sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 17k | content stringlengths 1 200k |
|---|---|---|---|---|
1c75c1813f6941469ffcaba01c5afbd15cce410d0561ba201d5eb0be92422e6a | Shell | 419 | 8 | #!/bin/bash
# this function is the wrapper to run the `CBIG_pMFM_step6_SWSTD_state_main.m`
# Written by Kong Xiaolu and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
cd ../../../part1_pMFM_main/scripts
matlab -nosplash -nodisplay -nodesktop -r "clear;clc;close all;CBIG_pMFM_step6_... |
5111c683602b26316fe54243d8ee85468d6b8a7be14aabe8a38c586018e44689 | Shell | 419 | 16 | #!/bin/bash
set -eu
dir="$1"
echo "dir: $dir"
mkdir -p "$dir/log"
sbatch_args="-p wav2vec --nodes=1 --ntasks-per-node=1"
sbatch_args="$sbatch_args --gpus-per-node=1 --cpus-per-task=8 --mem=0 --time=24:00:00"
sbatch_args="$sbatch_args -o $dir/log/decode_sweep_%A.out"
sbatch_args="$sbatch_args -e $dir/log/decode_swee... |
6b4a99d25b03a5c43245bee77e133a7e97d90b6b644b54c7f7e5c7aa37997c7a | Shell | 419 | 14 | #!/bin/bash
#SBATCH --job-name=salmon_generateDecoy
#SBATCH --output=slurm_logs/salmon_generateDecoy.out
#SBATCH --time=0-2:0
#SBATCH --nodes=1
#SBATCH --ntasks=1
mamba activate SQANTI3.env
./scripts/generateDecoyTranscriptome.sh \
-j 40 \
-g "${GENOMIC_DATA_DIR}"/GENCODE/GRCh38.primary_assembly.genome.fa \
-t proc/me... |
5f7cf1a6dac3b86bb521243d4ae97aaee4208b4f4d64852d701ae2ac0c7c18ef | Shell | 420 | 9 | #!/usr/bin/env bash
#SBATCH --job-name=TransDecoder_predict
#SBATCH --output=slurm_logs/TransDecoder_predict.out
#SBATCH --time=0-1:0
#SBATCH -n 1
#SBATCH -N 1
module apptainer
apptainer exec -e -B="/scratch/nxu/SFARI:/scratch/nxu/SFARI" ~/tools/transdecoder.v5.7.1.simg TransDecoder.Predict --single_best_only -t proc/... |
ad4a857498c03428ae6df4bb81f2a8814a961a4bf909cdd39df1377f0d18b5d7 | Shell | 420 | 9 | #!/bin/bash
# this function is the wrapper to run the `CBIG_pMFM_step3_test_conW.py`
# Written by Kong Xiaolu and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
cd ../../../../part2_pMFM_control_analysis/Constant_W/scripts
source activate pMFM
python CBIG_pMFM_step3_test_conW.py
m... |
c30d0398593c6826a53eec98e280eb19167c07e6d9c739e2e5e8c1f3f90a0ce6 | Shell | 420 | 9 | #!/bin/bash
# this function is the wrapper to run the `CBIG_pMFM_step3_test_conI.py`
# Written by Kong Xiaolu and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
cd ../../../../part2_pMFM_control_analysis/Constant_I/scripts
source activate pMFM
python CBIG_pMFM_step3_test_conI.py
m... |
794ed94dbc14f82071fc11a578304b558acd711ead72574c9817cd8b059c2fd4 | Shell | 421 | 9 | #!/bin/bash
# this function is the wrapper to run the `CBIG_pMFM_test_high_resolution.py`
# Written by Kong Xiaolu and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
cd ../../../../part2_pMFM_control_analysis/High_resolution/scripts
source activate pMFM
python CBIG_pMFM_test_high_r... |
c6b60084b8d21d2b8450f2fdb37572f43b9602c43eff0ab56ea04cde63f2491a | Shell | 423 | 15 | #!/bin/bash
set -eu
dir="$1"
echo "dir: $dir"
mkdir -p "$dir/log"
sbatch_args="-p wav2vec --nodes=1 --ntasks-per-node=1"
sbatch_args="$sbatch_args --gpus-per-node=1 --cpus-per-task=8 --mem=0 --time=24:00:00"
sbatch_args="$sbatch_args -o $dir/log/decode_sweep_%A.out"
sbatch_args="$sbatch_args -e $dir/log/decode_swee... |
dca55c3449bffcaccb91d4d12a6cb31e40c4c4d4e2bcb5ff4c2039da38d2fb11 | Shell | 427 | 18 | freeview \
-v mri/T1.mgz \
mri/brainmask.mgz \
mri/wm.mgz \
-f surf/lh.white:edgecolor=yellow \
surf/lh.pial:edgecolor=red \
surf/rh.white:edgecolor=yellow \
surf/rh.pial:edgecolor=red
###############
% just modified pial
recon-all -autorecon-pial -subjid S28_edited \
-sd /ifs/loni/groups/lo... |
1fe9ee268953b710ec0d0f334d86a7d4389ce3db4b7a60faf823fc2aed1a7f96 | Shell | 428 | 20 | #!/usr/bin/env bash
##
# @file train_neural.bash
# @author Simon Yu
# @date 12/06/2024
# @brief Script for training neural models.
##
# Go to script directory
cd "$(dirname $0)"
# Go to source directory
cd "../../src/npc-models"
./train_neural.py -b 256 -e 150 -s 42
./train_neural.py -b 256 -e 150 -s 52
./trai... |
8ecebd7966ca9374b00ecdba0ac988be23a7b50d961f759d2c4fcc607f611d3e | Shell | 430 | 9 | #!/bin/bash
# this function is the wrapper to run the `CBIG_pMFM_step1_training_fccost.py`
# Written by Kong Xiaolu and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
cd ../../../../part2_pMFM_control_analysis/FC_cost/scripts
source activate pMFM
python CBIG_pMFM_step1_training_fcc... |
229fac672b024feedd958b4eaba45e6c0512213954ab0d4c6b017870fe70bafe | Shell | 432 | 9 | #!/bin/bash
# this function is the wrapper to run the `CBIG_pMFM_step1_training_conw.py`
# Written by Kong Xiaolu and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
cd ../../../../part2_pMFM_control_analysis/Constant_W/scripts
source activate pMFM
python CBIG_pMFM_step1_training_co... |
fecabf13bfeb3415ae2d6e0e54b3dd4d24a387af673cdafb5f2c7dc466b8a6d8 | Shell | 432 | 9 | #!/bin/bash
# this function is the wrapper to run the `CBIG_pMFM_step1_training_conI.py`
# Written by Kong Xiaolu and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
cd ../../../../part2_pMFM_control_analysis/Constant_I/scripts
source activate pMFM
python CBIG_pMFM_step1_training_co... |
74b5562f0f6e3ec3da653749bf7021ab432f1c8e9aabc35ad6734389085ed0d3 | Shell | 434 | 9 | #!/bin/bash
# this function is the wrapper to run the `CBIG_pMFM_step3_test_gradient.py`
# Written by Kong Xiaolu and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
cd ../../../../part2_pMFM_control_analysis/Gradient_only/scripts
source activate pMFM
python CBIG_pMFM_step3_test_gra... |
93e3ba230792eebf01eb8893712381ddb93f1ea688b6a82984f81bea4882cb88 | Shell | 434 | 9 | #!/bin/bash
# this function is the wrapper to run the `CBIG_pMFM_step3_test_nonpara.py`
# Written by Kong Xiaolu and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
cd ../../../../part2_pMFM_control_analysis/Non_parametric/scripts
source activate pMFM
python CBIG_pMFM_step3_test_non... |
081c0bebc3a111835c86de12846961837a1486029f50b4a6889808a51f69cf23 | Shell | 436 | 9 | #!/bin/bash
# this function is the wrapper to run the `CBIG_pMFM_step3_test_consigma.py`
# Written by Kong Xiaolu and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
cd ../../../../part2_pMFM_control_analysis/Constant_sigma/scripts
source activate pMFM
python CBIG_pMFM_step3_test_co... |
3176534e550ba083eb1bb8b65ab614a5a24e32ae4e5bea63f31f2f1066916c08 | Shell | 436 | 14 | #!/bin/bash
set -euo pipefail
SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
python "${SCRIPT_DIR}/run_inference.py" \
--data-root "${SCRIPT_DIR}/../dataset" \
--dataset-names example_data \
--output-dir "${SCRIPT_DIR}/../outputs" \
--results-file results.xlsx \
--seg-ckpt "${SCRIPT_DIR}/../chec... |
76851dc58ded512c0cbf49e95715cc9e8b93cc7e21b4c082f95ff214a36e5630 | Shell | 436 | 9 | #!/bin/bash
# this function is the wrapper to run the `CBIG_pMFM_step2_validation_fccost.py`
# Written by Kong Xiaolu and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
cd ../../../../part2_pMFM_control_analysis/FC_cost/scripts
source activate pMFM
python CBIG_pMFM_step2_validation... |
13cbbe74090ab01e80859ac46dacec90e5c8f4fbe01c0fe7115a78a952c01739 | Shell | 438 | 9 | #!/bin/bash
# this function is the wrapper to run the `CBIG_pMFM_step2_validation_conI.py`
# Written by Kong Xiaolu and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
cd ../../../../part2_pMFM_control_analysis/Constant_I/scripts
source activate pMFM
python CBIG_pMFM_step2_validatio... |
82e51f0afcc150c8051f4f050ead0678a8da1ac4d36f90786a2be84c61af4a43 | Shell | 438 | 15 | #!/bin/bash
#SBATCH --account=def-kjerbi
#SBATCH --mail-user=gonnaride@gmail.com
#SBATCH --mail-type=ALL
#SBATCH --time=48:00:00
#SBATCH --nodes=1
#SBATCH --ntasks=4
#SBATCH --cpus-per-task=8
#SBATCH --mem-per-cpu=8G
#SBATCH --output=S-subtrain-%j.out
#SBATCH --error=S-subtrain-%j.err
source /home/vicolab/projects/... |
916759c89affeb5f8e7e3790d93e6f80b3c347601873a269bcee8d246f91c5e3 | Shell | 438 | 9 | #!/bin/bash
# this function is the wrapper to run the `CBIG_pMFM_step2_validation_conW.py`
# Written by Kong Xiaolu and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
cd ../../../../part2_pMFM_control_analysis/Constant_W/scripts
source activate pMFM
python CBIG_pMFM_step2_validatio... |
b38693d28577b47330c9935ed9c696cfd57b169169f48b82d490ca73b6ee04f2 | Shell | 438 | 15 | #!/bin/bash
#SBATCH --account=def-kjerbi
#SBATCH --mail-user=gonnaride@gmail.com
#SBATCH --mail-type=ALL
#SBATCH --time=46:00:00
#SBATCH --nodes=1
#SBATCH --ntasks=4
#SBATCH --cpus-per-task=8
#SBATCH --mem-per-cpu=8G
#SBATCH --output=S-subtrain-%j.out
#SBATCH --error=S-subtrain-%j.err
source /home/vicolab/projects/... |
f2a6be94e2be8a3564a911c64b0d50ef736ff9a57a2fd0ae350d961dc986379a | Shell | 438 | 15 | #!/bin/bash
#SBATCH --account=def-kjerbi
#SBATCH --mail-user=gonnaride@gmail.com
#SBATCH --mail-type=ALL
#SBATCH --time=38:00:00
#SBATCH --nodes=1
#SBATCH --ntasks=4
#SBATCH --cpus-per-task=8
#SBATCH --mem-per-cpu=8G
#SBATCH --output=S-subtrain-%j.out
#SBATCH --error=S-subtrain-%j.err
source /home/vicolab/projects/... |
c228b2237549d5322af4da4bb8bbb279f75f8e38bc0a734778e15a85d3f9c2ec | Shell | 439 | 20 | #!/bin/bash
if [ $# -ne 1 ]; then
echo "usage: $0 GENERATE_PY_OUTPUT"
exit 1
fi
GEN=$1
SYS=$GEN.sys
REF=$GEN.ref
if [ $(tail -n 1 $GEN | grep BLEU | wc -l) -ne 1 ]; then
echo "not done generating"
exit
fi
grep ^H $GEN | awk -F '\t' '{print $NF}' | perl -ple 's{(\S)-(\S)}{$1 ##AT##-##AT## $2}g' > $S... |
e3cf723a1dcafbecf86ddfee2ea4bb3b66fb3242a09d311dd0200f3fe0501844 | Shell | 441 | 9 | #!/usr/bin/env bash
#SBATCH --job-name=blastp
#SBATCH --output=slurm_logs/blastp.out
#SBATCH --time=0-4:0
#SBATCH -n 1
#SBATCH -N 1
module apptainer
apptainer exec -e -B="/scratch/nxu/SFARI:/scratch/nxu/SFARI" ~/tools/transdecoder.v5.7.1.simg blastp -query full_nt.fasta.transdecoder_dir/longest_orfs.pep -db uniprotkb_... |
af4c98943c0565314a99f4d33a189c6a584e0eebb6cf52175538327f1af962f0 | Shell | 442 | 9 | #!/bin/bash
# this function is the wrapper to run the `CBIG_pMFM_step3_test_conpara.py`
# Written by Kong Xiaolu and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
cd ../../../../part2_pMFM_control_analysis/Constant_parameter/scripts
source activate pMFM
python CBIG_pMFM_step3_test... |
fe7953b7690dfb1b072d755496293a0669632d447c388fb0f4ddfa240a414639 | Shell | 442 | 20 | #!/usr/bin/env bash
##
# @file train_blackbox.bash
# @author Simon Yu
# @date 12/12/2024
# @brief Script for training blackbox models.
##
# Go to script directory
cd "$(dirname $0)"
# Go to source directory
cd "../../src/npc-models"
./train_blackbox.py -b 256 -e 150 -s 42
./train_blackbox.py -b 256 -e 150 -s 5... |
202e76b3e9dd26d385e0c39d75571402c61eb71a0a55d23de7633155916abd33 | Shell | 445 | 8 | #!/bin/bash
#SBATCH --job-name=NPC_1_1_resub_S15_L001
#SBATCH --output=slurm_logs/NPC_1_1_resub_S15_L001.out
#SBATCH --time=0-5:0
#SBATCH --nodes=1
#SBATCH --ntasks=1
mamba activate patch_seq_spl
salmon quant -i proc/salmon_index -l A -1 data/illumina/SFARI_data/NPC_1_1_resub_S15_L001_R1_001.fastq.gz -2 data/illumina/S... |
02b91d19f63a6eee72e576342f3d3860c134040e02cb614c9838b39a6e1d4305 | Shell | 446 | 9 | #!/bin/bash
# this function is the wrapper to run the `CBIG_pMFM_step1_training_gradient.py`
# Written by Kong Xiaolu and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
cd ../../../../part2_pMFM_control_analysis/Gradient_only/scripts
source activate pMFM
python CBIG_pMFM_step1_trai... |
40369dca06012999a84e1479a0a8c907face65cda2a39b39b2d0f5107431b305 | Shell | 446 | 9 | #!/bin/bash
# this function is the wrapper to run the `CBIG_pMFM_step1_training_nonpara.py`
# Written by Kong Xiaolu and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
cd ../../../../part2_pMFM_control_analysis/Non_parametric/scripts
source activate pMFM
python CBIG_pMFM_step1_trai... |
beaf6ca04b16c154e346623d87aaf85c360fe8bf0478e6706cf4d76390780330 | Shell | 446 | 15 | nohup sh run_main.sh \
--model output/models/KeAP20/encoder \
--output_file ss8-KeAP20 \
--task_name ss8 \
--do_train True \
--epoch 5 \
--optimizer AdamW \
--per_device_batch_size 1 \
--gradient_accumulation_steps 32 \
--eval_step 50 \
--eval_batchsize 4 \
... |
c56f23bb470fc11a05c5ccb337568abe8638b4f826336ec43e84f5645a4c95c4 | Shell | 447 | 15 | nohup sh run_main.sh \
--model output/models/KeAP20/encoder \
--output_file ss3-KeAP20 \
--task_name ss3 \
--do_train True \
--epoch 5 \
--optimizer AdamW \
--per_device_batch_size 2 \
--gradient_accumulation_steps 16 \
--eval_step 50 \
--eval_batchsize 4 \
... |
8dda9d7f7b726fa210ad473e7007c0209c33e7624971b2695c6355c51ac5d255 | Shell | 448 | 9 | #!/bin/bash
# this function is the wrapper to run the `CBIG_pMFM_step1_training_consigma.py`
# Written by Kong Xiaolu and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
cd ../../../../part2_pMFM_control_analysis/Constant_sigma/scripts
source activate pMFM
python CBIG_pMFM_step1_tra... |
a9f510f43ecca802f486c3314be746ce804c8c8eca5f2211b4b1eadbb83e58a2 | Shell | 448 | 17 | #!/bin/sh
curr_dir=`pwd`
for folder in */
do
echo "[TEST](start) $folder"
cd $curr_dir
rsync -az $folder $CBIG_CODE_DIR/stable_projects/
git add $CBIG_CODE_DIR/stable_projects/$folder/*
git commit -m "test"
cd $CBIG_CODE_DIR
yes | $CBIG_CODE_DIR/hooks/pre-push
git reset HEAD~1
rm -... |
030e459bd354ae49eb4bab408ebc0f61f26dfca2c1442f3df34732ccd72c3c38 | Shell | 450 | 15 | #!/bin/bash
set -euo pipefail
SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
python "${SCRIPT_DIR}/run_inference.py" \
--data-root "${SCRIPT_DIR}/../dataset" \
--dataset-names example_data \
--output-dir "${SCRIPT_DIR}/../outputs" \
--results-file results.xlsx \
--seg-ckpt "${SCRIPT_DIR}/../chec... |
1eba43c527e117abef2f8da0f8b39acb5d651d7d289626de249306fece436d07 | Shell | 452 | 9 | #!/bin/bash
# this function is the wrapper to run the `CBIG_pMFM_step2_validation_nonpara.py`
# Written by Kong Xiaolu and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
cd ../../../../part2_pMFM_control_analysis/Non_parametric/scripts
source activate pMFM
python CBIG_pMFM_step2_va... |
c0649f52d6e997a41c851ee71a4338272307e5fc62799a0044ff77050f57f2dc | Shell | 452 | 9 | #!/bin/bash
# this function is the wrapper to run the `CBIG_pMFM_step4_generate_simulated_fc_fcd.py`
# Written by Kong Xiaolu and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
cd ../../../../part2_pMFM_control_analysis/FC_cost/scripts
source activate pMFM
python CBIG_pMFM_step4_ge... |
d8494e5d48d0c857de2e392cd54522dc9410f8b7a7a5d32341b00edffae1f671 | Shell | 452 | 9 | #!/bin/bash
# this function is the wrapper to run the `CBIG_pMFM_step2_validation_gradient.py`
# Written by Kong Xiaolu and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
cd ../../../../part2_pMFM_control_analysis/Gradient_only/scripts
source activate pMFM
python CBIG_pMFM_step2_va... |
ea3841398270230e3558e5277007ed28861c81ec9c57e8e01e2b915f016e3a25 | Shell | 453 | 18 | #!/bin/bash
#SBATCH --job-name=pfam_scan
#SBATCH --output=pfam_scan.out
#SBATCH --time=2-0:0
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=64
#SBATCH --mem=249G
#SBATCH --mail-user=nuoxu.xu@mail.utoronto.ca
#SBATCH --mail-type=FAIL,END
export PERL5LIB=/scratch/nxu/SFARI/PfamScan:$PERL5LIB
module load hm... |
a29a78f58f941f82a825be45f84eab6196c9f891fa7c468290a878e5200fba0f | Shell | 454 | 9 | #!/bin/bash
# this function is the wrapper to run the `CBIG_pMFM_step2_validation_consigma.py`
# Written by Kong Xiaolu and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
cd ../../../../part2_pMFM_control_analysis/Constant_sigma/scripts
source activate pMFM
python CBIG_pMFM_step2_v... |
d30b5262cdd3d19ff536ab10ed0f8ed42aa0a3b1f49e36caee14ff0e1635b84a | Shell | 454 | 9 | #!/bin/bash
# this function is the wrapper to run the `CBIG_pMFM_step1_training_conpara.py`
# Written by Kong Xiaolu and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
cd ../../../../part2_pMFM_control_analysis/Constant_parameter/scripts
source activate pMFM
python CBIG_pMFM_step1_... |
d6f892101e6ed7c533d8eb93546d000afbbb14c779e2ea4e31853db955267b27 | Shell | 454 | 13 | #!/bin/bash
for file in data/long_read/LUO26876.20240514/*/outputs/flnc.bam; do
if [[ -f "$file" ]]; then
first_field=$(samtools view "$file" | head -1 | cut -f1)
if [[ -n "$first_field" ]]; then
echo -e "$first_field\t$file" >> proc/id_to_sample.txt
else
echo -e "No ... |
ae2ca4a63682a677aafc0eeedafa24981a51dcbd8869b8b8a629022bd587aaa8 | Shell | 457 | 20 | #!/bin/bash
set -e
echo "=== Python: Ruff lint ==="
ruff check skfmm/
echo "=== Python: Ruff format check ==="
ruff format --check skfmm/
echo "=== Python: mypy ==="
mypy skfmm/
echo "=== C++: cppcheck ==="
cppcheck --enable=all --std=c++17 --suppress=missingIncludeSystem skfmm/
echo "=== C++: clang-tidy ==="
clan... |
1bf01cd1c7a92da1374df83f975bb94ce95a0f78f974ab34d44e4c766332bb56 | Shell | 458 | 9 | #!/bin/bash
#SBATCH --job-name=salmon_index
#SBATCH --output=slurm_logs/salmon_index.out
#SBATCH --time=0-5:0
#SBATCH --nodes=1
#SBATCH --ntasks=1
sbatch -J "slurm_logs/${1}.out" -o slurm_logs/"${1}".out -t 0-1:0 -N 1 -n 1 \
mamba activate patch_seq_spl; salmon quant -i proc/decoy_transcriptome -l A -1 data/illumina/S... |
8762df5fd4dca92d660434fe23751138cecfd24f67ad22307463437bfa9f0bed | Shell | 458 | 9 | #!/bin/bash
# this function is the wrapper to run the `CBIG_pMFM_step5_generate_STDFCD_correlation_main.m`
# Written by Kong Xiaolu and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
cd ../../../part1_pMFM_main/scripts
matlab -nosplash -nodisplay -nodesktop -r \
"clear;clc;close al... |
847ae2ad7e75e31d244617352df12b267edb8673367c1141a28577bfdd5b5d4b | Shell | 460 | 9 | #!/bin/bash
# this function is the wrapper to run the `CBIG_pMFM_step2_validation_conpara.py`
# Written by Kong Xiaolu and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
cd ../../../../part2_pMFM_control_analysis/Constant_parameter/scripts
source activate pMFM
python CBIG_pMFM_step... |
508b2aa31eda5caa6eb1dfcdd52de5fb5659b9b87be1ed21b6a0b5bed434994b | Shell | 461 | 15 | nohup sh run_main.sh \
--model output/pretrained/KeAP20/encoder \
--output_file contact-KeAP20 \
--task_name contact \
--do_train True \
--epoch 5 \
--optimizer AdamW \
--per_device_batch_size 1 \
--gradient_accumulation_steps 8 \
--eval_step 50 \
--eval_batch... |
a1a8a7b11585135dfecadd90961442b62e0563ff63b9e508776bb8b055419906 | Shell | 462 | 13 | #!/usr/bin/env bash
# Create the BASS conda environment named scmeb_env
# conda env create -f bass.yml -n bass_env
# Activate the environment
# source activate bass_env
# Install the required R packages
Rscript -e "remotes::install_github('xzhoulab/SPARK', ref = 'a8b4bf27b804604dfda53da42992f100b8e4e727', dependenci... |
a11a91127ed384951e935af492d0f7d06472c839eb4046b5f885d17c16e8b043 | Shell | 469 | 19 | #!/bin/bash
# Build the BEELINE Sphinx documentation.
# Output is written to docs/build/html/index.html.
# Run from the repository root or from the utils/ directory.
set -e
SCRIPT_DIR="$(dirname "$(readlink -f "$0")")"
REPO_ROOT="$(dirname "$SCRIPT_DIR")"
eval "$(conda shell.bash hook)"
conda activate BEELINE
sphi... |
7239b4c3b79d5ad6ff8fc8cdf01efd5c73f7427f60dd8134a4db3b93b8f077f9 | Shell | 470 | 12 | #!/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} ${affineTmp} ${outDir}${filename}_GMToAffineTmp -fnirt "--config=GM_2_MNI152GM_2mm.cnf"
# Generate G... |
d84588d2ed445543cdc222427496f6a0c1f5a3519dd5a34a7a6f90c28d609b91 | Shell | 472 | 18 | #!/bin/bash
BUCKET_NAME="vz-ultra-showcase"
OUTPUT_DIR="./merscope"
mkdir -p $OUTPUT_DIR
for BUCKET_FILE in $(gsutil ls -d gs://$BUCKET_NAME/*/region_*/*.h5ad); do
DATASET_NAME=$(basename $BUCKET_FILE)
if [ -f $OUTPUT_DIR/$DATASET_NAME ]; then
echo "File $DATASET_NAME already exists in $OUTPUT_DIR"
... |
fed7a3a40737057b66a9e899b7039b01533c429713dd47b3bdc1f36c310cf879 | Shell | 474 | 9 | #!/bin/bash
# this function is the wrapper to run the `CBIG_pMFM_step4_generate_simulated_fc_fcd.py`
# Written by Kong Xiaolu and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
cd ../../../../part2_pMFM_control_analysis/Constant_parameter/scripts
source activate pMFM
python CBIG_pM... |
7cfc468949d11558fa96539805364e7727124e37274ad4dccef6762de97de02f | Shell | 475 | 18 | #!/bin/bash
BUCKET_NAME="vz-merfish2-showcase"
OUTPUT_DIR="./merscope"
mkdir -p $OUTPUT_DIR
for BUCKET_FILE in $(gsutil ls -d gs://$BUCKET_NAME/*/region_*/*.h5ad); do
DATASET_NAME=$(basename $BUCKET_FILE)
if [ -f $OUTPUT_DIR/$DATASET_NAME ]; then
echo "File $DATASET_NAME already exists in $OUTPUT_DI... |
e320985c96d9c4e10227890ca2221fe6ae9c0b031b0716d1cddf97ebae93f0d0 | Shell | 476 | 9 | #!/bin/bash
# this function is the wrapper to run the `CBIG_pMFM_step8_gene_expression_analysis_desikan.m`
# Written by Kong Xiaolu and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
cd ../../../part1_pMFM_main/scripts
matlab -nosplash -nodisplay -nodesktop -r \
"clear;clc;close al... |
c9339c85dc8bcad7441948e27d174ef62839f33c32d4be6b48c410b92fd2e115 | Shell | 477 | 17 | #!/bin/bash
# converts 3d nii files into a single 4d nii file
# Cyrus Eierud, TReNDS 112025
DIR_PREV=$(pwd)
mkdir /out/tmp_dir
find /out/input_sbm -iname "*.nii" -exec mv {} /out/tmp_dir/. \;
find /out/input_sbm -iname "*.nii.gz" -exec mv {} /out/tmp_dir/. \;
cd /out/tmp_dir
ls *.nii* > /out/subject_file_name_order... |
4efba7b1e67483b6ee6fa80973c49666e27448b3af4ae95c2e36b4b8435f7ee2 | Shell | 480 | 5 | #!/bin/bash
python submit-umbrella-sampling.py chorismate 1 130185 $(readlink -f smd/charge/chorismate-130185-smd) 50 100000 --base_folder $(pwd)
python submit-umbrella-sampling.py chorismate 1 260822 $(readlink -f smd/charge/chorismate-130185-smd) 50 100000 --base_folder $(... |
838323ab81878a437ab17b89318cc0971854efe2f69e80cfb01c74634ea72547 | Shell | 482 | 17 | #!/bin/bash
set -eu
job_id="$1"
task_id="$2"
dir="$3"
echo "job_id: $job_id, task_id: $task_id, dir: $dir"
mkdir -p "$dir/log"
sbatch_args="-p wav2vec --nodes=1 --ntasks-per-node=1"
sbatch_args="$sbatch_args --gpus-per-node=1 --cpus-per-task=8 --mem=0 --time=24:00:00"
sbatch_args="$sbatch_args -d afterok:$job_id -o... |
e4a4abfa97cb97f2e35610674b055a000551bed729dfbdf8c60b0528f33fa496 | Shell | 485 | 15 | #! /bin/sh
#
# xor.sh
# Copyright (C) 2023 rkim <robert.f.kim@gmail.com>
#
# Distributed under terms of the MIT license.
#
for i in {1..5}; do \
python main.py --gpu 0 --gpu_frac $1 --n_trials 70000 --mode train \
--N 1000 --P_inh 0.20 --task instr --gain 1.5 --P_rec 0.20 \
--act sigmoid --loss_fn l2 --apply_da... |
9202e2f1ca8b789b34a2dc565b12ef4309b0d3b91f5ccebf8b42ea435e4efbbb | Shell | 486 | 27 | #!/bin/bash
if [ $# -ne 4 ]; then
echo "usage: $0 TESTSET SRCLANG TGTLANG GEN"
exit 1
fi
TESTSET=$1
SRCLANG=$2
TGTLANG=$3
GEN=$4
if ! command -v sacremoses &> /dev/null
then
echo "sacremoses could not be found, please install with: pip install sacremoses"
exit
fi
grep ^H $GEN \
| sed 's/^H\-//' \
|... |
c0ac5d6162c8e644947d7d1b3bfdcc30dea14c7799f23c1bd6d7f1acda293525 | Shell | 486 | 15 | #! /bin/sh
#
# xor.sh
# Copyright (C) 2023 rkim <robert.f.kim@gmail.com>
#
# Distributed under terms of the MIT license.
#
for i in {1..5}; do \
python main.py --gpu 0 --gpu_frac $1 --n_trials 70000 --mode train \
--N 1000 --P_inh 0.20 --task instr2 --gain 1.5 --P_rec 0.20 \
--act sigmoid --loss_fn l2 --apply_d... |
e117fb1ad891b036c229002e7e4476c4a18fe9fe934faea522f9d1f6e2b4f6c3 | Shell | 488 | 23 | #!/bin/bash -e
BOOST_DIR=${HOME}/dev/lib/boost_1_36_0/
YASMIC_DIR=.
source ccfiles.sh
OFILES=`echo ${CCFILES} | sed -e 's/\.cc/\.o/g'`
CFLAGS="-O2 -DMATLAB_BGL_LARGE_ARRAYS -fPIC -c -I${BOOST_DIR} -I${YASMIC_DIR}"
#CFLAGS="-g -W -DMATLAB_BGL_LARGE_ARRAYS -fPIC -c -I${BOOST_DIR} -I${YASMIC_DIR}"
function echocmd {
... |
716573c146891cdc4d7c6d19da379c661e4eb91ed68dd70916b2acbe1dca6f94 | Shell | 489 | 15 | #! /bin/sh
#
# xor.sh
# Copyright (C) 2023 rkim <rkim@salk.edu>
#
# Distributed under terms of the MIT license.
#
for i in {1..5}; do \
python main.py --gpu 0 --gpu_frac $1 --n_trials 70000 --mode train \
--N 1000 --P_inh 0.20 --task instr2_retro --gain 1.5 --P_rec 0.20 \
--act sigmoid --loss_fn l2 --apply_dale... |
061184b0b80e5627ffb79b19f9bf6f9eac13adc89d80e666908df2ef9b8cbf43 | Shell | 490 | 8 | #!/bin/sh
echo "\n\n[rebuildPortalAssets.sh] Downloading latest npm package from internal npm registry..\n\n"
rm -rf ./node_modules
rm -f ./static/external_assets/bundled.js
npm install aibs-portal-assets --save --registry http://dev_resource:4873
rm -f ./node_modules/aibs-portal-assets/dist/index.html
cp .... |
34d8e2ea58af7d3f79fa432d697e0ddb01905bcef1a91ea3781a9cdca2b9c62e | Shell | 492 | 5 | #!/bin/bash
python submit-umbrella-sampling.py 2cht-rcsb-aligned 5667 130185 $(readlink -f smd/2cht-rcsb-aligned-130185-smd) 50 100000 --base_folder $(pwd) --protein
python submit-umbrella-sampling.py 2cht-rcsb-aligned 5667 260822 $(readlink -f smd/2cht-rcsb-aligned-130185-smd) 50 100000 --base_folder $(pw... |
c3e0f74d8283f507f5586119d3bee204d6f23622d6cc71b0d7acf04e3cf0fcac | Shell | 496 | 11 | #!/bin/bash
# Written by Xiuming Zhang and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
brainList=/data/users/xzhang/storage/forPNASRelease/outputs/VBM_m24/brainList.txt
nuisanceVars=/data/users/xzhang/storage/forPNASRelease/outputs/VBM_m24/age_sex_icv_m24_matchBrainList.csv
K=3... |
c0c0107a15cc607721032cfd4bef779ba3f9f1b950d31b777a0d1264570e4409 | Shell | 497 | 23 | #!/bin/bash -xve
compile_options=(
crackle_wasm.cc
-Oz
-DNDEBUG
--no-entry
-fno-exceptions
-fno-rtti
-s FILESYSTEM=0
-s ALLOW_MEMORY_GROWTH=1
-s TOTAL_STACK=32768
-s TOTAL_MEMORY=64kb
-s EXPORTED_FUNCTIONS='["_crackle_decompress","_malloc","_free"]'
-s MALLOC... |
e67eaaaaef5b816f6895fe5a93e443ecefc87444427dc1875f5bfb21fcb3c525 | Shell | 497 | 17 | #!/bin/bash
set -eu
job_id="$1"
task_id="$2"
dir="$3"
echo "job_id: $job_id, task_id: $task_id, dir: $dir"
mkdir -p "$dir/log"
sbatch_args="-p wav2vec --nodes=1 --ntasks-per-node=1"
sbatch_args="$sbatch_args --gpus-per-node=1 --cpus-per-task=8 --mem=0 --time=24:00:00"
sbatch_args="$sbatch_args -d afterok:$job_id -o... |
914f7e2aa88c08caa8228951373cf3c10df6575b7a3c4e0b78583591bdf8a490 | Shell | 499 | 18 | #!/bin/bash
set -eu
job_id="$1"
task_id="$2"
dir="$3"
echo "job_id: $job_id, task_id: $task_id, dir: $dir"
mkdir -p "$dir/log"
sbatch_args="-p wav2vec --nodes=1 --ntasks-per-node=1"
sbatch_args="$sbatch_args --gpus-per-node=1 --cpus-per-task=8 --mem=0 --time=24:00:00"
sbatch_args="$sbatch_args -d afterok:$job_id -o... |
f1e407006dd629e41d5625748b33b1a2921aa85726bf3db8aa3dd23b51c6e953 | Shell | 499 | 16 | nohup sh run_main.sh \
--model output/models/KeAP20/encoder \
--output_file fluorescence-KeAP20 \
--task_name fluorescence \
--do_train True \
--epoch 15 \
--mean_output True \
--optimizer Adam \
--per_device_batch_size 4 \
--gradient_accumulation_steps 16 \
-... |
f1e138c5fbe326b8272318a3f6e4ecf898880d77bbd561044490d3a91e28e2fb | Shell | 500 | 16 | nohup sh run_stability.sh \
--model output/models/KeAP20/encoder \
--output_file stability-KeAP20 \
--task_name stability \
--do_train True \
--epoch 5 \
--mean_output False \
--optimizer AdamW \
--per_device_batch_size 2 \
--gradient_accumulation_steps 32 \
-... |
9ca4bca94660aad65a763c1ed2efb9b188ca379813f38d78dadf8adab411c12b | Shell | 501 | 23 | #!/bin/bash -xve
compile_options=(
compresso_wasm.cc
-O3
-DNDEBUG
--no-entry
-fno-exceptions
-fno-rtti
-s FILESYSTEM=0
-s ALLOW_MEMORY_GROWTH=1
-s TOTAL_STACK=32768
-s TOTAL_MEMORY=64kb
-s EXPORTED_FUNCTIONS='["_compresso_decompress","_malloc","_free"]'
-s MA... |
1abf7cd83eee1b780d8cd90627598c075e155082d5fee92d2b91abced7a9dad0 | Shell | 502 | 13 | #!/bin/sh
#PBS -l walltime=01:00:0
# Will come into play only if this script is qsub'ed
# Written by Xiuming Zhang and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
stdTmp=${FSL_DIR}/data/standard/tissuepriors/avg152T1_gray
fsl_reg ${GM} ${stdTmp} ${outDir}${filename}_GMToStdTmp... |
3125ca4392c23160a56861f8956216a0a6e80a9f7b34d2ff178c34a7ee661790 | Shell | 503 | 17 | #!/bin/bash
set -eu
job_id="$1"
task_id="$2"
dir="$3"
echo "job_id: $job_id, task_id: $task_id, dir: $dir"
mkdir -p "$dir/log"
sbatch_args="-p wav2vec --nodes=1 --ntasks-per-node=1"
sbatch_args="$sbatch_args --gpus-per-node=1 --cpus-per-task=8 --mem=0 --time=24:00:00"
sbatch_args="$sbatch_args -d afterok:$job_id -o... |
b58e3c382c4d63917e7efc578e4a7d42c521bfdec3e3b49576c3541b1b906acd | Shell | 503 | 15 | #! /bin/sh
#
# xor.sh
# Copyright (C) 2023 rkim <robert.f.kim@gmail.com>
#
# Distributed under terms of the MIT license.
#
for i in {1..5}; do \
python main.py --gpu 0 --gpu_frac $1 --n_trials 70000 --mode train \
--N 1000 --P_inh 0.20 --task instr --gain 1.5 --P_rec 0.20 \
--act sigmoid --loss_fn l2 --apply_da... |
92ceb6fa402deca9de3530d5c3357f942f50c8bb4773a124589e9553dd7803e7 | Shell | 504 | 22 | #!/bin/bash
#SBATCH --job-name=novae
#SBATCH --output=/gpfs/workdir/blampeyq/.jobs_outputs/%j
#SBATCH --mem=80G
#SBATCH --cpus-per-task=8
#SBATCH --partition=cpu_long
module purge
module load anaconda3/2023.09-0/none-none && source activate novae
cd /gpfs/workdir/blampeyq/novae
# Get config
DEFAULT_CONFIG=swav_cpu_0... |
ad99758993f8e2f92eccfa662af7a1d1f776600a0827aced3cf1c0bf6c6cfc69 | Shell | 507 | 12 | #!/usr/bin/env bash
# Create the stardust conda environment named stardust_env
# conda env create -f stardust.yml
# Activate the environment
# source activate stardust_env
# Install the required R packages
pip3 install torch==1.13.0 torchvision torchaudio --extra-index-url https://download.pytorch.org/whl/cpu --no-... |
8e32a2f19bf371554dfd562cf0dcc168ee920ff6a86c90f1e319e299eafa4c74 | Shell | 510 | 16 | nohup sh run_main.sh \
--model output/models/KeAP20/encoder \
--output_file remote_homology-KeAP20 \
--task_name remote_homology \
--do_train True \
--epoch 10 \
--mean_output True \
--optimizer AdamW \
--per_device_batch_size 2 \
--gradient_accumulation_steps 16 \
... |
a4abbe0b1eefb5fb4262a2f7ef0df9b3a52d6381575a6e166be8c573ea36e3eb | Shell | 513 | 19 | #!/bin/sh
# Written by Xiuming Zhang and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
progressFile=${1}
fullList=${2}
# Do not return until all jobs are finished
noJobs=`cat ${fullList} | wc -l`
noJobsDone=0
noJobsDonePrev=-1
while [ ${noJobsDone} -lt ${noJobs} ]; do
if [ !... |
5b4bbb13ddaa75a78865f109d22928076c19e933dc7e624142a2e02edce7acc7 | Shell | 515 | 22 | #!/bin/bash -xve
# This script builds `jxl_decoder.wasm` using emsdk in a docker container.
cd "$(dirname "$0")"
docker build -f compile.Dockerfile .
docker run \
--rm \
-v ${PWD}:/src \
-u $(id -u):$(id -g) \
$(docker build -f compile.Dockerfile -q .) \
/src/build_wasm.sh
docker ... |
d0809f81230499f5a4d94d611a2f1b9488f918b5926af49e025c0f3e9d2d7520 | Shell | 520 | 28 | #!/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 make test_$1 > /dev/null 2> .runtest.log ; then
if ! ./test_$1 r20 > /dev/null 2> .runtest.log ; then
echo -e $red Test $1 failed: $black
echo -e $blue
cat .runtest.log... |
fb95e0929c687e2799f7a407bd9b79dc59a93967ee1b418f15016613528fec09 | Shell | 521 | 18 | #!/bin/bash
# Written by Nanbo Sun and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
progress_file=${1}
total_no_jobs=${2}
# Do not return until all jobs are finished
no_jobs_done=0
no_jobs_done_prev=-1
while [ ${no_jobs_done} -lt ${total_no_jobs} ]; do
if [ ! ${no_jobs_done... |
8edf9474f408ff2aad92ea9125452f2f6ba06a27b1f3e813dc2d068afd6ee89f | Shell | 527 | 24 | #!/bin/bash
#SBATCH --job-name=novae
#SBATCH --output=/gpfs/workdir/blampeyq/.jobs_outputs/%j
#SBATCH --time=4:00:00
#SBATCH --partition=gpu
#SBATCH --mem=10G
#SBATCH --tmp=20G
#SBATCH --cpus-per-task=1
#SBATCH --gres=gpu:1
module purge
module load anaconda3/2023.09-0/none-none
module load gcc/15.1.0/gcc-15.1.0
modu... |
e0d16eed495f7b5d995c647f811a9fec630933d1273fa844fce9c3d1e5631ad7 | Shell | 535 | 15 | #!/bin/bash
if [ -f "cromwell-32.jar" ]; then
echo "Skip downloading cromwell."
else
wget -N -c https://github.com/broadinstitute/cromwell/releases/download/32/cromwell-32.jar
fi
CROMWELL_JAR=cromwell-32.jar
BACKEND_CONF=../backends/backend_with_db.conf
BACKEND=google
GC_PROJ=encode-dcc-1016
GC_ROOT=gs://encode-pi... |
de00502862ec9493e48663361f07063b99df97f4e5dd33963fcfc63f93dd021f | Shell | 538 | 27 | #!/bin/bash
# rename_prefix.sh
# Rename all files starting with prefix OLD to prefix NEW in a directory
if [ "$#" -lt 2 ]; then
echo "Usage: $0 OLD_PREFIX NEW_PREFIX [DIRECTORY]"
exit 1
fi
OLD="$1"
NEW="$2"
DIR="${3:-.}" # default: current directory
# Safety check
if [ ! -d "$DIR" ]; then
echo "Error: $DIR i... |
4fe725e55035bee1d7bf4c8e0ea2c396e0fac48365dbcfdf54fd6cd261e2c567 | Shell | 540 | 8 | #!/bin/bash
#SBATCH --job-name=CN_1_2_previous_tube_label_CN_1_3_S4_L001
#SBATCH --output=slurm_logs/CN_1_2_previous_tube_label_CN_1_3_S4_L001.out
#SBATCH --time=0-5:0
#SBATCH --nodes=1
#SBATCH --ntasks=1
mamba activate patch_seq_spl
salmon quant -i proc/salmon_index -l A -1 data/illumina/SFARI_data/CN_1_2_previous_tub... |
89451633fa399713f2fe64f338980e9fd99c2c547a68ed85ef49b8c5e6144c76 | Shell | 540 | 8 | #!/bin/bash
#SBATCH --job-name=CN_1_1_previous_tube_label_CN_1_2_S3_L001
#SBATCH --output=slurm_logs/CN_1_1_previous_tube_label_CN_1_2_S3_L001.out
#SBATCH --time=0-5:0
#SBATCH --nodes=1
#SBATCH --ntasks=1
mamba activate patch_seq_spl
salmon quant -i proc/salmon_index -l A -1 data/illumina/SFARI_data/CN_1_1_previous_tub... |
e24207f3b193163d0a030b358885b595a4ffff8c824ab4d7c730efd186bc9ebb | Shell | 541 | 14 | export MONQ=/home/whatizit/monq
export MONQLIB=$MONQ/lib
export PATH=$MONQ/bin:$PATH
export CLASSPATH=$MONQLIB/monq-1.0.jar
export CLASSPATH=$CLASSPATH:$MONQLIB/indexing.jar
export CLASSPATH=$CLASSPATH:$MONQLIB/xstream-1.4.7.jar
export CLASSPATH=$CLASSPATH:$MONQLIB/ie.jar
export CLASSPATH=$CLASSPATH:$MONQLIB/marie.ja... |
d2280fb6140e10dc52c396848dfb8971492fd819531533bd268d3645061103a2 | Shell | 542 | 21 | #!/bin/bash
# Stop on error
set -e
CONDA_ENV=encode-atac-seq-pipeline
CONDA_ENV_PY3=encode-atac-seq-pipeline-python3
SH_SCRIPT_DIR=$(cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd)
REQ_TXT=${SH_SCRIPT_DIR}/requirements.txt
REQ_TXT_PY3=${SH_SCRIPT_DIR}/requirements_py3.txt
if which conda; then
echo "=== Found Conda ... |
0e8513f965528c87a2ff8514f76619a3fdb9614dd4e868040e6e907d10fa5dda | Shell | 543 | 10 | #!/bin/bash
# this function is the wrapper to run the `CBIG_pMFM_test_different_window.py`
# Written by Kong Xiaolu and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
cd ../../../../part2_pMFM_control_analysis/Different_window_length/scripts
source activate pMFM
python CBIG_pMFM_te... |
6dd83c6061001bef1bd363c8f845e8ae5bea3a577952e81ab025a8df84fc9c7b | Shell | 543 | 11 | #!/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/docker110825/spect_bids/:/data \
-v /home/cyrus/ext4max/fromSsd/Documents/trends/work/2023/jeremy/keater/docker110825/spect_bids/derivatives/20blind/:/out \
-v /home... |
e4db3df0407213e9651999458e813499305d2fd3d3b1d14f3bd2746bc37a2b29 | Shell | 544 | 9 | #!/bin/bash
# this function is the wrapper to run the `CBIG_pMFM_step1_generate_permutation_order_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 -nosplash -n... |
75f6b311ecd5c5e5754c50dc362ad7b9b62657275e9ccb7bbdad075ea69d9605 | Shell | 548 | 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 $NO_CACHE -t doduo1.umcn.nl/nnunet_for_pathology:$VERS... |
9e55d7962d36d98ec4800a3b366e69a2326b1ae016336cf51d093aa3996760b4 | Shell | 548 | 15 | #!/bin/bash
#SBATCH --job-name=DeepTMHMM
#SBATCH --output=slurm_logs/DeepTMHMM.out
#SBATCH --time=0-5:0
#SBATCH --nodes=1
#SBATCH --ntasks=1
mamba deactivate
module load NiaEnv/2019b python/3.11.5
source .virtualenvs/DeepTMHMM/bin/activate
# This does not work in compute nodes because of the lack of internet access
#... |
b1425dd6057548ff2364d0b14a8c14e89534c70690fa774a1874f29c7c0cebfb | Shell | 548 | 24 | #!/bin/bash
#SBATCH --job-name=novae
#SBATCH --output=/gpfs/workdir/blampeyq/.jobs_outputs/%j
#SBATCH --time=00:30:00
#SBATCH --partition=cpu_short
#SBATCH --mem=20G
#SBATCH --cpus-per-task=8
module purge
module load anaconda3/2023.09-0/none-none
source activate novae
cd /gpfs/workdir/blampeyq/novae/scripts
# Get co... |
87cdee97feacb7a6b1596ad5628b8adbc0905f274e35b766646dc9f7362431f5 | Shell | 550 | 18 | export INCLUDE_PATH="${PREFIX}/include"
export LIBRARY_PATH="${PREFIX}/lib"
export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
export CFLAGS="-I${PREFIX}/include ${LDFLAGS}"
# disable Makefile driven build of htslib.a
sed -i.bak "s/'build_ext': HTSBuild//" setup.py
# just link to htslib
sed -i.bak 's/extra_objects.*//' bui... |
d5159c55b073562ffce9fabd46e2476ce325d3b4c43c09bda38f83c553a49905 | Shell | 550 | 8 | #!/bin/bash
#SBATCH --job-name=NPC_1_2_previous_tube_label_NPC_1_3_S2_L001
#SBATCH --output=slurm_logs/NPC_1_2_previous_tube_label_NPC_1_3_S2_L001.out
#SBATCH --time=0-5:0
#SBATCH --nodes=1
#SBATCH --ntasks=1
mamba activate patch_seq_spl
salmon quant -i proc/salmon_index -l A -1 data/illumina/SFARI_data/NPC_1_2_previou... |
00bb9e385dde50c5c72c2780903d2b7d5f39df43f772790245ee17e9ddcc90d7 | Shell | 555 | 22 | #!/bin/bash
#SBATCH --job-name=novae
#SBATCH --output=/gpfs/workdir/blampeyq/.jobs_outputs/%j
#SBATCH --time=24:00:00
#SBATCH --partition=gpua100
#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... |
63c022bdd64729d612c19441c12a41ffb0b8f959ad6246127ee6a9c0d8fa6f3d | Shell | 555 | 27 | dbdir=[path to directory containing G2S and JTI models]
### Run TWAS analyses
# adjust names in gwas_datapaths.txt to direct the code to the data downloaded from the PGC.
bash Code/run_twas.sh
### compile all results
bash Code/comp_twas_data.sh
### Perform tissue model-specific pvalue thresholding
bash Code/r... |
b55d5419bdb661a97f56dd48519d4559650356bd6c24f65488b4c97d056730f4 | Shell | 555 | 8 | #!/bin/bash
#SBATCH --job-name=NPC_3_2_previous_tube_label_NPC_3_3_S12_L001
#SBATCH --output=slurm_logs/NPC_3_2_previous_tube_label_NPC_3_3_S12_L001.out
#SBATCH --time=0-5:0
#SBATCH --nodes=1
#SBATCH --ntasks=1
mamba activate patch_seq_spl
salmon quant -i proc/salmon_index -l A -1 data/illumina/SFARI_data/NPC_3_2_previ... |
3083efb8b757f8612d556be736386546a7bf2cc223c544f21551b5e4a2a271f0 | Shell | 556 | 26 | #!/bin/bash
#SBATCH -p gpu
#SBATCH --mem=32g
#SBATCH --gres=gpu:rtx2080:1
#SBATCH -c 3
#SBATCH --output=example_3.out
source activate mlfold
path_to_PDB="../PDB_complexes/pdbs/3HTN.pdb"
output_dir="../PDB_complexes/example_3_outputs"
if [ ! -d $output_dir ]
then
mkdir -p $output_dir
fi
chains_to_design="A B"
p... |
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