sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
ef4c9de55187c200fc218bb4709e9d9c0b949cf1498b49725aa7c6bc8db41d0f | Shell | 513 | 20 | #! /bin/sh
cd tests
. ./compat.sh
sort -k2,2 > ${pref}.md5sum <<EOF
bbceae352707eaa945ce2057137f3a7a ${pref}.histo
c697577f78593fef303b5fcaad86e336 ${pref}.stats
EOF
echo "Count on a very small file" && \
${DIR}/generate_sequence -v -s 2609132522 -o small 148 && \
$JF count -m 20 -s 1M -t $nCPUs -o ${pref} -... |
f6ae2d3f3bedd52b4cbbf42ef7f8396fcd0c0c10f669a98ef203f04bd2706ced | Shell | 513 | 18 | mypython=$1
$mypython $MARINE/marine.py \
--bam_filepath \
$MARINE/tests/singlecell_tests/bams/9_3000526_only_5_cells.bam \
--annotation_bedfile_path \
$MARINE/annotations/cellranger-mm10-3.0.0.annotation.genes.bed \
--output_folder \
$MARINE/tests/singlecell_tests/only_5_cells_all_cells_coverage_no_tabulation_test \
... |
6cdd7a51e8d3b7236848392d08b7bec56688ba37303f6d5d64687fca8a2129d8 | Shell | 514 | 20 | #! /bin/sh
cd tests
. ./compat.sh
sort -k2,2 > ${pref}.md5sum <<EOF
8a0fe8ee1293f341fbde69e670beb74c ${pref}.histo
EOF
echo "Counting 22-mers, fastq format, no quality, on ${nCPUs} CPU" && \
$JF count --matrix seq10m_matrix_22 -m 22 -t $nCPUs \
-o ${pref} -s 10000000 --timing ${pref}.timing seq10m.fq && \
... |
d36da42cb735198eadc60fd99c2a29fe43a52d991705bdf8cbcecd22c6a1d58e | Shell | 514 | 20 | #!/bin/bash
set -e
bids_dir="/mnt/f/BIDS/WCH_SVD_3T_BIDS"
jobs_file="/mnt/f/BIDS/WCH_SVD_3T_BIDS/code/freesurfer/jobs.csv"
# 清理 BOM 和 CRLF
sed -i '1s/^\xEF\xBB\xBF//' "$jobs_file"
sed -i 's/\r$//' "$jobs_file"
run_one () {
local bids_dir=$1
local subject=$2
local session=$3
/mnt/f/BIDS/WCH_SVD_3T_BIDS/code/f... |
e346aeff04f7f734e0529e53abff171c5acdf66f43f9b245b7f9aa4bd27e293b | Shell | 514 | 20 | #! /bin/sh
cd tests
. ./compat.sh
sort -k2,2 > ${pref}.md5sum <<EOF
4fd24c05f7c18c47e7b69f77aa071f1f ${pref}_0
7059a4e90b6670b2d814e44e2bc7d429 ${pref}.histo
EOF
echo "Counting 22-mers on 1 CPU" && \
$JF count --matrix seq10m_matrix_22 -m 22 -t 1 -o ${pref} \
--timing ${pref}.timing -s 10000000 seq10m.fa && \... |
fb7c90fc2e1af6a787a75ea3444a94735627bb5ed9c73f83a9a0ca4a1a7d9402 | Shell | 514 | 25 | #!/bin/bash
# example script to train NCD using the kingdom fragment method
set -e
# Input paths
TRAIN_DATA="data/train"
TAXA_DATA="data/metadata"
# Parameters
FRAGMENT_SIZE=126
RANK="superkingdom"
N=100 # total samples/superkingdom
OUTPUT_DATASET="data/test_dataset"
# Run NCD training pipeline
python NCD.py... |
066329c60790ccb42949027e25c17f40818723dafbf7baa66c94ffdccf04885d | Shell | 515 | 26 | echo "Eval MedicalPatchNet_weights.pt"
python3 trainClassification.py \
-patchSize 64 \
-imgSize 512 \
-wb \
-wb_name MedicalPatchNetEvalOnly \
-evalOnly \
-loadPath "savedModels/MedicalPatchNet_weights.pt" \
echo " "
echo " "
echo " "
echo " "
echo " "
echo "Eval EfficientNetB0_weights.pt"
... |
e7235d5d3e8505e30c27f00298386f5860562df29e04a6a2dbf3033940b588b7 | Shell | 517 | 19 | #! /bin/sh
cd tests
. ./compat.sh
sort -k2,2 > ${pref}.md5sum <<EOF
8ebb01305cbb36754ef060c1e37d6e4d ${pref}.histo
EOF
echo "Counting 22-mers on ${nCPUs} CPU" && \
$JF count -q --matrix seq10m_matrix_22 -m 22 -t $nCPUs \
-o $pref -s 5000000 --timing ${pref}.timing seq1m_*.fq && \
$JF qhisto -f -l 0.0... |
2b3ab07a4887099fa1e6dad52e903d9ab59a7fb4e00279c0cc679b8184350388 | Shell | 519 | 21 | #!/bin/bash
set -e -E -u -o pipefail
pwsh -command "Install-Module -Name PSScriptAnalyzer -Scope CurrentUser -SkipPublisherCheck"
echo "Linting PowerShell code"
pwsh -file ./.ci/lint-powershell.ps1 || exit 1
conda create -q -y -n test-env \
"python=3.14[build=*_cp*]" \
'pre-commit>=3.8.0' \
'r-lintr>=3.3... |
b18fe231b69669c9deca6a07fc5da842271c1f654510dae27294914aa7e565dc | Shell | 519 | 9 | #!/bin/bash
fslreorient2std /Users/boo/Desktop/s0mask.nii /Users/boo/Desktop/ttts0mask.nii
flirt -in /Users/boo/Desktop/saaa01_ISO_IIHC_TAL.nii -ref /Users/boo/Desktop/fmri_script/brainmask/original_ima/MNI152_T1_2mm_template.nii -out /Users/boo/Desktop/ttt1.nii -omat /Users/boo/Desktop/ttt1.mat -dof 6
flirt -in ... |
b533d4842528a3da66a88a7c372c0bb6d48a3915806289854fb9f75b1eda8aee | Shell | 522 | 18 | #!/bin/bash
#SBATCH --time=1-00:00:00
#SBATCH --gres=gpu:1
#SBATCH --constraint=v100
#SBATCH --partition=gpu
#SBATCH -n 1
#SBATCH --mem 100G
#SBATCH --mail-type=FAIL
#SBATCH --mail-user=<EMAIL>
# Example SLURM script for running the Sei framework code
# on input sequences from a BED or FASTA file
input_filepath="${1:... |
354fa9e013fc39d8677f29ce993d17db66e16ad79b6c615dd25822b57062bfa6 | Shell | 523 | 18 | #!/bin/bash
# PediatricOpenTargets 2021
# Yuanchao Zhang
set -e
set -o pipefail
# This script should always run as if it were being called from
# the directory it lives in.
# copied from the run_in_ci.sh file at
# <https://github.com/AlexsLemonade/OpenPBTA-analysis/blob/master/scripts/>
script_directory="$(perl -e 'us... |
ef068f235cc41ec0777ff40c4b8ac135e3f0df5c1cacd7ee5332d1ff3f264d47 | Shell | 523 | 16 | #!/bin/bash -l
#SBATCH --job-name=model_build
#SBATCH --time=1:00:00
#SBATCH --account=proj83
#SBATCH --partition=prod
#SBATCH --mem=0
#SBATCH --exclusive
#SBATCH --constraint=cpu
module purge
module load unstable
source /gpfs/bbp.cscs.ch/home/pokorny/ReWiringKernel/bin/activate
connectome-manipulator build-model $1 $... |
766cb36692872d1d3441e9b9d5d793d7fba2d9b66131755fb65233ba13e8432f | Shell | 524 | 15 | #!/bin/bash -e
source config.sh
docker build -t ${image_name}:${version} .
# hack: comment the ENTRYPOINT and CMD lines to make it work for cromwell
# this will generate `Dockerfile.cromwell` and build it under the name `cromwell-${image_name}:${version}`
# https://github.com/broadinstitute/cromwell/issues/2461
cat ... |
66684409ad76e914fc4fa45e548033245a936309c964c52757f16bba27fa7e6c | Shell | 525 | 18 | #!/bin/bash
#
# anat_brain-extract_using-fs-reimport.sh <anat> <fsdir>
#
# - brain extraction of processed anatomy reimporting brain extracted freesurfer
# volume using coordinates of mp2rage and using it as a mask
anat=$1
fsdir=$2
mri_convert --out_orientation RAS -rt nearest --reslice_like ${anat} \
... |
d6728e4dc381c5e8cac87a35584f2be1b32ec4c18320c39ca6f523bbdc7f1c4b | Shell | 525 | 18 | #!/bin/bash -l
set -x
export CONFIG_DIR=../network_config/cifar10
declare -a config_files=(
20250827_EIANN_2_hidden_lrf_cifar10_van_bp_relu_SGD_config_G_zero_bias_optimized.yaml
20250829_EIANN_2_hidden_lrf_cifar10_bpDale_relu_SGD_config_G_zero_bias_optimized.yaml
20250829_EIANN_2_hidden_lrf_cifar10_DTP_config_... |
7c92096e788e1df03795682cbd795576d810d6f1529d5b9b2ceec1073351a90c | Shell | 529 | 18 | #!/bin/bash
## Gene function prediction task
wget -nv https://download.baderlab.org/PathwayCommons/PC2/v12/PathwayCommons12.All.hgnc.sif.gz
gunzip PathwayCommons12.All.hgnc.sif.gz
## Drug repurposing task
git clone https://github.com/mims-harvard/TxGNN
## Synthetic lethality task:
git clone https://github.com/Jie... |
7c5d1a40b105a3d88660267e37582a0c7e89f4853ef4cdc8a3e881241482069d | Shell | 535 | 18 | #!/bin/bash
BASE="output_$1"
firstfile=$(find . -name "${BASE}*-00000.vti" | head -1)
if [[ ! -f $firstfile ]]; then
echo "Can not find a file named '${BASE}*-00000.vti'"
exit 1
fi
OUTPUT=${BASE}.pvd
echo '<VTKFile type="Collection" version="1.0" byte_order="LittleEndian" header_type="UInt64">' > $OUTPUT
echo '... |
42d96493ac13108ab62d39f195f4020a492118f45dda41347fe5f70554dd6481 | Shell | 536 | 20 | #!/bin/bash
# Script to run all steps of dannce in a single job.
#
# Inputs: com_config - path to com config.
# dannce_config - path to com config.
# Example: sbatch com_and_dannce.sh /path/to/com_config.yaml /path/to/dannce_config.yaml
#SBATCH --job-name=com_and_dannce
#SBATCH --mem=5000
#SBATCH -t 5-00:00
#S... |
729427ab5e819866d892fc943f973ef57ed7e5c9ede22599ede3c7055b10f4ee | Shell | 536 | 9 | #!/bin/bash
for i in $(seq $(ctest -N | tail -1 | cut -d":" -f2)); do
lcov --zerocounters --directory CMakeFiles/
ctest -I $i,$i
lcov --capture --directory CMakeFiles/ --base-directory . --gcov-tool ../scripts/ci/llvm-gcov.sh --test-name "$(ctest -N -I $i,$i | sed -n "2p")" -o coverage_$i.info
lcov --remove cov... |
169aded1a0818f5f46e0bd615f1757457233cc5f359b9af49ac738f1f70a75b2 | Shell | 537 | 21 | mypython=$1
$mypython $MARINE/marine.py \
--bam_filepath \
$MARINE/examples/data/LR_single_cell.md.subset.filtered.sorted.bam \
--annotation_bedfile_path \
$MARINE/annotations/cellranger-mm10-3.0.0.annotation.genes.bed \
--output_folder \
$MARINE/tests/singlecell_tests/long_read_sc_test \
--min_dist_from_end \
0 \
--m... |
5723dc0757590ca33a7e731c887014553df071e7cf092bb0cff452a763496e38 | Shell | 537 | 14 | #!/bin/bash
# command used to packup distribution tar ball
UNAME=`uname`-`uname -m` # for instance Linux-x86_64
FNAME=hole2/hole2
FNAME+=-$HoleBuild # for instance NotForProfit
FNAME+=-$HoleVersion # for instance 2.004
FNAME+=-$UNAME # for instance Linux-x86_64
FNAME+=.tar.gz
echo "tarball name $FNAME"
cd ..
tar cvzf... |
e70e2fc53f38bf7861b4bc38cb1f0589565265aa0142fc205f17ac84396d232d | Shell | 538 | 10 | #!/usr/bin/env bash
set -euo pipefail
cd ..
device=0
for s in boxcar relu gaussian multi_gaussian sigmoid; do
python offline_main.py --model_type RLIF --nb_epochs 100 --nb_hiddens 1024 --normalization batchnorm --lr 0.005 --lr_step_size 5 --devices $device --new_exp_folder bptt-surrogate --nb_layers 3 --surrogate "... |
013803f51c72a7a55842e2a8846789475d738dcb2808d3e2bc644fa32e3a753a | Shell | 539 | 17 | #!/bin/bash
#SBATCH -J train_reID
#SBATCH -o unetpos.o%j
#SBATCH -t 40:00:00
#SBATCH -N 1 -n 8
#SBATCH --gres gpu:1
#SBATCH --mem=256GB
source activate Ali
python /home/lhuang37/repos/VisQ-Search-Engine/examples/graph_train.py\
-b 256 -a unet -d brain -dn myelo_panel_all -nc=7 --lr 0.00035 --weight-decay 5e-4\
-... |
f6e6b17e8eee0a6972ff7e28674524a142e59aad4a04be1edd9383994230029d | Shell | 539 | 23 | #!/usr/bin/env bash
set -x
PARTITION=$1
JOB_NAME=$2
CONFIG=$3
GPUS=${GPUS:-4}
GPUS_PER_NODE=${GPUS_PER_NODE:-4}
CPUS_PER_TASK=${CPUS_PER_TASK:-5}
SRUN_ARGS=${SRUN_ARGS:-""}
PY_ARGS=${@:4}
PYTHONPATH="$(dirname $0)/..":$PYTHONPATH \
srun -p ${PARTITION} \
--job-name=${JOB_NAME} \
--gres=gpu:${GPUS_PER_NODE} \... |
e69bab0af8fe60c9c6d35fd1edf7328df8175987003b8b9091568da6323ec29a | Shell | 540 | 21 | #! /bin/sh
cd tests
. ./compat.sh
sort -k2,2 > ${pref}.md5sum <<EOF
c448e173e5e18264ed00fad0008d5340 ${pref}.histo
EOF
echo "Counting 22-mers on ${nCPUs} CPU" && \
cat seq10m.fq | $JF count -q --matrix seq10m_matrix_19 -m 19 -t $nCPUs \
-o $pref -s 10000000 --timing ${pref}.timing /dev/fd/0 && \
$J... |
3128b90ddaeffbecb9c62aebfbab459022d15fe35630ed12d729172ab5c6cf72 | Shell | 541 | 10 | CONFIG_SOURCE_FILES="config_common.c config_parser.c postprocessor_config.c"
CONFIG_HEADER_FILES="config_common.h stim_config.h domain_config.h
purkinje_config.h assembly_matrix_config.h extra_data_config.h
linear_system_solver_config.h
config_parser... |
f2b23e3656e209308e9ec0b9d9df3feb01f146587b664eb02336e035db6fb246 | Shell | 541 | 26 | #!/bin/bash
set -e -E -u -o pipefail
# recreates 'configure' from 'configure.ac'
# this script should run on Ubuntu 22.04
AUTOCONF_VERSION=$(cat R-package/AUTOCONF_UBUNTU_VERSION)
echo "Creating 'configure' script with Autoconf ${AUTOCONF_VERSION}"
apt update
apt-get install \
--no-install-recommends \
-y \... |
113b48a43de3005cf5146813f33607be02d290d8eb41c47a180ed3f151b5686f | Shell | 543 | 22 | #!/usr/bin/env bash
#####################################################################
# Example script for computing the raw sequence class scores
# given Sei chromatin profile sequence predictions
# Usage:
# sh 2_raw_sc_score.sh <input-file> <output-dir>
##########################################################... |
0b0e36f41310869cfd1ad7539f962b0ba20f32fe5c50bab09186156aafdb4af4 | Shell | 545 | 27 | #!/bin/bash
function load_module() {
local MODULE_NAME="$1"
module load "${MODULE_NAME}" > /dev/null 2>&1
if [[ "$?" -ne 0 ]]; then
echo "failed to: module load ${MODULE_NAME}" 1>&2
return 1
fi
}
function load_modules() {
module purge || return 1
load_module cmake/3.15.4 || return 1
load_module ... |
309e520b6128bb7c0825940f09981ef0796cb5cc3210becdce5f8cfbac1ed89e | Shell | 545 | 15 | #!/bin/bash
#BSUB -J count_reads[1-2034]
#BSUB -o count_reads_windows.out
#BSUB -e count_reads_windows.err
#BSUB -We 5
#BSUB -q vshort
source activate ATACseq_preprocess
bampath=../input/sc-bams_nodup/
dirlist=(`ls $bampath*.bam`)
# echo ${dirlist[$LSB_JOBINDEX-1]}
mkdir -p count_reads_windows_output
echo ./count_rea... |
92bca21bc0188d5e997ecd208f1b4e9a4a91f247103f218d5577f6203711f608 | Shell | 545 | 15 | #!/bin/bash
#BSUB -J count_reads[1-5335]
#BSUB -o count_reads_windows.out
#BSUB -e count_reads_windows.err
#BSUB -We 5
#BSUB -q vshort
source activate ATACseq_preprocess
bampath=../input/sc-bams_nodup/
dirlist=(`ls $bampath*.bam`)
# echo ${dirlist[$LSB_JOBINDEX-1]}
mkdir -p count_reads_windows_output
echo ./count_rea... |
b940f2cde1fc02448b4424915137793e8538b322bd633b26f5333a45b4c9b8bf | Shell | 545 | 15 | #!/bin/bash
#BSUB -J count_reads[1-12178]
#BSUB -o count_reads_windows.out
#BSUB -e count_reads_windows.err
#BSUB -We 5
#BSUB -q vshort
source activate ATACseq_preprocess
bampath=../input/sc-bams_nodup/
dirlist=(`ls $bampath*.bam`)
# echo ${dirlist[$LSB_JOBINDEX-1]}
mkdir -p count_reads_windows_output
echo ./count_re... |
29490a7fedda46d4bbf1f969b5ca9b67efc83efa0d2cdf87f4d68e3fb99665ba | Shell | 548 | 23 | #!/bin/bash
set -eux
scriptdir=$(dirname "$0")
function compile_function()
{
local funcName="$1"
shift 1
local outdir="$scriptdir"/Compiled_"$funcName"
mkdir -p "$outdir"
"$MATLAB_HOME"/bin/mcc -m -v "$funcName".m "$@" -d "$outdir"
}
#addpath() adds to the front, while -I adds to the back, so rev... |
acb718410fa7e4e55b3d3533b31a57f657c12b371009a576f2879c1d18a96d8f | Shell | 548 | 20 | #!/bin/bash
set -e # Stop on error
SH_SCRIPT_DIR=$(cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd)
SRC_DIR=${SH_SCRIPT_DIR}/../src
PIPELINE_CONDA_ENVS=(
encd-chip
encd-chip-macs2
encd-chip-spp
)
chmod u+rx ${SRC_DIR}/*.py
echo "$(date): Updating WDL task wrappers on each Conda environment..."
for PIPELINE_CONDA... |
f6ad21f3a0264b5741b1803669a0b069c610b59d125f385a6958b7cd023c5b38 | Shell | 548 | 17 | #! /bin/sh
cd tests
. ./compat.sh
[ -z "$ENABLE_PYTHON_BINDING" ] && exit 77
export PYTHONPATH="$BUILDDIR/swig/python/.libs:$BUILDDIR/swig/python${PYTHONPATH+:$PYTHONPATH}"
K=$($PYTHON -c 'import random; print(random.randint(6, 20))')
I=$($PYTHON -c 'import random; print(random.randint(0, 4))')
$JF count -m $K -s 10M... |
e679ba201f9f01963c8ee58aeeaf89e51b11fc276061efe76c75fde503fa8a91 | Shell | 549 | 14 | #!/bin/bash
#
# Add the time and date onto reports and timeline names
nf_pipeline=$1
## Get current date ##
_date=$(date +"%d_%m_%Y")
_time=$(date +"%H:%M:%S")
## Appending a current date from a $_now to a filename stored in $_file ##
timing="${_date}-${_time}"
## Run nextflow in background with dated timeline and r... |
8c382849d5ee14e7bcfea1554e571e85051d5f2f7874ce41c520034b49aa695b | Shell | 550 | 17 | #!/bin/bash
dataset=$1
tract_list=$2
inputarray=()
while IFS= read -r line; do
inputarray+=("$line")
done < "${tract_list}"
# Get the tract for this SLURM array task
tract_name="${inputarray[$SLURM_ARRAY_TASK_ID]}"
# Run the R script for the specific dataset and tract
singularity run --cleanenv /cbica/projects... |
e6f77ca5dcc92dee5b97ee82adc0192bbf76ca7b6f6ab61a4abb38a70b521f1e | Shell | 550 | 7 | # aliases for converting sample read files
# `source conversion_utilities.sh` to add them to your environment
alias fastq_to_fasta="sed 'N;x;N;N;x;s/@/>/"
alias paired_to_tab5="paste <(sed 'N;x;N;g;N;s/\n/ /g' reads_1.fq) <(sed -n 'n;h;n;g;N;s/\n/ /g;p' reads_2.fq) > reads_12.tab5"
alias paired_to_tab6="paste <(sed '... |
11535ca90eabfced19e68634ec6df45921fc00592fe4f394f80c89d3aec7d211 | Shell | 551 | 21 | #!/bin/bash
#SBATCH --output=logs/param_%A_%a.out
#SBATCH --error=logs/param_%A_%a.err
#SBATCH --array=1-5000%500
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --mem=2G
#SBATCH --time=01:00:00
source ~/myenv/bin/activate
# Create variables
batch_id=$1
MODE=$2
Solut_per_batch=5000
OFFSET=(batch_id-1)*Solut_per_... |
2f00d5348b56d5bd1c0b66c4ead30ebaec7e25afd9355cd851f672dea2d9d878 | Shell | 551 | 21 | #!/bin/bash
#SBATCH --output=logs/param_%A_%a.out
#SBATCH --error=logs/param_%A_%a.err
#SBATCH --array=1-5000%500
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --mem=2G
#SBATCH --time=01:00:00
source ~/myenv/bin/activate
# Create variables
batch_id=$1
MODE=$2
Solut_per_batch=5000
OFFSET=(batch_id-1)*Solut_per_... |
4f1fefa94f42dc1ce66d29d0a41362d62edfa1d346bd2abab65f34f544c5bbcd | Shell | 551 | 21 | #!/bin/bash
#SBATCH --output=logs/param_%A_%a.out
#SBATCH --error=logs/param_%A_%a.err
#SBATCH --array=1-5000%500
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --mem=2G
#SBATCH --time=01:00:00
source ~/myenv/bin/activate
# Create variables
batch_id=$1
MODE=$2
Solut_per_batch=5000
OFFSET=(batch_id-1)*Solut_per_... |
5c0fa8a96f84c346ad6abb3d27eea0f300fa746525bf07fb273de30a7fd240c2 | Shell | 551 | 21 | #!/bin/bash
#SBATCH --output=logs/param_%A_%a.out
#SBATCH --error=logs/param_%A_%a.err
#SBATCH --array=1-5000%500
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --mem=2G
#SBATCH --time=01:00:00
source ~/myenv/bin/activate
# Create variables
batch_id=$1
MODE=$2
Solut_per_batch=5000
OFFSET=(batch_id-1)*Solut_per_... |
6601a170f891a62d61b518f8759e55da12eb1b2efa2a1dbbd3ca4b8657d76043 | Shell | 552 | 24 | #!/bin/bash
#
# importruns.sh <basename> <run1_file> <run2_file>
#
# -imports functional runs into current directory and names them as
# basename1 basename2 ...
# - uses fslmaths for copying, setting output data type to float
# -writes list of imported file names into runs.txt
fBase=$1
inFileNames="${@:2}"
i=0
> ${f... |
df9fca548c0eb9aa1e268635917675d3dff5399c2bdf6338134fd68dec35a2af | Shell | 553 | 14 | #!/bin/bash
#
# Add the time and date onto reports and timeline names
nf_pipeline=$1
## Get current date ##
_date=$(date +"%d_%m_%Y")
_time=$(date +"%H:%M:%S")
## Appending a current date from a $_now to a filename stored in $_file ##
timing="${_date}-${_time}"
## Run nextflow in background with dated timeline and r... |
eeee7459e80ee2cb3e6e81fc5c296cb4d03feb417784ad785266c3753e6b5a1f | Shell | 553 | 15 | #!/bin/bash
#BSUB -J count_reads[1-2034]
#BSUB -o count_reads_peaks.out
#BSUB -e count_reads_peaks.err
#BSUB -We 5
#BSUB -q vshort
source activate ATACseq_preprocess
bampath=../../input/sc-bams_nodup/
dirlist=(`ls $bampath*.bam`)
# echo ${dirlist[$LSB_JOBINDEX-1]}
mkdir -p count_reads_peaks_output
echo ./count_reads_... |
f1619ed2fbd14dbc0b76947b8f453767a6eeec47e009b34a937b6243a7251f53 | Shell | 554 | 16 | #!/bin/bash -l
#SBATCH --job-name=model_build
#SBATCH --time=1:00:00
#SBATCH --account=proj83
#SBATCH --partition=prod
#SBATCH --mem=0
#SBATCH --exclusive
#SBATCH --constraint=cpu
module purge
module load unstable
source /gpfs/bbp.cscs.ch/home/pokorny/ReWiringKernel/bin/activate
connectome-manipulator build-model $1 $... |
c45ad11d7ca3135227a826c2ff753cf0f82526c32c7dc01fc9b24c1c194ce56d | Shell | 556 | 26 | #!/bin/bash
#SBATCH --job-name=btmh5
#SBATCH --output=/home/users/surag/CS273B/model_zoo/stage1/log.txt
#SBATCH --error=/home/users/surag/CS273B/model_zoo/stage1/err.txt
#SBATCH --time=48:00:00
#SBATCH --partition=gpu,akundaje
#SBATCH --nodes=1
#SBATCH --mem=52G
#SBATCH --gres=gpu:1
#SBATCH --cores-per-socket=8
... |
6c454dad37bd74cffb9e08bf188dbb16af0d58fecde045a79c22e66816cb4f74 | Shell | 557 | 29 | #!/bin/bash
# step 1
docker run --rm -it \
-v /Users/sebastiandresbach/data/neurovascularCouplingVASO:/base nipy/heudiconv:latest \
-d /base/DICOM/sub-{subject}/ses-{session}/*.IMA \
-o /base/Nifti/ \
-f convertall \
-s 02 \
-ss 01 \
-c none \
--overwrite
# step 2
# make heuristics file
# step 3
docker run --rm -... |
d581ae8cb12f9ee784053e90b69ddbb48c7abfb9e3858b78a46126d5a39f6150 | Shell | 557 | 14 | #!/bin/bash
#
# Add the time and date onto reports and timeline names
nf_pipeline=$1
## Get current date ##
_date=$(date +"%d_%m_%Y")
_time=$(date +"%H:%M:%S")
## Appending a current date from a $_now to a filename stored in $_file ##
timing="${_date}-${_time}"
## Run nextflow in background with dated timeline and r... |
16e6da3aba017a3e01622c6df219a6a3774a131d5fa56827abeecfc96eddf711 | Shell | 558 | 25 | #! /bin/sh
cd tests
. ./compat.sh
sort -k2,2 > ${pref}.md5sum <<EOF
46c5d23c3560cf908fea997fff8abc1c ${pref}.histo
46c5d23c3560cf908fea997fff8abc1c ${pref}_q@.histo
d41d8cd98f00b204e9800998ecf8427e ${pref}_qi.histo
4faa0517f41d7dc808ec0b930fe0d88e ${pref}_qC.histo
EOF
count_histo () {
PREFIX=$1
shift
$JF... |
251db89c53283e01df0b2292818f51da861a5a50a1aa534b5404b2a2ad486618 | Shell | 558 | 16 | #!/bin/bash -l
#SBATCH --job-name=struct_comp
#SBATCH --time=1:00:00
#SBATCH --account=proj83
#SBATCH --partition=prod
#SBATCH --mem=0
#SBATCH --exclusive
#SBATCH --constraint=cpu
module purge
module load unstable
source /gpfs/bbp.cscs.ch/home/pokorny/ReWiringKernel/bin/activate
connectome-manipulator compare-connecto... |
00a474d78bf351b57112c2ccbdafa02fdf2b3720b0005450526abafc11e78f17 | Shell | 559 | 12 | SAVE_STATIC_DEPS="vtk_utils ensight_utils graph config_helpers utils sds alg tinyexpr miniz"
if [ -n "$CUDA_FOUND" ]; then
SAVE_STATIC_DEPS="$SAVE_STATIC_DEPS"
SAVE_DYNAMIC_DEPS="cudart"
fi
CHECK_CUSTOM_FILE
COMPILE_SHARED_LIB "default_save_mesh" "save_mesh_helper.c save_mesh.c ${CUSTOM_FILE}" "save_mesh_helper.... |
2110ac676f698470a91868b4a96bac0b469c1fec445cd25d5c974759f35cb95d | Shell | 560 | 19 | #!/bin/bash
#
# boldcorrect.sh <basename> <shiftFraction>
#
# - does bold correction of VASO by dividing nulled volumes by time shifted notnulled volumes
# - shiftFraction is shift relative to TR (usually a positive number)
fBaseName=$1
shiftFraction=$2
export FSLOUTPUTTYPE=NIFTI
# shift notnulled (BOLD)
slicetimer ... |
98d8f013c678b6e15d7682ff2c941b4321533bf329540b3e196b3f54c7812bb4 | Shell | 560 | 22 | #!/bin/bash -l
#
#SBATCH --nodes=1
#SBATCH --gres=gpu:a100:1
#SBATCH --partition=a100
#SBATCH --job-name=JETS_0.7mm_21dir
#SBATCH --time=23:59:59
#SBATCH --mail-user=zgtan@med.umich.edu
#SBATCH --mail-type=ALL
#
# do not export environment variables
#SBATCH --export=NONE
unset SLURM_EXPORT_ENV
module load cuda
module... |
f93399b1009888c75173c4df4514eff1807aac56924bb37ad12d107b0b476e81 | Shell | 560 | 13 | #!/bin/bash
echo "Start"
nvidia-smi -pm 1 #enable persistence mode
#nvidia-smi -q -d SUPPORTED_CLOCKS #check supported clocks, not all gpu support custom clocks, we used 3090.
nvidia-smi -lgc 1935 # set gpu clock to 1935 MHZ
nvidia-smi -lmc 810 # set memory clock to 810 MHZ
#nvidia-smi -lmc 9751 # set memory clock to 9... |
27d090d5511ccc76f2a99784942fa9e08c88fd93e343b58d4bfeef60f999b860 | Shell | 561 | 14 | #!/bin/bash
#
# Add the time and date onto reports and timeline names
nf_pipeline=$1
## Get current date ##
_date=$(date +"%d_%m_%Y")
_time=$(date +"%H:%M:%S")
## Appending a current date from a $_now to a filename stored in $_file ##
timing="${_date}-${_time}"
## Run nextflow in background with dated timeline and r... |
714300a42f47c8a5bda2d1cab5177738c0739becf6cae3aad89bab9c6de7afd2 | Shell | 562 | 17 | #!/bin/bash
dataset=$1
tract_list=$2
inputarray=()
while IFS= read -r line; do
inputarray+=("$line")
done < "${tract_list}"
# Get the tract for this SLURM array task
tract_name="${inputarray[$SLURM_ARRAY_TASK_ID]}"
# Run the R script for the specific dataset and tract
singularity run --cleanenv /cbica/projects... |
27d173590ab537b62827883e5b008e4e33f5eebe4a3627dc7b7d5a5cdd37a81a | Shell | 564 | 18 | #!/usr/bin/env bash
# Usage: ./get_ont_stats.sh
source ~/.bash_profile
module load miniconda/4.12.0
LRA=/net/eichler/vol28/projects/long_read_archive/nobackups
SCRIPT_PATH=/net/eichler/vol28/software/pipelines/compteam_tools/get_ont_stats.py
for cohort in pop clinical nhp; do
declare -a sample_array=($(ls -d ${LRA... |
a6dfcabebdad476369b8d55eed7d0b92e565f68023f554a98b511f04099f6ac3 | Shell | 564 | 16 | #!/bin/bash
for contrast in "motor" "ffa" "vwfa" "shape1" "shape3" "all_shapes"; do
python 03b_inflated_plots.py --task=category --contrast=$contrast &
python 03b_inflated_plots.py --task=category --contrast=$contrast --kids &
done
for contrast in "geom_theory" "geom_behavior_online" "geom_behavior_scanner"; do
... |
b6da867ef9c3b99849c967785209b39a0f86c4d803ac674fe336b0e85c25d002 | Shell | 564 | 18 | #!/bin/bash
set -e
#Tests each component of the demo
cd demo/markerless_mouse_1/
com-train ../../configs/com_mouse_config.yaml --epochs=3
dannce-train ../../configs/dannce_mouse_config.yaml --epochs=3
dannce-predict ../../configs/dannce_mouse_config.yaml
cp label3d_dannce.mat alabel3d_dannce.mat
com-predict ../../conf... |
1f7e2a939ff1101fbef86db250415b7de4c2db89f2b94619b55da84686eb8f03 | Shell | 566 | 24 | #!/usr/bin/env bash
set -x
PARTITION=$1
JOB_NAME=$2
CONFIG=$3
CHECKPOINT=$4
GPUS=${GPUS:-4}
GPUS_PER_NODE=${GPUS_PER_NODE:-4}
CPUS_PER_TASK=${CPUS_PER_TASK:-5}
PY_ARGS=${@:5}
SRUN_ARGS=${SRUN_ARGS:-""}
PYTHONPATH="$(dirname $0)/..":$PYTHONPATH \
srun -p ${PARTITION} \
--job-name=${JOB_NAME} \
--gres=gpu:${GP... |
6e4bf9b919277b8b4cd151c44c470bad9442b3b49a19e77135b6cb77a3f27b0e | Shell | 566 | 20 | #!/bin/bash
# PediatricOpenTargets 2021
# Yuanchao Zhang
set -e
set -o pipefail
# This script should always run as if it were being called from
# the directory it lives in.
# copied from the run_in_ci.sh file at
# <https://github.com/AlexsLemonade/OpenPBTA-analysis/blob/master/scripts/>
script_directory="$(perl -e 'us... |
3fdc02271bcb7503863dc3a634d125026ffa437c08b76c74ac2d64490750aea6 | Shell | 569 | 17 | #!/bin/sh
##
# push.sh
#
# Run this from the $BOWTIE2_HOME/doc/website subdirectory.
#
# Copies the files that comprise the website at
# http://bowtie-bio.sourceforge.net/bowtie2 to sourceforge. You must
# have the right sourceforge privileges to do this. The SF_USER
# environment variable must be set appropriately.... |
405c4fb7113e1b3fc89e461c83e46eebfd471d513e0e7b4718cc86e0d7da2319 | Shell | 569 | 11 | #!/bin/bash
#SBATCH --account account_name
#SBATCH --mem 32G
#SBATCH -t 24:00:00
R -e "bayesReact::bayesReact_parallel(lst_data = list(FC_rank = \"/path/to/FC_rank.rds\",
motif_probs = \"/path/to/motif_probs.rds\",
motif_co... |
ea46939af1b2810a4a0747c5958cdea7f0b264a5740bbbe2dc7abdc86c616666 | Shell | 569 | 18 | mypython=$1
$mypython $MARINE/marine.py \
--bam_filepath \
$MARINE/tests/singlecell_tests/bams/9_3000526_only_5_cells.bam \
--annotation_bedfile_path \
$MARINE/annotations/cellranger-mm10-3.0.0.annotation.genes.bed \
--output_folder \
$MARINE/tests/singlecell_tests/only_5_cells_all_cells_coverage_test \
--min_dist_fro... |
2b4d990f2ebdc9793663f1e7df85820acbd0a83bab0a20a922c253aa56e5360a | Shell | 573 | 26 | #!/bin/bash
set -eux
scriptdir=$(dirname "$0")
function compile_function()
{
local funcName="$1"
shift 1
local outdir="$scriptdir"/Compiled_"$funcName"
mkdir -p "$outdir"
"$MATLAB_HOME"/bin/mcc -m -v "$funcName".m "$@" -d "$outdir"
}
#addpath() adds to the front, while -I adds to the back, so rev... |
d650eab0dd45d7a6bb96d4a8c0a30bef0d8f4429f20a4676b1b698e48982422f | Shell | 574 | 17 | #!/bin/bash
echo $(date +"%Y-%m-%d %H:%M:%S")
for dataset in cifar100 imagenet
do
for model in snn_resnet18 snn_resnet50 snn_vgg16
do
for batchSize in 16 32 64 128
do
out_file="ncu_profile/"${dataset}_${model}_${batchSize}.txt
echo "start to get "$out_file
sudo rm -rf $out_file
sudo ncu --metrics dra... |
08dc4b491f850100285bcca5862fa3a6761890dfe3bb0b60de29f0df044ef10d | Shell | 576 | 13 | eval "$(/pollard/home/sdrusinsky/miniforge3/bin/conda shell.bash hook)"
source /pollard/home/sdrusinsky/miniforge3/bin/activate test_pt231
cd "$(dirname "${BASH_SOURCE[0]}")" #cd into the directory containing this script
cd .. #cd into `code` directory
script_path=./select_drivers_enformer.py
driver_method=forward_se... |
f36f01120c6e8f77ac47ee1eb8d58ca95a1a0e6d79f784b2a745a3e2c6022dc6 | Shell | 576 | 25 | #!/bin/bash
#SBATCH --account=def-rfm
#SBATCH --gres=gpu:1
#SBATCH --cpus-per-task=16
#SBATCH --mem=12G
module load python/3.8 blender/2.92 scipy-stack
## initialize variables
idstart=$1
idend=$2
IMAGEDIR=$3
scriptfile=$4
renderer=$5
counts=$6
archiv=$7
for imgid in $(seq $idstart 1 $idend)
do
## First render
ble... |
9c773d5cd9df440a2a146470e89b6fb8a79c51947b1d524b7e144872b4875959 | Shell | 577 | 23 | K=10
H=512
CUDA_VISIBLE_DEVICES=0 \
python run_pt.py \
--seed 12345 \
--noise_ratio 0.05 \
--noise_type mut \
--gnn egnn \
--gnn_config src/config/egnn.yaml \
--gnn_hidden_dim $H \
--plm facebook/esm2_t33_650M_UR50D \
--cath_dataset data/cath/cath_k$K \
--c_alpha_max_neighbors $K \
... |
d079d33880ce2fcb223538e090187bcc95e22edf30a1bc8c19d53d0d60226d00 | Shell | 577 | 17 | #!/bin/bash
dataset=$1
tract_list=$2
scalar=$3
inputarray=()
while IFS= read -r line; do
inputarray+=("$line")
done < "${tract_list}"
# Get the tract for this SLURM array task
tract_name="${inputarray[$SLURM_ARRAY_TASK_ID]}"
# Run the R script for the specific dataset and tract
singularity run --cleanenv /cbic... |
8510ff930bf846d0aa9b7b50ac113c89e0909191e0c7ffaf4f5b0f63ddbc33e0 | Shell | 578 | 17 | #!/bin/bash
dataset=$1
tract_list=$2
scalar=$3
inputarray=()
while IFS= read -r line; do
inputarray+=("$line")
done < "${tract_list}"
# Get the tract for this SLURM array task
tract_name="${inputarray[$SLURM_ARRAY_TASK_ID]}"
# Run the R script for the specific dataset and tract
singularity run --cleanenv /cbic... |
78d03fb62593c0a455cbe8e4a18aff4f19d68ac8263b8e8a46f550d5dc42198b | Shell | 580 | 10 | # 1. Get the list of files from the remote server and save it locally
files=$(ssh yroussel@bbpv1.epfl.ch "ls /gpfs/bbp.cscs.ch/data/project/proj84/csaba/aibs_10x_mouse_wholebrain/results/density_calculations/scaled_nrrd_CCFv3a")
# 2. Sample 10 evenly spaced files from the list
sample_files=$(echo "$files" | awk 'NR % ... |
873157bbec06ee12cf0ba12e391a3c73b28608ca3e5dff3f094c23dba5e8e157 | Shell | 582 | 19 | #!/bin/bash
#SBATCH --job-name=parallel_knn
#SBATCH --partition=compute
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --array=1-11
#SBATCH --mem=64G
#SBATCH --time=07:00:00
#SBATCH --cpus-per-task=1
#SBATCH --output=./outputs/parallel_knn.o%j
#SBATCH --error=./error/parallel_knn.e%j
source /etc/profile.d/conda.sh
#eva... |
f95a23962007ace85c7f979a668e62e0a0236b2eed4931e17430ace6a355790b | Shell | 582 | 15 | #!/bin/bash -e
source config.sh
docker build -t ${image_name}:${version} -f Dockerfile-${version} .
# hack: comment the ENTRYPOINT and CMD lines to make it work for cromwell
# this will generate `Dockerfile.cromwell` and build it under the name `cromwell-${image_name}:${version}`
# https://github.com/broadinstitute/... |
220629e417e0e423137a04c1cd679b948fdf25cc371d05dcbf01323a8b21cebd | Shell | 583 | 24 | #!/bin/bash
# PediatricOpenTargets 2022
# Eric
set -e
set -o pipefail
# This script should always run as if it were being called from
# the directory it lives in.
script_directory="$(perl -e 'use File::Basename;
use Cwd "abs_path";
print dirname(abs_path(@ARGV[0]));' -- "$0")"
cd "$script_directory" || exit
# Set u... |
149a10130bce95621ae96deda68674f23d3931e1f7e5272aed2bc22a330647b7 | Shell | 584 | 19 | #!/bin/bash
# PediatricOpenTargets 2021
set -e
set -o pipefail
# This script should always run as if it were being called from
# the directory it lives in.
# copied from https://github.com/AlexsLemonade/OpenPBTA-analysis/blob/master/scripts/run_in_ci.sh
script_directory="$(perl -e 'use File::Basename;
use Cwd "abs_p... |
414e507a83daceeac09905a4447caccf0612a856c2b83d3e3cd430708c9457bf | Shell | 584 | 31 |
# ==================== #
# Sorted Position Bins #
# ==================== #
python -m rscvp.statistic.persistence_agg.main_trial_avg_position \
-D 250916,250918,251018 \
-A YW102,YW071,YW109 \
-P ,, \
--region aRSC,aRSC \
--session close \
--used_session close \
--sort close \
-T spks \
--page ap_v... |
52b37949918e097bec57c200f50ebfd4308fc9d75b25236f49f86efa8ffc840a | Shell | 585 | 28 | #!/usr/bin/env bash
# Usage: ./run.sh 30
JOB_COUNT=$1
shift
DRMAA_ARGS=" -V -cwd -j y -o ./log -e ./log -l h_rt={resources.hrs}:00:00 -l mfree={resources.mem}G -pe serial {threads} -w n -S /bin/bash"
# Load the module where snakemake is installed
module load miniconda/4.12.0
# Make log directory
mkdir -p log
# Ru... |
b40340671a117833275204757e0916cb8f8ecf39c3a5ec8655833862e8f57686 | Shell | 587 | 26 | #!/bin/bash
#SBATCH --time=16:00:00
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --job-name=gnn_ddd_pars_est_model_train
#SBATCH --output=logs/gnn_ddd_pars_est_model_train-%j.log
#SBATCH --mem=16GB
#SBATCH --partition=regular
ml Python/3.8.16-GCCcore-11.2.0
source $HOME/venvs/eve/bin/activate
# Check if the correct n... |
3fde6723868f52bc9083937e41bb3cdd0b3caec9f6648a3e2f8cd159d8d0ce2f | Shell | 592 | 22 | #!/bin/bash
#$ -M mzarodn2@nd.edu # Email address for job notification
#$ -m abe # Send mail when job begins, ends and aborts
#$ -pe mpi-24 48 # Specify parallel environment and legal core size
#$ -q debug # Specify queue
#$ -N genomeGenerate # Specify job name
module load bio/star/2.... |
0f12a0c7c3a88fb5fbb0141f98158f8002ecb62e3eef532aec05125538e0b54e | Shell | 594 | 18 | #!/usr/bin/env bash
# Usage: ./get_ont_stats.sh
source ~/.bash_profile
module load miniconda/4.12.0
LRA=/net/eichler/vol28/projects/long_read_archive/nobackups
SCRIPT_PATH=/net/eichler/vol28/software/pipelines/compteam_tools/get_pb_stats.py
for cohort in pop clinical nhp; do
declare -a sample_array=($(ls -d ${LRA}... |
b61c317d3acf4551867c52925ce0ce7eed6d5c45ecb8aa4d79928109ecaa2be5 | Shell | 594 | 24 | #!/bin/bash -l
#
#SBATCH --nodes=1
#SBATCH --gres=gpu:a100:1
#SBATCH --partition=a100
#SBATCH --constraint=a100_80
#SBATCH --job-name=zsssl
#SBATCH --time=16:59:59
#SBATCH --mail-user=zgtan@med.umich.edu
#SBATCH --mail-type=ALL
#SBATCH --output=%x.%j.out
#
# do not export environment variables
#SBATCH --export=NONE
un... |
a16c4e43ae320b42b9f70a21425828334fecd8076f695a3003a3f96945a616aa | Shell | 595 | 11 | #!/bin/bash
# It only runs FROM Elias' local TO server rn
read -p "Enter subj num(s) to upload with no leading 0s (but with spaces): " SUBJ_NUMS
for SUBJ_NUM in ${SUBJ_NUMS[@]}; do
printf -v SUBJ_NUM_4D '%04d' $SUBJ_NUM
# can't scp into symlinked folders, must go to the original
scp ~/OneDrive\ -\ Emory\ Univ... |
aff6eca5185e4e9802742432f64fd794b3dd8dcce77926af26c9e10d392adf36 | Shell | 595 | 27 | #!/bin/bash
#SBATCH --time=02:00:00
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --gpus-per-node=1
#SBATCH --job-name=gnn_bd_poly_val_diffpool
#SBATCH --output=logs/gnn_bd_poly_val_diffpool-%j.log
#SBATCH --mem=64GB
#SBATCH --partition=gpu
ml Python/3.8.16-GCCcore-11.2.0
source $HOME/venvs/eve/bin/activate
# Check if... |
d32f17b59c4eaeeedd5538570c55172c706e20280e22a64d530a722f8461ea58 | Shell | 595 | 18 | #!/bin/bash
# Ultralytics 🚀 AGPL-3.0 License - https://ultralytics.com/license
# Download latest models from https://github.com/ultralytics/assets/releases
# Example usage: bash ultralytics/data/scripts/download_weights.sh
# parent
# └── weights
# ├── yolov8n.pt ← downloads here
# ├── yolov8s.pt
# └── ..... |
99defc428af914a57c6d89182f52329c396ad9f0a2f2edabae4b0c420f813a83 | Shell | 597 | 27 | #!/bin/bash
#SBATCH --time=10:59:00
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --gpus-per-node=1
#SBATCH --job-name=gnn_ddd_pars_est_gps
#SBATCH --output=logs/gnn_ddd_pars_est_gps-%j.log
#SBATCH --mem=64GB
#SBATCH --partition=gpu
ml Python/3.8.16-GCCcore-11.2.0
source $HOME/venvs/eve/bin/activate
# Check if the cor... |
6874e4e6e18aa5f65fcf5b2af89c7eefe256818e283e87c121ffa63d8123584d | Shell | 599 | 21 | #!/bin/bash
# Author: Francois Aguet
set -euo pipefail
IFS=$'\n\t'
source_bam=$1
target_bam=$2
prefix=$3
output_bam=${prefix}.Aligned.sortedByCoord.out.patched.bam
bamsync ${source_bam} ${target_bam} -o ${output_bam}
samtools index ${output_bam}
# verify that both BAMs have same number of reads
nreads_in=$(samtools... |
944b8351ee700c3967aafb0f8b77e52209cd7580bcb3c8470c3ee62a53cbf4d4 | Shell | 600 | 15 | # install Julia and make sure it's in the PATH of the current shell
curl -fsSL https://install.julialang.org | sh -s -- --yes
# Julia startup file
mkdir -p ~/.julia/config
cp .devcontainer/julia_startup.jl ~/.julia/config/startup.jl
# Github CLI autocomplete (https://www.ajfriesen.com/github-cli-auto-completion-with... |
c68c841e1debdf610e660d82e3d4b2a065d3b36d24ea40ae13a244385ee83819 | Shell | 600 | 20 | #!/usr/local/fsl/bin/bash
# glm analysis for a simple [rest activation] x repeat paradigm
basename=$1
T_rest=$2
T_act=$3
TR=$(3dinfo -tr ${basename}.nii)
NumVol=$(3dinfo -nv ${basename}.nii)
run_duration=$(bc -l <<< "${TR}*${NumVol}")
ITI=$(bc -l <<< "${T_rest}+${T_act}")
3dDeconvolve -input ${basename}_preproc_bol... |
ba701d634a0a0b9b3bbc4b6b690cad148efc2d28ea0449bdfba2bc3c50fb5227 | Shell | 601 | 21 | #!/bin/bash
#
# This source code is licensed under the license found in the
# LICENSE file in the root directory of this source tree.
set -e
# Configure download location
DOWNLOAD_PATH="$BIOBERT_DATA"
if [ "$BIOBERT_DATA" == "" ]; then
echo "BIOBERT_DATA not set; downloading to default path ('data')."
DOWNLOA... |
6ee7e4fc311a7ee5310d8cb271a668ebf1bf0240e56a615c879db81cfa0eb8f9 | Shell | 602 | 20 | #! /bin/sh
cd tests
. ./compat.sh
sort -k2,2 > ${pref}.md5sum <<EOF
c448e173e5e18264ed00fad0008d5340 ${pref}.histo
554c9c76fb1f54f2c7526dd1af5aa252 ${pref}_lines.dump
174c7b3873c8aaa5ffee36d5d405bbce ${pref}.stats
EOF
echo "Counting 19-mers qmers, on ${nCPUs} CPU"
$JF count --quake --matrix seq10m_matrix_19 -m 19 -t... |
02f954bb214e0b63e328a997a7abcf3808d8c84784b6d01e9912ced597a42681 | Shell | 603 | 11 | # Run nucmer
nucmer --maxmatch -t 10 -c 100 -b 500 -l 50 tair10_chr4.fa.gz ler_chr4.fa.gz # Whole genome alignment. Any other alignment can also be used.
delta-filter -m -i 90 -l 100 out.delta > out.filtered.delta # Remove small and lower quality alignments
show-coords -THrd out.filtered.delta > out.filtered.... |
3838d689f93464930c24543304ae923f374d7b353d39e83690f80b7e8d8e54cf | Shell | 603 | 25 | #!/bin/bash
#SBATCH --time=6:00:00
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --job-name=gnn_bd_training
#SBATCH --output=logs/gnn_bd_training-%j.log
#SBATCH --mem=32GB
#SBATCH --partition=regular
ml Python/3.8.16-GCCcore-11.2.0
source $HOME/venvs/eve/bin/activate
# Check if the correct number of arguments is provi... |
efe2eedc461ac318f5e72d82a719d323f6bee819d717e245edaeff4a1e7906f9 | Shell | 605 | 26 | #!/usr/bin/env bash
# Usage: ./run_hifiasm.sh 30
JOB_COUNT=$1
shift
DRMAA_ARGS=" -V -cwd -j y -o ./log -e ./log -l h_rt={resources.hrs}:00:00 -l mfree={resources.mem}G -pe serial {threads} -w n -S /bin/bash"
# Load the module where snakemake is installed
module load miniconda/4.12.0
# Make log directory
mkdir -p l... |
1864d311425802d9c5693349ca153768f7a003af8920c7aa5e82b98c838faec4 | Shell | 606 | 15 | ############## TROVATO_2019 ##############################
MODEL_FILE_CPU="trovato_2019.c"
MODEL_FILE_GPU="trovato_2019.cu"
COMMON_HEADERS="trovato_2019.h"
COMPILE_MODEL_LIB "trovato_2019" "$MODEL_FILE_CPU" "$MODEL_FILE_GPU" "$COMMON_HEADERS"
##########################################################
############## T... |
ba637515c5c61e92e09dc49ff6bdf5fadd86cf088c89620ece2d133e3955d8f3 | Shell | 607 | 27 | #!/bin/bash
#SBATCH --time=05:00:00
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --gpus-per-node=1
#SBATCH --job-name=gnn_bd_pars_est_val_diffpool
#SBATCH --output=logs/gnn_bd_pars_est_val_diffpool-%j.log
#SBATCH --mem=64GB
#SBATCH --partition=gpu
ml Python/3.8.16-GCCcore-11.2.0
source $HOME/venvs/eve/bin/activate
# ... |
d9c0bae13c8d4690d70e8cbd6366c51c3be8ae6ecfae5324d07590f992e4f483 | Shell | 607 | 13 | #!/usr/bin/env bash
set -euo pipefail
cd ..
device=0
for lr in 0.02 0.01 0.005 0.002 0.001
do
python online_main.py --model_type RLIF --nb_epochs 100 --method esd-rtrl --nb_hiddens 1024 --devices "$device" --normalization none --lr $lr --lr_step_size 5 --etrace_decay 0.93 --nb_layers 3 --state_init rand --pdrop 0.1 ... |
50a27bfa9a4c392c975e129d652aab47ceb5fdaf80be1350a629e9d7fb7da277 | Shell | 608 | 20 | #!/bin/bash
# PediatricOpenTargets 2021
# Yuanchao Zhang
set -e
set -o pipefail
# This script should always run as if it were being called from
# the directory it lives in.
# copied from the run_in_ci.sh file at
# <https://github.com/AlexsLemonade/OpenPBTA-analysis/blob/master/scripts/>
script_directory="$(perl -e 'us... |
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