sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
2b3fea3f211fab2e6c5622350acf5090c3347ddc070c6412bd07a951c06b044c | Shell | 574 | 21 | #!/bin/bash
mkdir -p plots
mkdir -p clusters
python ../scripts/calculate_combined_clusters.py --write --wss \
--ref_file_a 'traj/condition-a_receptor.gro' \
--trj_file_a 'traj/condition-a_receptor.xtc' \
--ref_file_b 'traj/condition-b_receptor.gro' \
--trj_file_b 'traj/condition-b_receptor.xtc' \
--label_a 'A' \... |
909ee7fd2405850fb794eec5999aaa4decab8b9b1e6e20ae6fcbf8d6bd28fa3c | Shell | 574 | 29 | #!/bin/bash
helpFunction() {
echo ""
echo "Usage: $0 -d DESTINATION_DIR -n NIFTI_FILEPATH"
exit 1
}
while getopts d:n: opt; do
case "${opt}" in
d) DESTINATION_DIR=${OPTARG} ;;
n) NIFTI_FILEPATH=${OPTARG} ;;
?) helpFunction ;;
esac
done
main() {
echo running ...
}
if [ -z "$NIFTI_FILEPATH" ] || [ -z... |
a4836e54b3b00b14a9e03989a1a05dd8bfb81e8bb63dcea65c63bc054d1cacba | Shell | 574 | 28 | #!/bin/bash
#$ -cwd -V
#$ -l mem_free=30G,h_vmem=30G,h_fsize=50G
#$ -N torus_priors
#$ -e torus.out
#$ -o torus.out
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAME}"
## List current modules for reproduc... |
5a25b2a1dbc5311781add93036d77cedaa3863ae73e62322a6c72c3234bb99b0 | Shell | 575 | 12 | #!/bin/sh
set -e
echo "This script only works with ODK 1.3.2 and later. For ODK 1.3.1 or earlier, use https://raw.githubusercontent.com/INCATools/ontology-development-kit/v1.3.1/seed-via-docker.sh"
ODK_IMAGE=${ODK_IMAGE:-odkfull}
ODK_TAG=${ODK_TAG:-latest}
ODK_GITNAME=${ODK_GITNAME:-$(git config --get user.name)}
OD... |
571c6b7a3a7ca35b5441666d1a983c781c7af5ca77596060f0ce662e0e6aa214 | Shell | 576 | 28 | #!/bin/bash
#$ -cwd -V
#$ -l mem_free=30G,h_vmem=30G,h_fsize=50G
#$ -N torus_priors
#$ -e torus.out
#$ -o torus.out
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAME}"
## List current modules for reproduc... |
ccaed6560e8bdfae7969e6bf9a502895bf540d6dcf11907cb13c98fba7ab5a95 | Shell | 577 | 27 | #!/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="../inputs/PDB_complexes/pdbs/3HTN.pdb"
output_dir="../outputs/example_3_outputs"
if [ ! -d $output_dir ]
then
mkdir -p $output_dir
fi
chains_to_design="A B"
... |
2651ba35e4e4cb1c9a3738b98b185b9f97fbf68a756fed9beecb37d36b8493ba | Shell | 579 | 9 | #!/bin/sh
GPU=3
CUDA_VISIBLE_DEVICES=${GPU} python ../src/main_fast_new.py --GPU --J2=0 --lr=0.001 --dataname='108_triangular_lattice'\
--savefolder='108_triangular_lattice_pbc_J2_0_f_64_non_local_preact_regularconv_clip_grad_-1_lr_decay_4000' --data_dir='../dataset/' --save_dir='../result/Heisenberg/' \
--checkpoi... |
2e540689d26c65233805247e1d91480f00206168dfe99df685692ae08e7d589b | Shell | 580 | 9 | #!/bin/sh
GPU=0
CUDA_VISIBLE_DEVICES=${GPU} python ../src/main_fast_new.py --GPU --J2=0.125 --lr=0.001 --dataname='6_6_triangular_lattice'\
--savefolder='6_6_triangular_lattice_pbc_J2_0125_f_64_non_local_preact_regularconv_clip_grad_2_lr_decay_4000' --data_dir='../dataset/' --save_dir='../result/Heisenberg/' \
--ch... |
3c6c7150752a8f14598e6799c4703e37085588df712e84c01dd74011dca0a3e0 | Shell | 580 | 16 | export nnUNet_results="nnUNet_training/nnUNet_results"
export nnUNet_raw="nnUNet_training/nnUNet_raw"
export nnUNet_preprocessed="nnUNet_training/nnUNet_preprocessed"
export nnUNet_predictions="nnUNet_training/nnUNet_predictions"
GPU_ID=0 # Put the GPU IDs here
DATASET=558
TRAINER=nnUNetTrainerNoMirroring
nnUNetv2_pl... |
a04a5970ee4fe3da1abb99d93c596573a7e138149da73202cb7bb242f49a3ac4 | Shell | 580 | 28 | #!/bin/bash
#$ -cwd -V
#$ -l mem_free=30G,h_vmem=30G,h_fsize=50G
#$ -N torus_priors
#$ -e torus.out
#$ -o torus.out
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAME}"
## List current modules for reproduc... |
e8a2abffa220c00a3e01ef1623d224cf408e5e71521a0762298e9ad9a90453ab | Shell | 582 | 9 | #!/bin/sh
GPU=3
CUDA_VISIBLE_DEVICES=${GPU} python ../src/main_fast_new.py --GPU --J2=0 --lr=0.001 --dataname='6_6_triangular_lattice'\
--savefolder='6_6_triangular_lattice_pbc_J2_0_f_64_non_local_preact_regularconv_clip_grad_2_lr_decay_4000' --data_dir='../dataset/' --save_dir='../result/Heisenberg/' \
--checkpoin... |
039c14b0dd92ffd7d561a1ff28a69c3c1922a3d1a90ab4ee980aec5f8ab37bb6 | Shell | 584 | 31 | #!/bin/bash
#$ -cwd
#$ -l caracol,mem_free=50G,h_vmem=50G,h_fsize=100G
#$ -N gene_tensorqtl
#$ -o ./summary.log
#$ -e ./summary.log
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAME}"
## List current modu... |
2a8088f5e2df1fb225f18f91b3a3806fbbe3cd1c9c70a120c505c56a0d79c2e7 | Shell | 587 | 6 | cd lasagna
mkdir results
# python program.py <dataset> <column_index_of_label> <result_location> <id_for_embeddings: 0=onehot, 1=a_c, 2=a_{ph}, 3=[a_c,a_{ph}]> <hidden_dim> <epochs_per_fold>
CUDA_VISIBLE_DEVICES=2 python rcnn.py ../../../yeast/preprocessed/protein.actions.tsv -1 results/yeast_wvctc_rcnn_50_5.txt 3 50 1... |
88b88427b96d181efb6dc3aeb8289ef1c127592c7748e3d0dccf866d567b59e2 | Shell | 587 | 9 | #!/bin/sh
GPU=7
CUDA_VISIBLE_DEVICES=${GPU} python ../src/main_fast_new.py --GPU --J2=-0.02 --lr=0.001 --dataname='36_kagome_lattice'\
--savefolder='36_kagome_lattice_pbc_J2_-002_f_64_non_local_preact_regularconv_V2_clip_grad_1_lrdecay_4000' --data_dir='../dataset/' --save_dir='../result/Heisenberg/' \
--checkpoint... |
b4e453fccc993d273284fe6193dca778ddca5751e388879c994358cb03176393 | Shell | 587 | 9 | #!/bin/sh
GPU=9
CUDA_VISIBLE_DEVICES=${GPU} python ../src/main_fast_new.py --GPU --J2=0.08 --lr=0.001 --dataname='6_6_triangular_lattice'\
--savefolder='6_6_triangular_lattice_pbc_J2_008_f_64_non_local_preact_regularconv_clip_grad_2_lr_decay_4000' --data_dir='../dataset/' --save_dir='../result/Heisenberg/' \
--chec... |
507cbe34f632bc6b6a8b54dc872b1393b1fc4a6fe45acbe3fa3163da5d59f198 | Shell | 588 | 32 | #!/bin/bash
#$ -cwd -V
#$ -t 1-23663:1
#$ -N gen_sbams
#$ -e ./logs/sbams_$TASK_ID.out
#$ -o ./logs/sbams_$TASK_ID.out
#$ -tc 50
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAME}"
## List current modules... |
a27067706d928199eb27c38f608c4a48dbc0b787eb115601e851c9dd6a4389c9 | Shell | 590 | 32 | #!/bin/bash
#$ -cwd -V
#$ -t 1-25979:1
#$ -N gen_sbams
#$ -e ./logs/sbams_$TASK_ID.out
#$ -o ./logs/sbams_$TASK_ID.out
#$ -tc 75
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAME}"
## List current modules... |
9f8c14a8be6d6bb492b8513f89324affe4d4c44a4bcff4239c94edee1da6a844 | Shell | 591 | 31 | #!/bin/bash
#$ -cwd
#$ -l mem_free=10.0G,h_vmem=10G,h_fsize=50G
#$ -N pca_dlpfc
#$ -o ./summary_dlpfc.log
#$ -e ./summary_dlpfc.log
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAME}"
## List current modu... |
1605c9b2cf5185dfef2a61c9421ab111e68dbbc37a888ae670c90945522b15af | Shell | 592 | 16 | #!/bin/bash
# Export the model
export MODEL_FILE=$(pwd)"/src/test/resources/encryptedACPmodel.jar"
# Export the encryption key (here as plain text)
export ENCRYPTION_KEY=Kt6gqo8lds7mVyYr0gOdpg==
# Go into service_utils and install a new version (required during development and testing, when updated continuously)
cd .... |
3c8aee703e2ef29fdbbd77b79698d417596a23cfa5649e846e3865c3669abc5f | Shell | 592 | 31 | #!/bin/bash
#$ -cwd
#$ -l mem_free=15.0G,h_vmem=15G,h_fsize=50G
#$ -N de_sex_tx_hippo
#$ -o ./summary_tx.log
#$ -e ./summary_tx.log
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAME}"
## List current modu... |
f2bab68505a9ef83467925275f7a7915f19680ed59fb0c4cf3f5ea342c2e66f1 | Shell | 592 | 31 | #!/bin/bash
#$ -cwd
#$ -l mem_free=15.0G,h_vmem=15G,h_fsize=50G
#$ -N de_sex_tx_dlpfc
#$ -o ./summary_tx.log
#$ -e ./summary_tx.log
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAME}"
## List current modu... |
23ed323d41027f60feb46ed0193b174747b330711b374ac4949dbf4d97a1dfb5 | Shell | 593 | 9 | #!/bin/sh
GPU=1
CUDA_VISIBLE_DEVICES=${GPU} python ../src/main_fast_new.py --GPU --J2=0.125 --lr=0.001 --dataname='108_triangular_lattice'\
--savefolder='108_triangular_lattice_pbc_J2_0125_f_64_non_local_preact_regularconv_clip_grad_2_lr_decay_4000' --data_dir='../dataset/' --save_dir='../result/Heisenberg/' \
--ch... |
0784cfa063ea4e9c0e6edcf89b623b2860555d9b8f36fd84f918acd3b2f90f99 | Shell | 594 | 31 | #!/bin/bash
#$ -cwd
#$ -l mem_free=35.0G,h_vmem=35G,h_fsize=50G
#$ -N de_sex_exon_hippo
#$ -o ./summary_exon.log
#$ -e ./summary_exon.log
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAME}"
## List curren... |
1a334a0c23309b6522785e411cf8fff99612f826c2160751bd7c281100993b62 | Shell | 594 | 31 | #!/bin/bash
#$ -cwd
#$ -l mem_free=35.0G,h_vmem=35G,h_fsize=50G
#$ -N de_sex_exon_dlpfc
#$ -o ./summary_exon.log
#$ -e ./summary_exon.log
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAME}"
## List curren... |
4de2cf9d94777d43b165f19fc8827cbf125da94353997472e2f13f1bd9f10e62 | Shell | 594 | 31 | #!/bin/bash
#$ -cwd
#$ -l mem_free=45.0G,h_vmem=45G,h_fsize=50G
#$ -N de_sex_jxn_dlpfc
#$ -o ./summary_jxn.log
#$ -e ./summary_jxn.log
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAME}"
## List current m... |
50c2d072f5a239144e1f10c334707be0e929ec5ee837f36395f92b53a2f58a16 | Shell | 594 | 32 | #!/bin/bash
#$ -cwd -V
#$ -t 1-22388:1
#$ -N gen_sbams
#$ -e ./logs/sbams_$TASK_ID.out
#$ -o ./logs/sbams_$TASK_ID.out
#$ -tc 50
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAME}"
## List current modules... |
652e7c761baec2212699e853e7b36443e0c3003a64be6002807717b9f29f8973 | Shell | 594 | 31 | #!/bin/bash
#$ -cwd
#$ -l mem_free=10.0G,h_vmem=10G,h_fsize=50G
#$ -N de_sex_gene_dlpfc
#$ -o ./summary_gene.log
#$ -e ./summary_gene.log
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAME}"
## List curren... |
8f1107e88b2c8eeedca6d75a43672cf7d4d8d996c7a56ca6e320dbfe87a12ce7 | Shell | 594 | 31 | #!/bin/bash
#$ -cwd
#$ -l mem_free=45.0G,h_vmem=45G,h_fsize=50G
#$ -N de_sex_jxn_hippo
#$ -o ./summary_jxn.log
#$ -e ./summary_jxn.log
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAME}"
## List current m... |
a61471fe2f3226c6c79f6066b6e04d294ab1ab686611721d10b4bf6fc63a2408 | Shell | 594 | 31 | #!/bin/bash
#$ -cwd
#$ -l mem_free=15.0G,h_vmem=15G,h_fsize=50G
#$ -N de_sex_tx_caudate
#$ -o ./summary_tx.log
#$ -e ./summary_tx.log
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAME}"
## List current mo... |
b0088af4c8d8ca504964ddb2ca5bc232c5ad08e40027d724264f2b54eacb4f4d | Shell | 594 | 31 | #!/bin/bash
#$ -cwd
#$ -l mem_free=10.0G,h_vmem=10G,h_fsize=50G
#$ -N de_sex_gene_hippo
#$ -o ./summary_gene.log
#$ -e ./summary_gene.log
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAME}"
## List curren... |
05c52422d926e88dd13fca81e55a83fd6137854371c67af51ba57a11a77e5d7f | Shell | 595 | 31 | #!/bin/bash
#$ -cwd
#$ -R y
#$ -l mem_free=50G,h_vmem=50G,h_fsize=100G
#$ -N mash_allpairs_chunking
#$ -o ./chunking.log
#$ -e ./chunking.log
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAME}"
## List cu... |
0b44aac6978e918b907a66fc77e7bf7607b6abd4be2cadeca2873330df538e26 | Shell | 596 | 31 | #!/bin/bash
#$ -cwd
#$ -l mem_free=45.0G,h_vmem=45G,h_fsize=50G
#$ -N de_sex_jxn_caudate
#$ -o ./summary_jxn.log
#$ -e ./summary_jxn.log
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAME}"
## List current... |
47b5a9c113585253440f66f25ad04ebb1479429fa67d77bcf61cdee4068f494e | Shell | 596 | 31 | #!/bin/bash
#$ -cwd
#$ -R y
#$ -l mem_free=50G,h_vmem=50G,h_fsize=100G
#$ -N mash_allpairs_chunking
#$ -o ./chunking.log
#$ -e ./chunking.log
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAME}"
## List cu... |
699c948df560fac6fca1b4a4e5793305ee15ace4f1f9fb0c46d05d806dce7482 | Shell | 596 | 31 | #!/bin/bash
#$ -cwd
#$ -l mem_free=10.0G,h_vmem=10G,h_fsize=50G
#$ -N de_sex_gene_caudate
#$ -o ./summary_gene.log
#$ -e ./summary_gene.log
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAME}"
## List curr... |
833916a92d1ceee40be11d672fe8471ec36e2c639470aaf16d3b6385f088f2f7 | Shell | 596 | 31 | #!/bin/bash
#$ -cwd
#$ -l mem_free=35.0G,h_vmem=35G,h_fsize=50G
#$ -N de_sex_exon_caudate
#$ -o ./summary_exon.log
#$ -e ./summary_exon.log
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAME}"
## List curr... |
928ec9cda81a648038544cf12477f10daa9745dd11e4f638b215b74a5a902ba2 | Shell | 596 | 29 | #!/bin/bash
echo "ENTER STARTUP"
logrotate -vf /etc/logrotate.conf
# Redirect stdout to a log file
exec > >(tee /var/log/container.log)
# Redirect stderr to a different error log file and also to stderr
exec 2> >(tee /var/log/container.log >&2)
# Activate the Conda environment
echo "ENTER PFP"
#mamba env update -n pfp... |
d7ce823f9f87a26a3232115cd79ad34804e5c7ee733f012797fb5474f1dcde72 | Shell | 596 | 31 | #!/bin/bash
#$ -cwd
#$ -R y
#$ -l mem_free=80G,h_vmem=80G,h_fsize=100G
#$ -N mash_allpairs_chunking
#$ -o ./chunking.log
#$ -e ./chunking.log
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAME}"
## List cu... |
e77f74fb510963f73b44db449161838168a0774aec31f626b460a354bdb89045 | Shell | 596 | 31 | #!/bin/bash
#$ -cwd
#$ -pe local 8
#$ -l mem_free=5.0G,h_vmem=5G,h_fsize=50G
#$ -N region_tx
#$ -o ./summary_tx.log
#$ -e ./summary_tx.log
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAME}"
## List curre... |
47e434adb0344d37b14f13ab4115ca8f7c5d4394eaa98351c5e0d357a814946d | Shell | 597 | 17 | #!/bin/bash
#Purpose: Submit tedana restart script for each subject
#Written by M. Peterson, Nielsen Brain and Behavior Lab
#PATHS
CODE_DIR=/fslgroup/fslg_spec_networks/compute/code/Utah_analysis/CBIG2016_preproc_ALL
for subj in `cat ${CODE_DIR}/subjids/preproc_failed_ids2.txt`; do
mkdir -p ${CODE_DIR}/subject_scri... |
44089c4d07a65cc1c08a5bde1c0b9e66e5c0c72912b496d63692faa2c8093688 | Shell | 598 | 18 | #!/usr/bin/env bash
###############################################################################
#
# Create conda virtual environment for MAPP
#
# AUTHOR: Maciej_Bak
# AFFILIATION: University_of_Basel
# AFFILIATION: Swiss_Institute_of_Bioinformatics
# CONTACT: wsciekly.maciek@gmail.com
# CREATED: 20-03-... |
8fd7ebc4d68efefd22ef53794a568a9635fc7fa7861ea20f67f6f0e3b64711fb | Shell | 598 | 31 | #!/bin/bash
#$ -cwd
#$ -pe local 8
#$ -l mem_free=2.0G,h_vmem=2G,h_fsize=50G
#$ -N region_gene
#$ -o ./summary_gene.log
#$ -e ./summary_gene.log
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAME}"
## List... |
b0f3c37286eb226d95360a86f09f39453d7c58a7e1ef429db10c28473102278a | Shell | 598 | 20 | # Set up ProteinMPNN
mkdir -p packages
cd packages
git clone https://github.com/dauparas/ProteinMPNN.git
# Set up ESMFold
pip install "fair-esm[esmfold]"
pip install "dllogger @ git+https://github.com/NVIDIA/dllogger.git"
pip install "openfold @ git+https://github.com/aqlaboratory/openfold.git"
pip install modelcif
#... |
de1e7c2ab1e1f36283c3106db49060c8297af852d304d01d3f4327ce77751131 | Shell | 598 | 31 | #!/bin/bash
#$ -cwd
#$ -l mem_free=15.0G,h_vmem=15G,h_fsize=50G
#$ -N de_sex_tx_hippocampus
#$ -o ./summary_tx.log
#$ -e ./summary_tx.log
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAME}"
## List curren... |
43eeb2ecca8e2b7b109ca71ae38b530945fcfb9012cb4fdaa80597106d9c0467 | Shell | 599 | 21 | #!/bin/bash
#SBATCH -A <id>
#SBATCH -p node
#SBATCH -t 20:00:00
#SBATCH -n 10
#SBATCH -J cr_arc_merge_brain
#SBATCH --mail-user <email-id>
#SBATCH --mail-type=ALL
#SBATCH -e wjob-%J.err
#SBATCH -o wjob-%J.out
module load bioinfo-tools
cd ../../../multiome_data/merged
../../programs/cellranger-arc-2.0.0/cellranger-ar... |
7b090090b50e864ed68980e6de5187121a0d8ecb020080bfef3e89477accc97a | Shell | 599 | 16 | #!/usr/bin/env bash
###############################################################################
# This script builds the Dockerfiles in the dockerfiles/ directory.
# assumes that the dockerfiles/ directory is a sibling of the scripts/ directory, and the script is being run
# from the scripts/ directory
set -eux
c... |
ebbe5c010afd19e43aa53b4309fdf48e3dafe60d4c4da0c29c3cbc26ba0760fe | Shell | 599 | 32 | #!/bin/bash
#$ -cwd
#$ -l mem_free=2G,h_vmem=2G,h_fsize=10G
#$ -N eQTLplots_caudate
#$ -o ./logs/summary.log
#$ -e ./logs/summary.log
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAME}"
## List current mo... |
fcb4bad409bd7d6692e6d90f6f0a582c6e50757b7a2684292087ea44c8afd085 | Shell | 599 | 31 | #!/bin/bash
#$ -cwd
#$ -l mem_free=10.0G,h_vmem=10G,h_fsize=50G
#$ -N pca_caudate
#$ -o ./summary_caudate.log
#$ -e ./summary_caudate.log
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAME}"
## List curren... |
3b02c0f07bbc5aa88463ffb3e0853f427e47810c7dc4535810400881fa9e5a7b | Shell | 600 | 31 | #!/bin/bash
#$ -cwd
#$ -l mem_free=35.0G,h_vmem=35G,h_fsize=50G
#$ -N de_sex_exon_hippocampus
#$ -o ./summary_exon.log
#$ -e ./summary_exon.log
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAME}"
## List ... |
3dd7164e622bcbbae6cafe251f03eb8cfb029d0f8ae368b58db1f8ad1f69cf2d | Shell | 600 | 31 | #!/bin/bash
#$ -cwd
#$ -l mem_free=45.0G,h_vmem=45G,h_fsize=50G
#$ -N de_sex_jxn_hippocampus
#$ -o ./summary_jxn.log
#$ -e ./summary_jxn.log
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAME}"
## List cur... |
bb2facddf3fec241127f618e07c2a607ab6ed75c5497d7afc426cd861b50dc3c | Shell | 600 | 31 | #!/bin/bash
#$ -cwd
#$ -l mem_free=10.0G,h_vmem=10G,h_fsize=50G
#$ -N de_sex_gene_hippocampus
#$ -o ./summary_gene.log
#$ -e ./summary_gene.log
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAME}"
## List ... |
87ba4ea1fb7b4bc8e64c9b85d123bf8ed122d08e31a9f2ceb70440a39cef80ff | Shell | 601 | 31 | #!/bin/bash
#$ -cwd
#$ -pe local 10
#$ -l mem_free=12.0G,h_vmem=12G,h_fsize=50G
#$ -N region_jxn
#$ -o ./summary_jxn.log
#$ -e ./summary_jxn.log
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAME}"
## List... |
ac29c23ebc458afb620830746dd292ddf843e30a710334a4cb284ac1470261d6 | Shell | 601 | 31 | #!/bin/bash
#$ -cwd
#$ -pe local 10
#$ -l mem_free=12.0G,h_vmem=12G,h_fsize=50G
#$ -N region_exon
#$ -o ./summary_exon.log
#$ -e ./summary_exon.log
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAME}"
## L... |
ed4524ca2bcd680d00055dc7950e25d117b208bbb65b4192ce845d497e1861d7 | Shell | 601 | 20 | # bert base
python -m train \
experiment=hg38/promoter \
wandb.mode=online \
wandb.group=Promoter \
wandb.name=train_inf_bert_base_step1 \
hydra.run.dir=./outputs/promoter/train_inf_bert_base_step1 \
task=DNA_masked_gen \
model=bert \
dataset.load_prob=True \
model.config.block_size=... |
9749cc382d3d789de0aa2be044ccad49a5d7e5d02150b4ea45ea27ada9b12506 | Shell | 602 | 21 | #!/bin/bash
set -Eeuxo pipefail
trap "echo ERR trap fired!" ERR
#This script generates atac qc tsv report and write the output to a gcp bucket.
#Usage : bash src/qc2tsv.sh <gcp_path_path_to_croo_outputs> <output_qc_report_name>
gcp_path=$1
outfile_name=$2
random_string=$(openssl rand -hex 8)
mkdir "$random_string"
cd... |
9c368186c738a42452badb8ddbe7f91e3dd878c4b9e076002b9125fb520631df | Shell | 603 | 31 | #!/bin/bash
#SBATCH --job-name=xci_exploration
#SBATCH --mail-type=FAIL
#SBATCH --mail-user=jbenja13@jh.edu
#SBATCH --nodes=1
#SBATCH --cpus-per-task=1
#SBATCH --output=summary.log
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${SLURM_JOBID}"
echo "Job name: ${SLURM_J... |
a0b2a4160c2a29ba41767fa4ebf7bcf47c17b89b0312d2155696276ea46fc2bc | Shell | 604 | 29 | #!/bin/bash
#$ -cwd
#$ -R y
#$ -t 1-2:1
#$ -l mem_free=5G,h_vmem=5G,h_fsize=100G
#$ -N mash_allpairs_combine
#$ -o ./allpairs_mash.log
#$ -e ./allpairs_mash.log
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOS... |
d9d221d41c4ad0297fb796fc83d74404f00292e17a4823d282b4fdcb33f2047d | Shell | 605 | 18 | # create_tabix_gtex_sigpairs.sh
# by Brian Chen
# This script takes GTEx v8 eQTL significant pair files and outputs index file for tabix
# $1 is path to tissue file
module load htslib #or module load tabix
module load vcftools
tissueName=$(echo "${1##*/}" | cut -f 1,2 -d '.')
echo $tissueName
cat $1 | sed '1D' | tr ... |
94280b4998372904fdfe8a7deeddf411c78458df6b12297163a076ca300d7ea8 | Shell | 607 | 14 | # open and run docker
docker run -d -it \
--name run_pfam \
--mount type=bind,source=/data/user/efjones/230227_EJ_MouseBrainIsoDiv/data/switchlist_fasta,target=/opt/PfamScan/fasta,readonly \
--mount type=bind,source=/data/user/efjones/230227_EJ_MouseBrainIsoDiv/data/Pfam,target=/opt/PfamScan/results \
pfam_test:1.0.36
... |
e3391e5b0209d6526e965e0f18cefc04d21e3e6ee2dac16c8f012327e50b97a8 | Shell | 609 | 31 | #!/bin/bash
#SBATCH --job-name=heatmap_plotting
#SBATCH --mail-type=FAIL
#SBATCH --mail-user=jbenja13@jh.edu
#SBATCH --nodes=1
#SBATCH --cpus-per-task=1
#SBATCH --output=summary.log
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${SLURM_JOBID}"
echo "Job name: ${SLURM_... |
1ffe2ab3e3db0b035387aff37ae54abf673f22cc63112d4a89906f5421c6f375 | Shell | 610 | 19 | #!/bin/bash
#Copyright 2023. TU Graz. Institute of Biomedical Imaging.
#Author: Moritz Blumenthal
set -eu
SCRIPT_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )
cd $SCRIPT_DIR
if [ -z "${RECODIR:-}" ]; then
RECODIR="$(readlink -e $SCRIPT_DIR/../)"
fi
SRC=$RECODIR/21_recos_rt/vol0082_vis1_s... |
33972293b6c9ed859442ac1bd3b83835f7db44b4aaafb6ed0064deedfde55d64 | Shell | 610 | 19 | #!/bin/bash
#Copyright 2023. TU Graz. Institute of Biomedical Imaging.
#Author: Moritz Blumenthal
set -eu
SCRIPT_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )
cd $SCRIPT_DIR
if [ -z "${RECODIR:-}" ]; then
RECODIR="$(readlink -e $SCRIPT_DIR/../)"
fi
SRC=$RECODIR/21_recos_rt/vol0056_vis1_s... |
d5b480d536bbe2b93a95896124d6785da275ceeee6d38fb7ae1d4df5a4a27313 | Shell | 611 | 25 | #!/bin/bash
folders=( \
"nora_221116_114205" \
"nora_221117_225954" \
"nora_221118_222513" \
"nora_221122_185629" \
"nora_221130_094643" \
"nora_221204_204553" \
"nora_221207_081815" \
"nora_221213_224340" \
)
rootfolder=/media/G1/xl_spinal_cord_electrode/Animals/active_Animals/Nora_112... |
fcc9f68f1023ee3f9239c9a45d7126efd562bf02d53c73e6322cfcff2921341f | Shell | 611 | 24 | #!/usr/bin/env bash
set -e
# # make truth set and sort the BAMs
# BAM=/gscmnt/gc2802/halllab/sv_aggregate/MISC/realigned_BAMs/NA12878/NA12878.bam
# BAM_BASE=`basename $BAM .bam`
# python -m svtyper.core \
# -i data/example.vcf \
# -B $BAM \
# -l data/$BAM_BASE.bam.json \
# -w data/$BAM_BASE.target_loc... |
7195733e6d182ac84cd1e489a7adfc576212d15dc8899da560adfab3fa55949b | Shell | 612 | 29 | #!/bin/bash
#$ -cwd
#$ -l mem_free=10G,h_vmem=10G,h_fsize=100G
#$ -N combine_parquet
#$ -o ./combine.log
#$ -e ./combine.log
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAME}"
## List current modules for... |
239721727ad16b3f1e3f36870949dc4370f681b0bdd95e2c763c8325c473f885 | Shell | 614 | 28 | #!/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="../inputs/PDB_complexes/pdbs/3HTN.pdb"
output_dir="../outputs/example_3_score_only_outputs"
if [ ! -d $output_dir ]
then
mkdir -p $output_dir
fi
chains_to_des... |
b7bda044089a3b55a9b91476f1f35d2be08b2139911332d270285593f4ad57fe | Shell | 615 | 31 | #!/bin/bash
#$ -cwd
#$ -l mem_free=10.0G,h_vmem=10G,h_fsize=50G
#$ -N pca_hippocampus
#$ -o ./summary_hippocampus.log
#$ -e ./summary_hippocampus.log
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAME}"
##... |
cb9316c1c55c44cb3a9e2b7d85c88853259d5a12d137c28250e119c1d43f7af1 | Shell | 616 | 19 | #!/bin/bash
CURRENT_DIR="$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )"
export XP_SCRIPT_DIR=${CURRENT_DIR}
export XP_TARGET_DIR=${CURRENT_DIR}/..
bash ${XP_SCRIPT_DIR}/build.sh setup
bash ${XP_SCRIPT_DIR}/build.sh local
export BASE_SERVICE_NAME=base
if [[ $(lsmod | grep nvidia) ]]; then
ex... |
19a2c5473213d0ca5d93e2f29c7717086684878eef17daf09230791e1ab5e308 | Shell | 619 | 23 | #!/bin/bash
# Gets a list of all the workflows that have been run, and deletes the corresponding input json files
if [ $# -lt 2 ]; then
echo "Usage: ./delete_json.sh [SUBMITTED_LABELS] [JSON_DIR]"
echd
echo "Example: delete_json.sh labels.txt jsons"
echo
echo "[SUBMITTED_LABELS]: a file containing a list of ... |
2ed9025bab2efca4986770640dd09697737d14d3dd909ebfce2730fe52c92f63 | Shell | 619 | 19 | python -m train \
experiment=hg38/enhancer_mel_debug \
wandb.mode=online \
wandb.group=Enhancer_Mel \
wandb.name=train_inf_bert_base_step1_lr1e-4 \
hydra.run.dir="./outputs/enhancers_mel/train_inf_bert_base_step1_lr1e-4" \
task=DNA_masked_gen \
model=bert \
dataset.load_prob=True \
m... |
7ecd35f3a7c4da980ba71fc9e6cbdc47d24f21be1bf0fe607e1108e051aec318 | Shell | 619 | 28 | #!/usr/bin/env bash
# ============================
# Run script for VANTAGE
# ============================
VENV_NAME="venv_vantage"
SCRIPT_NAME="VANTAGE_MAIN.py"
# ===== Check that venv exists =====
if [ ! -d "$VENV_NAME" ]; then
echo "Virtual environment '$VENV_NAME' not found."
echo "Please run setup.sh fi... |
7c07b35888756ce39cc168bd9e89b2175a81b568113d2e2f047df95089d5219d | Shell | 621 | 24 | #!/bin/bash
# Check if the correct number of arguments are provided
if [ "$#" -ne 2 ]; then
echo "Usage: $0 source_directory target_directory"
exit 1
fi
# Assign arguments to variables
source_directory=$1
target_directory=$2
# Check if the target directory exists, and delete it if it does
if [ -d "$target_di... |
30eec8eb836bbdcfb15ddf472ee09931dc2bff2f05d10bbc0e9e836947117182 | Shell | 622 | 31 | #!/bin/bash
#$ -cwd
#$ -l mem_free=10.0G,h_vmem=10G,h_fsize=50G
#$ -N dRFE_gene_dlpfc
#$ -o ./summary_gene.log
#$ -e ./summary_gene.log
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAME}"
## List current ... |
a460f48612f1e475b9de97d392a3bae7a7a7c209064511a6c11f62c7f6291ade | Shell | 622 | 31 | #!/bin/bash
#$ -cwd
#$ -l mem_free=20.0G,h_vmem=20G,h_fsize=50G
#$ -N dRFE_tx_dlpfc
#$ -o ./summary_tx.log
#$ -e ./summary_tx.log
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAME}"
## List current module... |
f842abab70cebd646b5f6918e35bc702d922e9714d807115d2e96c7e994298ca | Shell | 622 | 31 | #!/bin/bash
#$ -cwd
#$ -l mem_free=30.0G,h_vmem=30G,h_fsize=50G
#$ -N dRFE_exon_dlpfc
#$ -o ./summary_exon.log
#$ -e ./summary_exon.log
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAME}"
## List current ... |
312a322aa5bd4d0fe60bb5eedea117c0eaa5640c4f9bc11f9b28ccdd02c9b142 | Shell | 623 | 17 | # create_tabix_gtex_sqtl_sigpairs.sh
# by Brian Chen
# This script takes GTEx v8 sQTL significant pair files and outputs index file for tabix
# $1 is path to tissue file
module load htslib #or module load tabix
module load vcftools
tissueName=$(echo "${1##*/}" | cut -f 1,2 -d '.')
echo $tissueName
cat $1 | sed '1D' ... |
85343f14626af4ec2ce5629431b4b5134405bd1823e1a4d1cff4a5268f9a94e7 | Shell | 623 | 31 | #!/bin/bash
#$ -cwd
#$ -l mem_free=20.0G,h_vmem=20G,h_fsize=50G
#$ -N dRFE_jxn_dlpfc
#$ -o ./summary_jxn.log
#$ -e ./summary_jxn.log
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAME}"
## List current mod... |
86336fff88cfc8bf384673c07952754810a726ee67800c38a4ff4cf340c4ec5c | Shell | 624 | 19 | python -m train \
experiment=hg38/enhancer_flybrain_debug \
wandb.mode=online \
wandb.group=Enhancer_Fb \
wandb.name=train_inf_bert_base_step1_lr1e-4 \
hydra.run.dir="./outputs/enhancers_fb/train_inf_bert_base_step1_lr1e-4" \
task=DNA_masked_gen \
model=bert \
dataset.load_prob=True \
... |
0a103535a0641314899edf17a56e1d06924f967ca9f620442aab1769eb80cb0d | Shell | 625 | 16 | metric_list=(FA MD L1 RD)
test_list=(scd_story scd_age age_story)
cd tbss/stats
module load fsl/6.0.5
for metric in "${metric_list[@]}"; do
for test in "${test_list[@]}"; do
fsleyes -std1mm all_${metric} lower_cingulum_mask -cm green \
${metric}/${metric}_llc_${test}_tfce_corrp_tstat1 -cm red-yellow -dr 0... |
4ddccaed643669e690b1e6c684b82bc432dd7c29494e8e9cd987667ee5e61c16 | Shell | 626 | 31 | #!/bin/bash
#$ -cwd
#$ -l mem_free=10.0G,h_vmem=10G,h_fsize=50G
#$ -N dRFE_gene_caudate
#$ -o ./summary_gene.log
#$ -e ./summary_gene.log
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAME}"
## List curren... |
5379d044b658c3e1f76ceb656915fb570e60bfaf112913e1d2db63cd35dfe8d8 | Shell | 626 | 31 | #!/bin/bash
#$ -cwd
#$ -l mem_free=30.0G,h_vmem=30G,h_fsize=50G
#$ -N dRFE_exon_caudate
#$ -o ./summary_exon.log
#$ -e ./summary_exon.log
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAME}"
## List curren... |
7b8913a776034cac5ad208df22fc4a0e7595e912f4181c868e191bba86a01da8 | Shell | 626 | 31 | #!/bin/bash
#$ -cwd
#$ -l mem_free=20.0G,h_vmem=20G,h_fsize=50G
#$ -N dRFE_tx_caudate
#$ -o ./summary_tx.log
#$ -e ./summary_tx.log
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAME}"
## List current modu... |
27fbc10dd7bc4f49d0f7f10e8fc50e8ab11ff766933d0400575d448eebb5c10b | Shell | 627 | 45 | #!/usr/bin/env bash
# definitions
workDir=/vols/Scratch
scriptDir=/vols/Scratch/comparative_scripts
mkdir -p $workDir/connectivity_maps_mice
subjList="001
002
003
004
005
006
007
008
009
010
011
012
013
014
015
016
017
018
019
020"
seedList=""
template=/vols/Scratch/Valerio_data/Template/QBI_atlas_2mm_v6.nii
for s... |
479e24f29807d3c856181fc0f6429777db7d2633111ec5323def80b618277b01 | Shell | 627 | 31 | #!/bin/bash
#$ -cwd
#$ -l mem_free=20.0G,h_vmem=20G,h_fsize=50G
#$ -N dRFE_jxn_caudate
#$ -o ./summary_jxn.log
#$ -e ./summary_jxn.log
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAME}"
## List current m... |
9c274dd6b569b6e058ab47fd400626bce45518ca55f0282870105e6c434f506d | Shell | 627 | 11 | export SUBJECTS_DIR=./
cut -f1 anat_over_55.tsv > recon-all-clinical/subjectsfile.txt
cd recon-all-clinical
sed -i '' '1d' subjectsfile.txt
#generate stats tables with Freesurfer
aparcstats2table --subjectsfile=subjectsfile.txt --hemi lh --tablefile=lh_aparctable.tsv --measure=thickness --common-parcs
aparcstats2tabl... |
4235051060785146035378f75b4f661ca57fc9e8b36ded01f37e0b33a0204860 | Shell | 628 | 17 | SBATCH_OPTIONS=" -p gpu-a100 -t 0-13:00:00 --ntasks=4 --gres=gpu:4"
SPOKES=13
SPLIT="0.75"
SPLIT_FLAG=2
OS=1.5
COS=1.25
DATASET=01_rt_svd
TIME=3
ITER=3
NETWORK="--scaling-flags=$(bart bitmask 10) --init-rtnlinv --conv-time=$TIME -i$((6+ITER)) --resnet-block=no-batch-normalization,F=64 --iter-net=$ITER"
TRAINING="--a... |
e09da97384180643a1c93cacbde083d8abf6df6ef45e809d3bb1cb7d9574673e | Shell | 628 | 17 | SBATCH_OPTIONS=" -p gpu-a100 -t 0-13:00:00 --ntasks=4 --gres=gpu:4"
SPOKES=13
SPLIT="0.75"
SPLIT_FLAG=2
OS=1.5
COS=1.25
DATASET=01_rt_svd
TIME=3
ITER=3
NETWORK="--scaling-flags=$(bart bitmask 10) --init-rtnlinv --conv-time=$TIME -i$((6+ITER)) --resnet-block=no-batch-normalization,F=64 --iter-net=$ITER"
TRAINING="--a... |
84b60c1162acd668daf86402f85de2baba73081641388d4027a69cb9e1fc5d74 | Shell | 629 | 19 | #!/bin/bash
#Copyright 2023. TU Graz. Institute of Biomedical Imaging.
#Author: Moritz Blumenthal
set -eu
SCRIPT_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )
cd $SCRIPT_DIR
if [ -z "${RECODIR:-}" ]; then
RECODIR="$(readlink -e $SCRIPT_DIR/../)"
fi
SRC=$RECODIR/21_recos_rt/vol0056_vis1_s... |
fdd558125dc515b180f32692d0936b4438e3feb7708e002dbaf44939e88f9334 | Shell | 629 | 13 | #!/bin/bash
## OURS ALL vs GTEx ENSEMBL 107 ALL
singularity exec ../../../../singularity_containers/nanopore.sif gffcompare -r \
../../../data/processed/other/novel_only_annotations/leung_annotation_clean.gtf \
../../../data/processed/other/novel_only_annotations/all_novel_bambu.gtf \
-o OURS_ALL_vs_leung
... |
f1b546c3e626ee4307bc0c1b5b2413b0918cd25bad4c4b90482e2590d890812d | Shell | 631 | 21 | #!/bin/bash
#Copyright 2023. TU Graz. Institute of Biomedical Imaging.
#Author: Moritz Blumenthal
set -eu
SCRIPT_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )
cd $SCRIPT_DIR
if [ -z "${RECODIR:-}" ]; then
RECODIR="$(readlink -e $SCRIPT_DIR/../)"
fi
SRC=$RECODIR/21_recos_rt/vol0082_vis1_s... |
fd5fa3e98073ea95c6874bf9dde29d7ef51280481310067c2679f1abfee3c3d3 | Shell | 631 | 16 |
###### Segment VCF files according to genome block segmentation information provided by lddetect
bed_file=lddetect_1KG_EUR_hg19.bed
### To segment the genome block with chromosome, start position, end position provided in the 6th row of the BED file
chr=$(awk 'NR==6{print $1}' lddetect_1KG_EUR_hg19.bed)
vcf_file=CHR$... |
1afb49d450658b38c6714250934811116e0e228bf232a1c9c0325a720931f588 | Shell | 634 | 20 | #!/bin/sh
gistic2 \
-b /apps/home/lulab_liuxiaofan/qhsky/project/multi_omics_paper/data_TCGA/1.raw_data/gistic2/BRCA \
-seg /apps/home/lulab_liuxiaofan/qhsky/project/multi_omics_paper/data_TCGA/1.raw_data/BRCA.CNV_masked_seg_filter.txt \
-mk /apps/home/lulab_liuxiaofan/qhsky/project/multi_omics_paper/reference/snp6.n... |
554b6ce5cf14561f48a00deb696b36c70bcb9a8b8d3c8d60741f6916b3f471e6 | Shell | 634 | 31 | #!/bin/bash
#$ -cwd
#$ -l mem_free=20.0G,h_vmem=20G,h_fsize=50G
#$ -N dRFE_tx_hippocampus
#$ -o ./summary_tx.log
#$ -e ./summary_tx.log
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAME}"
## List current ... |
5f27d1de9490942c65824ec942d108ad7dc677510e5482e84fcd4c40ec516de8 | Shell | 634 | 31 | #!/bin/bash
#$ -cwd
#$ -l mem_free=10.0G,h_vmem=10G,h_fsize=50G
#$ -N dRFE_gene_hippocampus
#$ -o ./summary_gene.log
#$ -e ./summary_gene.log
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAME}"
## List cu... |
f7dd220e327a4ae5f352c045527ebaea44ea2eba38816648f34c1cf9f776d696 | Shell | 634 | 31 | #!/bin/bash
#$ -cwd
#$ -l mem_free=30.0G,h_vmem=30G,h_fsize=50G
#$ -N dRFE_exon_hippocampus
#$ -o ./summary_exon.log
#$ -e ./summary_exon.log
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAME}"
## List cu... |
90c185c016191b3467615d20b10d23920b91fd7cd2c2f8e54a5498dbcd48a068 | Shell | 635 | 31 | #!/bin/bash
#$ -cwd
#$ -l mem_free=20.0G,h_vmem=20G,h_fsize=50G
#$ -N dRFE_jxn_hippocampus
#$ -o ./summary_jxn.log
#$ -e ./summary_jxn.log
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAME}"
## List curre... |
01f04e057371671fc777d95745669379fe22a25a574a8c021cc47521a718eca4 | Shell | 639 | 17 | SBATCH_OPTIONS=" -p gpu-a100 -t 0-13:00:00 --ntasks=4 --gres=gpu:4"
SPOKES=13
SPLIT="0.75"
SPLIT_FLAG=2
OS=1.5
COS=1.25
DATASET=01_rt_svd
TIME=3
ITER=3
NETWORK="--scaling-flags=$(bart bitmask 10) --init-rtnlinv --conv-time=$TIME -i$((6+ITER)) --resnet-block=no-batch-normalization,F=64 --iter-net=$ITER"
TRAINING="--a... |
e106aa784a03ea7d471cd71b3cef0867ceaddc42666df64f1d939212077ecd6b | Shell | 639 | 17 | SBATCH_OPTIONS=" -p gpu-a100 -t 0-13:00:00 --ntasks=4 --gres=gpu:4"
SPOKES=13
SPLIT="0.75"
SPLIT_FLAG=2
OS=1.5
COS=1.25
DATASET=01_rt_svd
TIME=3
ITER=3
NETWORK="--scaling-flags=$(bart bitmask 10) --init-rtnlinv --conv-time=$TIME -i$((6+ITER)) --resnet-block=no-batch-normalization,F=64 --iter-net=$ITER"
TRAINING="--a... |
2b171c79a780d6f4bf673c2a2e22e4ab6376a9ff46ef4525a20f357a3149475a | Shell | 640 | 20 | #!/bin/bash
# run this script to set up a xtb environment
# requirements: $XTBHOME is set to `pwd`
if [ -z "${XTBHOME}" ]; then
XTBHOME="$(cd -P "$(dirname "${BASH_SOURCE[0]}")" && pwd)/../../"
fi
# set up path for xtb, using the xtb directory and the users home directory
XTBPATH=${XTBHOME}/share/xtb:${HOME}
# to ... |
8e9a6564415ec441400a4da9e1dc4eebeedc8398d38a435b9ea3b9c20ee64297 | Shell | 640 | 11 | #!/bin/bash
# Here, we're running one of the motif-scaffolding benchmark examples
# Specifically, we're scaffolding site 5 from RSV-F protein
# We specify the output path and input pdb (the RSV-F protein)
# We specify the protein we want to build, with the contig input:
# - 10-40 residues (randomly sampled)
# - res... |
a936e2532a12c50cdd41a722c6b1e93bfa0b69d53409409722eb909b7be9219a | Shell | 640 | 32 | #!/bin/bash
#SBATCH --job-name=xci_plotting
#SBATCH --mail-type=FAIL
#SBATCH --mail-user=jbenja13@jh.edu
#SBATCH --nodes=1
#SBATCH --cpus-per-task=1
#SBATCH --output=summary.log
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${SLURM_JOBID}"
echo "Job name: ${SLURM_JOB_... |
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