sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
52de7a0e7085adf0065ef50c111843a28db091876116392da7a9658f2870eadf | Shell | 594 | 27 | #!/bin/bash
#================================
# Step 3: Remove ethnic outliers
#================================
prefix=rosmap
# merge adc and 1000g filesets
python code/prep/merge_plink_filesets.py \
-b tmp/"$prefix"_2 \
-b1 data/1000g/1000g \
-o tmp/"$prefix"_1000g_merged
# prune
plink \
--bfile tmp/"$pref... |
e613dd954e706e483186faf9950d34cf77d6eb41a9f44d6cf4500194afd6bb5e | Shell | 594 | 18 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../data"
mkdir -p outputs_from_test
./str_calc -select:bb -in::pdb:path=./test_inputs \
-in:pdb:listfile=./test_inputs/input_pdb_list \
-calc:phi_psi -in:pdb:header -select::aa > str_calc.results
grep -v "#" str_calc.results | awk '{print $5,$6}' > phi_psi.resul... |
51cc4da29366b5995a6c079aaa6c5c35937a3a91d1609f9e31ab5e41bbf553bf | Shell | 595 | 6 | #! /usr/bin/env bash
python /opt/elephant/script/generate_seg_labels.py --st --3d --cr 0.4 /workspace/datasets/ISBI2021/Fluo-C3DH-A549/
python /opt/elephant/script/generate_seg_labels.py --st --3d --cr 0.4 /workspace/datasets/ISBI2021/Fluo-C3DH-H157/
python /opt/elephant/script/generate_seg_labels.py --st --3d --cr 0.4... |
9595be01fe4022c0fb14a6954bf0cedba932fb7861838f4713599c25e2211f5e | Shell | 595 | 13 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
export PYTHONPATH="../../../../../bin"
echo "#Running python3 partial_thread.py test_inputs/2azaA_2pcyA-ali.fasta test_inputs/2aza.pdb A > 2azaA-thread.pdb"
python3 partial_thread.py test_inputs/2azaA_2pcyA-ali.fasta test_inputs/2aza.pdb A > 2azaA-thread.pdb
... |
d316b31e38e3044f01195863480d655defc2967ccc39e5570cfb5313c869b675 | Shell | 595 | 16 | #!/usr/bin/env bash
scanphyslog2bids \
--file ../sub-02/func/sub-02_task-face_run-1_physio.log \
--fmri ../sub-02/func/sub-02_task-face_run-1_bold.nii.gz \
--sf 496 # use 500 when using a wireless physio recorder
--triggermethod gradient_log \
--outdir ../sub-02/func \ # default
--plottraces \... |
a97b7a76256533926d3c2369f9816aa3fe628236d07513635176971f4180cb02 | Shell | 597 | 7 | python3 -W ignore scperb.py --model_name CD4T --exclude_celltype CD4T --data pbmc
python3 -W ignore scperb.py --model_name CD14+Mono --exclude_celltype CD14+Mono --data pbmc
python3 -W ignore scperb.py --model_name B --exclude_celltype B --data pbmc
python3 -W ignore scperb.py --model_name CD8T --exclude_celltype CD8T ... |
e2b55c45f7556f271073e0baf021f30a7bfe56ff44165f1a3604fc1a06347244 | Shell | 597 | 14 | # intra-experiments
python main.py --dataset Zheng\ 68K --data_dir /home/xyfan/data/Datasets/baseline_datasets \
--train_prop 0.6 --valid_prop 0.2 \
--use_graph --use_knn --use_HVG \
--epochs 20 --batch_size 256 \
--runs 1 --device 0 --save_result
# cross-platforms
# python main.py --d... |
7a03c85bbc6f44b0c1914916ac4050824eb66036b55423c31611cbb28f55c5a4 | Shell | 598 | 24 | #!/bin/bash
INPUT="2gb1A"
mkdir -p outputs_from_test
~/src.git/bioshell/bin/surpass_annealing -verbose=FINEST \
-model:random \
-in:ss2=test_inputs/$INPUT.ss2 \
-sample:t_start=2.2 \
-sample:t_end=0.9 \
-sample:t_steps=15 \
-sample:mc_outer_cycles=10 \
-sample:mc_inner_cycles=10 \
-sample:mc_cycle_factor=10 ... |
4b08f3e73c9c5cef7bd09f13529804c71859f1026d29d1c977ff06fb8621f390 | Shell | 599 | 17 | #!/bin/bash
#
FILES=($(ls *.log)) # assuming the output format is [phenotype]_rg.log
N=$(echo ${#FILES[@]}) # and that all combinations of penotypes have been analysed
for I in ${FILES[@]}; do
PHEN=$(echo $I | sed 's/.log//')
# subset log files to relevant output
tail -n$(($N+4)) $I | hea... |
4e3fa2ee675a8f85e93632194eba8bc57dd3b14dc70a6433880fee7650be8388 | Shell | 599 | 25 | #!/bin/bash
#SBATCH --time=2-23:00:00
#SBATCH --mail-type=ALL
#SBATCH --cpus-per-task=1
#SBATCH --partition=gpu
#SBATCH --mem=20G
#SBATCH --gres=gpu:1
#SBATCH --output=slurm-nucleus-%j.out
# submit as sbatch run_nucleus.sh
ml Anaconda3/2019.07
source activate nucleus
python -m ipykernel install --user --name=nuc... |
2194501e0f4c739278e4d866ada041f99c7ac7e325189ad42f910c87857b2b4e | Shell | 600 | 17 | #!/bin/bash
########## FMRI PREPROCESSING
id_list=$1
task=$2
scripts_dir=`dirname "$(readlink -f "$0")"`
root_dir="$(dirname "$(dirname "$(readlink -fm "$0")")")"
mkdir -p ${scripts_dir}/logs
for id in `cat $id_list`
do
id=${id/NDAR_/NDAR}
cmd="$scripts_dir/CBIG_ABCD_proc_brain_mask.sh ${id} ${task} 50"
er... |
aab3dfb2893f7512703ef9d4fbb2df03c9f32293ffb136f6ee49c78c5102edd6 | Shell | 601 | 14 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
echo "# Running ./ap_stiff_docking_crmsd test_inputs/2m56-ref.pdb CAM test_inputs/00199.pdb test_inputs/00963.pdb test_inputs/04473.pdb"
./ap_stiff_docking_crmsd test_inputs/2m56-ref.pdb CAM test_inputs/00199.pdb test_inputs/00963.pdb test_inputs/04473.pdb
... |
3bc60d047e93436cf5e8b47666fb2285bfb23b8b6b1846b50fd5a16bb1d9fe61 | Shell | 602 | 23 | function show_help {
echo "example usage: ./VCF_to_CSV.sh 1998"
echo "Options:"
echo " -h, --help Show this help message and exit"
echo ""
echo "Arguments:"
echo " numbrer of observations Example: 1998"
echo ""
echo "Pipeline steps:"
echo " 1. Run VCF_MS_... |
ac73b1e8f84dcadd57c3da6a8cdc8d773f2351a756dd163d33eaecdcb7639904 | Shell | 604 | 21 | #!/bin/bash
email=a.alemany@hubrecht.eu
Dt=15:00:00
Dmem=20G
threads=5
if [ $# -ne 3 ]
then
echo "Please, give these following inputs:"
echo "1) input fastq file to map"
echo "2) root for output file (no .sam or .bam exntesion)"
echo "3) reference file [mouse, elegans, human, zebrafish, GFP, full path... |
9f2ee6d57b7251b6a6d170c606212a20d5b591730fe41b38de74d5f75a460b77 | Shell | 608 | 26 | #!/bin/bash
#SBATCH -N 1
#SBATCH --mem 350G
#SBATCH --time=20:00:00
#SBATCH --job-name=basic_props_network
#SBATCH --account=proj9
#SBATCH --partition=prod
#SBATCH --output=logs/basic_props_network
source /gpfs/bbp.cscs.ch/home/egassant/connalysis/bin/activate
declare -a
configs=(#"Celegans_basics.json"
#"Drosophil... |
caae687aafea4b09293ecb85c40f15a3d4f53b5724efaa1ca40bf6bcea192028 | Shell | 609 | 21 | #!/bin/bash
email=a.alemany@hubrecht.eu
Dt=15:00:00
Dmem=30G
threads=12
if [ $# -ne 3 ]
then
echo "Please, give these following inputs:"
echo "1) input fastq file to map"
echo "2) root for output file (no .sam or .bam exntesion)"
echo "3) reference file [mouse, elegans, human, zebrafish, GFP, full pat... |
d033fa002078b9bc2bea028cb45b5b9466e7ed86234842547b73233c77890390 | Shell | 612 | 29 | #!/bin/bash
set -ex
## Installing Ubuntu APT packages (required sudo privileges)
export DEBIAN_FRONTEND=noninteractive
apt-get -yq update \
&& apt-get install -yq --no-install-recommends \
"build-essential" \
"bzip2" \
"cmake" \
"gcc" \
"libboost-all-dev" \
"libboost-python-dev"... |
4ffe496faa78fa864b1e1ab7833e8b705897f54393ea8eb990da496e3b1306ea | Shell | 616 | 27 | #!/bin/sh
# Generate test results
TESTS="ffghemical ffuff ffmmff94 formula formalcharge rings smarts strip"
unset BABEL_LIBDIR
unset BABEL_DATADIR
if [ -d ../src/formats/.libs ]; then
if [ "x${BABEL_LIBDIR}" = "x" ]; then
BABEL_LIBDIR="`pwd`/../src/formats/.libs:`pwd`/../src/formats/xml/.libs"
export BABEL_LIB... |
70bd052eeb40d803689347924e565f12a48a90dc1c7fc85eeeab02ec216117c7 | Shell | 617 | 13 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
DIR="test_inputs"
echo -e "# Running ./ap_docking_crmsd $DIR/2m56-ref.pdb CAM $DIR/00199.pdb $DIR/00963.pdb $DIR/04473.pdb"
./ap_docking_crmsd $DIR/2m56-ref.pdb CAM $DIR/00199.pdb $DIR/00963.pdb $DIR/04473.pdb
echo -e "# Running ./ap_docking_crmsd - CAM $DI... |
73471f693252624a77bf17f4b09549d77a08a8aba90cf386a77235277370b32c | Shell | 620 | 20 | #!/bin/sh
current_dir=`pwd`
code_dir="./../../../Core_code/"
ncores=90
output_folder="/home/asantoro/COST/Project2_Higher_Order_Brain/Brain_HORS/Figure2/Results/HO_localmeasures/"
file_input_format="TS_Schaefer100S_gsr_bp_z_rest300_tasks_EMO_GAM_LAN_MOT_REL_SOC_WM"
cd ${code_dir}
for subjID in `ls -d /home/asantoro... |
d4519360ebf1f4843a897dd201a81f950fa3963b0b682795d24f5cade184d52a | Shell | 621 | 21 | #!/bin/sh
current_dir=`pwd`
code_dir="./../../../Core_code/"
ncores=90
output_folder="/home/asantoro/COST/Project2_Higher_Order_Brain/Brain_HORS/Figure2/Results/HO_localmeasures/"
file_input_format="TS_Schaefer100S_gsr_bp_z_rest300_tasks_EMO_GAM_LAN_MOT_REL_SOC_WM"
cd ${code_dir}
for subjID in `ls -d /home/asantoro... |
ead0a9638299ec21583ba9fe0f01e6dfa6ae63be942b7e5f32e19b3e7ca95691 | Shell | 621 | 40 | #!/bin/bash
N=20
function loopLittleR {
echo
echo -n " --- our r calling summary() $N times"
i=0
while [ $i -lt $N ]
do
./summary2.R >/dev/null
i=$((i + 1))
done
}
function loopRscript {
echo
echo -n " --- GNU R's Rscript calling summary() $N times"
i=0
while [ $i -lt $N ]
... |
ec40a411888809643ee9102fc0769ea76250315390a86f75af94db92ccb0665f | Shell | 621 | 15 | mkdir blast && cd blast
wget -c https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.16.0+-x64-linux.tar.gz
wget -c https://github.com/rcedgar/muscle/releases/download/v5.2/muscle-linux-x86.v5.2
tar zxvf ncbi-blast-2.16.0+-x64-linux.tar.gz
mv ncbi-blast-2.16.0+/bin ./bin
mv muscle-linux-x86.v5.... |
145ec317f79a71f7ac9d4d78ae46174aa501c1707f167a7363dcf3da29e03da3 | Shell | 624 | 14 | #!/bin/bash
# Written by Jianzhong Chen and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
id_list=$1
if [ -z "${id_list}" ];then
#id_list=$CBIG_REPDATA_DIR/stable_projects/predict_phenotypes/ChenTam2020_TRBPC/lists/release2_subjects_with_rs_and_t1.txt
id_list=/home/leon_oo... |
5615e36f232d52b34d7a42cab4d019cbb35288774fb01e92e5281fe65eb57275 | Shell | 625 | 20 | #!/bin/sh
current_dir=`pwd`
code_dir="./../../../Core_code/"
ncores=86
output_folder="/home/asantoro/COST/Project2_Higher_Order_Brain/Brain_HORS/Figure2/Results/HO_localmeasures/"
file_input_format="TS_Schaefer100S_gsr_bp_z_rest300_tasks_EMO_GAM_LAN_MOT_REL_SOC_WM"
cd ${code_dir}
for subjID in `ls -d /home/asantoro... |
b8db2e586c0b64f3092b10b936f3d02a124cd8642d08aa720c0e795fcc2a4642 | Shell | 625 | 17 |
# (c) Coraline Rinn Iordan 07/2017, 10/2017, 10/2019
# call from ./107/fmri as ./scripts/preprocess.sh
afni_proc.py -script AFNIprocess \
-out_dir ./processed \
-scr_overwrite \
-dsets ./raw/run??.nii.gz \
-tcat_remove_first_trs 6 ... |
c3387a6c6653591ed094b0c95a97cfc298e0956081976bea2e433e20456f66f0 | Shell | 625 | 21 | #! /bin/bash
################################################################################
# Auditory pathway processing pipline
################################################################################
if [ $# -ne 1 ]; then
"usage: $(basename $0) subject_dir"
exit 1
fi
workflow=$(cd $(dirname ${0}); c... |
f80795e1171fe282dbc3bb73f6803eca376e849eb5be80c4731c8dbb0244c39a | Shell | 625 | 20 | #!/bin/bash
###############################
# Run Montreal Forced Aligner #
###############################
eval "$(conda shell.bash hook)"
conda activate linfeatures
CONFIG_FILE="/Users/elenauzh/Projects/rantext-speech/rantext-speech/speech/speech_config.yaml"
INPUT_FOLDER=$(yq -r '.stimuli_parameters.stimuli_fold... |
264a1c97cca729aa30bfbad712d5ea7b68013f732e2b9d6436901458d1488b71 | Shell | 626 | 25 | #!/bin/bash
email=a.alemany@hubrecht.eu
Dt=5:00:00
Dmem=10G
threads=1
if [ $# -ne 2 ]
then
echo "Please, give these following inputs:"
echo "1) bam file"
echo "2) genome"
exit
fi
inf=${1%.bam}
if [ $2 == 'mouse' ]
then
ref=/hpc/hub_oudenaarden/aalemany/bin/mapandgo2/transcript2geneID_mm10_fromGTF... |
85e6c75a60a728b8a492e713c542192d41da505975eb8694dc8621a58a46897e | Shell | 626 | 20 | #!/bin/sh
current_dir=`pwd`
code_dir="./../../../Core_code/"
ncores=86
output_folder="/home/asantoro/COST/Project2_Higher_Order_Brain/Brain_HORS/Figure2/Results/HO_localmeasures/"
file_input_format="TS_Schaefer100S_gsr_bp_z_rest300_tasks_EMO_GAM_LAN_MOT_REL_SOC_WM"
cd ${code_dir}
for subjID in `ls -d /home/asantoro... |
fd69364644a33c82b745bf5373e0821c2868ce9e45b7753e2825921401718286 | Shell | 628 | 32 | #!/bin/bash
if [ $# -ne 2 ]
then
echo "Please, give input root file and protocol (celseq1, celseq2, nla/mspj1)"
exit
fi
p2s=/hpc/hub_oudenaarden/aalemany/bin/mapandgo2
in=$1
protocol=$2
out=${in%_*_S*_L*}
# merge data
${p2s}/mergeLanes.sh $in $out
# extract barcodes
${p2s}/extractBC.sh $out $protocol
# t... |
bd68dd601193eb7fd40c56cebafe2a39ce33ee722f0fdb64886cad0b31b95fd5 | Shell | 630 | 27 | #!/bin/bash
set -e
### Save working directory
cwd=$(pwd)
function cleanup {
echo "Installation failed"
cd "${cwd}"
exec $SHELL
}
trap cleanup ERR
export UBUNTU_VERSION=$(lsb_release -sc)
### install SDK
sudo apt-key adv --keyserver keys.gnupg.net --recv-key C8B3A55A6F3EFCDE || \
sudo apt-key adv --keyserver h... |
4efe8a982b4d58b1525006d2b1b428e26b04c1882f35abf724c355e1bc374523 | Shell | 631 | 30 | #MOLGENIS walltime=23:59:00 mem=8gb ppn=2
#string gapVersion
#string Project
#string logsDir
#string intermediateDir
#string optiCallDir
#string optiCallVersion
#string chr
set -e
set -u
set -o pipefail
module load "${optiCallVersion}"
module list
makeTmpDir "${optiCallDir}/"
tmpOptiCallDir="${MC_tmpFile}"
"${EBR... |
da1c550eb8c9c8b89a05f064d0cbc21d91b800a2e16c4bf74c894d770a65ebc3 | Shell | 634 | 11 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
echo -e "# Running ./ap_PairwiseSequenceIdentityProtocol test_inputs/small50_95identical.fasta 4 0.28 0 5"
./ap_PairwiseSequenceIdentityProtocol test_inputs/small50_95identical.fasta 4 0.28 0 5
echo -e "# Running ./ap_PairwiseSequenceIdentityProtocol test_inp... |
66a31a7672fa4aedbbf69003da8cfd0679c097c2cf443ce217b0b75218a7b02f | Shell | 635 | 20 | #!/bin/sh
# Generate misc.cpp.md from misc_template.cpp
cat << EOL
The Misc File Explained
=======================
<!-- This file is autogenerated. Do not edit directly! See makefile for details. -->
EOL
sed '
s/\/\*//g; s/\*\///g; # remove comment blocks /* */ -> display as code
s/^\s*\(\/\/ \)\+/\//; # double quo... |
42b0fa6ee41c6ab6e07cd344d982166c873edf43e20916f7dcb4887b5923a064 | Shell | 640 | 25 | #!/bin/bash
INPUT="2gb1A"
mkdir -p outputs_from_test
./surpass_annealing -verbose=INFO \
-model:random \
-in:ss2=test_inputs/$INPUT.ss2 \
-sample:t_start=2.2 \
-sample:t_end=0.7 \
-sample:t_steps=15 \
-sample:mc_outer_cycles=10 \
-sample:mc_inner_cycles=10 \
-sample:mc_cycle_factor=10 \
-sample:perturb:rang... |
ffaff804914155c75c3fb98357562fe9624b482e85f932b403db9a825d405be0 | Shell | 641 | 15 | #!/usr/bin/bash
#SBATCH --nodes=4
#SBATCH --ntasks=160
#SBATCH --ntasks-per-node=40
#SBATCH --partition=dev_multiple
#SBATCH --time=00:30:00
#SBATCH --job-name=monoatrial_PEERP_CV_0.8_S_LA_ntasks_160_dev_multiple
#SBATCH --output=jobs/%x.out
#SBATCH --error=jobs/%x.err
#SBATCH --mail-type=ALL
#SBATCH --mail-user=patr... |
1d73d822eb02b965361fa8e81eab32f085a8a361190cc430ed6b68dabd95440e | Shell | 647 | 22 | #!bin/sh
# chkconfig: 2345 96 14
us_region_name="us-east-1"
ami_id=""
temp_snapshot_id=""
my_array=( $(aws ec2 describe-images –image-ids $ami_id –region $us_region_name –output text –query ‘Images[*].BlockDeviceMappings[*].Ebs.SnapshotId’) )
my_array_length=${#my_array[@]}
echo "Deregistering AMI: "$ami_id
aws ec... |
84193bed085c54339eff5dfb383d680abddf2d1c5ffe16d5c193c75caf25dabb | Shell | 649 | 24 | #!/bin/bash
# Activate environment (Python 3.7.3)
source activate SAMPL7-PHIP2
# Update requirements
conda list --export > requirements.txt
# Generate user map
#python get_usermap.py
python create_separate_usermaps.py
# Run analysis for stage1 and create collection file
python analyze_stage1.py
# Compile LaTeX st... |
b7fabe6c18bac668fa7380ed04d4ecfc27d19831bdba656a372de68d86ddc377 | Shell | 649 | 31 | #!/bin/bash
set -euo pipefail
# Disable glob expansion. "*" in filenames are handled within hmftools java code
set -f
# Parse arguments
jvm_mem_opts=""
jvm_gen_opts=""
declare -a app_args
for arg in "$@"; do
case ${arg} in
'-Xm'*)
jvm_mem_opts="${jvm_mem_opts} ${arg}"
;;
'-D'* | '-XX'*)
jv... |
032a594d66406e98ce3265fb11c538ba58e9f4a7590935c1d9d70b9e6e299139 | Shell | 650 | 19 | #!/bin/bash
# File: run_compute_TdP_error.sh
# Author: Kelly Chang
# Date: Oct 2017
# Version: 1.0
#
# Description: Bash script to perform logistic regression on AP simulation
# results.
#
# classification with fixed-input simulation results
Rscript compute_TdP_error.R > log... |
32c490a799be0ef5d4a17bcbacc307956b9482b405fbce6a6792a8afaa6c46e3 | Shell | 650 | 18 | #!/bin/bash
module load python/3.9
for i in `ls /project/picsl/jtduda/data/Allen/DevCCF/subjects_corrected_v2/*.csv`; do
base=`basename $i .csv`
p1=`echo $base | cut -d _ -f1`
p2=`echo $base | cut -d _ -f2`
p3=`echo $base | cut -d _ -f3`
#echo "$p1 $p2 $p3"
img="/project/picsl/jtduda/data/Allen/DevCC... |
f0484cc645926b7dc4d35c8ff6c77ed8848c13c97cf9841340422d5876e5b16e | Shell | 651 | 27 | #!/bin/bash --login
#SBATCH --nodes=3
#SBATCH --ntasks-per-node=192
#SBATCH --time=0:15:01
#SBATCH --job-name='LFPy Circuit'
#SBATCH --account=rrg-etayhay
#SBATCH --mail-type=ALL
#SBATCH --mail-user=agmccrei@gmail.com
#SBATCH -o output_regular.out
#SBATCH -e error_regular.out
module load StdEnv/2023
module load gcc/1... |
06a2e61f8fb36f554dbac0ae5bbf12e6c556bc930e5e53c2684dd02a1ce74c59 | Shell | 655 | 24 | #!/bin/bash
# Script to run lasso_range_gene.ipynb for several different sets of simulation
# parameters using papermill, writing the resulting plots to the
# simulation_plots directory.
# Note that this must be run from the parent directory
# {repo_root}/02_cancer_type_classification.
kernel_name="pc-eval"
papermi... |
f664ebce12461d3182cba553db2608112d7e7165ad97237a56cc29671ff38c41 | Shell | 657 | 18 | #!/bin/bash
echo -e "# Running ./ap_SequenceProfile test_inputs/cyped.CYP109.aln > cyped.CYP109.profile"
./ap_SequenceProfile test_inputs/cyped.CYP109.aln > cyped.CYP109.profile
mkdir -p outputs_from_test
mv cyped.CYP109.profile outputs_from_test/
echo -e "# Running ./ap_SequenceProfile test_inputs/cyped.CYP109.aln... |
5ffb0daab2c50c5dc672c2fae92fff149d015fcebf6422f68b6c798ad89db377 | Shell | 659 | 19 | sigfile="twas/info"
line_count=$(awk 'END{print NR}' "$sigfile")
gwasfolder=cFDR/traitfolder/
modelfolder=predixcan/elastic_net_models/
for i in $(seq 1 $line_count);do
IDP=`cat $sigfile|awk 'NR=='$i' {print $1}'`
tissue=`cat $sigfile|awk 'NR=='$i' {print $2}'`
predixcan/MetaXcan-master/software/SPrediXcan.py \
--model... |
b78b36455e5ef602ee0cd7d1e1076a99fea32b4ab86241e7ea5ea06b1b082618 | Shell | 659 | 15 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../data"
echo -e "Running: ./seqc -in::pdb=./test_inputs/1rrx.pdb -out::fasta"
./seqc -in::pdb=./test_inputs/1rrx.pdb -out::fasta
echo -e "Running: ./seqc -in::pdb=./test_inputs/1ofz.pdb -out::fasta"
./seqc -in::pdb=./test_inputs/1ofz.pdb -out::fasta
echo -e "Running: ... |
0764d610c95ce3944edad271bf000427e2e90eab97fb2232eb6f402195e7c4a7 | Shell | 660 | 38 | # command interpreter to be used
#$ -S /bin/bash
#
# name
#$ -N uni_2nd_analysis
#
# merge stdout and stderr stream of job
#$ -j y
#
# output file
#$ -o ./results/uni_2nd_speedup.log
#
# use current working directory
#$ -cwd
#
# define mail notification events
#$ -m n
#
# request the given resources
# maximal run time ... |
0166e9cff76ba5fad6b68551203972f670e3b961db0f2d13ab39f2b3e6dc97e3 | Shell | 663 | 26 | #!/usr/bin/env bash
LOG_ALIAS=$1
LOG_DIR="ckpts/logs"
mkdir -p ${LOG_DIR}
LOG_FILE="${LOG_DIR}/`date +'%Y-%m-%d_%H:%M.%S'`.log"
python3 main_train.py --arch="mobilenet_v2" \
--start-epoch=1 \
--snapshot="ckpts/SynergyNet" \
--param-fp-train='./3dmm_data/param_all_norm_v201.pkl' \
--warmup=5 \
--b... |
eaaa007ae334c327ad9c382b86c577463266664373980c12b4a769c701848119 | Shell | 668 | 35 | #!/bin/bash
# Script to run plot_ridge_results.ipynb for several different
# genes using papermill, writing the results to the fs_plots directory.
# Note that this must be run from the parent directory
# {repo_root}/08_cell_line_prediction.
kernel_name="pc-eval"
papermill_output_dir="./papermill_output_nbs"
mkdir -... |
3dd53af1ba8d2d13fd5073db9339192c14b6628750ce76a26914cb662d05a41e | Shell | 672 | 7 | #!/bin/bash
# reformat the space-delimited file into a tab-delimited one
perl -nle '@a=split;print join "\t", @a' /Users/siyuansmac/bioinfo/temp/mean_depth.txt >/Users/siyuansmac/bioinfo/temp/mean_depth_format.txt
# generate a table with contig name, ref_seq accession and chromosomes assigned by Kapun
join -t "$(echo ... |
f200f2022cbc46e2b836ffd993f87bf5f2bb97f50d15a4129a9e94ea0d113e38 | Shell | 672 | 34 |
PPI="ppi_remove_self_loop.txt"
FOLDER="Human_350K"
# SEED=0
DEVICE=0
K=1200
echo "PPI = $PPI"
echo "FOLDER = $FOLDER"
# echo "SEED = $SEED"
echo "DEVICE = $DEVICE"
echo "K = $K"
for SEED in {1..10}
do
echo "SEED = $SEED"
python ./main.py \
--rand_seed $SEED \
--device $DEVICE \
--pretraine... |
315803704cf8d2d9d1931ddc0752048a238735880dc4267dc6ed8aaa45f5ec55 | Shell | 673 | 31 | #!/bin/bash
echo "Testing value of 'q(status=...)' exits for r:"
echo "q(status=123)" | ../r
echo " Got: $? via stdin"
echo "q(status=124)" | ../r -
echo " Got: $? via file '-'"
../r -e "q(status=125)"
echo " Got: $? from 'r -e'"
tempfile=`tempfile`
echo "q(status=126)" > $tempfile
../r $tempfile
echo -n " G... |
e40092b1ecd62919bd05e0c266b73fc5638e3d611b60b999102687c1b55c19b6 | Shell | 674 | 34 | #MOLGENIS walltime=23:59:00 mem=20gb ppn=6
#string pennCNVVersion
#string intermediateDir
#string tmpTmpdir
#string tmpDir
#string workDir
#string tmpName
#string Project
#string logsDir
#string finalReport
#string samplesheet
#string pennCNVInputDir
#string pennCNVVersion
set -e
set -u
set -o pipefail
module load "... |
83bc04e4a12b0b63f9a8ca5e302a021a77c6feb16585c21debbb353951113692 | Shell | 675 | 24 | # This script only works with my base environment
# conda deactivate
cd ../bin/GO-Figure
InputDir=${1}
Ontology=${2}
mkdir -p ${1}/go-figure
OutputDir=${1}/go-figure
for GOTerms in ${InputDir}/*.txt
do
FileName=${GOTerms##*/}
echo "${FileName%.txt}"
./gofigure-mac --input ${GOTerms} --input_type standard-plus ... |
2e1d581f390a1f4814ed9de7dc12826ed171601efff537b327565f89cab28e82 | Shell | 677 | 7 | rm -rf helmquadcorr.o
MWPATH=/cm/shared/sw/pkg/vendor/matlab/R2020a/bin/glnxa64
gfortran -fPIC -march=native -O3 -c helmquadcorr.f -o helmquadcorr.o -L/mnt/home/mrachh/lib -lfmm3d -lfmm3dbie_matlab
gfortran -fPIC -march=native -O3 -c read_plane_geom.f -o read_plane_geom.o -L/mnt/home/mrachh/lib -lfmm3d -lfmm3dbie_matla... |
ed7d2a3add982b317cd201deda75613482bf274d83b48fce5e2adc68e37c2671 | Shell | 681 | 12 | FMMLIBNAME=-lfmm3d
FMM3DBIELIBNAME=-lfmm3dbie_matlab
FMMPATH=/mnt/home/mrachh/lib
FMM3DBIEPATH=/mnt/home/mrachh/lib
LLNAME=flattrirouts
MWNAME=${LLNAME}.mw
GATEWAY=${LLNAME}.c
rm -rf lpeval_flattri.o
rm -rf potint2.o
gfortran -fPIC -march=native -fopenmp -O3 -c lpeval_flattri.f90 -o lpeval_flattri.o -L${FMMPATH} ${FMML... |
119b75b30474d3bfb522d79567810f75b7322130a26f950ada4cdda6c910a284 | Shell | 682 | 15 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
echo -e "Running ./ex_SelectChainResidueAtom test_inputs/1ofz.pdb A:aa"
# Here we select all amino acid residues of chain A, water molecules, ligands etc. are removed
./ex_SelectChainResidueAtom test_inputs/1ofz.pdb A:aa
echo -e "Running ./ex_SelectChainResi... |
2c6e74aa7481212b1629735ae5a825be1f60650856596afc5757409425556b66 | Shell | 682 | 14 | #! /bin/bash
cd /home/sfeng77/jobs/EAA/bayescenv/chtc/split_jobs/test_para_p
## this script submit dag for all environmental variables
# for env_var in Altitude
for env_var in Altitude Annual_Precipitation Precipitation_Seasonality Mean_Diurnal_Range Mean_Temperature_of_Coldest_Quarter Mean_Temperature_of_Warmest_Q... |
0dd0bce90b0f9bfd0f5687c981b28f4150d3002b9c81bfe742eb2a483af23b32 | Shell | 683 | 22 | #!/bin/bash
#SBATCH --time=05:00:00
#SBATCH --output=/home/intoumanis/sugar/code/logs/post_processing_subject-%A-%a.out
#SBATCH --error=/home/intoumanis/sugar/code/logs/post_processing_subject-%A-%a.err
#SBATCH --array=32,34,36-38,43
module load Python/Anaconda_v11.2021
source activate expert_power
sub=$SLURM_ARRAY_... |
5cedd80a9117738706201d82db00b631864494516e0693f90de7939392c47d0e | Shell | 684 | 20 | # Create meshes
# for refinement in 0 1 2 3 4 5 6 7 8
# do
# python3 main.py phosphorylation-preprocess --num-refinements $refinement --rect --curRadius 2.0 --mesh-folder "meshes-phosphorylation/rect_refined_${refinement}"
# done
partition=defq
# Diffusion, Refinements, timestep
for timestep in .64 .32 .16 .08 .0... |
ebe122294d6af00f8c928a12c3ff70f306f51787cbf6fefabe534b3d5ebfddce | Shell | 685 | 22 | #!/bin/bash
email=a.alemany@hubrecht.eu
Dt=20:30:00
Dmem=50G
threads=1
if [ $# -ne 6 ]
then
echo "Please, give in this order the following inputs"
echo "1) library name (name until 1_R*_001.fastq.gz)"
echo "2) pool lanes [y, n]"
echo "3) protocol [celseq1, celseq2, n]"
echo "4) trim cbc.fastq file ... |
6db1c1233cfe5f224e71d52ab4ca2d42db5c6afeac3cb2f52b10550a7843d0ef | Shell | 689 | 35 | #!/bin/bash
# Script to run plot_f_dist_heatmaps.ipynb for several different
# genes using papermill, writing the results to the ./heatmaps directory.
# Note that this must be run from the parent directory
# {repo_root}/01_stratified_classification.
kernel_name="pc-eval"
papermill_output_dir="./papermill_output_nbs... |
b66f912ca80aa7a12ae25cde699a077a074b2bcf1659b2b23f8104ce31ab21f1 | Shell | 689 | 13 | #!/bin/bash
#cat /sc/arion/projects/roussp01b/resources/databases/PEC_RNAseq_REFERENCE_HG38_GENCODE30/gencode.v30.annotation.gtf |
# gtf2bed | grep -w gene > gencodeGenes.bed
/sc/arion/projects/roussp01b/resources/software/bedtools/bin/sortBed -i /hpc/users/songl05/PF_25BR/data/gwas_sig.avinput > /hpc/users/song... |
8ac062c843a15d478e199987c306789e7266494e5b120b0eaa69dd7a534b9b7f | Shell | 690 | 36 | #!/bin/bash
# Script to plot sample distribution using download_data.ipynb for several
# different genes using papermill, writing the results to the fs_plots
# directory.
# Note that this must be run from the parent directory
# {repo_root}/08_cell_line_prediction.
kernel_name="pc-eval"
papermill_output_dir="./paper... |
07ae489bc6930a684e11a2cbe35b0cb518bdcd24d79210f63bd9d73e80fe9bf2 | Shell | 692 | 6 | rm -rf helmquadcorr.o
gfortran -O3 -march=native -fPIC -fopenmp -c helmquadcorr.f -o helmquadcorr.o -L/usr/local/lib -lfmm3d -lfmm3dbie_matlab
gfortran -fPIC -march=native -O3 -c read_plane_geom.f -o read_plane_geom.o -L/mnt/home/mrachh/lib -lfmm3d -lfmm3dbie_matlab
../../mwrap/mwrap -c99complex -list -mex fmm3dbierout... |
704202b679cf91184c5144fbce7380acbd58aa4847263d699bc6e6957bd44b14 | Shell | 692 | 30 | #!/bin/bash
#SBATCH -N 1
#SBATCH --mem 350G
#SBATCH --time=4:00:00
#SBATCH --job-name=plastic_rewire
#SBATCH --account=proj9
#SBATCH --partition=prod
#SBATCH --output=logs/plasticity_rewiring_100s
source /gpfs/bbp.cscs.ch/home/egassant/connalysis/bin/activate
declare -a
configs=("V5_placement_4k_rewire.json"
"V5_pl... |
79757c4ad60ed4e5fbbee28c3163b4a58686567bd4bc37f81a00da2c3707ad24 | Shell | 692 | 17 | #!/bin/bash
export DATADIR="/public/home/yancg/YANWork/Data/Test"
# Should have BIDS and subjects.txt
export SingularityDIR="/public/home/yancg/YANWork/Soft/Singularity"
# Should have dpabisurfslurm.sif. You can get it by singularity pull dpabisurfslurm.sif docker://cgyan/dpabisurfslurm:latest
# Should have freesurfe... |
26e421c72322216dbdbd3a67c9bc8bfd0735207e0ad63e0db2e54c5e1e86ea77 | Shell | 693 | 19 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../data"
# calculate a map of minimal distances between residues
echo -e "Running: ./str_calc -in::pdb=./test_inputs/2gb1.pdb -calc::distmap::min -calc::distmap::describe"
./str_calc -in::pdb=./test_inputs/2gb1.pdb -calc::distmap::min -calc::distmap::describe
# calculat... |
99ba114e8fb2e14b6da3204c77a8f75725000a27e431ccb2ffc20d3b796df9c9 | Shell | 693 | 12 | $OVDIR/../bin/wfoverlap.x -f ciov_all.in > ciov_all.out
$OVDIR/../bin/wfoverlap_ascii.x -f ciov_fc.in > ciov_fc.out
$OVDIR/../bin/wfoverlap.x -f dyson.in > dyson.out
export OMP_NUM_THREADS=4 # If there are more threads, then more memory would be needed!
$OVDIR/../bin/wfoverlap.x -f ciov_fc.in -m 9 > ciov_low-mem.out... |
4096e2086d86b56cf85217b808844bae4d743307d59dfec249d110a87030022d | Shell | 694 | 26 |
source samples.sh
for i in ${SAMPLES[@]};
do
mkdir results/star_pass1/${i};
STAR --runThreadN 16 \
--outSAMtype BAM Unsorted \
--sjdbOverhang 124 \
--outFilterType BySJout \
--outFilterMismatchNoverLmax 0.04 \
--alignEndsType EndToEnd \
--alignSJDBoverhangMin 4 \
--alignIntronMax 1000000 \
--alignMat... |
facdce458d57a3bc80874a55928a06b252f40c6cfbf37aed9ba7104621023366 | Shell | 695 | 30 | #!/bin/bash
# Check the first argument to determine the method
method=$1
# Shift the first argument (train_<method>) off, leaving the rest of the arguments
shift
# Handle different methods based on the first argument
case "$method" in
train_wavelet)
echo "Running Wavelet model..."
Rscript Wav_lin.R "$@"
... |
342fbebbceda5e8ef96cae759fc9524f6aab3a44fde805d445f82254ab608dbb | Shell | 698 | 34 | #!/bin/bash
# author : sjn
# date : Dec.2022
set -euox pipefail
if [[ $# != 2 ]]; then
printf "Require a reference fasta file and an output file\n"
exit -1
fi
inp=$1
outp=$2
awk 'BEGIN {OFS="\t"; pos=0; prev=""; chr=""} ; { \
if ( $1 ~ /^>/ ) { chr=substr($1, 2); prev=""; pos=0; next; } \
lng=split(... |
4baf478085301fa5dcec04bab4f837b7cb3998cfcd8bec453ee9f219a6eae45d | Shell | 698 | 19 | #!/bin/bash
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable ... |
c942feae11cae1c8f166b47051f2c6e35b64300563fb638e13bcc50cc69487bf | Shell | 700 | 19 | #!/bin/sh
#
# Written by Tong He and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
cd ~/storage
rsync -a --exclude .git CBIG/* Standalone_He2019_KRDNN
# remove useless stable projects
rm -r Standalone_He2019_KRDNN/stable_projects/brain_parcellation
rm -r Standalone_He2019_KRDNN/s... |
3d0ce303b082d0cc5b227a61ae777ce29d80364b9f2fa5df63cf43ea36c42330 | Shell | 704 | 35 | #!/bin/bash
# Script to run plot_univariate_fs_results.ipynb for several different
# genes using papermill, writing the results to the fs_plots directory.
# Note that this must be run from the parent directory
# {repo_root}/08_cell_line_prediction.
kernel_name="pc-eval"
papermill_output_dir="./papermill_output_nbs"... |
69774b8e92fca10d982d50b8eafea1d40ec16ac2366f0ff5242a898e111ef460 | Shell | 707 | 21 | #!/bin/bash
# Set your paths here
HOME=/fslgroup/fslg_spec_networks/compute
code_DIR=${HOME}/code/HCPD_analysis/CBIG2016_preproc
data_DIR=${HOME}/data/HCPD_BIDS
# Create that special CBIG subjids text file for each subject (data must be in BIDS format)
# CBIG example format: 001 /fslhome/NETID/Downloads/CBIG_Data/Sub... |
531bbd211855c5f028f846888400c70292f1c67eb7a71d6453f75e7b5113f857 | Shell | 708 | 33 |
# mkdir data/adc/plink
# # make chromosome-specific plink filesets
# for chr in $(seq 1 22)
# do
# plink \
# --bfile data/adc/adc_np \
# --chr "$chr" \
# --make-bed \
# --out data/adc/plink/adc_np_chr"$chr"
# done
# mkdir data/rosmap/plink
# # make chromosome-specific plink filesets
# for chr i... |
b840e68ebf933f39721d4002b7853c1854efc54052470e4cc45ec47e0e5a4b1b | Shell | 708 | 22 | #!/bin/bash
# Set output directory
output_dir="nt"
mkdir -p "$output_dir"
# URL to the metadata file
metadata_url="https://ftp.ncbi.nlm.nih.gov/blast/db/nt-nucl-metadata.json"
# Fetch the metadata file and extract file URLs
curl -s "$metadata_url" | grep -o '"ftp://[^"]*"' | sed 's/"//g' | sed 's/ftp:/https:/g' | wh... |
3b87861facec414ffebbf6745861201d96a4e240de0e4eb9a1aecf2069e5635e | Shell | 710 | 37 | #MOLGENIS walltime=59:59:00 mem=20gb ppn=6
#string pythonVersion
#string beadArrayVersion
#string gapVersion
#string bpmFile
#string projectRawTmpDataDir
#string intermediateDir
#string tmpTmpdir
#string tmpDir
#string workDir
#string tmpName
#string Project
#string logsDir
#string finalReport
#string samplesheet
#str... |
79cff6d18863b536a6f3d32950a831120f57b025776f96dd6ba5b490fb31f00f | Shell | 714 | 33 | #!/bin/sh
#$ -N hidden-size-effect-2
#$ -cwd
#$ -q cuda.q
#$ -S /bin/bash
#$ -M lukas.galke@mpi.nl
#$ -m beas
# Halt on error
set -e
module load miniconda/3.2021.10
conda activate pytorch
pip install -r requirements.txt
NUM_ITER=1000
SEED=42000
OUTDIR="./results_ll_hidden_size_effect_2"
NUM_LAYERS=2
# Iterate ... |
5689354c582c561416ee3777a341baeaddc565aa3adcc53ce2bc70132b30e914 | Shell | 715 | 36 | #!/bin/bash
# Script to run plot_univariate_fs_results.ipynb for several different
# genes using papermill, writing the results to the fs_plots directory.
# Note that this must be run from the parent directory
# {repo_root}/02_cancer_type_classification.
kernel_name="pc-eval"
papermill_output_dir="./papermill_outpu... |
fd9ad6f0d5fca8873e3f8a968fa7bf45e9c1e40790ebb1fabaf4a8090ea00e9c | Shell | 715 | 22 | #!/bin/bash
# File: run_AP_uncertainty.sh
# Author: Kelly Chang
# Date: Oct 2017
# Version: 1.0
#
# Description: Bash script to run AP simulations for the 12 CiPA training
# drugs using uncertainty inputs (i.e. drug parameters from
# sampling distributions).
#
... |
cd835e283baa967bb1c38b4eb6e5ddc30f7b6418537f601dcbaff2a0b3e4d4ba | Shell | 716 | 28 | #!/bin/bash
set -ex
# Install and set first the solver to accelarte package installation
source $PWD/soft/miniconda3/bin/activate
conda install conda-libmamba-solver --yes \
&& conda config --set solver libmamba \
&& conda install --yes --solver=libmamba \
--channel conda-forge --channel anaconda python=3.7 \
... |
23fbbffe6b471712d8f3a36bc83e43052a1f20d4048b26ec9b9864a5c02ae945 | Shell | 717 | 20 | #!/bin/bash
# Set your paths here
HOME=/fslgroup/fslg_spec_networks/compute
code_DIR=${HOME}/code/HCP_analysis/CBIG2016_preproc
data_DIR=/fslgroup/grp_proc/compute/HCP_analysis/HCP_download
# Create that special CBIG subjids text file for each subject (data must be in BIDS format)
# CBIG example format: 001 /fslhome/... |
2bb1ff44960eb41c14e0a45cf261f6bf782a634e6e9b856f72e063aae5b09657 | Shell | 719 | 13 | #!/bin/bash -l
python3 model_eval.py \
--tpu_name="pod1" \
--tpu_zone="europe-west4-a" \
--wandb_project="enformer_rampage_atac_ft_test" \
--wandb_user="njaved" \
--wandb_sweep_name="enformer_rampage_atac_ft_test" \
--gcs_path="gs://genformer_euro... |
8f60587b8267d83e729b88f2529039325281b30bf21fc6d87118a22158f6c459 | Shell | 719 | 14 | #!/usr/bin/env bash
/etc/init.d/rabbitmq-server start
rabbitmqctl add_user $RABBITMQ_USER $RABBITMQ_PASSWORD 2>/dev/null
rabbitmqctl set_user_tags $RABBITMQ_USER administrator
rabbitmqctl set_permissions -p / $RABBITMQ_USER ".*" ".*" ".*"
/etc/init.d/rabbitmq-server stop
echo "*** User '$RABBITMQ_USER' with password '... |
2c341193bf3fbfcdd651b7257044862d6d88db6ec24f5e7d4ad5a42141483f96 | Shell | 720 | 25 | #!/bin/bash
# # convert imputed VCF files to PLINK 2 binary filesets
# seq 1 22 | \
# xargs -n 1 -P 22 -I % \
# ./code/imputation/vcf_to_plink2.py \
# --vcf /data_global/ADC_imputed/chr%_all_adcs.dose.vcf.gz \
# --out tmp/adc_chr%
# merge PLINK 2 chromosomal binary filesets
list_file=tmp/adc_prefix_list.t... |
95ca37f4449b67af5234a43283416a27f0112eb6a93d22f0e29be582c6d45449 | Shell | 720 | 7 | CUDA_VISIBLE_DEVICES=3 python test.py --resume ./M4Raw_exp/ALL_UNET/snapshot/net_100.pth --modal FLAIR --net_name UNET
CUDA_VISIBLE_DEVICES=3 python test.py --resume ./M4Raw_exp/ALL_UNET/snapshot/net_100.pth --modal T1 --net_name UNET
CUDA_VISIBLE_DEVICES=3 python test.py --resume ./M4Raw_exp/ALL_UNET/snapshot/net_10... |
38077bad84b885f772bf3c86b4c958049bc2f91f1169b1f96aa2f0be1250a31b | Shell | 721 | 31 | #!/bin/bash
#================================
# Step 3: Remove ethnic outliers
#================================
prefix=tmp/adc_qc1.tmp
# # convert to PLINK 1.9 fileset
# # (merging in PLINK 2.0 is currently limited in features)
# plink2 --pfile "$prefix" --make-bed --out "$prefix"
#
# # merge adc and 1000g filesets... |
0ced9c826a23f00e75955fef4d9fa9d50d5d20a38c671fab43b9db5ebac4dd2c | Shell | 722 | 22 | #!/bin/bash
#
# Gokberk Alagoz - 02.03.2023
#
# This script will extract GCTB results from all SBayesS
# analysis .parRes files and annotate each result's trait.
#
########################
# PATHS
inDir="/data/clusterfs/lag/users/gokala/beat-dyslexiaevol/results/GCTB/"
for i in ${inDir}*.parRes; do
tmp1=$(bas... |
20ab21981ef869b72e029a843801d67c1b2dbd8088224abfb5cf811661b48b71 | Shell | 724 | 33 | #MOLGENIS walltime=05:59:00 mem=10gb ppn=6
#string intermediateDir
#string Project
#string logsDir
#string runID
set -e
set -u
set -o pipefail
# Touch log file for GAP_Automated for starting copying project data to PRM
if [[ -f "${logsDir}//${Project}/${runID}.pipeline.started" ]]
then
mv "${logsDir}/${Project}/${... |
80a292a77e99b7bd338b05cf46604a17c103a44c56151daab29c0cd1b4073d6e | Shell | 727 | 8 | python3 -W ignore scperb.py --model_name Endocrine --exclude_celltype Endocrine --data hpoly
python3 -W ignore scperb.py --model_name Enterocyte --exclude_celltype Enterocyte --data hpoly
python3 -W ignore scperb.py --model_name Enterocyte.Progenitor --exclude_celltype Enterocyte.Progenitor --data hpoly
python3 -W igno... |
ef78915dbdcdc548bf255b33eb685e65427609e922dd16dbc168dd22417372d9 | Shell | 727 | 31 | #!/bin/sh
set -e
DATA_ROOT=""
TRAIN_ID="multiclass-id1"
# train models
item=1
while [ $item -le 18 ]; do
python train_classifier.py --data-root "$DATA_ROOT" \
--results-dir "./spaceml-results" \
--id $TRAIN_ID \
--item $item \
--n_blocks 4 \
--batch-size 64 \
--epochs 30 \
--eval-test
... |
fb4273c36729f540df8ad23fa103a231b9d6578f7855adabcce7b0f9a962d90a | Shell | 727 | 37 | #!/bin/bash
set -e
if [ -z ${AWS_SSH_PRIVATE_KEY_FILE} ]
then
echo "ERROR: You must set AWS_SSH_PRIVATE_KEY_FILE in the environment."
exit 1
fi
d=`dirname $0`
for possibleH2oJarFile in ${d}/h2o.jar ${d}/../h2o.jar ${d}/../target/h2o.jar
do
if [ -f ${possibleH2oJarFile} ]
then
h2oJarFile=${pos... |
186217542938c9bad1d9889580a425ca61578e45a69b309d61ea0d418b0bfa33 | Shell | 728 | 30 | viewpoint=V11O2
for viewpoint in ep0
do
python3 ../train_vit.py \
--lars_wrapper \
--max_epochs 100 \
--batch_size 128 \
--data_dir /data/lpandey/UT_Austin_EgocentricDataset/output_64x64Squished/train3_80k/${viewpoint} \
--seed_val 0 \
--temporal \
--window_s... |
6c14d54ca5b1a425fa3ba420b8ab722dee2da8f8be7dfa0bc25683a41e2b74bb | Shell | 728 | 15 |
# (c) Coraline Rinn Iordan 07/2017, 10/2017, 10/2019
# Align prototype
# $1 : PARAMS.TEMPLATEDIR
# $2 : PARAMS.LOCALIZERANAT
# $3 : PARAMS.CURRENTANAT
# $4 : PARAMS.LOCALIZERTEMPLATE
# $5 : PARAMS.NIFTIDIR
# $6 : PARAMS.PROTOTYPE.FINALFILE
\@Align_Centers -base "$1"/"$2"+orig -dset "$1"/"$3"+orig -child "$5"/Prototy... |
b32138ba5a8dd13403a1b55415f28e418ba2385b7adeb13656d61d1005556710 | Shell | 731 | 25 | #!/bin/bash
# File: run_hERG_fit_boot.sh
# Author: Kelly Chang
# Date: Oct 2017
# Version: 1.0
#
# Description: Bash script to fit hERG model to bootstrap samples of Milnes
# protocol data.
#
# change CMA-ES default hyperparameters
POP_SIZE="80"
STOPTOL="0.001"
DRUGNAMES=(d... |
15e722ae0206350b4058dacef174127c97bdbcf49b606c62a6446a615cb59656 | Shell | 732 | 22 | #!/bin/bash
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable ... |
ab77fa71048c01eeee7f7169b7b4f585d4cc6c06729aaf8cf7eae6c0da2e0cc4 | Shell | 732 | 45 | #!/bin/sh
# clean prior results
rm -rf amp_sub*
# prepare directories
AMP_SUB_DIRS=$(ls configs/ | sed 's/config/amp_sub/g' | sed 's/.csv//g' )
mkdir $AMP_SUB_DIRS
# execute notebooks from templates and configs
for d in amp_sub*
do
#echo $d
cd $d
CONTRAST=$(echo $d | sed 's/amp_sub_//g')
echo "computing $CONTRAST... |
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