPUT=/home/Mpzhang/8.CN_RSS_pigs/5.normal_analysis/3.Admixture
cd ${INPU... |
903f11f8e5983273d8de39caf8aef505709185a75718fa1db40962f9f9f05ed1 | Shell | 1,046 | 24 | #!/bin/bash -e
#SBATCH slurm/HPC parameters
#SBATCH --mem=488G
cd /path/to/hmm_ecotype
module add hmmer/3.3
module load clustal-omega/1.2.4
clustalo -i env0_train.fasta --auto -o env0_train_aln.fasta -v
hmmbuild ecotype_0.hmm env0_train_aln.fasta
clustalo -i env1_train.fasta --auto -o env1_train_aln.fasta -v
hmmbuil... |
1d29d549b1d8c44bf49e32fafe52d85de2566b8eba3e7662abf777d1710e2433 | Shell | 1,048 | 22 | #!/usr/bin/env bash
# Matched ResNet18-GLASS baseline on additional dataset: concrete.
# Same split/schedule/config as the proposed model; ONLY the backbone differs.
# Faithful GLASS light backbone: layer2 (/8) + layer3, NO gate.
# Maskless dataset: fg=0, forced distribution 2, image-level metrics only.
# NOTE: layer2 ... |
85413a6d13c0bb0124414c91510e020bae3f3ce7c945fbdc4ce95c851fbb9459 | Shell | 1,052 | 55 | #!/bin/bash
############
# Usage
############
# bash script_main_SBMs_node_classification_PATTERN_PE_GatedGCN_500k.sh
############
# GNNs
############
#MLP
#GCN
#GraphSage
#GatedGCN
#GAT
#MoNet
#GIN
#3WLGNN
#RingGNN
############
# SBM_PATTERN - 4 RUNS
############
seed0=41
seed1=95
seed2=12
seed3=35
code=ma... |
6e5f29ddf3001b345eadba94819c8bd0fbb241fde4b22c8dc3a7042c008d4bbc | Shell | 1,053 | 18 | #! /bin/bash
# activate conda env with openmeeg installed
__conda_setup="$('/Users/pault/miniconda3/bin/conda' 'shell.bash' 'hook' 2> /dev/null)"
eval "$__conda_setup"
conda activate openmeeg
export OMP_NUM_THREADS=7
proc_dir=$1
# calculate forward model with openmeeg
om_assemble -HeadMat ${proc_dir}/subject.geom ${... |
7a582b9e7a1824a999d283c22484f15dfb59f46ec9dc9af287a0ab15504d963f | Shell | 1,053 | 55 | #!/bin/bash
############
# Usage
############
# bash script_main_SBMs_node_classification_CLUSTER_PE_GatedGCN_500k.sh
############
# GNNs
############
#MLP
#GCN
#GraphSage
#GatedGCN
#GAT
#MoNet
#GIN
#3WLGNN
#RingGNN
############
# SBM_CLUSTER - 4 RUNS
############
seed0=41
seed1=95
seed2=12
seed3=35
code=m... |
9b1e1b4ce443342c430ff6f010037e2b468920bbdf8e5e252235fae754b09c5e | Shell | 1,063 | 17 | #!/bin/bash -x
SMC=$(which smc++)
set -e
LENGTH=100000000
# ./make_split.py $LENGTH > /tmp/split.vcf
# bcftools view -Oz -o /tmp/split.vcf.gz /tmp/split.vcf
# bcftools index /tmp/split.vcf.gz
# $SMC vcf2smc --length $LENGTH -v /tmp/split.vcf.gz /tmp/example.1.smc.gz 1 msp1:$(echo msp_{0..24} | sed 's/ /,/g')
# $SMC vcf... |
6b33952e0699ef22e331ae0add0ee75ae98c5ec403c69355e62db805d8a300fa | Shell | 1,064 | 35 | CUDA_VISIBLE_DEVICES=3 python run_exp_spk.py \
--dataset_name vox1 \
--data_folder /home/zeyang/data/VoxCeleb1\
--nb_epochs 200 \
--nb_hiddens 512 \
--nb_layers 3 \
--batch_size 256 \
--frontend fbank\
--model_type adLIF \
--exp_name adLIF_alpha096_099 \
--log_tofile True \
-... |
d3ebc95519b2129cf4520edd347397729c887c9bc39b4cc71b31952844fe0d1c | Shell | 1,066 | 31 | #!/bin/bash -e
#SBATCH # HPC/slurm parameters here
#SBATCH --mem=498G
module add kraken2
cd /path/to/folder
line=$( sed "${SLURM_ARRAY_TASK_ID}q;d" /path/to/metadata/files/kraken_md.txt) # containing filepaths to spades output folders
sample_id=$(echo $line)
if [ -f "${sample_id}/scaffolds.fasta" ] && [ ! -f "${sampl... |
09d6fe065950dd448068efc607386d6cc7de7300c995ad54798c1ad5b023c1ae | Shell | 1,069 | 43 | #!/usr/bin/env bash
# Additional dataset: PillQC. Image-level metrics only (no GT masks). Defects: dirt + chip.
# Locked model: MobileNetV2 dw2 + gate, 100 epochs, fg=0, forced hypersphere distribution.
datapath=/content/anomaly_extra # output root from prepare_datasets.py
augpath=/content/dtd/images
python main.... |
031733cfb451fb85c2782c4710a2169d58dd30daaa3414c655feafb8ade66a7c | Shell | 1,070 | 43 | #!/usr/bin/env bash
# Additional dataset: Concrete Crack (Ozgenel). Image-level metrics only (no GT masks).
# Locked model: MobileNetV2 dw2 + gate, 100 epochs, fg=0, forced manifold distribution.
datapath=/content/anomaly_extra # output root from prepare_datasets.py
augpath=/content/dtd/images
python main.py \
... |
77fa87c994a61620872b70a2a59e5cbd04a64c8fd93935bb4649e54ec989ecf8 | Shell | 1,074 | 36 | #!/bin/bash
Help()
{
# Display Help
echo "Syntax: scriptTemplate [-d|t]"
echo "options:"
echo "d Directory"
echo "t Taxonomy id"
echo "n Name of gene in labels"
}
while getopts d:t:n: flag
do
case "${flag}" in
d) DIR=${OPTARG};;
t) TAX=${OPTARG};;
n) NAME=${O... |
d77614c4f7e2a83cb6421fcd1013b85a911941351cfca9d2f6a2352c9f496758 | Shell | 1,074 | 47 | #!/bin/sh
#
# Downloads sequence of C. elegans from WormBase and builds Bowtie index.
#
GENOMES_MIRROR=ftp://ftp.wormbase.org/pub/wormbase/species/c_elegans/sequence/genomic
BOWTIE_BUILD_EXE=./bowtie-build
if [ ! -x "$BOWTIE_BUILD_EXE" ] ; then
if ! which bowtie-build ; then
echo "Could not find bowtie-build in c... |
94e15c6a400e3bc23c66399da94e2bd77d525bb43364bf78686fd1e312226945 | Shell | 1,080 | 44 | #!/usr/bin/env bash
# 100-epoch matched run: run-wrn50-100ep
# Compare ONLY against the other 100-epoch run (same schedule).
datapath=/content/mvtec_anomaly_detection
augpath=/content/dtd/images
python main.py \
--gpu 0 \
--seed 0 \
--test ckpt \
--run_name wrn50_100ep \
net \
-b wideresnet50 \
... |
afc03eeb99c63510a8264e2b00e7dc0eacc15e7016be5f1c30b88e6ac2693ee0 | Shell | 1,081 | 35 | CUDA_VISIBLE_DEVICES=2 python run_exp_spk.py \
--dataset_name vox1 \
--data_folder /home/zeyang/data/VoxCeleb1\
--nb_epochs 200 \
--nb_hiddens 512 \
--nb_layers 3 \
--batch_size 256 \
--frontend fbank\
--model_type RhyadLIF \
--exp_name RhyadLIF_b0-3_c1-30_dc07-1_p0 \
--log_tofil... |
7eb20e7ef68e8868623e532334cf7cc283204c3ca287d5ffa76c9d163047d44d | Shell | 1,095 | 46 | #!/bin/sh
#
# Downloads the sequence for a strain of e. coli from NCBI and builds a
# Bowtie index for it
#
GENOMES_MIRROR=ftp://ftp.ncbi.nlm.nih.gov/genomes
BOWTIE_BUILD_EXE=./bowtie-build
if [ ! -x "$BOWTIE_BUILD_EXE" ] ; then
if ! which bowtie-build ; then
echo "Could not find bowtie-build in current directory... |
ae2a7008e9ae1bd2d469608e512c520fc7ac9f2809002d30831e2194d8cb1617 | Shell | 1,101 | 47 | #!/bin/bash
#$ -cwd
#$ -j y
#$ -l h_fsize=100G
#$ -l mem_free=6G
#$ -l h_vmem=6G
#$ -l h_rt=96:00:00
#$ -pe local 8
#$ -t 1-41
module load bowtie2
module load samtools
CORES=8
umask g+w
# Inputs
fqdir="../fastq"
outdir="../bam"
scratchdir="tmp"
## align with alternates
refgenome="/dcl01/scharpf/data/pipeline-hub/pip... |
2cb9a991f83a2080582bbf978b0dcada1221fe4819eeb328c0f1fa23b16857df | Shell | 1,103 | 49 | #!/bin/bash
set -e
# Define the SQLite database file
DATABASE="onsides.db"
cd database/
# Remove any existing database file to start fresh
if [ -f "$DATABASE" ]; then
echo "Removing existing database file: $DATABASE"
rm "$DATABASE"
fi
# Import the schema into the database
echo "Creating SQLite database and... |
f29352b22a83728ae602890cc2e0e11676b45195193c24d4007a99f733c9cc58 | Shell | 1,112 | 44 | #!/usr/bin/env bash
# 100-epoch matched run: run-dw2gate-100ep
# Compare ONLY against the other 100-epoch run (same schedule).
datapath=/content/mvtec_anomaly_detection
augpath=/content/dtd/images
python main.py \
--gpu 0 \
--seed 0 \
--test ckpt \
--run_name mnv2_dw2gate_100ep \
net \
-b mobilen... |
2050c215276e6daed4a1f63659571e2a23e0996025c85a891d27f44ccef12cbb | Shell | 1,114 | 48 | #!/bin/bash
#SBATCH --partition=gpu4_dev
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --mem=20G
#SBATCH --job-name=08_CoxReg_ind
#SBATCH --output=rq_08_CoxReg_ind_%A_%a.out
#SBATCH --error=rq_08_CoxReg_ind_%A_%a.err
unset PYTHONPATH
module load condaenvs/gpu/pathgan_SSL37
all_ind=os_event_ind
all_data=o... |
19f72cb1cf21733280bd90800f0f103b3ca8063157ae21f664a02eb34d8f237a | Shell | 1,120 | 57 | #!/bin/bash
############
# Usage
############
# bash script_main_molecules_graph_regression_ZINC_PE_GatedGCN_500k.sh
############
# GNNs
############
#MLP
#GCN
#GraphSage
#GatedGCN
#GAT
#MoNet
#GIN
#3WLGNN
#RingGNN
############
# ZINC - 4 RUNS
############
seed0=41
seed1=95
seed2=12
seed3=35
code=main_molecu... |
219375a36a695bbae87bcdedd478bb6f300ce2a436ea5fb93d6dfa600e484048 | Shell | 1,120 | 39 | #!/bin/bash
corrected_args=()
docker_args=()
mounts=0
for var in "$@"
do
if [ -d "${var}" ]; then
echo "$var is a directory" >&2
var=$(realpath "${var}")
host_dir=$(dirname "${var}")
((mounts+=1))
container_dir="/data/mount_${mounts}"
docker_args+=("-v ${host_dir}:${cont... |
62227b77f0cfa328624f1ca2dc9841b8c87e2dcf98ec2690f5a903c271ec7b6c | Shell | 1,120 | 49 | #!/bin/sh
#
# Downloads sequence for a D. melanogaster from flybase.
#
GENOMES_MIRROR=ftp://ftp.flybase.net/genomes/Drosophila_melanogaster
F=dmel-all-chromosome-r5.48.fasta
REL=dmel_r5.48_FB2012_06
IDX_NAME=d_melanogaster_fb5_48
get() {
file=$1
if ! wget --version >/dev/null 2>/dev/null ; then
if ! curl --versi... |
a6af9f70d74bbaf1f354841e3cde0679b64695c136505fb18f9ac122a00ccf88 | Shell | 1,122 | 39 | #!/bin/bash
corrected_args=()
docker_args=()
mounts=0
for var in "$@"
do
if [ -d "${var}" ]; then
echo "$var is a directory" >&2
var=$(realpath "${var}")
host_dir=$(dirname "${var}")
((mounts+=1))
container_dir="/data/mount_${mounts}"
docker_args+=("-v ${host_dir}:${cont... |
cb43b569a9b07eda15672d022c9e59fbc36b6ca136e78309762cd786ffd93f24 | Shell | 1,125 | 31 | #!/bin/bash
# SPDX-FileCopyrightText: Copyright (c) 2020-2025, NVIDIA CORPORATION.
# SPDX-License-Identifier: Apache-2.0
set -euo pipefail
rapids-logger "Create checks conda environment"
. /opt/conda/etc/profile.d/conda.sh
rapids-logger "Configuring conda strict channel priority"
conda config --set channel_priority ... |
c554f31139b2d5ae026e062b58b0381e3af9ceb7011c81b28b81b511b4e7d6ed | Shell | 1,127 | 47 | #!/bin/sh
#
# Downloads sequence for a S. cerevisiae from CYGD. This script
# was used to build the Bowtie index for S. cerevisiae.
#
GENOMES_MIRROR=ftp://ftpmips.gsf.de/yeast/sequences
BOWTIE_BUILD_EXE=./bowtie-build
if [ ! -x "$BOWTIE_BUILD_EXE" ] ; then
if ! which bowtie-build ; then
echo "Could not find bow... |
cff64b76c692e1cd3d3172f2d94ed589bf6da5e41b9caa74d73977c5b0e88c77 | Shell | 1,127 | 57 | #!/bin/bash
############
# Usage
############
# bash script_main_molecules_graph_regression_AQSOL_PE_GatedGCN_500k.sh
############
# GNNs
############
#MLP
#GCN
#GraphSage
#GatedGCN
#GAT
#MoNet
#GIN
#3WLGNN
#RingGNN
############
# AQSOL - 4 RUNS
############
seed0=41
seed1=95
seed2=12
seed3=35
code=main_mole... |
4ac2f12893ac4a1b5f3d584ec228578211fb171634073f875b76ed696a872db5 | Shell | 1,128 | 27 | #!/usr/bin/env bash
set -euo pipefail
# Reset US download artifacts so Snakemake will re-scrape and re-download.
ROOT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")/.." && pwd)"
US_DIR="${ROOT_DIR}/_onsides/us"
rm -f \
"${US_DIR}/download_page.html" \
"${US_DIR}/map_page.html" \
"${US_DIR}/parsed.done" \
"${US_DIR... |
6975012fb45a4c3a5724598b5d3507de592becadd2466efcb0ece1df633fc1ec | Shell | 1,130 | 39 | #!/bin/bash
corrected_args=()
docker_args=()
mounts=0
for var in "$@"
do
if [ -d "${var}" ]; then
echo "$var is a directory" >&2
var=$(realpath "${var}")
host_dir=$(dirname "${var}")
((mounts+=1))
container_dir="/data/mount_${mounts}"
docker_args+=("-v ${host_dir}:${cont... |
f8ae2d4815d2e49aa3cd5fde5e0c33aca18d81cd0870ffa6247e6ba4e3a4c6ef | Shell | 1,132 | 64 | #!/bin/bash
# check :
# bash script.sh
# tmux attach -t script_tsp
# tmux detach
# pkill python
# bash script_main_COLLAB_edge_classification_PE_GatedGCN_40k.sh
############
# GNNs
############
#GatedGCN
#GCN
#GraphSage
#MLP
#GIN
#MoNet
#GAT
############
# OGBL-COLLAB - 4 RUNS
############
seed0=41
seed... |
0dd584ce4b3d019fd8d34330fa342a72735dc9fae58217c9feb95819b6105551 | Shell | 1,145 | 29 | DATETIME=$(date +%Y%m%d_%H%M%S)
OUTPUT_FOLDER=outputs/experiment/pert/mnist/pert_trigger_$DATETIME
export WANDB_API_KEY=YOUR_WANDB_KEY
python perturb_mnist.py --pert.model-type trigger \
--pert.perturbation-num 32 \
--pert.trigger.replace-num-candidates 32 \
--pert.trigger.use-optim-eval \
--trainer.da... |
f5ae9523a14c250db21c27e988cbeccb6ca1bb39898c5e67e043657df5c036b3 | Shell | 1,145 | 29 | DATETIME=$(date +%Y%m%d_%H%M%S)
OUTPUT_FOLDER=outputs/experiment/pert/mnist/pert_trigger_$DATETIME
export WANDB_API_KEY=YOUR_WANDB_KEY
python perturb_mnist.py --pert.model-type trigger \
--pert.perturbation-num 32 \
--pert.trigger.replace-num-candidates 32 \
--pert.trigger.use-optim-eval \
--trainer.da... |
fc9214e2ce614afab781e300b8dd9092660f22b25b64514a2decc0528d399a0f | Shell | 1,148 | 39 | #!/bin/sh
# script for execution of deployed applications
#
# Sets up the MCR 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\> args
else
... |
6574ebbc94df51c8a36fdf4ba8f4f3d5d80b8459e728f30931154454f3fc740b | Shell | 1,149 | 22 | #!/usr/bin/env bash
# VisA (all 12 categories): proposed model = MobileNetV2 dw2 + gate, 100 epochs.
# VisA is in MVTec layout WITH real ground-truth masks and fg_mask/ foreground masks,
# so this uses --fg 1 (real foreground) and reports full image + pixel metrics.
# Forced manifold distribution (--distribution 2), si... |
95da94edc553be7d4cba05e195d631612125d7be3fce422f50edb77b46189177 | Shell | 1,150 | 17 | #!/bin/bash
#SBATCH --account=rrg-bourqueg-ad
#SBATCH --output=%x.o%j
#SBATCH --error=%x.e%j
#SBATCH --mem=20G
#SBATCH --time=04:00:00
module purge 2>/dev/null
module load mugqic/homer/4.11
cd $SLURM_SUBMIT_DIR
findMotifsGenome.pl inputs/WT_genes_not_exp_musc_myob_mf_RPM1_annotated_to_H3K4me3_TSS_1KB_homer_input.txt... |
bd7beb69bd337d7c6cdeb268e8eda2727534207b8d0d2b837fbb57a5719b9f3e | Shell | 1,155 | 39 | #!/bin/sh
# script for execution of deployed applications
#
# Sets up the MCR 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\> args
else
... |
fd2eda3fd2486d1ec3cdcd12aa3abbaead3abfad4eb8d93f422fde1eb9f13395 | Shell | 1,159 | 41 | #! /bin/bash
# make sure to use correct Freesurfer version
#export FREESURFER_HOME=/home/prior/vep_pipeline/freesurfer_v7
#source $FREESURFER_HOME/SetUpFreeSurfer.sh
# downsample the cortical mesh using freesurfer surface registration tool
# it will register and resample the cortical surface onto
# that of fsaverage... |
5006689575d58f811e571056aca4b77078376fec78f476febeb330e4fb9be423 | Shell | 1,163 | 34 | #!/bin/bash
# SPDX-FileCopyrightText: Copyright (c) 2025-2026, NVIDIA CORPORATION.
# SPDX-License-Identifier: Apache-2.0
# This script runs the umap tests with the cuml.accel plugin.
# Any arguments passed to this script are forwarded directly to pytest.
#
# Example usage:
# ./run-tests.sh # Run ... |
1bfe3b1c3eb28f8a7dcf927a90d47db3896d8dc65cde0d6dad1c8c8526df325c | Shell | 1,167 | 25 | #!/bin/bash
set -e
echo -e "\n START: CreateDenseTimeSeries"
DownSampleFolder="$1"
Subject="$2"
LowResMesh="$3"
NameOffMRI="$4"
SmoothingFWHM="$5"
ROIFolder="$6"
OutputAtlasDenseTimeseries="$7"
GrayordinatesResolution="$8"
TR_vol=`fslval "$NameOffMRI" pixdim4 | cut -d " " -f 1`
#Some way faster and more concise cod... |
6cbda0e48d7757766a07f6dab860ea3940fa2c7587108120cf0d155c4357e866 | Shell | 1,173 | 20 | #!/bin/bash
#
#./mlp_train.sh ~/Documents/run_umap/examples/balbc10DLabeled134k.csv balbc10D 50
#
#./mlp_predict.sh ~/Documents/run_umap/examples/balbcFmo10D133k.csv balbc10D ~/Documents/run_umap/examples/balbcFmo10D133k_mlp.csv
#suh_pipelines pipe match training_set balbcFmo10DLabeled133k.csv test_set balbcFmo10D133k_... |
3cef85aedc078b50754a1e95d8cd37bc5a62240a5d02b7310eeab328a738b200 | Shell | 1,180 | 32 | #!/bin/bash
set -e
echo " "
echo " START: T2w2T1Reg"
WD="$1"
T1wImage="$2"
T1wImageBrain="$3"
T2wImage="$4"
T2wImageBrain="$5"
OutputT1wImage="$6"
OutputT1wImageBrain="$7"
OutputT1wTransform="$8"
OutputT2wImage="$9"
OutputT2wTransform="${10}"
T1wImageBrainFile=`basename "$T1wImageBrain"`
cp "$T1wImageBrain".nii.gz... |
af513e8c8d0767dbe3c8f94a762fbe47b8bcf7b893bbe25b87f4f8f37099f1fc | Shell | 1,183 | 56 | #!/bin/sh
#
# Downloads sequence for A. thaliana from TAIR and builds Bowtie index.
#
GENOMES_MIRROR=ftp://ftp.arabidopsis.org/home/tair
get() {
file=$1
if ! wget --version >/dev/null 2>/dev/null ; then
if ! curl --version >/dev/null 2>/dev/null ; then
echo "Please install wget or curl somewhere in your PATH"... |
16171248e03f7288dfd0726030284fde8949334f7cd2a4122bce7f9ac8d386ac | Shell | 1,198 | 55 | #!/usr/bin/env bash
## Compare overlap similarity between segmentations:
## CNN and manual labels
## XCorrelation
TMPDIR=$(mktemp -d --tmpdir)
trap "rm -rf $TMPDIR" 0 1 2 15
set -ux
# Directories
HERE="${HVR_VALIDATION_DIR:-$(git -C "$(dirname "$0")" rev-parse --show-toplevel)}"
MANUAL_LABS=${HERE}/data/labels_doro... |
f0977c8fca963e2d0a9e1aa5a8570298c03426edf99f9153c86a767f19de10a9 | Shell | 1,203 | 28 | #!/bin/bash
parentDirect=$1
phenoBasename=$2
snpPrefix=$3
genelocs=`basename $4 .locs`
GRM=$5
cisDist=$6
permutations=$7
celltype=$8
#for i in ${phenoDirect}/*.bed
#for i in ${phenoDirect}/expressiontable_matrixeqtl_geschwind_coarse*
#name=expressiontable_matrixeqtl_geschwind_coarse_control10_oRG_cpm-inorm.bed
snpFil... |
ed6edbe0c3ebe8a4b4ac2a6bdbda5634b3d7c6c08f7b4034f91e5a08934219f0 | Shell | 1,212 | 55 | #!/bin/bash
#$ -cwd
#$ -j y
#$ -l h_fsize=100G
#$ -l mem_free=10G
#$ -l h_vmem=10G
#$ -l h_rt=96:00:00
## #$ -pe local 8
#$ -t 1-41
module load bowtie2
module load samtools
PATH="/users/scristia/.linuxbrew/bin:$PATH"
FASTP=/users/scristia/fastp
CORES=1 ##CORES=8
umask g+w
# Inputs
fqdir="../fastq"
outdir="../bam"
b... |
fb23b02435717168d05d700d414cf734aacd1405c1efc751e003b4177168f3e0 | Shell | 1,232 | 36 | #!/bin/bash
# SPDX-FileCopyrightText: Copyright (c) 2022-2026, NVIDIA CORPORATION.
# SPDX-License-Identifier: Apache-2.0
# Support invoking test_python_singlegpu.sh outside the script directory
cd "$(dirname "$(realpath "${BASH_SOURCE[0]}")")"/../ || exit 1
# Common setup steps shared by Python test jobs
source ./ci/... |
9068a145afbab5eccf8087ac07b94797f1500e08ef874650f828e2cbac6d5f74 | Shell | 1,244 | 38 | #!/bin/bash
##################################### Match sample base on genotype and create new annotation file for the merging #####################
if [ -v $1 ]
then
echo 'to run this script you need R with the following packages installed: argparse, circlize, ComplexHeatmap, RColorBrewer, doParallel'
echo 'this sc... |
ff94ddfe19c9c0315853e752397d760b9cbb42a979d48a8cbb85e1bc51059ce9 | Shell | 1,245 | 39 | #!/bin/bash
# SPDX-FileCopyrightText: Copyright (c) 2022-2026, NVIDIA CORPORATION & AFFILIATES. All rights reserved.
# SPDX-License-Identifier: Apache-2.0
set -euo pipefail
source rapids-configure-sccache
source rapids-datetime-string
export CMAKE_GENERATOR=Ninja
rapids-print-env
rapids-logger "Begin cpp build"
s... |
8199e185808654352b9c00a6b9f4e2722214fc41ade21ba646adbd84349f8833 | Shell | 1,258 | 52 | #!/bin/bash
#$ -cwd
#$ -j y
#$ -l h_fsize=1000G
#$ -l mem_free=2G
#$ -l h_vmem=2G
#$ -l h_rt=96:00:00
#$ -o ./logs
module load conda_R
#############################
#YOU MUST SET THESE PATHS
#Where are the granges
granges= #Folder with the granges (this is an output of the DELFI pipeline in https://github.com/cancer-... |
82ab7704b79a8c98eb819eb9d923d1d26c64727292b5566d60d97a5fd83ff4af | Shell | 1,259 | 21 | #!/bin/bash -x
SMC=$(which smc++)
TMP=$(mktemp -d)
set -e
$SMC vcf2smc -v example/example.vcf.gz $TMP/example.1.smc.gz 1 msp1:msp_0
$SMC vcf2smc -v example/example.vcf.gz $TMP/example.11.smc.gz 1 msp1:msp_1
$SMC vcf2smc -d msp_0 msp_0 example/example.vcf.gz $TMP/example.2.smc.gz 1 msp2:msp_0,msp_3,msp_4
$SMC vcf2smc -d... |
2a5d439cb68fb845baa9d5e0ae61e2df0071a3835a68b65fc93aa1ea1b08436a | Shell | 1,270 | 58 | #!/bin/bash
############
# Usage
############
# bash script_main_molecules_graph_regression_ZINC-full_PE_GatedGCN_500k.sh
############
# GNNs
############
#MLP
#GCN
#GraphSage
#GatedGCN
#GAT
#MoNet
#GIN
#3WLGNN
#RingGNN
############
# ZINC-full - 4 RUNS
############
seed0=41
seed1=95
seed2=12
seed3=35
code=m... |
bf1c2a5581bc2298c5f91a6310fcb89e34e870624b1cccf041e58b90d165c85e | Shell | 1,271 | 40 | #!/bin/bash
################## Merge two complete (LRR and BAF annotated) vcf files ###############################
if [ -v $1 ]
then
echo 'to run this script you need vcftools and bcftools installed globally'
echo 'this script should be run like this:'
echo './Merge_vcf.sh <path folder> <path folder 1> <path folde... |
6a4ae983c6917781d11d9bbe00eaf807bd947b92dd626a05d96391e2f4758c7f | Shell | 1,291 | 34 | #!/bin/sh
#
# Copyright (C) 2020 Genome Research Ltd.
#
# Author: James Bonfield <jkb@sanger.ac.uk>
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including with... |
3c6ba912bd2a0f83f0067ca8e315a09af6c282a9d3cc6f9c364afd79f89b0b11 | Shell | 1,295 | 34 | #!/bin/sh
#
# Copyright (C) 2017-2018 Genome Research Ltd.
#
# Author: Robert Davies <rmd@sanger.ac.uk>
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including ... |
ae1662be6bd3ec55ebda99433c1ebbc2d43792a03b4646e546c5ad378030b2c8 | Shell | 1,298 | 47 | #!/usr/bin/env bash
# 100-epoch ResNet18-GLASS baseline (faithful: layer2+layer3, NO gate).
# Matches the GLASS paper's light backbone (lit. img 99.1/px 98.0/PRO 94.7 @640ep).
# Run at SAME schedule as your model for the in-house comparison;
# landing near 99.1 also validates the pipeline reproduces GLASS.
# layer2 is ... |
190049017f7c4fc7dc98d0e24a9120425ed977bfb94bf6d1fd71ef1b22ec14e5 | Shell | 1,310 | 57 | #! /bin/bash
clobber=true
set -xe
## Run MALF ADNI subjects from list
# Directories
BASE_DIR="${HVR_VALIDATION_DIR:-$(git -C "$(dirname "$0")" rev-parse --show-toplevel)}"
LIB_DIR=${BASE_DIR}/libraries/malf_dorothee
TMP_DIR=${BASE_DIR}/tmp/malf_hcvc
QC_DIR=${BASE_DIR}/plots/qc_adni-bl/malf/all
OUT_DIR=${BASE_DIR}/da... |
97e8ef8d9067c42bcb9916a21d4d29a6836290a5f1f2f455950b9f3ca7a2002e | Shell | 1,312 | 35 | #!/bin/sh
#
# Copyright (C) 2017-2018 Genome Research Ltd.
#
# Author: Robert Davies <rmd@sanger.ac.uk>
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including ... |
1a607c7d6b2d4d3e27829546ccbcdd0360b811683afdd518aff57e51bee92dc9 | Shell | 1,318 | 32 | #!/bin/sh
#
# Copyright (C) 2020 Genome Research Ltd.
#
# Author: James Bonfield <jkb@sanger.ac.uk>
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including with... |
86902d27fb66b4273d007c3230ba5c83ec6909d0bd029636363764d76b549ad3 | Shell | 1,318 | 59 | #!/bin/bash
# Simple fine-tuning script for RCM Lesion Classification on 4th Generation Images
# Usage: bash scripts/run_lesion_finetune.sh --pretrained_model PATH_TO_MODEL
# Set CUDA device order
export CUDA_DEVICE_ORDER=PCI_BUS_ID
# Default values
CONFIG_FILE="configs/lesion_finetune_config.yaml"
PRETRAINED_MODEL=... |
cfa223e28085fadcc26637583fab9946814f9b4f309adcee80198cee8e6c4742 | Shell | 1,318 | 61 | #!/bin/sh
#
# Downloads sequence for the canFam2 version of C. familiaris (dog)
# from UCSC.
#
i=2
BASE_CHRS=chr1
while [ $i -lt 39 ] ; do
BASE_CHRS="$BASE_CHRS chr$i"
i=`expr $i + 1`
done
BASE_CHRS="$BASE_CHRS chrX chrM chrUn"
CHRS_TO_INDEX=$BASE_CHRS
CANFAM2_BASE=ftp://hgdownload.cse.ucsc.edu/goldenPath/canFam2/... |
934d5b238a0e8d101548b44f6748dcee5a43d9136927d3478314c82b023c9ec3 | Shell | 1,326 | 63 | #!/bin/bash
#$ -cwd
#$ -j y
#$ -l h_fsize=1000G
#$ -l mem_free=2G
#$ -l h_vmem=2G
#$ -l h_rt=96:00:00
#$ -o ./logs
module load conda_R
#############################
#YOU MUST SET THESE PATHS
#Where are the fastq
fastq=
#Where do you want the kmer counts to go
outdir=./counts
#Where are the bams
bams=
#where do you... |
4e8fa4a536bbe2fab1a995d242a42dcce67635b2b398d091850fa2c69946e40b | Shell | 1,331 | 35 | #!/bin/sh
#
# Copyright (C) 2020 Genome Research Ltd.
#
# Author: James Bonfield <jkb@sanger.ac.uk>
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including with... |
486b9c61f6cef4f7cd5a84549bb7569400c389f617e3cca5bde534255286e356 | Shell | 1,334 | 32 | #!/bin/bash -e
#SBATCH slurm/HPC parameters here
#SBATCH --mem=48G
module add Prodigal/2.6.3
cd /path/to/folder
line=$(sed "${SLURM_ARRAY_TASK_ID}q;d" /path/to/metadata/files/run_kraken_md.txt) # contains accessions
sample_id=$(echo "$line")
if [ -d "$sample_id" ]; then
if [ -f "$sample_id/prokaryotic.fasta" ] && ... |
ba7a94c2e1e8268c6faba7d800fb0216f2fb77594928afb85a351f56b93f239b | Shell | 1,336 | 48 | #!/usr/bin/env bash
# 100-epoch: dw2 + GATE + WAVELET. Matched partner to run-dw2gate-100ep.
# ONLY difference vs dw2+gate@100 (0.9923) is --wavelet 1. Compare pair.
# Read pixel_ap / pixel_pro on textural classes (carpet, wood, grid):
# that is where the wavelet showed durable-looking signal at 20ep.
datapath=/content... |
880d674e69fbd684139e484a0ba77acfa0718c7f4256ff0ea08c891bc91c33c2 | Shell | 1,349 | 31 | DATETIME=$(date +%Y%m%d_%H%M%S)
OUTPUT_FOLDER=outputs/experiment/train/pancreas/ode_model_all_$DATETIME
export WANDB_API_KEY=YOUR_WANDB_KEY
python train.py --model.dim 64 \
--model.input-dim 668 \
--trainer.train-batch-size 64 \
--trainer.train-num-steps 2000 \
--trainer.train-lr 1e-4 \
--trainer.s... |
7226510477d0d9a87d2cb36e853a60eae610a75de0937646041c0efd4e69aa2b | Shell | 1,352 | 52 | #! /bin/bash
dirname="temp"
mkdir -p -- "$dirname"
task_name=""
config_num=""
moment=$(date +"%m%d_%T")
log_file="train_log_$moment.txt"
function usage
{
echo "-t or --task for task_name; -i or --config for config_num; -l or --log for log_file"
}
while [ "$1" != "" ]
do
case "$1" in
-t | --task ) ... |
2ad1e6c632fc4e6f5f3ecc1aa2d42ceebe5ac5f2df7ca8262417fed36c067571 | Shell | 1,358 | 25 | #!/bin/bash
#SBATCH --account=def-lpenacas
#SBATCH --time=00:30:00
#SBATCH --cpus-per-task=16
# module load gcc
# module load gnuplot
# module load hisat2
# module load sra-toolkit
# module load trimmomatic
# module load fastqc
module load fastp
bash qc.sh -r SRR15049591,SRR15049592,SRR15049593 -d ../../operons/data_o... |
8a26ed6ae798ef0f534adaa22f0effb676fcce8687768ac09a03e84bc539b22e | Shell | 1,366 | 51 | # Name: restructure_for_tensorboard.sh
#
# Desc:
# Creates a new directory structure that's more tensorboard-friendly
# It restructures the dictionary to be grouped by src/dst/arch through
# symlinking the original dirs
#
# Note:
# If a task was restarted early on then Tensorboard may crap out because there
# ... |
9447fc3a8ab245b29b2647a8cba8e15a49c19df39416f9c428075ba534c07ae2 | Shell | 1,368 | 26 | #!/bin/bash
#SBATCH --account=def-lpenacas
#SBATCH --time=5:00:00
#SBATCH --mem-per-cpu=13G
module load gcc
module load sra-toolkit
# mkdir ../data_odb
bash sra.sh -r SRR15049591,SRR15049592,SRR15049593 -t 224308 -o ../data_odb
# bash sra.sh -r SRR7977557,SRR7977561,SRR7977565 -t 196627 -o ../data_odb
# bash sra.sh ... |
663c6bbd32c4c913a64a30147b787b131f382396dbd867c1f886202e43dca227 | Shell | 1,373 | 47 | #!/usr/bin/env bash
# ============================================================
# GLASS baseline: toothbrush only, full paper settings (Colab/Linux).
# --distribution 2 forces the MANIFOLD hypothesis (toothbrush's shipped
# baseline value), so it needs no distribution xlsx lookup.
# EDIT the two paths below to y... |
83570a711e91a39a5883577e1fdadaf13a313a34e7aa938ae5077923f13dee84 | Shell | 1,379 | 31 | DATETIME=$(date +%Y%m%d_%H%M%S)
OUTPUT_FOLDER=outputs/experiment/train/dentategyrus/ode_model_all_$DATETIME
export WANDB_API_KEY=YOUR_WANDB_KEY
python train.py --model.dim 64 \
--model.input-dim 1087 \
--trainer.train-batch-size 64 \
--trainer.train-num-steps 2000 \
--trainer.train-lr 1e-4 \
--trai... |
066ddb3a055f94cda1cc600027203a84ecc004149b4eb92caed80188a0b1a48b | Shell | 1,380 | 50 | #!/bin/bash
################## Merge more than 2 complete (LRR and BAF annotated) vcf files ###############################
if [ -v $1 ]
then
echo 'to run this script you need vcftools and bcftools installed globally'
echo 'this script should be run like this:'
echo './Merge_vcf.sh <path folder> <path folder 1> <pa... |
7a929089e768ca4cdd9ed61fae72c74cd19c575e2115db85c08bd4b74761ca72 | Shell | 1,382 | 54 | #!/bin/bash
# SPDX-FileCopyrightText: Copyright (c) 2024-2026, NVIDIA CORPORATION & AFFILIATES. All rights reserved.
# SPDX-License-Identifier: Apache-2.0
set -euo pipefail
package_dir=$1
wheel_dir_relative_path=$2
RAPIDS_CUDA_MAJOR="${RAPIDS_CUDA_VERSION%%.*}"
cd "${package_dir}"
rapids-logger "validate packages ... |
879e92e02785ada9c190724a95742ab0132ad64cb5f2360fabba749c9bda1f1e | Shell | 1,383 | 37 | DATETIME=$(date +%Y%m%d_%H%M%S)
OUTPUT_FOLDER=outputs/experiment/pert/mnist/pert_sage_$DATETIME
export WANDB_API_KEY=YOUR_WANDB_KEY
python perturb_mnist.py \
--trainer-method sage \
--pert.model-type sage \
--pert.perturbation-num 10 \
--pert.sage.trigger-pert-type trigger_perturbation \
--pert.sag... |
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