sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
348816278013dd74e6fb16945978c6e38b3fcd83f8adc371d22377b01e4f17ce | Shell | 2,593 | 98 | #!/bin/bash
#: Title : test_maskinv
#: Date : 2017-08-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../maskinv
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"... |
7c3f8ab5aa77d9815639d59055fe76a8b25967afadc567f2df21d5c651fa8fa0 | Shell | 2,597 | 85 | #!/usr/bin/env bash
# =============================================================================
# 06_extract.sh — Extract Lead / Novel Variants
# =============================================================================
# Extract genome-wide significant loci or novel variants (not in GWAS Catalog).
#
# Usage:
#... |
e5d9a103ce7f233cfb16f431b7df21369bc2f3f1ab534a1020a8e35879aa37ad | Shell | 2,598 | 81 | #!/usr/bin/env bash
# =============================================================================
# 03_liftover.sh — Genome Build Liftover
# =============================================================================
# Lift GWAS summary statistics from one genome build to another.
# If --qc is not specified, CLI ru... |
7e465fe3b685eeacf47cf069a01ed51233eb877e75c9dbcb15c628ab0943d54a | Shell | 2,600 | 87 | #!/bin/sh -e
# Genome name (in SnpEff's config file)
VER="GRCh38"
SUBVER="p7"
GENOME="$VER.$SUBVER.RefSeq"
# Path to scripts
SNPEFF_DIR="$HOME/snpEff"
SCRIPTS_DIR="$SNPEFF_DIR/scripts"
SCRIPTS_BUILD_DIR="$SNPEFF_DIR/scripts_build/data/$VER.RefSeq"
DB_DIR="$SNPEFF_DIR/data/$GENOME"
# File names
GFF_REF="ref_$VER.$SUB... |
a0127d6b81a00f9bf89747a4968ca533f88e2e4ecb055b54dc67bbe13f619031 | Shell | 2,604 | 60 | Rscript step2_SPAtests.R \
--vcfFile=./input/genotype_10markers_triallelic.vcf.gz \
--vcfFileIndex=./input/genotype_10markers_triallelic.vcf.gz.tbi \
--vcfField=GT \
--chrom=1 \
--minMAF=0 \
--minMAC=0.5 \
--maxMAFforGroupTest=0.01 \
--sampleFile=./i... |
843d703143028886aaab755ad7c281925b873318691fedefd620f60505ff300e | Shell | 2,607 | 122 | #!/bin/bash
set -e
export VFC_BACKENDS_SILENT_LOAD="true"
export VFC_BACKENDS_LOGGER="true"
run() {
local TYPE=$1
local TEST=$2
local DEBUG_MODE=$3
local OPTIONS=$4
local LOG=log_${TEST}_${TYPE}
export VFC_BACKENDS="libinterflop_ieee.so ${DEBUG_MODE} ${OPTIONS}"
./test_options_${TYPE} 2>${... |
5fd7d7b526a0fd55791456c4e1004dd388dbef1686222066ac862b16e3b4643b | Shell | 2,609 | 57 | python launcher_scripts/run_from_config.py configs/marason/marason_gen_predict_train_nist20.yaml
python launcher_scripts/run_from_config.py configs/marason/marason_gen_predict_train_msg.yaml
# Assign intensities to prediction for next training run
# python data_scripts/dag/add_dag_intens.py \
# --pred-dag-path resu... |
a821a23501e03d2df22dcf80a62c796ee49064e5d46490eb3725963315117b89 | Shell | 2,611 | 89 | #!/bin/bash
#: Title : test_imgfrsmo
#: Date : 2016-09-16
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../imgfrsmo
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\... |
e32ef528cea55a17bae6befc3e7c6aaab09c24156e6bac77f629500cfac8a083 | Shell | 2,612 | 95 | #!/bin/bash
#: Title : test_dcmframe
#: Date : 2017-11-04
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../dcmframe
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\... |
d29b44c8a8a559d359101c14387027832b6c687c1046e28d72ffcd829906087f | Shell | 2,615 | 68 | #!/bin/bash
##bash script for creating a conda environment called perturb_seq with all necessary software, as well as scGPT model files
host=$(hostname)
if [[ $host =~ "gamma" ]]; then
echo "host is gamma"
source ~/miniconda3/etc/profile.d/conda.sh
else
echo "host is not gamma"
source ~/.bashrc
fi
##... |
b261c047cc5d028d7e93a72e1e5277b97c5e304d60818a999137601715ec824b | Shell | 2,616 | 84 | #!/bin/bash
#: Title : test_fit_suri
#: Date : 2025-08-27
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../fit_suri
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\... |
5a8517551cf4ab76a09061d5af76cd5951e49b85687f27de3667600d40c85ba1 | Shell | 2,622 | 71 | #!/bin/bash
# interflop_call(INTERFLOP_ROUND_DW_ID, ...) rounds a double-word number x + e
# with the PRISM backend.
#
# Validates:
# 1. RN at reduced precision: the low part e breaks a tie of x on the
# virtual grid, so the call rounds x + e and not x alone.
# 2. SR in binary64 and binary32: x + ulp/4 rounds ... |
6ea79891d486ff32cdf437cda2360c41dabb16d70b19f402e370aad8d56b0aa9 | Shell | 2,622 | 75 | #!/usr/bin/bash
# ==============================================================================
# ==============================================================================
# DEFINE ALL PATHS:
# ==============================================================================
# path to the current code folder:
# defi... |
37746c5d9b4d4484eec179fe652b28399dd9c0cc0d1ca934f211af249fe3d229 | Shell | 2,623 | 99 | #!/bin/bash
# This script builds portable minimap2 binaries using the Holy build box environment
# options:
# -b|-bits|--bits: 32 for 32 bits build (default 64)
# -d|-builddir|--builddir: top directory to build external software in (default ~/build/bin-$arch)
# -a|-all|--all: if 1 (default) all binaries are (re)build,... |
6d390733ea14a3be50c64febeb18b0316c4db9580e9a74f21360750a8f72f339 | Shell | 2,623 | 72 | #!/bin/bash
#
# A plug-in for the micapipe module 02_proc-func.sh that replaces the T1w-FUNC transform computation
# Uses a nonlinear SyN method with an initial translation step to align the images by their geometric center
#
# INPUTS:
# $1 : moving image
# $2 : fixed image 1
# $4 : prefix for output filen... |
25767aa88f5ba7c13ba5ce80ef599be2b89cfeb802ce6f4d0c51b6c457787353 | Shell | 2,628 | 60 | Rscript step2_SPAtests.R \
--vcfFile=./input/genotype_10markers_triallelic.vcf.gz \
--vcfFileIndex=./input/genotype_10markers_triallelic.vcf.gz.tbi \
--vcfField=GT \
--chrom=1 \
--minMAF=0 \
--minMAC=0.5 \
--maxMAFforGroupTest=0.01 \
--sampleFile=./i... |
8052f92fe42c995bc70d4ce4c65463485db6f02fe6bc3041318609821cca9791 | Shell | 2,648 | 82 | #!/bin/bash
#: Title : test_tac2nii
#: Date : 2021-11-11
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../tac2nii
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"... |
ed5ec480219c878a48bb18f2474dff4e4df62176415f132430e2ba9024064809 | Shell | 2,657 | 82 | #!/bin/bash
#: Title : test_e7evhdr
#: Date : 2014-09-23
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../e7evhdr
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"... |
e8e4310fa7146046a84ce6eabc0bf442dbeeddd2d9d2f172857ff2ad7c9eda41 | Shell | 2,660 | 81 | #!/bin/bash
#
#
# move FC connectomes around
#
# Inputs:
# $1 : source directory
# $2 : target directory
#
# note: files should conform to expected naming structure: e.g., sub-01_ses-1_func_space-conte69-32k_atlas-schaefer-400_desc-FC.txt
#
# 2021 Mark C Nelson, McConnell Brain Imaging Centre, MNI, McGill
#------------... |
a19b25f77c06f2eeb3963bcc0457c0250625722ae5ebb42eb2cfbd009df8b44c | Shell | 2,666 | 64 | #!/bin/bash
# Build one ISA variant of verificarlo/fuzzy:v2.6.0-pytorch2.2.1-<isa>.
#
# docker/pytorch/build.sh <sse2|sse4|avx2|avx512> [podman|docker]
#
# Two stages: Verificarlo v2.6.0 with PRISM's static kernels compiled for the
# variant's -march (Dockerfile.verificarlo), then PyTorch compiled with it
# (Dockerfi... |
1afd1c6dd53c5ffdda13de6631573e1b4596755c08b025fb84cfeb2b46ff0298 | Shell | 2,684 | 100 | #!/bin/bash
#: Title : test_asc2flat
#: Date : 2014-09-21
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../asc2flat
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\... |
7db510ab29f0e8ba7185af131f2026f7b76a2b395dce0bc2cd5c3e8d37a36a39 | Shell | 2,691 | 60 | #!/usr/bin/bash
# ==============================================================================
# SCRIPT INFORMATION:
# ==============================================================================
# SCRIPT: CREATE GROUP-LEVEL MRIQC REPORTS FOR A BIDS-STRUCTURED DATASET
# ONLY RUN AFTER ALL PARTICIPANT-LEVEL REPORTS ... |
2a656211dfb2b35a2f3d205bf1c42958238c2a4c24950fc9b5146a9494280e63 | Shell | 2,695 | 93 | #!/bin/bash
#: Title : test_imgki_big
#: Date : 2021-11-15
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../imgki
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"... |
786c1ae5ab6a8d3b8dd2990f7022623c75ce559064ad30eac423a57172dd17a6 | Shell | 2,697 | 93 | #!/bin/bash
#: Title : test_res2html
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../res2html
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\... |
251de5df0e574279748dbbf99b47f5d6c0cf366c77dad407dd33c875727ff999 | Shell | 2,704 | 110 | #!/bin/bash
cd ./data/logs
## Remove all `cet_training` custom logfiles
find . -name '*cet_training*custom.txt' -delete
## Remove unwanted logfiles
rm -f '3011h-stories_R1-20231130-160614-WYLBD.log'
rm -f '0212d-stories_R1-20231202-121637-OYMRK.log'
rm -f '0512a-stories_R1-20231205-091750-JZSCO.log'
rm -f '0712b-s... |
71fb3c1fb5eecffd1d5f9c5df4f1e1b2c7b551b007db3653146b32f6d2b245f4 | Shell | 2,706 | 107 | #!/bin/bash
echo !!! in common.sh
echo nargs: $#
echo args: $*
echo mydir: $mydir
echo arrayid: $SLURM_ARRAY_TASK_ID
if [[ x$mydir == x ]]; then
echo missing project diretory!
exit 1
fi
# default BD and STAGE
BD=11
STAGE=train
# parsing args from commandline
while [[ $# -gt 0 ]]; do
arg=$1;shift
args=(${arg/... |
dceed43dac64b96e07a454618030636927746b5ac2940716c2598bc1276757f0 | Shell | 2,718 | 98 | #!/bin/bash
# This script builds the genomecomb binaries using the Holy build box environment
# options:
# -b|-bits|--bits: 32 for 32 bits build (default 64)
# -d|-builddir|--builddir: top directory to build external software in (default ~/build/bin-$arch)
# -c|-clean|--clean: 1 to do "make clean" before building (def... |
752e8798f021ccc6320a76d9e1bbd064371f49c07bad58e0ad416d96b9402d88 | Shell | 2,719 | 98 | #!/bin/bash
cd ../..
# source ~/.bashrc
source ./scripts/utils.sh
source /fs1/software/modules/bashrc
module load loginnode
module load CUDA/11.2
module load cudnn/8.4.1-cuda11.x
export PYTHONUNBUFFERED=1
root_path="../../../.."
export PYTHONPATH="$(pwd)/$root_path/":$PYTHONPATH
finetune_model=$1
init_model=$2
da... |
185e6f169c713e74fb5ca3caacb62c22803d9c186dc0d905ecbdada63e8f3b69 | Shell | 2,725 | 51 | #!/bin/bash
# Training nnUNet on just the Zurich dataset
# define arguments for nnUNet
dataset_name="Dataset276_tSCICombinedSeed7"
dataset_num="276"
nnunet_trainer="nnUNetTrainer_2000epochs" # default: nnUNetTrainer
configuration="3d_fullres" # for 2D training, use "2d"
cuda_visible_devices=... |
72d715ee73c07e6090d7c3df03cdec966804b19d4aad2f57f10c61ad691cc4ee | Shell | 2,733 | 68 | #!/bin/bash
# Build verificarlo/fuzzy:<verificarlo>-x86-64-v<N> for one x86-64 level:
#
# docker/fuzzy/build.sh <v1|v2|v3|v4> [podman|docker]
#
# 1. The level's Verificarlo image, with PRISM's static kernels compiled for
# its -march (docker/pytorch/Dockerfile.verificarlo). Skipped when
# localhost/verificarlo/... |
cbf772d9385df563a6fb2eb427856a05fd4af153d3d4f470511987155d91c6ec | Shell | 2,739 | 64 | #!/bin/bash
#
# Combine subjects from sci-zurich and sci-colorado datasets into a single BIDS-like folder, example output:
#
# ├── derivatives
# │ └── labels
# │ ├── sub-5416 # sci-colorado subject
# │ │ └── anat
# │ │ ├── sub-5416_T2w_lesion-manual.json
# │ │ ├── sub-5416_T2w_lesion-m... |
63a8b9349cd28d25bd1c9730fef6b7b86cbe390bd4c2bba68302759446fac4c3 | Shell | 2,761 | 99 | #!/bin/bash
#: Title : test_tacdel
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../tacdel
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"
... |
e6b1d54e5dd151527f193d8945200d9357f835e82fdaf8259118fdd39d713311 | Shell | 2,785 | 91 | #!/bin/bash
#: Title : test_imgzavg
#: Date : 2022-02-09
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../imgzavg
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"... |
331f9607a33de46b3d96c18954fb5cc864ae665db16d9427eb25971f3afa7880 | Shell | 2,793 | 83 | #!/bin/bash
#: Title : test_extrapol
#: Date : 2014-10-05
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../extrapol
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\... |
c03fea24870b7b222dc0444d306757924b412bcb2e2bde1ced448ee5bb9a4041 | Shell | 2,798 | 94 | #!/bin/bash
#: Title : test_tacfr2x
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../tacfr2x
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"... |
85e85543a0667b719c1a75e81d551bc362aeca51c3d3651d2185de658a4af538 | Shell | 2,837 | 54 | #!/bin/bash
#PBS -q emconnectome
#PBS -l nodes=1:ppn=32 -n
#PBS -l walltime=03:00:00
#PBS -N em_lens_correction
#PBS -r n
#PBS -j oe
#PBS -o /allen/programs/celltypes/workgroups/em-connectomics/danielk/em_lens_correction/log/pbs.log
metafile=/allen/programs/celltypes/production/wijem/long_term/reference_2018_02_21_01... |
800cc65dc7d9fa34a8f0afd8847a9e785676f11bb9732353f0e0938c5e58eff3 | Shell | 2,842 | 91 | #!/bin/bash
#: Title : test_dftscale
#: Date : 2014-11-02
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../dftscale
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\... |
a7e148237edd6d7346b9acc1ea310fd35731e289291b01928944235bc50bc084 | Shell | 2,848 | 92 | #!/bin/bash
#: Title : test_fit_line
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../fit_line
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\... |
769c834ac5a45b56e7761f86dce55e39db863fd34a7f780982a90fa65d6337d8 | Shell | 2,851 | 93 | HTKTools=$1
HTKSamples=$2
NMIXMONO=$3
MINTESTMONO=$4
NPASSPERMIX=$5
# template for a prototype model should be in
# conf/simp.pcf
exp=exp
mkdir -p $exp
# generate a prototype model
echo proto > exp/protolist
(cd exp ; echo N | $HTKSamples/HTKDemo/MakeProtoHMMSet ../conf/sim.pcf)
$HTKTools/HCompV -T 1 -m -S data/... |
557b5e59b20a07b62ea11c84980e562126415341aad23fab990ec9d503465af0 | Shell | 2,855 | 89 | #!/bin/bash
PathToDropSeqTools=/home/goodwintracking/Genomics/Software/Drop-seq_tools-2.1.0
PICARD=/home/goodwintracking/Genomics/Software/Drop-seq-master/lib/picard-2.18.14.jar
WorkingDirectory=/mnt/LocalData/Genomics/VNC/20190709_analysis
DataLocation1=/mnt/LocalData/Genomics/VNC/20190709_analysis/RawData/190109_K0... |
33b4f4d091c70accc35740ca928487902528bab9b165014c17d8f2f2be96c285 | Shell | 2,856 | 78 | #!/bin/bash
#
# Process data.
#
# Usage:
# ./process_data.sh <SUBJECT>
#
# Manual segmentations or labels should be located under:
# PATH_DATA/derivatives/labels/SUBJECT/<CONTRAST>/
#
# Authors: Julien Cohen-Adad
# The following global variables are retrieved from the caller sct_run_batch
# but could be overwritten ... |
a8859f4a70f91776252277f79d0030fa0fc4fb8ca75caa2f6bff46fa097e4fa2 | Shell | 2,856 | 109 | #!/bin/bash
# This script builds portable sniffles binaries using the Holy build box environment
# options:
# -b|-bits|--bits: 32 for 32 bits build (default 64)
# -d|-builddir|--builddir: top directory to build external software in (default ~/build/bin-$arch)
# -a|-all|--all: if 1 (default) all binaries are (re)build,... |
2a606c6ec09e7daf8ec8e2f43aee19929cf0188ffac5526bf3e45d487064e2bd | Shell | 2,876 | 102 | #!/bin/bash
#: Title : test_tac4frpl
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../tac4frpl
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\... |
1ec4d0e3dede368e76414dbbc1aa29b26fa8d5bd26971981b39b7cb4f1f8b6c8 | Shell | 2,882 | 85 | ########conda
# conda install multiqc
# conda install trim-galore
# conda install RSeQC
# conda install subread
# conda install hisat2
# conda install samtools
conda activate rna
module load alignments/hisat2-2.1.0
module load utils/samtools-1.9
module load stringtie-2.1.5
module load tools/subread-1.6.3
m... |
40f6cc837a8c7e182b031ae4f04d29b94e3bbbecc56d89a65e80d1717d3dc985 | Shell | 2,884 | 65 | #!/bin/bash
# $1 : path to sim_folder (eg "lite")
# $2 : path to synth config file
# $3 : name of cell_collection file of morphs to synthesize axons
# $4 : path to axon-projection out folder
deactivate > /dev/null; \
module purge; \
module load archive/2024-01 py-mpi4py; \
module load archive/2024-01 py-dask-mpi; \
\
e... |
24fb975d72d7c6f42b36b87c614b79d47bbadaf13126ad2df73f9ec46b2beb87 | Shell | 2,908 | 90 | #!/bin/bash -l
#SBATCH --account=the_tucanos
#SBATCH --partition=mlgpu_long
#SBATCH --job-name=ViTucano-pretraining
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=8
#SBATCH --threads-per-core=1
#SBATCH --cpus-per-task=16
#SBATCH --time=7-00:00:00
#SBATCH --gres=gpu:a40:8
#SBATCH --exclusive
source /lustre/mlnvme/data/the... |
0fc3fbfd587711f3aa548550b76550dfa889af9eb314b9d9501600c4eed41042 | Shell | 2,913 | 82 | #!/bin/bash
# Training nnUNet on just the Zurich dataset
path_data_dir=$1
# get the base name of the path_data_dir
dataset_name=$(basename $path_data_dir)
if [ $dataset_name == "Dataset901_tumMSChunksRegion" ]; then
# site="muc_stacked_lesion"
site="muc_lesion_chunk-3"
training_type="single-channel"
... |
dfe836f75e1db00f1271fa167ab02a74da43a205a8a2b4fd9e6f8b56ffcdfaec | Shell | 2,936 | 85 | #!/usr/bin/env bash
# Load and re-save a session, so that trash files and/or customTrash tables can be moved
# to the locations specified by hg.conf's sessionDataDir and sessionDataDbPrefix.
HELP_STR="usage: sessionDataConvert.sh userName sessionName
Both userName and sessionName must be %-encoded as they are in name... |
a8270a11acc1d7e7844dffbd0c601c49ebb5c7b987c347e8ba56cfe6e56a59bd | Shell | 2,945 | 95 | #!/bin/bash
#: Title : test_fit_xsur
#: Date : 2019-02-17
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../fit_xsur
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\... |
3e9b81729622e9e8f3c7c662f23cdc873a0868e303d75a0190262468a62d16d1 | Shell | 2,960 | 68 | #!/bin/bash
echo "Choose your task"
select task in "classification" "regression"; do
break;
done
echo "You have selected $task task"
echo "Choose your finetune model"
select finetune_model in "only_geometry" "geometry_cm5_wiberg" "geometry_espc_wiberg" "geometry_hirshfeld_wiberg" "geometry_npa_wiberg" "cm5_wiberg... |
abb8f85d29767b7cb2e58d4ce41a310ba020b5c366512f2df85122f1bbab770a | Shell | 2,984 | 92 | #!/bin/bash -l
#SBATCH --account=the_tucanos
#SBATCH --partition=mlgpu_long
#SBATCH --job-name=ViTucano-sft
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=8
#SBATCH --threads-per-core=1
#SBATCH --cpus-per-task=16
#SBATCH --time=7-00:00:00
#SBATCH --gres=gpu:a40:8
#SBATCH --exclusive
source /lustre/mlnvme/data/the_tucanos... |
cf877870205b80b89e637838bbb3f133aa051fb1de228a2e9487e43cd79beed9 | Shell | 2,985 | 81 | #!/bin/bash
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --time=01:00:00
#SBATCH --job-name=daskml
#SBATCH --mem=40G
#SBATCH --signal=B:SIGUSR1@120
#SBATCH --mail-type=end
#SBATCH --... |
70273f79f97d1dfa29cc70e5ccc26a698527d16fad1cffab6c00331a4d6d911a | Shell | 2,986 | 96 | #!/usr/bin/env bash
# =============================================================================
# 08_utility.sh — Utility Subcommands
# =============================================================================
# Examples of GWASLab's utility subcommands:
# version — show installed version
# config ... |
7d69b3c7a57a7ad5fd2349a5ffd5da7ee77542405ecd09bd6adde0ab204f6c60 | Shell | 2,995 | 64 | # Zeiss
OUTDIR='/home/miguel/Projects/smlm_z/publication/models/zeiss_green_beads/out2_1'
# PX_SIZE=106;
# ZSTEP=10;
NUP_OUTDIR='out_bac_1'
DEFAULT_LOCS='/media/Backup/smlm_z_data/20240606_bacteria_Miguel_zeiss/FOV1/storm_3/storm_3_MMStack_Default.ome_locs_alt.hdf5';
DEFAULT_SPOTS='/media/Backup/smlm_z_data/202406... |
a8c8fa8ba079f2f8b7a7129da0c01e58b493f9c9497bdc85f27839005945809d | Shell | 3,022 | 100 | #!/bin/sh -e
#-------------------------------------------------------------------------------
#
# Example on how to annotate human variants using SnpSift
# Note: It is assumed that the organism is "human"
#
# Pablo Cingolani 2012
#--------------------------------------------------------------------------... |
9408b523d8a5d99d59944f19d13a9cb64b5fefacd6f5e11d47378cfb740a6baa | Shell | 3,024 | 67 | #!/usr/bin/env bash
# Copyright 2020 The HuggingFace Team. All rights reserved.
#
# 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 r... |
bafbdedd63043e63c5861e45c04858088ec12f13d834ffd2c35edf8341213c71 | Shell | 3,030 | 70 | #!/usr/bin/env bash
# Copyright 2020 The HuggingFace Team. All rights reserved.
#
# 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 r... |
fc30aecbc3eb55dccfb0748adb740bcc7115a4a19aec5b926891b5203a6ad17e | Shell | 3,033 | 121 | set -e
bash get_gm12878.sh 100000 22
bash get_gm12878.sh 10000 22
BEDPATH=hic_data/GM12878_combined_22_10kb.bed
#Chromosome3D
#create input
#INPUT_PATH=Chromosome3D/input/GM12878_combined_22_10kb.txt
#if [ ! -e $INPUT_PATH ]
# then
# python chromosome3d_input.py $BEDPATH $INPUT_PATH
#fi
#rep 1
#perl Chromosome3D... |
66941e4605304ed2f1d8455255edab640171e8a23c05ac6b9c1a9a805b26ac30 | Shell | 3,040 | 97 | #!/bin/bash
#: Title : test_avgttac
#: Date : 2016-03-02
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../avgttac
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"... |
9ccedd1ee8897c2a64e9d647b18228bafa439a63cc64e1c070689e5093e629ad | Shell | 3,064 | 100 | #!/bin/bash
#: Title : test_sifcat
#: Date : 2016-11-24
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../sifcat
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"
... |
9bf8e553ffd9a77ca2263f0cbfe1ce6ccdc0c9dad2b6fbcfd7b3ed27f2ecad17 | Shell | 3,066 | 62 | #!/bin/bash
# Script extracts FreeSurfer measurements of precentral and postcentral gyri of all analyzed scans
# into .csv files containing measurements of all subject for specific hemisphere side and gyrus.
#
# Subject-specific results of all atlas-based regions of interest are stored in separate files:
# APARC=$SUB/s... |
59a7dd4098adf26cb50ffc85ca29b1b73fd52af59904b6a542bf9038f6fd783e | Shell | 3,092 | 98 | #!/bin/bash
#: Title : test_o2_p2w
#: Date : 2016-02-17
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../o2_p2w
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"
... |
d86b025268891ed733cc32273bd5812227b93a10ab7fdbd981e92817a3ac93fb | Shell | 3,092 | 94 | #!/bin/bash
#: Title : test_lhtest
#: Date : 2023-04-14
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../lhtest
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"
... |
e7a9539fc111d61bd190eacbddc713e66668f6ec6513e2fe9298460d98ceba38 | Shell | 3,097 | 57 | #!/bin/bash
#SBATCH -A p20023
#SBATCH -p short
#SBATCH -N 1
#SBATCH -n 2
#SBATCH -t 04:00:00
#SBATCH --mem=20G
#SBATCH --mail-user=viriyakeo2023@u.northwestern.edu
#SBATCH --mail-type=END,FAIL
#SBATCH --job-name=z_apa
#SBATCH -o "%x.o%j"
source ~/.bashrc
conda activate peakachu
h="/projects/p20023/Viriya/analysis/fo... |
a739420645a1ac510d9e7606b7cbc4309d94f4db1ec46346144cd19c4e3b1c65 | Shell | 3,098 | 100 | #!/usr/bin/env bash
# This script installs a dedicated Miniconda (not added to $PATH), installs
# ReproZip and runs `reprozip trace ...` on an arbitrary number of commands.
#
# This script accepts an arbitrary number of arguments, where each argument is
# a command to be traced. It is recommended to initialize an envi... |
71fd36fc2273b519ea49dbe12fa6fd0dc8770aa270f6bdb1a39d12580acecd6f | Shell | 3,105 | 105 | #!/bin/bash
#: Title : test_rmcmnts
#: Date : 2016-11-25
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../rmcmnts
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"... |
0961eabcebc9864aa56657686fa26ed96c99eea037dfb615df42a4c19045eb0e | Shell | 3,114 | 51 | #!/bin/bash
#SBATCH -N 1 # use 1 node
#SBATCH -n 1 # 1 task
#SBATCH --cpus-per-task 4 # cpu cores to use
#SBATCH -t 2-00:00:00 # 0 days, 6 hours, 0 minutes, 0 seconds
#SBATCH -p gpu_batch # use the gpu partition
#SBATCH -J RetroDiffusion # Job nam... |
37663e363e682dfc6a2524184bcb727dab354a09793579b592b4062c205dd03d | Shell | 3,117 | 108 | #!/bin/bash
# Test that the arithmetic of vectorized floating-point reductions
# (llvm.vector.reduce.fadd/fmul) is instrumented:
# - no fixed-width reduction intrinsic is left in the instrumented IR,
# - MCA and PRISM results vary across runs,
# - the IEEE backend reproduces the native result bit for bit (the
# ... |
eef6507888a7330b398cab942cc12fb23d3a1afd1476da850669dea18e913b7f | Shell | 3,122 | 54 | #!/bin/bash
#
# Useful for getting location of raw & derivative data, as well as code related to the MWC project
# Defines several variables that can be used to quickly access materials
#
# Input:
# $1 : subject numeric ID (2 digit e.g., 01, 10, 25, etc)
# $2 : session numeric tag (1 digit: 1 or 2)
#
# 2023 Mark C Ne... |
93aa63a1984ecc10a6a687f00b17a4133d4dd59cb999b3e695ee9d4395b72f98 | Shell | 3,123 | 112 | #!/bin/bash
# Test that loops auto-vectorized for SVE on AArch64 do not abort the
# instrumentation passes:
# 1. By default, verificarlo keeps the loop vectorizer on fixed-width
# vectors, so the vector operations are instrumented (MCA and PRISM).
# 2. When the user forces scalable vectors, compilation still s... |
97dd77a3b8691c71b33ea16717ee2d1e92dc0ed568fe954322c667659b2b2446 | Shell | 3,148 | 115 | #!/bin/bash
#: Title : test_e7to63
#: Date : 2016-11-02
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../e7to63
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"
... |
f31d50ca394facfb606f512a43b5cac1a30d518fa6c48c85d0203ceb24b24d9d | Shell | 3,150 | 123 | #!/bin/bash
# This script builds portable pigz binaries using the Holy build box environment
# options:
# -b|-bits|--bits: 32 for 32 bits build (default 64)
# -d|-builddir|--builddir: top directory to build external software in (default ~/build/bin-$arch)
# -a|-all|--all: if 1 (default) all binaries are (re)build, if ... |
a115a090543a623c476ab43362a53186527c6714b5e329949329b3b19059b165 | Shell | 3,162 | 91 | #!/bin/bash
# This script runs an infant brain morphometry pipeline using iBEATv2, infant FreeSurfer (iFS), and standard FreeSurfer (FS). The following pipeline assumes that iBEATv2 tissue segmentations have already been generated.
# 1. Runs FS up to step 15 (https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all#StepD... |
6f6eaa56324c376a8cd11c412d0664e9ed71ef4af81b9caf6576c03e9cf1d905 | Shell | 3,166 | 87 | #!/usr/bin/env bash
set -euo pipefail
ROOT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
BUILD_DIR="${ROOT_DIR}/build"
NEST_CONFIG="${NEST_CONFIG:-$(command -v nest-config)}"
if [[ -z "${NEST_CONFIG}" ]]; then
echo "nest-config not found. Set NEST_CONFIG or add nest-config to PATH." >&2
exit 1
fi
NEST_COMP... |
8aa8469adf14379df8cda68bbdbe5559a5a7bce208f673e12cfb177e7cb46cf6 | Shell | 3,193 | 104 | #!/bin/bash -l
#SBATCH --account=the_tucanos
#SBATCH --partition=sgpu_long
#SBATCH --job-name=filtering-gigaverbo
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=4
#SBATCH --threads-per-core=1
#SBATCH --cpus-per-task=32
#SBATCH --time=7-00:00:00
#SBATCH --gres=gpu:a100:4
#SBATCH --exclusive
source /lustre/mlnvme/data/the_... |
47d93ac6522e30286cd9adb1b6db74e7d17ae56892828e8b82ca7de5cd173fd9 | Shell | 3,197 | 56 | #!/bin/sh
set -e
# Generate Dockerfile using neurodocker 0.7.0
generate() {
docker run --rm neurodocker:local generate "$1" \
--base=ubuntu:bionic-20201119 \
--pkg-manager=apt \
--install "gcc g++ lsb-core bsdtar jq libopenblas-dev tree openjdk-8-jdk libstdc++6" \
--dcm2niix version=v1.0.20190902 me... |
7cde00d408d7ce4bba317f70ca923b7054d4c5c93ce39242ab11a65baa08804a | Shell | 3,201 | 107 | #!/bin/sh
# the next line restarts using tclsh \
exec cg source "$0" "$@"
# Script to download and prepare all reference databases (including genome) for sacCer3
# call using
# makedbs_sacCer3.sh ?options? ?dest? ?webcache?
# where
# * dest: the directory where the reference databases will be installed (default /comp... |
afa734bc74fc723905c05886914f7eb907aa73ec616e3cfe1c9afbc1b68f203f | Shell | 3,204 | 119 | #!/bin/bash
# This script builds portable gatk3 binaries using the Holy build box environment
# options:
# -b|-bits|--bits: 32 for 32 bits build (default 64)
# -d|-builddir|--builddir: top directory to build external software in (default ~/build/bin-$arch)
# -a|-all|--all: if 1 (default) all binaries are (re)build, if... |
48929459099f2bf2a4ec1bbe040d35626bf408940ffbb8c39be80ca6e9956593 | Shell | 3,205 | 109 | #!/bin/bash
#: Title : test_simelli
#: Date : 2023-02-20
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../simelli
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"... |
90eb8d56b97f9748e153d050b27b9feb9bac61983385344e4bdbe0e490a9cd3f | Shell | 3,205 | 115 | #!/bin/bash
#: Title : test_tacdelna
#: Date : 2018-06-06
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../tacdelna
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\... |
5769998ac0d0fbd37504f34be99be604244abcc260783cf3a5823284654d449d | Shell | 3,211 | 84 | #!/bin/bash
#
# A plug-in for the micapipe module 02_proc-dwi.sh that replaces the T1w-DWI transform computation
# Uses a nonlinear SyN method with 2 equally weighted fixed images
#
# INPUTS:
# $1 : moving image
# $2 : fixed image 1
# $3 : fixed image 2
# $4 : prefix for output filenames
# $5 : log filen... |
08bc36eac96264b11e266bb5cf7e47dd26a5d330a66e411f416b6d742fdc5170 | Shell | 3,217 | 121 | #!/bin/bash
# cd ..
source /fs1/software/modules/bashrc
module load loginnode
# module load CUDA/11.2
# module load cudnn/8.4.1-cuda11.x
module load CUDA/10.2
module load cudnn/8.0.5-cuda10.2
export PYTHONUNBUFFERED=1
root_path="../../../../../.."
export PYTHONPATH="$(pwd)/$root_path/":$PYTHONPATH
export CUDA_VISIBL... |
52b219a91b71ddf311e197352ef7bacbe1daeb9cae68be1ac303bb96bac09eab | Shell | 3,221 | 113 | #!/bin/bash
CURRENT_DIR=$(
cd $(dirname ${BASH_SOURCE:-$0})
pwd
)
cd $CURRENT_DIR
BUILD_TYPE="Debug"
INSTALL_PREFIX="${CURRENT_DIR}/out"
SHORT=r:,v:,i:,b:,p:,
LONG=run-mode:,soc-version:,install-path:,build-type:,install-prefix:,
OPTS=$(getopt -a --options $SHORT --longoptions $LONG -- "$@")
eval set -- "$OPT... |
66ce33d50a08ecfe10773c8761ca1d0a28c29d771542838137d90ae89c4bb815 | Shell | 3,232 | 108 | #!/bin/bash
#: Title : test_tacslope
#: Date : 2019-08-21
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
#: ToDo : Test all options.
# Set the name of executable to test
PROGRAM=../../tacslope
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: ex... |
a3c5d580d66ec07f9f9891be512388646dff3eb768f0e91cac9fe177d3a991e8 | Shell | 3,238 | 78 | #!/bin/bash
# ==============================================================================
# SCRIPT INFORMATION:
# ==============================================================================
# SCRIPT: DEFACING ANATOMICAL MRI DATA IN A BIDS DATASET
# PROJECT: SFGPI
# WRITTEN BY LENNART WITTKUHN, ADAPTED BY SAM HALL... |
7f789eed6ecf285d30259c91a5046c7162dc92ec5e134bae18758e5acf34d0ea | Shell | 3,250 | 103 | #!/bin/bash
#: Title : test_dftdblf
#: Date : 2019-12-20
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the exit status of a pipeline to the exit status of failed, not the last command in the pipeline
set -o pipefail
# Set the name of executable to test
PROGRAM=../../dftdbl... |
bb275ccca160275707bdeb532569165cc0977a3d136794d398382f338a605cfd | Shell | 3,261 | 105 | #!/bin/bash
cd ../..
# source ~/.bashrc
source ./scripts/utils.sh
source /fs1/software/modules/bashrc
module load loginnode
module load CUDA/11.2
module load cudnn/8.4.1-cuda11.x
export PYTHONUNBUFFERED=1
# echo "Choose your finetune model"
# select finetune_model in "only_geometry" "geometry_cm5_wiberg" "geometry... |
e8135c685cbd873a7ecf7c7a2fd27a35312a2bafce6537c3743a2de271275be0 | Shell | 3,261 | 86 | #!/bin/bash
#
# Make user information HTML pages of each of TPCCLIB applications that are found in ./bin folder.
# These are made by calling each program with option --helphtml.
# HTML files are placed in ./doc folder. Also a web page ./doc/index.html, containing download
# links and links to application docs, is c... |
d83f1accdbe97ea564b8104df07a6475cb4d56e247bb2cbc89b4d8bfb5b9cc76 | Shell | 3,282 | 71 | #!/usr/bin/env bash
# Copyright 2020 The HuggingFace Team. All rights reserved.
#
# 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 r... |
a8a2de90e809726b5d0a27216e9302bce04701a908bc62f8cb110eac41896767 | Shell | 3,285 | 109 | #!/bin/bash
#: Title : test_tacmultx
#: Date : 2014-10-05
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../tacmultx
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\... |
5a5e4913584957ace0b8b24a990e9e02f874fbb82d57a096689bb9012a752c0d | Shell | 3,315 | 89 | #!/bin/sh
#============================================================
# iso2mesh inline documentation to wiki convertor
#
# Author: Qianqian Fang <fangq at nmr.mgh.harvard.edu>
#============================================================
print_help()
{
awk '/^%/ {dp=1} /-- this function is part of iso2mesh/ {... |
3c4b87044910a5d0e5036a774becbe3791d07aa228679f29eda62c34e4ec71d0 | Shell | 3,319 | 99 | #!/usr/bin/env bash
set -u
SFTP_HOST="${SFTP_HOST:-iceberg-ms.mit.edu}"
SFTP_PORT="${SFTP_PORT:-2222}"
SFTP_USER="${SFTP_USER:-runzhong@mit.edu}"
SSH_USER="${SSH_USER:-coley-group}"
REMOTE_ROOT="${REMOTE_ROOT:-/home/coley-group/atlas_nist/h_plus_out_mgf}"
VIRTUAL_ROOT="${VIRTUAL_ROOT:-/nist23/h_plus}"
TARGET_DIR="${T... |
9aff9148dcc8edbed1ca2dc9c69fe6f3289b244d49ff1fe80e02daa1708fe42d | Shell | 3,322 | 70 | #!/bin/bash
#
# Runs NODDI on preprocessed diffusion data (micapipe preprocessing modules are run before this!)
# Requires Matlab, AMICO & MRtrix!
# See: AMICO_process.m
#
# INPUTS:
# $1 : SUBJECT (i.e. 01, 02, ... , 50)
# $2 : FUNCTION ID (DEPRECATED)
#
# OUTPUTS:
# See ${NODDI_DIR}, ${NODDI_DIR}/AMICO & ${NODDI_D... |
ed6b6a459d42f2efce4c0089720f57df6195f8bd4cb2bd15f4f7fbff21daf2e8 | Shell | 3,325 | 82 | #!/bin/bash
# Verify that no directory makefile overrides the compiler flags that
# inc/common.mk sets for the whole tree.
#
# hg/hgTracks/makefile carried "COPT = -ggdb" from 2019 to 2026. Every
# directory makefile includes inc/common.mk on its first line, so that
# assignment came after the tree default and silent... |
44704e9b0aec2c9fff2e59759a6b548be4ed3fd7cb308d08abe8b375693b3f45 | Shell | 3,341 | 89 | #!/bin/sh
#============================================================
# iso2mesh inline documentation to wiki convertor
#
# Author: Qianqian Fang <fangq at nmr.mgh.harvard.edu>
#============================================================
print_help()
{
awk '/^%/ {dp=1} /-- this function is part of iso2mesh/ {... |
786c394a74433dd208d19f2ce5f1f68036bb84e4ce46bc42f4ef3cbd1ac67c4d | Shell | 3,347 | 98 | #
# HTK script to train three state monophones
#
HTKTools=$1
# template for a prototype model should be in
# conf/simp.pcf
exp=exp
mkdir -p $exp
# generate a prototype model
cat << "EOF" > exp/proto
~o <VecSize> 39 <MFCC_E_D_A_Z>
~h "proto"
<BeginHMM>
<NumStates> 5
<State> 2
<Mean> 39
0.0 0.0 0.0 0.0 0.0 0.0 0.0 ... |
523339ca3761085abf1adef808e17691ff61baba03753615689abb1398d3985e | Shell | 3,353 | 113 | #!/bin/bash
#: Title : test_dftavg
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../dftavg
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"
... |
30875b49296136827705aa498b64beb8599b855cd6fb2af8efa49940773d543f | Shell | 3,354 | 113 | #!/bin/sh
# the next line restarts using tclsh \
exec cg source "$0" "$@"
# Script to download and prepare all reference databases (including genome) for dm6
# call using
# makedbs_dm6.sh ?options? ?dest? ?webcache?
# where
# * dest: the directory where the reference databases will be installed (default /complgen/ref... |
5c2574c95a66558af55b3a2a6239a24c3185105ebc8f62684025551b8fd7923a | Shell | 3,361 | 102 | #!/bin/bash
#
# Generate QCs for T2w images:
# - sagittal lesion QC
# - single slice sagittal spinal cord QC (to check FOV coverage (C/Th/L))
#
# Dependencies (versions):
# - SCT 6.0 and higher
#
# Usage:
# sct_run_batch -script generate_qc.sh -path-data <PATH-TO-DATASET> -path-output <PATH-TO-OUTPUT> -jobs <nu... |
22015ed0eed33a3bebd15cc99f9dad9b6e926eea1f61bc7b746b356e5fc5aa62 | Shell | 3,370 | 111 | #!/bin/bash
set -beEu -o pipefail
umask 002
# Given two directories: one containing files with URLs of files that need
# to be downloaded and the other as a destination for those files,
# perform the downloads. Locks are used to prevent multiple instances
# from colliding. On error, an error file is generated and th... |
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