sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
49680dc779f2b3eb1ba983eb071419c53cb02d265328494dd9d980f9460b5a61 | Shell | 6,391 | 215 | #!/bin/bash
### 1. set paths ###
## set parameter parsings for user-specified paths ##
usage="## this script calculates genome-wide window-based pairwise Reynolds Fst.\n
usage: bash $0 [-h/--help] [-w/--work_directory <path>] [-s/--dir_snp <path>]\n
[-m/--dir_mpileup <path>] [-c/--chr_assignment <path>] [-a/--sample_s... |
1437d58bbe4b9152cb9429b8f513ad9926e2bf21804e92621278052a63d3d499 | Shell | 6,447 | 197 | #MOLGENIS walltime=02:00:00 mem=4gb
#list SentrixBarcode_A,SentrixPosition_A
#string intermediateDir
#string resultDir
#string computeVersion
#string Project
#string projectJobsDir
#string projectRawTmpDataDir
#string intermediateDir
#string genScripts
#string pipeline
#string runID
#string logsDir
#string perlVersion
... |
54f9074a5c7ffe246e3631be601dee7f1b80187f174601e1f4ab1d394a636090 | Shell | 6,467 | 213 | #!/bin/bash -f
#*********************************************************************************************************
# Vivado (TM) v2018.2 (64-bit)
#
# Filename : system.sh
# Simulator : Xilinx Vivado Simulator
# Description : Simulation script for compiling, elaborating and verifying the project source files... |
80eaa38043e010cdcd1f4206942a22682dc1db306aed12769f9ae9070bb6e6ea | Shell | 6,511 | 159 | #!/usr/bin/env bash
# Written by Wu Jianxiao and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
# This function runs RF-ANTs vol2surf mapping creation and projection using 1 subject
RF_DIR=$CBIG_CODE_DIR/stable_projects/registration/Wu2017_RegistrationFusion
RF_SURF2VOL_DIR=$RF_DIR... |
d47a2bbdc39f1f2da56edc5c19fe95eeaf0f3c10d97b45652ad2aaadfaf33334 | Shell | 6,526 | 136 | #!/usr/bin/env bash
#
# bench_run.sh — one timed extractor config (one tool, one mode, one --parallel),
# repeated R times, emitting one CSV row per rep. Part of the full-dataset
# benchmark campaign (plans/05302026_extractor-fulldata-validation/PLAN.md).
#
# Captures, per rep:
# wall_s — GNU /usr/bin/time -v "... |
cde9e40b3fc5ce365702704faa7e7ef0aa211781b738d5f14d2c80b1c4d7d0cd | Shell | 6,555 | 220 | #!/bin/bash
### 1. set paths ###
## set parameter parsings for user-specified paths ##
usage="## this script calculates genome-wide window-based pairwise Reynolds Fst.\n
usage: bash $0 [-h/--help] [-w/--work_directory <path>] [-s/--dir_snp <path>]\n
[-m/--dir_syn_snp <path>] [-c/--chr_assignment <path>] [-a/--sample_s... |
1a35a7ae22e5e0b361e6a5152799f2eb8c7093c3f9035460cb5525b31ad1da26 | Shell | 6,562 | 168 | #!/usr/bin/env bash
# Written by Wu Jianxiao and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
# This function runs RF-ANTs surf2vol mapping creation and projection using 5 subjects
RF_DIR=$CBIG_CODE_DIR/stable_projects/registration/Wu2017_RegistrationFusion
RF_SURF2VOL_DIR=$RF_DI... |
99c53585374ec4353e0fdf06f11aef49ec3aa143a2b7692f80706012c345c57b | Shell | 6,661 | 146 | #!/bin/bash
# This script will generate replication input data for:
# 1) group priors estimation
# 2) individual parcellation generation
# The user need to specify the output directory, which will later contain two folders:
# 1) estimate_group_priors
# 2) generate_individual_parcellations
# Written by Ru(by) Kong and ... |
f344934af839c848b3646dc7f9473fee9d55db3a5d93c70fdfbebae9412c255c | Shell | 6,733 | 112 | #! /bin/bash
# run freesurfer surface extraction on uBrain volume
mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 atlas/temp/rh.inflated
mris_sphere atlas/temp/rh.inflated atlas/temp/rh.sphere
# create subject directory structure
export SUBJECTS_DIR='./atlas/'
export SUBJ='fs_atlas'
echo 'Creating a subject d... |
7c1ad54998f62a699b7f6ac8a993628a08317ef839073c4dd7d6f496b5b09b74 | Shell | 6,830 | 208 | #!/bin/bash -f
# Vivado (TM) v2015.4 (64-bit)
#
# Filename : clk_wiz_0.sh
# Simulator : Synopsys Verilog Compiler Simulator
# Description : Simulation script for compiling, elaborating and verifying the project source files.
# The script will automatically create the design libraries sub-directories ... |
2ca5339c55f3b63b8460f54f6e2589f20059bb565eddb5a3bbe0cf1ed7c7e3b1 | Shell | 6,841 | 166 | #!/usr/bin/env bash
#
# Generate hermetic byte-identity goldens for filter_non_conversion_rs by
# running the REAL Perl `filter_non_conversion` (v0.25.1) + samtools on tiny
# synthetic Bismark BAM fixtures. Commits, per success case:
# tests/data/<case>/in.bam (or a non-.bam name)
# tests/data/<case>/exp... |
68bcfaa189c04cc4de5964306356405ffc67e88d0a885fb08a4b99c619d68158 | Shell | 6,854 | 187 | #!/usr/bin/env bash
# Written by Wu Jianxiao and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
#This script runs ANTs registration from subject's T1 space to MNI152 template for a specified number of GSP subjects
###########################################
#Define paths
##########... |
5ce47462485de1dfe4017922ade4344c18b99225098668836751f5bb1fbdad88 | Shell | 6,863 | 152 | #!/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 ... |
e426cc7ca7494b5e48fc3d9d2bf1953dad6b085e03755d438d0ab34896ba44d7 | Shell | 6,874 | 169 | #!/usr/bin/env bash
# Written by Wu Jianxiao and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
#This script computes average mapping from fsaverage to the volumetric atlas space across a specified number of GSP subjects for the specified approach approach (by supplying the correspo... |
284d699cbbb93cd5c81c83697cdce9121cfb08626a326d71391ccee60077e5c6 | Shell | 6,902 | 207 | #!/bin/bash -f
# Vivado (TM) v2015.4 (64-bit)
#
# Filename : clk_wiz_0.sh
# Simulator : Cadence Incisive Enterprise Simulator
# Description : Simulation script for compiling, elaborating and verifying the project source files.
# The script will automatically create the design libraries sub-directorie... |
20bf6894bceef9187fa4b68c9cb5c693461224f0d1c80073c6b974f310e27804 | Shell | 6,955 | 240 | #!/bin/bash
# Example:
# sh CBIG_gwMRF_unit_test.sh ~/storage/Temporary/CBIG_gwMRF_unit_test
#
# Written by Yang Qing and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
user=`whoami`
###############################
# Set paths and create log file
############################... |
7e5b278e13715615c8f16372b8385162cf6a22b37b5882d581a2fc64370a6d69 | Shell | 6,982 | 128 | #!/bin/bash
# Phase-9b oxy WORKER-INVARIANCE gate (--multicore/--parallel).
#
# Gate (PLAN §1): for any N, the Rust output is byte-identical across worker counts
# AND equals Perl SINGLE-CORE:
# bismark_rs --parallel 4 == bismark_rs --parallel 1 == Perl bismark (single-core)
#
# 🔴 A-Imp6: the Perl oracle is ru... |
3d870ec166285bbad1673f880ec21cc68b074498cbd07bcdf49ebbd69d0a9436 | Shell | 7,027 | 182 | #!/usr/bin/env bash
# Setup script for octopi-software environment
# -------------------------------------------------------
# Usage
# -------------------------------------------------------
# brew install git (MacOS)
# sudo apt-get install git (Linux)
#
# git clone git@github.com:sohamazing/octopi-software.git
# cd o... |
9b5e95d3d7d37256a80a5279e4c85001c5adc7868bb81b2e5669efcd9969dbfe | Shell | 7,076 | 139 | ##Sample match check (QTLtools and NGSmakecheck)
ls RNA-seq/BAM/*Aligned.sortedByCoord.out_Pit_re_marked.bam | awk '{split($1,a,"/");split(a[5],b,".");print b[1]}' | while read line; do QTLtools_1.0_CentOS6.8_x86_64 match --bam RNA-seq/BAM/"$line".sortedByCoord.out_Pit_re_marked.bam --vcf DNA-seq/VCF/Combine/chr22.vcf.... |
fe158f02cd37c9b10ae8fcc23d4eba7c1a2207cd20560688537bc540239602e7 | Shell | 7,318 | 110 | ########### MOST OF THESE STEPS HAVE PRECOMPUTED RESULTS
#run the following in the base Xpresso folder to retrieve these precomputed results:
wget -r -np -nH --reject "index.html*" --cut-dirs 5 https://krishna.gs.washington.edu/content/members/vagar/Xpresso/data/datasets/
########### EXTRACT PROMOTERS FROM FANTO... |
ee40610725e3fe08a1286b494d52684a2e66145ae2feae9600c10084589a2194 | Shell | 7,336 | 166 | #!/usr/bin/env bash
# Written by Wu Jianxiao and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
# This script uses the mappings generate using Registration Fusion approach to project batch data in a volumetric space to fsaverage surface
###########################################
#... |
5a4bd1a8c11bd3afe2362f6da78205fe8f06b7f6019c52e206a55c2c1e1fa0ec | Shell | 7,348 | 166 | #!/usr/bin/env bash
# Written by Wu Jianxiao and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
# This script uses the mappings generate using Registration Fusion approach to project batch data in a volumetric space to fsaverage surface
###########################################
#... |
32d5031bf21bce77876540fa75189df0f5ba0c8f1109a310eca6846d4996273c | Shell | 7,399 | 192 | #!/bin/bash
# ==============================================================================
# Ginkgo - Command line version
# ==============================================================================
# Determine root directory (http://stackoverflow.com/a/246128)
DIR_ROOT="$( cd "$( dirname "${BASH_SOURCE[0]}" )... |
174bc426efa858d587990df78934a79e89715ce2c024ed60e5f54be6f15e0d96 | Shell | 7,407 | 315 | #!/bin/bash
set -e
# ============================================================
# GSvar macOS DMG creation script
# ============================================================
APP="GSvar.app"
EXECUTABLE="$APP/Contents/MacOS/GSvar"
FRAMEWORKS="$APP/Contents/Frameworks"
# =========================================... |
0045b9c824820cf0fce1732b2593f31d5aada5ec28ef4bcc778910f320135650 | Shell | 7,428 | 141 | #!/bin/bash
STAR --genomeDir /media/NAS1/Sammi_NAS1/ref/rna-GRCh38-mm10/refdata-gex-GRCh38-and-mm10-2020-A/star/ \
--runThreadN 6 \
--readFilesIn /media/Home_Raid1_Voyager/sammi/sammi_Scratch/bulk_teratoma/M_1_S1_L001_R1_001.fastq.gz /media/Home_Raid1_Voyager/sammi/sammi_Scratch/bulk_teratoma/M_1_S1_L001_R2_001.fastq... |
d7a3b4dd1ae217ba1c8cd820ac6722ec94c22bbd83a1e1ace3e0c86141698754 | Shell | 7,483 | 57 | #! /usr/bin/env bash
# BF-C2DL-HSC
# python /opt/elephant/script/train.py --baseconfig /opt/elephant/script/train_configs/base_train_seg.json seg /opt/elephant/script/train_configs/BF-C2DL-HSC-GT-seg.json
# python /opt/elephant/script/train.py --baseconfig /opt/elephant/script/train_configs/base_train_seg.json seg /opt... |
32112323241fe313989b576c6c52b3ca92d3b8a927ad23326e7ac8f936be0aad | Shell | 7,496 | 222 |
# Aim of this script is to calculate local Fst (per-river) Per-site and sliding windows (10kb)
# In addition, the script calculates PBS per river
# move to correct directory before running
######################################################
######################################################
echo "1. Calculate... |
22b2b0a27365a2d3b9c0fd89f6ad3207d308a354ce15bbb993aff955b8c3ef32 | Shell | 7,499 | 182 | #!/bin/sh
#
# There are two subjects (with two sessions of data) in the CoRR_HNU dataset involved in the example. To be able to
# separate the data into training and test sets, these two subjects will be treated as 4 subjects (each session is
# considered as a subject). Then the RSFC of each session will be duplicate... |
ef5f314a9dc990110791c1de98e4dccc6d917e5c8a85f79498cd2c544bae9f22 | Shell | 7,707 | 242 | #!/bin/bash -f
#*********************************************************************************************************
# Vivado (TM) v2018.2 (64-bit)
#
# Filename : ila_0.sh
# Simulator : Synopsys Verilog Compiler Simulator
# Description : Simulation script for compiling, elaborating and verifying the project s... |
797860c158c500549fdd852ce4ed685821bfe1cc8f394604db028069fa005494 | Shell | 7,839 | 195 | #!/bin/bash
#
# Gokberk Alagoz - 13.03.2023
#
# This script will convert .starch files to .bed format
# and merge all of chromosome in one file. Then, it will
# reformat all genomic coordinate files into UCSC bed
# format which is necessary for LDSC to run. This format
# looks like this:
# chr1 1 2
# chr1 10 11
# chr1 ... |
e676ccd7a6599d393fe5e8ab5878afdedcd791d1206650510c5f9ce7001cec6f | Shell | 7,862 | 229 | #!/bin/sh
#
# Written by Jingwei Li and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
data_csv=$CBIG_LiGSR_REP_GSP_DIR/scripts/subjects/GSP_extended_140630.csv
ystem=""
root_dir="$CBIG_CODE_DIR/stable_projects/preprocessing/Li2019_GSR/VarianceComponentModel/scripts/"
main() {
##... |
1ad974f91a0a6b9d76f5df1eea28ead0530a2a568ed5ca3f62525147404e47b1 | Shell | 7,895 | 255 | #!/bin/bash
### 1. set paths ###
## set parameter parsings for user-specified paths ##
usage="## this script calculates pairwise genetic distance dxy.\n
usage: bash $0 [-h/--help] [-w/--work_directory <path>] [-s/--dir_snp <path>]\n
[-m/--dir_mpileup <path>] [-c/--chr_assignment <path>]\n
[-v/--mincov <path>] [-x/--ma... |
70d4e4d0b9b35bfa9cb374068e80513f455d6734b16b9554fddf66ec069df88c | Shell | 7,972 | 244 | #!/bin/sh
#
# Written by Jingwei Li and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
data_csv=$CBIG_LiGSR_REP_GSP_DIR/scripts/subjects/GSP_extended_140630.csv
outstem=""
num_test_folds=20
num_inner_folds=20
with_bias=0
root_dir="$CBIG_CODE_DIR/stable_projects/preprocessing/Li2... |
063946ff83c80eb101409e3400f8b23ed60992dc8664ead780958372f1fdc052 | Shell | 7,988 | 217 | #!/bin/sh
#
# This script should be run via curl:
# sh -c "$(curl -fsSL https://raw.githubusercontent.com/replicate/cog/main/tools/install.sh)"
# or via wget:
# sh -c "$(wget -qO- https://raw.githubusercontent.com/replicate/cog/main/tools/install.sh)"
# or via fetch:
# sh -c "$(fetch -o - https://raw.githubuserco... |
a74ea1fe293e51a4a92af1e96e274a2c71d0f8d532281e766be17d8178108f0e | Shell | 8,007 | 201 | #!/usr/bin/env bash
# Written by Wu Jianxiao and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
# This script projects MNI152 index volumes to a specifiec number of GSP subjects' T1 space, using talairach.m3z
# transform, and then to fsaverage surface.
############################... |
ca68e90884febbd27c090f411afac537c9d04e76c73c5fd2a82391ee6f3328ac | Shell | 8,031 | 260 | #!/bin/bash
### 1. set paths ###
## set parameter parsings for user-specified paths ##
usage="## this script calculates pairwise genetic distance dxy.\n
usage: bash $0 [-h/--help] [-w/--work_directory <path>] [-s/--dir_snp <path>]\n
[-m/--dir_mpileup <path>] [-c/--chr_assignment <path>]\n
[-v/--mincov <path>] [-x/--ma... |
99adbfc52edc014592b41d482ef170372e1770a9407286dd47db349d4017ee66 | Shell | 8,092 | 168 | # Written by Tong He and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
# UKBB
## FNN
### Age
python3 ../cbig/He2019/CBIG_ukbb_fnn.py --pred_item 1 --weight_decay 2.798810e-05 \
--lr 9.122903e-03 --dropout 0.308501 --scheduler_decrease 32 --n_l1 9 --n_layer 2 --gpu 0
# Best validat... |
1c9f20c8dd97cad05d48891d9b661564a1a06dd12c4bdd03f36b5574e063e0ef | Shell | 8,159 | 191 | #!/usr/bin/env bash
# Written by Wu Jianxiao and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
# This script project xyz index files in a specified number of subjects' surface space to the subject's T1 space, and
# then to a volumetric atlas space
################################... |
34ef151ad96847d8fdbcad27eceaaab628e743259d9d90471704be94579ac9a1 | Shell | 8,197 | 203 | #!/usr/bin/env bash
# Written by Wu Jianxiao and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
# This script projects MNI152 index volumes to a specifiec number of GSP subjects' T1 space, using ANTs transforms,
# and then to fsaverage surface.
####################################... |
6b129bec3bab714a8819ebe101ada604e21ca763b45769d077e50777e37ef5ca | Shell | 8,225 | 243 | #!/bin/bash
Vaa3dPath=$1
TeraFlyBrains=$2
annotationpath=$3
outputpath=$4
threadNum=$5
logFile=${outputpath}/logFile.txt
function outFoldercheck() {
for swcpath in $(ls ${annotationpath}/*swc);
do
read -u6
{
swcname=${swcpath##*/}
outputDataPath="${outputpath}/${swcname:0:11}"
... |
4eb378dacfc7225b287950d7cd1275be9bc16eed30999612f687c480af7acdaf | Shell | 8,347 | 255 | #!/bin/sh
#
# Written by Jingwei Li and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
data_csv=$CBIG_LiGSR_REP_GSP_DIR/scripts/subjects/GSP_extended_140630.csv
num_test_folds=20
num_inner_folds=20
evaluations=15
tree=3
root_dir="$CBIG_CODE_DIR/stable_projects/preprocessing/Li201... |
fd2174bd06015a70c11a28cde59f4f195f29f284281548a0cf22f87573114a31 | Shell | 8,350 | 215 | #!/usr/bin/env bash
#
# generate_goldens.sh — produce byte-identity goldens for bismark-bam2nuc by
# running the REAL Perl `bam2nuc` (v0.25.1) over synthetic fixtures.
#
# Provenance: re-running this script regenerates every fixture (genome dirs,
# SAM→BAM inputs) AND every golden byte-for-byte. The committed `goldens/... |
7bf633779e6f890a6296af8d5f0afac80ba1eaf20edb441a43112e21c921231f | Shell | 8,503 | 68 | # Copyright 2022 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 law or agree... |
0177b39e10eaac2f7ee09e31f15db8d5facc75786e527bc38a755014c97cc387 | Shell | 8,529 | 155 | #!/bin/bash
# Phase-4 (v1.x) oxy SE byte-identity gate — minimap2 backend.
#
# Runs Perl bismark v0.25.1 --minimap2 + minimap2 2.31-r1302 and the Rust
# bismark_rs --minimap2 with IDENTICAL argv into the SAME -o (Perl moved aside),
# then diffs DECOMPRESSED SAM content (samtools @PG-filtered) + the report
# (wall-clock... |
8cb6b01934c2d607e635a905e7c2dcf064ed489ecf049ea1b74a470f1b7c7766 | Shell | 8,558 | 152 | #!/bin/bash
source ../multiNodeUtils.sh
# Argument parsing
if [ "$1" = "jacoco" ]
then
JACOCO_ENABLED=true
else
JACOCO_ENABLED=false
fi
# Clean out any old sandbox, make a new one
OUTDIR=sandbox/multi
MKDIR=mkdir
SEP=:
case "`uname`" in
CYGWIN* )
MKDIR=mkdir.exe
SEP=";"
;;
esac
rm -fr $... |
5dd2e8e18dd6cf4781a77786e912aa9a0ac2c4ed3d8ee86f171afa8ce696d9e6 | Shell | 9,048 | 188 | #!/bin/bash
#
# This script will reformat summary statistics from
# various external sources for LDSC munge.
#
# Gokberk Alagoz - 24.01.23
#
#############################################################
# 1) Reformat PGC sumstats. Extract the columns below (column
# order doesn't matter):
#
# rsID EffAllele RefAllele ... |
7ac510d256698f7a41f830e9c56740f45a2e27c6a322ec2db9781d55c0b50a6c | Shell | 9,129 | 267 | #!/bin/sh
#
# Written by Jingwei Li and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
HCP_dir="$CBIG_LiGSR_REP_HCP_DIR/S1200/scripts"
restricted_csv="$HCP_dir/restricted_hcp_data/\
RESTRICTED_jingweili_4_12_2017_1200subjects_fill_empty_zygosityGT_by_zygositySR.csv"
unrestricted_c... |
56863c37996fe7fff9a15649fb2246a1bd65dbf93030f65ac8a492d2710c4714 | Shell | 9,242 | 225 | #!/bin/bash
# =============================================================================
# Author: Gerard Martí, Eloy Martínez de las Heras
# Description: Implements pipeline to extract SC weights and length tracts from
# generated tractography, using a segmentation based on freesurfer
# NOTE: it is required to ch... |
ca5748904f8b95da0ecfdf780ab15eeae96b6a5a349a0ea686538bc31a348281 | Shell | 9,377 | 229 | #!/bin/bash
#
##########################
# define a helper function
##########################
warn_msg () {
# only output warning msg when the shell is interactive
if [[ $- == *i* ]]; then
echo $1
fi
}
####################################################
# export paths for subdirectories of CBIG repositor... |
3e40e9989a1aae5738d77e95c93beff7ad9e68bf5278d980968f56df444877cc | Shell | 9,393 | 274 | #!/bin/sh
#
# Written by Jingwei Li and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
HCP_dir="$CBIG_LiGSR_REP_HCP_DIR/S1200/scripts"
restricted_csv="$HCP_dir/restricted_hcp_data/\
RESTRICTED_jingweili_4_12_2017_1200subjects_fill_empty_zygosityGT_by_zygositySR.csv"
unrestricted_cs... |
7b43e0bac1d191e53af7eafcf9d9c8c7fdd81af899e116ac926c6315924a02f0 | Shell | 9,443 | 221 | #!/usr/bin/env bash
# Written by Wu Jianxiao and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
# This script projects xyz index files in a specified number of subjects' surface space to the subjects' T1 space, and
# then to the volumetric atlas space
#############################... |
25cb4632f20c071b1ad3573a58d0f655f748935802ec50063017143c08488a8f | Shell | 9,567 | 273 | #!/usr/bin/env bash
set -euo pipefail
# One-command Colab bootstrap using the proven legacy install pattern:
# - Installs Miniforge (if missing)
# - Installs OpenMM stack in a dedicated openmm_env environment
# - Installs ColabMDA
# - Verifies GPU/OpenMM/CLI
#
# Usage:
# bash bootstrap_colab_openmm_gpu.sh
# bash b... |
e99453026fb732683bdeae8b4d5a17d8ffea1624bd591924cbcf95c0b66f0980 | Shell | 9,610 | 260 | #!/bin/sh
#
# Written by Jingwei Li and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
HCP_dir="$CBIG_LiGSR_REP_HCP_DIR/S1200/scripts"
restricted_csv="$HCP_dir/restricted_hcp_data/\
RESTRICTED_jingweili_4_12_2017_1200subjects_fill_empty_zygosityGT_by_zygositySR.csv"
unrestricted_cs... |
2f6c2c00a31ad2468465e3af6d84c76e2255d0a4a6993c79215eaa237cb3b538 | Shell | 9,858 | 156 | #!/bin/bash
# ==========================================================================
# Phase-5 (v1.x) combined real-data gate — 10M single-core strict.
#
# For each cell: Perl Bismark v0.25.1 + the pinned aligner (single-core) vs
# bismark_rs (single-core), IDENTICAL argv into the SAME -o (Perl moved aside).
# Comp... |
0133252690f2a3261c9a97c589a829c0fa5dde5d09589016d512b27a3877d8c5 | Shell | 10,243 | 217 | #!/bin/sh
#
# There are two subjects (with two sessions of data) in the CoRR_HNU dataset involved in the example. To be able to
# separate the data into training and test sets, these two subjects will be treated as 4 subjects (each session is
# considered as a subject). Then the RSFC of each session will be duplicate... |
0b8dfbea320791df363618cc6b55d2dd425275d2a2278f53cb4d22bb3c2475e2 | Shell | 10,375 | 254 | #!/bin/bash
### 1. set paths ###
## set parameter parsings for user-specified paths ##
usage="## this script builds maximum-likelihood tree using TreeMix.\n
usage: bash $0 [-h/--help] [-w/--work_directory <path>] [-s/--dir_snp <path>]\n
[-c/--chr_assignment <path>] [-a/--sample_size <path>] [-l/--window_len <int>]\n
[... |
3477ef774733d124046501e1546a9e8d355f39f113d0f65865ef67a97b3fe06b | Shell | 10,425 | 203 | #!/bin/bash
#
#SBATCH --job-name=phaselocknet_localization_train
#SBATCH --out="slurm-%A_%a.out"
#SBATCH --cpus-per-task=8
#SBATCH --mem=16G
##SBATCH --gres=gpu:a100:1
#SBATCH --gres=gpu:1 --exclude=node[017-094,097,098],dgx001,dgx002
#SBATCH --array=0-119
#SBATCH --partition=normal --time=2-0
#SBATCH --requeue
offset... |
fcb9ab5e7b87ae6e42e6a3d2923c6d4df54b6f33876287b76f0ef3eb2f98dc89 | Shell | 10,809 | 214 | #!/bin/bash
#
#SBATCH --job-name=phaselocknet_localization_eval
#SBATCH --out="slurm-%A_%a.out"
#SBATCH --cpus-per-task=8
#SBATCH --mem=24G
##SBATCH --gres=gpu:a100:1
#SBATCH --gres=gpu:1 --exclude=node[017-094,097,098],dgx001,dgx002
#SBATCH --array=0-119
#SBATCH --partition=normal --time=2-0
#SBATCH --requeue
offset=... |
4d55f3989d7090ccacbcc714444eeb6e48e84595201739d479ce504a67b41b6c | Shell | 10,911 | 188 | #!/usr/bin/env bash
#
# overnight_driver.sh — unattended full-dataset benchmark + byte-identity campaign.
# Part of plans/05302026_extractor-fulldata-validation/PLAN.md.
#
# Sequence:
# STAGE — copy the 3 S3-symlinked BAMs to local disk; dedup the WGBS-SE for
# parity with WGBS-PE (RRBS stays non-dedup'... |
889e76200ea83ae62705799f4d06e2341d37a55c0e2f028fe49c7d1ad021950c | Shell | 11,021 | 338 | #!/bin/bash
##### Setting default options #####
outdir="$PWD"
diamond=0
diamond_path=''
threads=4
diamond_sensitivity="--sensitive"
minlength=500
filterlength=0
##### FUNCTIONS #####
#Help function
usage()
{
cat << EOF
usage: viper-classify.sh [OPTIONS]
This script takes a fasta file as input and uses Diamond and Kr... |
27958944305c57ce53410b09adac99e10a9056de1d91dfc83ac50a0173f7d3f0 | Shell | 11,424 | 425 | # Aim of this script:
# 1. Prepare input files for Baypass
# 2. Run Baypass and examine outliers
###################################
###################################
# 1. Prepare input files for Baypass
###################################
###################################
# Steps
# A. Get sites file based on... |
8407cf8f0671a5f4fefef16118b771ba803990a89f883ed3cebf2cd210a500aa | Shell | 11,491 | 241 | #!/bin/bash
## this script is used for calculating nucleotide diversity for each sample (population), based on previously called SNPs, high-quality sites and indel positions.
## this is a modified version of 'calc_diversity.sh', with a change that we discard a whole site with at least one sample failing to meet the min... |
6f615aa2abd2e29cfd508a4b8105bf5ca3de18c79bf9a41ff312381000c60593 | Shell | 12,280 | 224 | #!/bin/bash
# ==========================================================================
# Phase-10 Gate A — subset strict byte-identity + worker-invariance + the
# direct A1-assumption check (PLAN rev 1 §3.1 Gate A).
#
# Per cell, three legs — all on DECOMPRESSED content, @PG block filtered,
# report wall-clock line f... |
47b47a91b7265a19001af8e669e8a30bb100aa13429b2f433cc0a3410aad26dd | Shell | 12,285 | 251 | #!/bin/bash
#
#SBATCH --job-name=phaselocknet_spkr_word_train
#SBATCH --out="slurm-%A_%a.out"
#SBATCH --cpus-per-task=8
#SBATCH --mem=8G
##SBATCH --gres=gpu:a100:1
#SBATCH --gres=gpu:1 --exclude=node[017-094,097,098],dgx001,dgx002
#SBATCH --array=0-189
#SBATCH --partition=normal --time=2-0
#SBATCH --requeue
offset=0
j... |
cd3150022253bdee6457a1f839490e120ec5bf0828cd1ad890fe6d5aad2efa83 | Shell | 12,650 | 266 | #!/bin/bash
#
#SBATCH --job-name=phaselocknet_spkr_word_eval
#SBATCH --out="slurm-%A_%a.out"
#SBATCH --cpus-per-task=8
#SBATCH --mem=8G
##SBATCH --gres=gpu:a100:1
#SBATCH --gres=gpu:1 --exclude=node[017-094,097,098],dgx001,dgx002
#SBATCH --array=0-189
#SBATCH --time=2-0
#SBATCH --partition=use-everything
#SBATCH --requ... |
d226c871e5d284d911379ee94da3f0b5f161c994166f9547d26acfddb45d1ded | Shell | 13,817 | 231 | #!/bin/bash
# ==========================================================================
# Phase-10 Gate B — full-scale content-identity + perf (PLAN rev 1 §3.1 Gate B).
#
# Per cell, on the FULL dataset, Perl --parallel P (timed) vs Rust --parallel P
# (timed) with identical argv (orchestration flags aside):
# B0 ... |
22c30268cde2005cb6bdb0170b461157f32432f4bb39ab53ef8a0ae4359528f6 | Shell | 14,050 | 390 | #!/bin/bash
# how to run:
# source forest_brain.sh [complete path to folder with files] [scan_number] [number of echos] [dyn to exclude]
# ex - source forest_brain.sh /home/user/case_number_001 59 3 1,2,3
# this example is for a 3 echo sequence where the first 3 dynamics are motion corrupted
# if no dynamics are bad,... |
517cef45aaf52e45f6a159d7d5f9d27c0e9859c44a2ac0032648cac861999664 | Shell | 14,219 | 363 | w#!/bin/bash
### 1. set paths ###
## set parameter parsings for user-specified paths ##
usage="## this script calculates synonymous nucleotide diversity.\n
usage: bash $0 [-h/--help] [-w/--work_directory <path>] [-s/--dir_snp <path>]\n
[-n/--sample_size <path>] [-m/--dir_mpileup <path>] [-c/--chr_assignment <path>]\n
... |
fbd05d30de47c60f6fc19d9747a4cfa37419e6112d60dd785387ee313087aebc | Shell | 14,421 | 361 | #!/bin/bash
### 1. set paths ###
## set parameter parsings for user-specified paths ##
usage="## this script generate 4-fold synonymous SNP data.\n
usage: bash $0 [-h/--help] [-w/--work_directory <path>] [-s/--dir_snp <path>]\n
[-n/--sample_size <path>] [-m/--dir_mpileup <path>] [-c/--chr_assignment <path>]\n
[-v/--mi... |
669956cef8290fd2b00c6d0f78d9a2c790864b282901720527e1a6fcb76c04ef | Shell | 15,260 | 407 | #!/bin/bash
# how to run:
# source forest_body.sh [complete path to folder with files] [scan_number] [number of echos] [dyn to exclude]
# ex - source forest_body.sh /home/user/case_number_001 59 3 1,2,3
# this example is for a 3 echo sequence where the first 3 dynamics are motion corrupted
# if no dynamics are bad, p... |
c8d376984b06020e9fc25ffc50c0283c3f906b6f771946bd26c4c9ff5a8c4b27 | Shell | 15,689 | 143 | #!/bin/bash
#run this from LCModel source directory
# This adds LCModel to your path
gfortran -c -fno-backslash -fno-f2c -O3 -fall-intrinsics -std=legacy -Wuninitialized -ffpe-summary=none LCModel.f
gfortran LCModel.o -o lcmodel
control_files="
/Volumes/catherine_team/mvperdue/preschool/mrs/data_acg/PS10001_PS14_006_... |
72954527cb24960780af2a8bbd87e559a6ddb71d919bcc5d2303368465279f7f | Shell | 16,026 | 370 | ### ToDO:
# Neurodesktop tools to use:
ml afni
ml fsl
ml laynii
cd /neurodesktop-storage/5T4/Alejandro/sosp_vaso/data
folder="05192023_sv_paper"
scan="cv_01"
r_a_tr=7 # rest/activity TRs paper=sv(8), cv(7)
tr=1.81 # volume TR paper=sv(1.66), cv(1.81)
# Spiral reconstruction options
traj="_nom" && cs="_cs" ... |
d5f0e968f1d2bf2cc21c70d68c6239793d7cdcec6536d5c65309fb9f5e7b4f96 | Shell | 16,664 | 215 | #!/bin/bash
cd /m/cs/scratch/networks-pm/effects_externalfactors_on_functionalconnectivity/data/mri/decoder
Text2Vest contrast.txt contrast.con
Text2Vest movie_awake_time1_design.txt movie_awake_time1_design.mat
Text2Vest movie_awake_time2_design.txt movie_awake_time2_design.mat
Text2Vest movie_awake_time3_design.txt... |
bd79ebcde3683ce02722884f5ae28f4df91a0c51c34cae70bb833ab9cbb91260 | Shell | 16,697 | 313 | #!/bin/bash -f
#*********************************************************************************************************
# Vivado (TM) v2018.2 (64-bit)
#
# Filename : system.sh
# Simulator : Synopsys Verilog Compiler Simulator
# Description : Simulation script for compiling, elaborating and verifying the project ... |
0c646aa0fddc5db158dbfe852b554fac14f4eaec33e42595a121276d57e27e68 | Shell | 17,104 | 226 | #!/bin/bash
#Batch Processing for LCModel
#Adapted for the pre-processed data from FID-A/MM
#Orig Tiffany Bell
#Adapted M DeMayo
#2020/Aug/23
# in_path=COT0201/
# out_path=COT0201/
list_of_files=list_controlfiles.csv
basis_set_path='/Volumes/catherine_team/mvperdue/preschool/mrs/BasisSet/PRESS30.basis'
atth2o=0.7
wc... |
f203bc0dac44b99fb82c50ef02263a38b52f84c612e5657e7de05b9f84d92a63 | Shell | 17,138 | 350 | #!/bin/bash
# =============================================================================
# Author: Gerard Martí
# Description: Process the DT image and create the full brain tracking, which
# will be preprocessed later
# =============================================================================
################... |
f30efb516a3c62a9a936fdad54c047e6e61b53124f95a7c9d83f58e62f0d9e9d | Shell | 18,151 | 390 | #!/usr/bin/env bash
#
# phase_h_smoke.sh — Phase H per-cell byte-identity smoke against real WGBS data.
#
# Runs both the Perl `bismark_methylation_extractor` and the Rust
# `bismark-methylation-extractor-rs` on the same BAM input, then compares
# every output file. Also measures wall-clock for both runs to validate
# ... |
34f84b7b9aed489d281e51e7ca3e455f57c42756700d4c06fc5857ec9537feca | Shell | 21,758 | 150 | # For each setting, metrics are: encoder_test_rmse_last, decoder_test_rmse_[2-6]-step
# tumor growth dataset (run standard supervised learning experiments first)
## standard supervised learning
### MSM
PYTHONPATH=. python runnables/train_msm.py -m +dataset=cancer_sim +target_dataset=cancer_sim +dataset.tr_te_type=src_... |
5ed95ae4a30f359405b4757ef5025d924d089c474304b0fcf660e67a880ae7bf | Shell | 22,136 | 486 | #!/bin/bash
mkdir -p HFA_v3/trimmed_fastq_HFA_20230711
mkdir -p HFA_v3/aligned_bam_HFA_20230711
mkdir -p HFA_v3/alignedfiltered_bam_HFA_20230711
mkdir -p HFA_v3/collapsed_bam_HFA_20230711
mkdir -p HFA_v3/tagged_bam_HFA_20230711
mkdir -p HFA_v3/dedupped_bam_HFA_20230711
mkdir -p HFA_v3/tmp_20230711
mkdir -p AEI_HFA_v5/... |
b4792534294b58fd5a3d67df00048eeddb052849b989c63c68b4784e19a0b460 | Shell | 24,769 | 827 | #!/bin/bash
function trap_exit_handle() {
echo "(exit_handle)"
if [ -n "${lock_pid_file}" ]; then
rm ${lock_pid_file}
fi
print_stage_status
if [ -n "${PID_PERF_PROFILE}" ]; then
echo "(kill perf-profile)"
kill -- -${PID_PERF_PROFILE}
fi
# kill 0
}
trap trap_exit_han... |
96a71392e2fe314d4d544b649424d1814fcd08037d070d50b6968766222c5381 | Shell | 28,037 | 552 | #!/usr/bin/env bash
#
# c2c_byte_identity_matrix.sh — bismark-coverage2cytosine release gate.
#
# Runs the Rust `coverage2cytosine_rs` and Perl `coverage2cytosine` (v0.25.1)
# over a 15-cell representative flag matrix against a Perl-bismark2bedGraph
# `.bismark.cov.gz` + genome, and asserts RAW-BYTE-IDENTITY Rust≡Perl ... |
0b05fddac8992082a38253d6075fa3e542df7e746096bec6550e0638431ce0a6 | Shell | 28,349 | 721 | #!/usr/bin/env bash
#
# phase_h_se_matrix.sh — Phase H sub-gate 1 SE byte-identity + speedup matrix.
#
# Runs the per-cell Phase H smoke (scripts/phase_h_smoke.sh) over the 5-cell
# representative SE matrix at --parallel ∈ {1, 4} (configurable). Asserts
# SPEC §8.3 row 4 N-invariance per ignore-pair (Rust-N=1 ≡ Rust-N=... |
c5c1f0d9afb46f6ec0add2468ce494be99c59334ae4bad4e15ed27d773e16c7c | Shell | 29,116 | 589 | natDir='test_data/native_reads/'
ampDir='test_data/amplified_reads/'
rcsvDir='test_data/recursive_test/'
natFsq="test_data/fastqs.native.fasta"
natFqDir='test_data/native_reads.for_fastq_ann/'
nrModFn='../tombo/tombo/tombo_models/tombo.DNA.model'
altModFn='../tombo/tombo/tombo_models/tombo.DNA.5mC.model'
poreModel="r9... |
b05c0995c1e3471410cce4e0d2f0328bcfb876a61cf9b92709b81b7270ebe4d6 | Shell | 29,745 | 355 | #!/bin/bash
set -e
set -o pipefail
set -o verbose
root=`pwd`
src=$root/../src/
# Get data_folder path
SETTINGS_FILE=$root/../settings.ini
if [ ! -f "$SETTINGS_FILE" ]; then
SETTINGS_FILE="$root/../settings.ini.default"
fi
DATA_FOLDER=$(grep -E "^data_folder" "$SETTINGS_FILE" | awk -F ' = ' '{print $2}' | sed "s|\... |
7349711556cc102e88a0ba5830b9c56a5a505757d8ffe84486347f48fec17a5f | Shell | 31,030 | 1,126 | #!/bin/bash
# file: tests/test-runPipeline.sh
if [ ! -f tests/test-helper.sh ]; then
echo "test-helper.sh not exist"
exit
fi
. tests/test-helper.sh
SHUNIT2_SRC_DIR=/mp/nas1/share/lib/shunit2
INPUT_IMAGE_DIR=/mp/nas1/share/ExSEQ/AutoSeq2/test-data/xy01/1_deconvolution
BASENAME="exseqauto-xy01"
#CHANNELS="'ch0... |
d676362324c351a9913585912d78a5bba1d7525b244681eef84e921027bfdab6 | Shell | 33,920 | 811 | #!/usr/bin/env bash
#
# phase_h_pe_matrix.sh — Phase H sub-gate 1 PE byte-identity + speedup matrix.
#
# Runs the per-cell Phase H smoke (scripts/phase_h_smoke.sh) over the 5-cell
# representative PE matrix at --parallel ∈ {1, 4} (configurable). Asserts
# SPEC §8.3 row 4 N-invariance per CELL_ID (Rust-N=1 ≡ Rust-N=4 ra... |
2536cd4baa7901406da4f73cfe8c0e7cb4f999e8d977f315c21c61c486ffd588 | Shell | 37,599 | 1,032 | #!/bin/bash
viper_command="$0 $@"
printf '%s\n' "$viper_command"
##### Setting default options #####
outdir="$PWD"
contaminome=''
spades_k_mer=21,33,55,77
diamond=0
diamond_path=''
threads=4
host_removal=0
host_genome=''
contaminome_removal=0
triple=0
trimmomatic_primer="$CONDA_PREFIX/share/trimmomatic/adapters/Nexter... |
62c3cfcd64573e12c5a449077f6a139d92c65c84056c19024355b2d7e768811b | Shell | 39,246 | 429 | #!/bin/bash
#Batch Processing for LCModel
#Adapted for the pre-processed data from FID-A/MM
#Orig Tiffany Bell
#Adapted M DeMayo
#2020/Aug/23
# in_path=COT0201/
# out_path=COT0201/
list_of_files=list_controlfiles.csv
basis_set_path='/Volumes/catherine_team/mvperdue/preschool/mrs/BasisSet/PRESS30.basis'
atth2o=0.7
wc... |
e225fa14372c59b3ee639635e50103e96e9fa6b97d3cd413c62932c3234ba3fc | Shell | 39,610 | 346 | #!/bin/bash
#run this from LCModel source directory
# This adds LCModel to your path
gfortran -c -fno-backslash -fno-f2c -O3 -fall-intrinsics -std=legacy -Wuninitialized -ffpe-summary=none LCModel.f
gfortran LCModel.o -o lcmodel
control_files="
/Volumes/catherine_team/mvperdue/preschool/mrs/data_lag/PS10006_PS14_120_3... |
fe841e7fb1cb3ab0181c63639db7cba0e185c1a47e365f0bdedcb9e26a847b99 | Shell | 198,965 | 6,930 | # ltmain.sh - Provide generalized library-building support services.
# NOTE: Changing this file will not affect anything until you rerun configure.
#
# Copyright (C) 1996, 1997, 1998, 1999, 2000, 2001, 2003, 2004, 2005, 2006,
# 2007 Free Software Foundation, Inc.
# Originally by Gordon Matzigkeit <gord@gnu.ai.mit.edu>... |
2e46e47507dc5136c19b321ec9822a28243c8ac06d460eb015de780f6ab43a7e | Shell | 200,000 | 2,722 | ./ms 48 1 -t 18.0009 -r 881.135217200136 20001 >> autotet.all.LD.sims.txt
./ms 48 1 -t 18.0009 -r 27.2706078011852 20001 >> autotet.all.LD.sims.txt
./ms 48 1 -t 6.0003 -r 4.87867093703502 20001 >> autotet.all.LD.sims.txt
./ms 48 1 -t 60.003 -r 410.260276446122 20001 >> autotet.all.LD.sims.txt
./ms 48 1 -t 24.0012 -r 13... |
6d80b1b217cc8f2c8ea689d03431379a8dfee0349bd191a4c23358b330ef05d8 | Shell | 200,000 | 3,048 | ./ms 50 1 -t 6.0003 -r 266.956266549913 20001 >> all.LD.sims.txt
./ms 50 1 -t 1.20006 -r 5.58685354484189 20001 >> all.LD.sims.txt
./ms 50 1 -t 6.0003 -r 148.563415383436 20001 >> all.LD.sims.txt
./ms 50 1 -t 12.0006 -r 59.7492525857357 20001 >> all.LD.sims.txt
./ms 50 1 -t 18.0009 -r 297.658012649852 20001 >> all.LD.s... |
9843567d295a8162a5a01278dae4eeb49719d5cf85965cbdc6b943a4c1af0370 | Shell | 200,000 | 2,516 | ./ms 48 1 -t 24.0012 -r 308.282954898289 20001 >> autotet.test.data.LD.sims.txt
./ms 48 1 -t 18.0009 -r 388.803897445349 20001 >> autotet.test.data.LD.sims.txt
./ms 48 1 -t 24.0012 -r 203.335153066788 20001 >> autotet.test.data.LD.sims.txt
./ms 48 1 -t 18.0009 -r 21.0699166920815 20001 >> autotet.test.data.LD.sims.txt
... |
99c34c59d2a0c7ddd09db702afb9f566b9c3d79a088f12fdbf4ac85d4a405e2e | Shell | 200,000 | 3,036 | ./ms 50 1 -t 42.0021 -r 2023.467911258 20001 >> gap.LD.sims.txt
./ms 50 1 -t 48.0024 -r 2639.54538586607 20001 >> gap.LD.sims.txt
./ms 50 1 -t 54.0027 -r 186.650670021069 20001 >> gap.LD.sims.txt
./ms 50 1 -t 48.0024 -r 1534.58119574007 20001 >> gap.LD.sims.txt
./ms 50 1 -t 42.0021 -r 101.926158587693 20001 >> gap.LD.s... |
50946aed4050b64b34cdfe34f67d0955902016670e0e12763108b84bc3a1b923 | Stan | 2,479 | 124 | functions {
vector side_choice_kern(array[] int choice, real alpha, int N) {
vector[N] choice_kernel = rep_vector(0, N);
for (t in 1:N-1) {
choice_kernel[t+1] = choice_kernel[t] + alpha * (choice[t] - choice_kernel[t]);
}
return choice_kernel;
}
vector ses_si... |
4fb604adbe4d757738d5b793634526bb6e43e8ac411822539d1ffc815de4d2ef | Stata | 151 | 7 | set pack_assert_off {numeric_std std_logic_arith}
database -open waves -into waves.shm -default
probe -create -shm -all -variables -depth 1
run
exit
|
2f1cf0be469f71875e76dd358b73dcc1d31602a8ab53f0646d434edae0b0d0a7 | Stata | 171 | 16 | onbreak {quit -f}
onerror {quit -f}
vsim -t 1ps -lib xil_defaultlib ila_0_opt
do {wave.do}
view wave
view structure
view signals
do {ila_0.udo}
run -all
quit -force
|
c99eae36f0e9126e9bd6baf701716e3b238794bdc7b876952b00b7fd6faaefe0 | Stata | 173 | 16 | onbreak {quit -f}
onerror {quit -f}
vsim -t 1ps -lib xil_defaultlib system_opt
do {wave.do}
view wave
view structure
view signals
do {system.udo}
run -all
quit -force
|
31c09d9f66dff20004cc74258d9dc14652aa146d17215cb088ef7e034038ed80 | Stata | 175 | 1 | vopt -64 +acc -l elaborate.log -L unisims_ver -L unimacro_ver -L secureip -L xil_defaultlib -work xil_defaultlib xil_defaultlib.clk_wiz_0 xil_defaultlib.glbl -o clk_wiz_0_opt
|
fd19030e3c431748f0ce16c9031ba4b2f44dd030a2a1e24528e89490a709475c | Stata | 238 | 16 | onbreak {quit -f}
onerror {quit -f}
vsim -t 1ps -pli "C:/Xilinx/Vivado/2015.4/lib/win64.o/libxil_vsim.dll" -lib xil_defaultlib clk_wiz_0_opt
do {wave.do}
view wave
view structure
view signals
do {clk_wiz_0.udo}
run -all
quit -force
|
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.