sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
b207b0834cd84cfaa3c6e14e6930d3f58aec6945622095908fbbcf54a45ec937 | Shell | 1,366 | 38 | mkdir /scratch/edickie/saba_PINT/bids_in/ds000030
chuncks='sub10159-10299
sub10304-10388
sub10428-10575
sub10624-10697
sub10704-10893
sub10912-10998
sub11019-11098
sub11104-11156
sub50004-50008
sub50010-50038
sub50043-50059
sub50060-50085'
for chunck_name in ${chuncks}; do
if [ ! -f ds000030_R1.0.5_${chunck_name}.z... |
a89ea304edc3e001d68efa8db734dc488abe7b57135d3d88f4efb5ffe7ae4e2b | Shell | 1,367 | 36 | #!/bin/bash
codeDir=/home/OBIWAN/CODE/PREPROC/06-smoothing_unzip/
smoothScript=${codeDir}smoothFunctional.sh
anatomicalScript=${codeDir}anatomicalClean.sh
# loop over subjects
group='obese2'
#for subjID in 00 01 02 03 04 05 06 07 08 09 11 13 15 17 18 20 21 24 25 26 27 28 29 30 31 32 34 35 36 37 38 39 41 42 44 45... |
897dfbab54f1dfbee6d3ce6587e05bda513ab854f0a2e18fa877d372ad0addf7 | Shell | 1,381 | 56 | #!/bin/bash
## Companion script for ops/pipeline/nightly-test-cccl.sh
set -eo pipefail
# Cannot set -u before Conda env activation
if [[ "$#" -lt 1 ]]
then
echo "Usage: $0 [cccl_version]"
exit 1
fi
cccl_version="$1"
# Set up Conda env
cuda_version="$(nvcc --version | awk '/release/ {gsub(/,/, "", $5); print $5}'... |
20e4e1f28c7edf62479328276217bb78f6ae31eb27c8a29e747d08d8db5edb80 | Shell | 1,394 | 38 | #!/bin/bash
# #############
codeDir=/home/OBIWAN/CODE/PREPROC/05-ANTS_coreg/
# scripts to run
anatScript=${codeDir}ANTsCoregAnatomical.sh
funcScript=${codeDir}ANTsCoregRefAndFunc.sh
# loop over subjects
group='obese2'
#00 01 02 03 04 05 06 07 08 09 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 ... |
7b660bcefd62e966f7dcdc4f6f76fa50f16048972421142bd9d930072a3d01cf | Shell | 1,407 | 29 | #!/bin/bash
# #############
codeDir=/home/OBIWAN/CODE/PREPROC/05-ANTS_coreg/
# # re-slice target anatomical T1/T2 to match subject (moving) image resolution
# # This only needs to be done once for the whole project
# tmpDir=/home/OBIWAN/DERIVATIVES/EXTERNALDAT/CANONICALS/
# fixedT1=CIT168_T1w_MNI
# fixedT2=CIT168_T2w... |
1191c102b77d0b5685b017402b6d05f0931f6713dc76e800a8cea19eb2029293 | Shell | 1,440 | 41 | #!/bin/sh
############################################
############################################
# #
# **GRADE in PBS Cluster** #
# General RNAseq Analysis for #
# Differential Expression #
# ... |
77341bf2edecfc9da6b278b19d2739a84bca3a319b2587db51451a20915a6b42 | Shell | 1,449 | 41 | #!/bin/sh
############################################
############################################
# #
# **GRADE in PBS Cluster** #
# General RNAseq Analysis for #
# Differential Expression #
# ... |
45b07bef5e91e885d23d48bcfa855e267074b5e920587a0b0c5a52a10f307498 | Shell | 1,452 | 41 | #!/bin/sh
############################################
############################################
# #
# **GRADE in PBS Cluster** #
# General RNAseq Analysis for #
# Differential Expression #
# ... |
2b78e95a54b575e53595f4989d5fb58a6cc997e4451c81bcd01b535ca1263161 | Shell | 1,453 | 48 | #!/bin/bash
# Generates The toolSet macro file from the individaal macros of the Angle2Ablation Timelapse workflow
# To run, open a terminal where this file and where the individual macro files are located and run the line: $ bash A2AWF_ToolSet_Template.sh > Angle2ablation_Workflow_ToolSet.ijm
echo 'var ImageOne;'
ec... |
c327e79185e4cbef8b8be6afb2e48075db109c16084c37bc07633b70ad031831 | Shell | 1,455 | 24 | #!/bin/sh
# Training implicit network + NeuralODE + SecondOrder
mkdir -p ./Results/Pendulum/
mkdir -p ./Results/Pendulum/
########################################################
################ Batch time 3 ##########################
########################################################
python Pendulum_SecondOr... |
4369d4482a45a27b5558e3d70141da492702fc12d2c5cca2575ee5c64e1dbe62 | Shell | 1,461 | 41 | #!/bin/sh
############################################
############################################
# #
# **GRADE in PBS Cluster** #
# General RNAseq Analysis for #
# Differential Expression #
# ... |
12f86e06636d79f353dd9f049fd5379db7a8b0ff7316e348e1f1ff0b690ebb66 | Shell | 1,464 | 36 | #!/bin/bash
# pull in subject
subjectID=$1
# pull in session
sessionID=$2
# pull in task
taskID=$3
echo "Preparing subject ${subjectID}, ${sessionID} session functionals, for FEAT"
# directory containing raw nifti data
dataDir=/home/OBIWAN/DATA/STUDY/RAW/BIDS/sub-${subjectID}/ses-${sessionID}/func/
# output direct... |
ee0f6a3309e768acd2179c36927ebf0d383f498e9d42f678de0f4d93f26a0b45 | Shell | 1,488 | 57 | #!/bin/bash
###LOCATIONS AND SAMPLE NAMES#########################################################################################
file="/media/labcomputer/AWLABEX2/Asela/202204011_DAPseq_GmRav4/00_data/20220427_filenames.txt"
PROJECT_SAMPLE_DIR=/media/labcomputer/AWLABEX2/Asela/202204011_DAPseq_GmRav4
RAW_DATA=00... |
72ec36801c889fe0f1f0bd9e241a7cffb48a902dfb348ecc489e3b3b4a10e4d9 | Shell | 1,522 | 58 | #!/bin/csh
# JHK
# C-shell script for 5x5 occlusion sensitivity (OS)
# function selection
setenv op_gpu 'off'
# set experiment name
setenv exp_name 'dd_v01'
# set main directory
setenv h_dir '/home/jhkim/model/deep_detection'
# set gpu number (for multi-GPU environment)
setenv n_gpu 0
# number of ense... |
7f62ea5dd02d24f2c82b2807ce7484328be22b197cd7e3f657ca46c8740e2497 | Shell | 1,527 | 42 |
#!/bin/sh
# User must supply the directory name.
dir=$1; currdir=`pwd`
ref=$2
# Retrieve number of clusters:
nclusters=`sort -nbr -k2,2 ${currdir}/${dir}/SeuratResults/Cell_Clusters.tsv | head -n1 | cut -f2`
echo "===> Clusters 0 to ${nclusters} were found."
echo ""
# Enter input directory and create output di... |
8d98a5909f4c5dacb65c4a831cb16675da85ae01c0ae837b40e8cb59997e91b8 | Shell | 1,534 | 66 | #!/bin/bash
help()
{
echo "Usage: createDataset [ -p | --path_data PATH_DATA ]
[ -n | --nbSamplesPerCase ]
[ -f | --matrixfilename MATRIXFILEMANE]
[ -h | --help ]"
exit 2
}
SHORT=p:,n:,f:,h
LONG=path_data:,nbSamplesPerCase:,matrixfilename:,help
OPTS=$(getopt -a -n ... |
8e60bc1f04e9ea85b1b49e13bfb2af223011ed2e60b8929d09df172f755f96a3 | Shell | 1,544 | 43 | #!/bin/sh
############################################
############################################
# #
# **GRADE in PBS Cluster** #
# General RNAseq Analysis for #
# Differential Expression #
# ... |
d3effdb4c9f31788f2a5085ebf8d3c153612222aee8f352e24dd0b3f9570a5e3 | Shell | 1,555 | 48 | #!/bin/sh
############################################
############################################
# #
# **GRADE in PBS Cluster** #
# General RNAseq Analysis for #
# Differential Expression #
# ... |
f25c2ceaff5a62e71d2ed535b37b08aa11bb80984314f51dcc402a40b9fcb6cb | Shell | 1,578 | 48 | # This bash script can be used to regenerate the tables used
# in possible parameters when parameters changed in tracksclasses.
# As well as updating the usage part in the README.md
if [ -e docs/content/tracks/auto ]; then
rm -r docs/content/tracks/auto
fi
mkdir -p docs/content/tracks/auto
python pygenometracks/get... |
50b61db76706997f70bb9a4ad1f0187cee77a367574243c0dbe17af0e5f7d789 | Shell | 1,586 | 49 | #!/bin/csh
# JHK
# function selection
setenv op_train 'off'
setenv op_test 'on'
setenv exp_name 'reg' # experiment name
setenv input_var 'prcp' # input variable
# # set test dataset (ERA5, IMERG)
setenv o_name 'ERA5' # test set
setenv h_dir '/home/jhkim/model/deep_detection' # ... |
7fa7f900999e3aa2b942d714d40e8612d8e82f0ace132cb5069d5ec7fbd02829 | Shell | 1,588 | 50 | #!/usr/bin/env bash
# Build the full PTSA conda matrix locally, one cell per conda-build
# invocation (mirrors what .github/workflows/build.yml does per
# strategy.matrix cell). Per-cell invocation is REQUIRED: a single
# `conda-build` run driven by a zipped python/numpy variant list in
# conda_build_config.yaml mis-re... |
02969fd8b92fcc0db9eef415f46cc2bdd88ff52ab24d9204992f3386100a162d | Shell | 1,611 | 50 | #!/bin/bash
# pull in subject
subjectID=$1
#subjectID='obese262'
# pull in session
sessionID=$2
#sessionID='third'
# pull in task
taskID=$3
#taskID='pav'
echo "Preparing subject ${subjectID}, ${sessionID} session, ${taskID} task"
# directory containing scripts and templates
#codeDir=/home/OBIWAN/ANALYSIS/fsl_script... |
8b74d9e1d95b4e2ce54e4b7e90e9bb274af8d83f4350d1e64e4395bbfa15168c | Shell | 1,612 | 59 | #!/bin/bash
####################################CONFIGERATION INFORMATION#########################################################
###LOCATIONS AND SAMPLE NAMES#########################################################################################
PROJECT_SAMPLE_DIR=/media/labcomputer/AWLABEX2/Asela/202204011_DAPse... |
a474148e44d6373a5e76744758ef283c7f140c7b3dd9cb1baf8adc4b1ca5aac4 | Shell | 1,612 | 40 | #!/bin/sh
dir=$1; currdir=`pwd`
cd ${currdir}/${dir}
echo "Running marker assignment for folder ${dir}..."
parent="/working/lab_julietF/mainaB/scRNAseq"
cut -f1 Cell_Clusters.tsv | sort | uniq | while read cell; do grep "$cell" ${parent}/SRAinformation/SraRunInfo_PRJNA450* | cut -d',' -f11 | while read id; do grep... |
8d698a69bcd383b96576161c264b18d8515db87aa1e507256668f840f5eb06a4 | Shell | 1,642 | 43 | #!/bin/bash
# pull in subject
subjectID=$1
# input directory containing anatomical data
anatDir=/home/OBIWAN/DATA/STUDY/DERIVED/ICA_ANTS/sub-${subjectID}/ses-first/anat/
# output directory for preprocessed data
outDir=/home/OBIWAN/DATA/STUDY/CLEAN/sub-${subjectID}/ses-first/anat/
anatDav=/home/OBIWAN/DERIVATIVES/PRE... |
2e81165631b7ad6d2b6dc534ba5056648fc93e84b438ae45c453c6273ae9fe71 | Shell | 1,647 | 48 | #!/bin/bash
# pull in subject
subjectID=$1
# pull in session
sessionID=$2
# pull in task
taskID=$3
echo "Preparing FIX training data for subject ${subjectID}, session ${sessionID}, task ${taskID}"
# input MELODIC directory
melodicDir=/home/OBIWAN/DATA/STUDY/DERIVED/ICA_ANTS/sub-${subjectID}/ses-${sessionID}/func/t... |
ccfd57066e2675ae4d446e24cbb3b713e0ed09d5fd88fd8b17828a8f851c1322 | Shell | 1,648 | 36 | inter_type="pixel";
# ===== basic settings =====
gpu_id=0; dirname="result"; pretrained=True; ckpt_DIR="timm_hub/";
dataset="imagenet"; class_number=1000; image_size=224; grid=14; seed=1; # ImageNet: 224x224, grid 14x14
# ===== model settings =====
arch="resnet";
ckpt="resnet50_a1_0-14fe96d1.pth"
# arch="mlpmixer"... |
a788f7bc522b30e30c465f36490d3263b937586907423ca928c3e14ba38af67b | Shell | 1,656 | 48 | #!/bin/sh
######################################################
# #
# ** DENTAL (de Novo Transcriptome Assembly Line) ** #
# #
######################################################
#################################... |
e030abb91e2ac3fa6cb83a85bf3800c6e66f1fe9f89b3fa14665e15a01cc4069 | Shell | 1,658 | 59 | #!/bin/csh
# JHK
# c-shell script for integrated gradient (IG)
# function selection
setenv op_gpu 'on'
setenv exp_name 'dd_v01' # experiment type
setenv h_dir '/home/jhkim/model/deep_detection' # Main directory
setenv n_gpu 3 # GPU number
setenv n_ens 5 ... |
b3c3bc689f731f5b295ab541e5a07c6f1466cd8180c10781127852257581c579 | Shell | 1,667 | 61 | #!/bin/bash
###LOCATIONS AND SAMPLE NAMES#########################################################################################
file="/media/labcomputer/AWLABEX2/Asela/202204011_DAPseq_GmRav4/00_data/20220427_filenames.txt"
PROJECT_SAMPLE_DIR=/media/labcomputer/AWLABEX2/Asela/202204011_DAPseq_GmRav4
RAW_DATA=00_... |
3bc813a134d260544ca72615e25420b41bd81305990ec335c15eeb95c0942993 | Shell | 1,680 | 41 | #!/bin/bash
#codeDir=/home/OBIWAN/ANALYSIS/fsl_scripts/preproc/fsl_ANTS/01-prepForICA/
codeDir=/home/OBIWAN/CODE/PREPROC/01-prepForICA/
anatomicalScript=${codeDir}prepAnatomical.sh
functionalScript=${codeDir}prepFunctional.sh
fmapScript=${codeDir}prepFmap.sh
# loop over subjects
group='control1'
#group='obese2'
#... |
e2ce4efae04ca29fd01003b64a7da765e1e5ad0bd20252f5881beb97ade8b9e7 | Shell | 1,713 | 63 | #!/bin/csh
# JHK
# C-shell script for 7x7 occlusion sensitivity (OS)
# function selection
setenv op_gpu 'off'
# set experiment name
setenv exp_name 'dd_v01'
# set output name
set o_name = 'ERA5'
# set main directory
setenv h_dir '/home/jhkim/model/deep_detection'
# set gpu number (for multi-GPU enviro... |
bf0d3342e69bf48df9cf114639497cac95619bb265f941d53448d4d390f202c2 | Shell | 1,737 | 40 | # This script generates a subsetted genome index for use in unit tests
# The index is hosted at: http://aryee.mgh.harvard.edu/guideseq/data/Homo_sapiens.GRCh38.dna.subset.masked.fa.index.zip
# Requirements: samtools, bedtools
mkdir -p genome_prep
cd genome_prep
# Download chromosomes 1 2 3 6 15
wget ftp://ftp.ensembl... |
5d51dfcc3ef37b6151d8f16a2aeef345aaf7d024ae849f0efdbbf4c1b65c4215 | Shell | 1,740 | 56 | #!/bin/bash
####################################CONFIGERATION INFORMATION#########################################################
###LOCATIONS AND SAMPLE NAMES#########################################################################################
PPROJECT_SAMPLE_DIR=/home/labcomputer/Documents/Asela/data/20_DAPs... |
243523051d24d9e977fa611dcb79d023328316adde6dbe8581a4f64084a44f39 | Shell | 1,746 | 52 | #!/bin/sh
######################################################
# #
# ** DENTAL (de Novo Transcriptome Assembly Line) ** #
# #
######################################################
#################################... |
c284867294a26398d5f64c85d721eae9cdd9c56dc874f1dd830ddcd92485601b | Shell | 1,775 | 62 | #!/bin/csh
# JHK
# C-shell script for Shapley Additive exPlanations (SHAP) with Gradient explainer
# function selection
setenv op_gpu 'on'
setenv exp_name 'dd_v01' # experiment type
setenv h_dir '/home/jhkim/model/deep_detection' # Main directory
setenv n_gpu 0 # GPU number... |
7bbcf62e7a9c51ed8cd2a166324f3ac40b12e0db9bf9248456ed8f0aee7a38b7 | Shell | 1,831 | 45 |
#!/bin/sh
# User must supply the directory name.
dir=$1; currdir=`pwd`
ref=$2
stats="/working/lab_julietF/mainaB/Scripts/Statistics.sh"
ttestr="/working/lab_julietF/mainaB/Scripts/Ttest.R"
# Retrieve number of clusters:
nclusters=`sort -nbr -k2,2 ${currdir}/${dir}/SeuratResults/Cell_Clusters.tsv | head -n1 | c... |
e39dd0a76137a945964f2fc9c6b5a17e8b8c0864d4b457ad8d3d325d64ad096f | Shell | 1,853 | 65 | #!/bin/bash
#SBATCH --job-name=fastqc_20210628_capture
#SBATCH --partition=comp01
#SBATCH --output=fastqc_20210628_capture_%j.txt
#SBATCH --error=fastqc_20210628_capture_%j.err
#SBATCH --mail-type=ALL
#SBATCH --mail-user=awijeratne.astate.edu
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=32
#SBATCH --time=01:00:00
##... |
8582b51fdf5ae86c8e5af436778162f6c97e736eabf6c2cb736dac5f599a44b9 | Shell | 1,880 | 52 | #!/bin/sh
######################################################
# #
# ** DENTAL (de Novo Transcriptome Assembly Line) ** #
# #
######################################################
#################################... |
b004e77722ce7b9d5ad50b18bfcbc18015ad1294cde680f94472d4f4c3b04763 | Shell | 1,900 | 58 | #!/bin/sh
######################################################
# #
# ** DENTAL (de Novo Transcriptome Assembly Line) ** #
# #
######################################################
#################################... |
bdfcf5f04ca19bb17215b65ab4c38fdff125e25e69f3dd2d6c45abeca3d0cede | Shell | 1,903 | 58 | #!/bin/sh
######################################################
# #
# ** DENTAL (de Novo Transcriptome Assembly Line) ** #
# #
######################################################
#################################... |
5850cc465b7fce1b81ea0215ec7d629e4670ad4b2d30340d73cc05a6f6fa53cf | Shell | 1,904 | 52 | #!/bin/bash
channels=$1
fold=$2
tfold=$fold
if [[ $fold == "1" ]]
then
echo "WARNING: fold 1 is set to empty string!"
fold=""
fi
conda activate gfcn
if [[ $channels == "4ch" ]]
then
echo "running 4ch"
echo " Deleting files gendo_"
# rm data/gisles2018/processed/TRAINING/gendo_*.pt
echo "Training upool pro... |
5734998ec913e4df14f09e93a85ae8800b15926852da2843444224945a02ed6b | Shell | 1,906 | 58 | #!/bin/sh
######################################################
# #
# ** DENTAL (de Novo Transcriptome Assembly Line) ** #
# #
######################################################
#################################... |
1541c5894f64f7d1c550ca337f5f37a4c6359a4006d2f1b6d99e006b15fd9378 | Shell | 1,918 | 43 | #!/usr/bin/env bash
# Copyright 2015 The TensorFlow Authors. 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... |
06340223dea3f07b3cbdadda2501860cdfe44fb6084e19d48e329a0d2501b6ad | Shell | 1,933 | 22 | #!/bin/bash
set -x -e -o pipefail
#Step 1: Find low-read genes and cells for removal
normalisr -v qc_reads -s data/highmoi/0_read.mtx.gz data/highmoi/0_gene.txt data/highmoi/0_cell.txt data/highmoi/1_gene.txt data/highmoi/1_cell.txt
#Step 2: Remove found low-read genes and cells, and single-valued covariates
normalis... |
1b70ff8dc5e00c3a3bba87d3b1dda143866d25e490d3573aecaeb0aacb1f3b38 | Shell | 1,935 | 32 | # Create output directory:
mkdir AllOutMGFR
# Create 500 input files for MGFR:
seq 1 500 | while read n; do echo "Basal Her2 LumA LumB Normal" | tr ' ' '\n' | while read subtype; do grep $subtype FullSampleIDs_withType.sorted | sort -R | head -n3 >> ThreeReplicates_$n; done; done
seq 1 500 | while read n; do cut -f1 ... |
99f78ca5b85aac2086f02932712af23b75821536d948a836e7e608701db6ebfa | Shell | 1,947 | 66 | #!/bin/bash
## Build XGBoost with CUDA
## Companion script for ops/pipeline/build-cuda.sh
set -euox pipefail
# PRs and master's cache-warming pass share the same SM75 compiler-cache entries.
cuda_arch_args=()
if [[ -n "${GITHUB_BASE_REF:-}" || "${BRANCH_NAME:-}" == "master" ]]; then
# PRs reuse the SM75 cache popul... |
9db88ab9accb4a4ff1bc15c9a7f6d71e5a2d65d1d90ab6f62a8e1bd5c801e9e8 | Shell | 1,947 | 51 | #!/bin/bash
channels=$1
fold=$2
tfold=$fold
if [[ $fold == "1" ]]
then
echo "WARNING: fold 1 is set to empty string!"
fold=""
fi
conda activate gfcn
if [[ $channels == "4ch" ]]
then
echo "running 4ch"
echo "Deleting files gendo_"
# # rm data/gisles/processed/TRAINING/gendo_*.pt
tid="Pre4Ch$fold"
echo "GFC... |
c13b1d517eb35a1a54f8be5792c29babde893e100c0891316d1f357f1478d940 | Shell | 1,954 | 60 | #!/bin/sh
############################################
############################################
# #
# **GRADE in PBS Cluster** #
# General RNAseq Analysis for #
# Differential Expression #
# ... |
2f236ce783a7098c89df6de4c1194732b43b21fec05d4b22f7fb0da426be301d | Shell | 1,964 | 52 | #!/bin/bash
channels=$1
fold=$2
tfold=$fold
if [[ $fold == "1" ]]
then
echo "WARNING: fold 1 is set to empty string!"
fold=""
fi
conda activate gfcn
if [[ $channels == "4ch" ]]
then
echo "running 4ch"
echo " Deleting files gendo_"
# rm data/gisles2018/processed/TRAINING/gendo_*.pt
echo "Training upool pro... |
6f1ea000af5d40fd06b9763b82df38fc33bd739bd31d6ad42117024e29b6189c | Shell | 1,969 | 60 | #!/bin/sh
############################################
############################################
# #
# **GRADE in PBS Cluster** #
# General RNAseq Analysis for #
# Differential Expression #
# ... |
796ab93de453d4aa4a5f6b4caa88011bb3a949b5591ad36e8cd2cc646e535ec3 | Shell | 1,971 | 48 | #!/bin/sh
######################################################
# #
# ** DENTAL (de Novo Transcriptome Assembly Line) ** #
# #
######################################################
#################################... |
3ee0c459c983d2d670db1d320eb1fb256f487076f003498815c54f3542def1d4 | Shell | 1,982 | 52 | #!/bin/bash
# pull in subject
subjectID=$1
# pull in session
sessionID=$2
# pull in task
taskID=$3
# input directory containing unsmoothed data
funcDir=/home/OBIWAN/DATA/STUDY/DERIVED/ICA_ANTS/sub-${subjectID}/ses-${sessionID}/func/task-${taskID}.ica/
# output directory for preprocessed data
outDir=/home/OBIWAN/DAT... |
565940622489247068b029c282a37d4585433c41aa23b7ecd70aedeeea3d33fa | Shell | 2,011 | 49 | #!/bin/sh
######################################################
# #
# ** DENTAL (de Novo Transcriptome Assembly Line) ** #
# #
######################################################
#################################... |
eaaa5a15fef5af7d68da4e43609098dc71bc1c48fee43d21fe9fe701b587eed4 | Shell | 2,052 | 52 | #!/bin/sh
############################################
############################################
# #
# **GRADE in PBS Cluster** #
# General RNAseq Analysis for #
# Differential Expression #
# ... |
2d4d6b2afaf908befb5a1a63e6699807358ee94d6b4cb15cd949ffac81710815 | Shell | 2,056 | 52 | #!/bin/bash
#SBATCH --nodes=1
#SBATCH --cpus-per-task=40
#SBATCH --time=11:00:00
#SBATCH --job-name fmriprep_anat_ds30
#SBATCH --output=fmriprep_anat_ds30_%j.txt
source ${HOME}/code/bids-on-scinet/env/source_qbatch_python_env.sh
module load gnu-parallel/20180322
## change this to the name of your dataset
dataset="ds0... |
6c68b9a3277c3c43b7d4dcc3f0a2eaeeabbf3a6b48f35ef6c8d7271fb3d42071 | Shell | 2,075 | 27 | #!/bin/bash
set -x -e -o pipefail
#Step 1: Find low-read genes and cells for removal
normalisr qc_reads -s --gene_cell_count 500 data/de/0_read.mtx.gz data/de/0_gene.txt data/de/0_cell.txt data/de/1_gene.txt data/de/1_cell.txt
#Step 2: Remove found low-read genes and cells, and single-valued covariates
normalisr subs... |
c7da855503f9d0c44dc4ba484062a3545d07fdcdfe0186294a418d5909a8ab41 | Shell | 2,078 | 52 | #!/bin/bash
channels=$1
fold=$2
tfold=$fold
if [[ $fold == "1" ]]
then
echo "WARNING: fold 1 is set to empty string!"
fold=""
fi
conda activate gfcn
if [[ $channels == "4ch" ]]
then
echo "running 4ch"
echo "Deleting files gendo_"
# rm data/gisles/processed/TRAINING/gendo_*.pt
tid="Pre4Ch$fold"
echo "GFCN... |
11bd16952a7fb6fce6f9922a7e856d66c75d04b57264ce528ea79d4d5d170f69 | Shell | 2,112 | 55 | #!/bin/sh
######################################################
# #
# ** DENTAL (de Novo Transcriptome Assembly Line) ** #
# #
######################################################
#################################... |
e52513b86bb3704a830f6563d95236ff13f12feb2c2bb6ecea69c9c630b08a6a | Shell | 2,135 | 97 | #!/bin/bash
## Build XGBoost with CUDA
## This script runs inside a container (via GitHub Actions container support)
##
## Usage:
## build-cuda.sh --cuda-version <12|13> --use-rmm <0|1>
##
## All parameters are required (no defaults).
##
## Examples:
## # CUDA 12 xgboost-cu12 package build
## build-cuda.sh --cuda... |
eaf88c44c2b5e272ecab0434e7ee948cb30a15ca05c7313670f031757161a78b | Shell | 2,195 | 65 | #!/bin/bash
####################################CONFIGERATION INFORMATION#########################################################
###LOCATIONS AND SAMPLE NAMES#########################################################################################
file="/media/labcomputer/AWLABEX2/Asela/202204011_DAPseq_GmRav4/00_da... |
6f5d0cc49105c8beb5a0c9940d8367c7f7fac40aa5d16a480a686097394728af | Shell | 2,282 | 66 | #!/bin/bash
# pull in subject
subjectID=$1
# pull in session
sessionID=$2
# pull in task
taskID=$3
echo "Preparing subject ${subjectID}, session ${sessionID}, task ${taskID} for classification"
# T2 scan
subT2=/home/OBIWAN/DATA/STUDY/DERIVED/ICA_ANTS/sub-${subjectID}/ses-first/anat/*T2_reoriented_brain.nii.gz
# d... |
77a287b89a9e59aefb8e1d0e58fb42e6af72b360f1fc803b8839bb69f504e965 | Shell | 2,348 | 56 | #!/bin/bash
channels=$1
fold=$2
tfold=$fold
if [[ $fold == "1" ]]
then
echo "WARNING: fold 1 is set to empty string!"
fold=""
fi
conda activate gfcn
if [[ $channels == "4ch" ]]
then
echo "running 4ch"
echo "Deleting files gendo_"
# rm data/gisles/processed/TRAINING/gendo_*.pt
tid="4Ch$fold"
echo "PointNe... |
3fa3b0b32e76d886fa31b8d81fbdad7dd9f7a9e0f32b407d45d5bdf8216b2a32 | Shell | 2,428 | 43 | #!/bin/bash
# pull in subject
subjectID=$1
# pull in session
sessionID=$2
# pull in task
taskID=$3
echo "Preparing subject ${subjectID}, ${sessionID} session fieldmaps, for FEAT"
# directory containing raw nifti data
dataDir=/home/OBIWAN/DATA/STUDY/RAW/BIDS/sub-${subjectID}/ses-${sessionID}/fmap/
# output director... |
1ffedd0a090c3aa64e98a9c99a175fcdf89d03a2677d87ff8928bd91ded7427a | Shell | 2,430 | 54 | #!/bin/sh
######################################################
# #
# ** DENTAL (de Novo Transcriptome Assembly Line) ** #
# #
######################################################
#################################... |
aa77d15f64479a9fb519e98432899516d5c21347766afdc858ea18aec808a8fd | Shell | 2,484 | 80 |
#!/bin/sh
# User must supply the directory name.
dir=$1; currdir=`pwd`
MarkersHeatmap=/working/lab_julietF/mainaB/Scripts/MarkersHeatmap.R
## Markers from Literature:
markerslist=/working/lab_julietF/mainaB/Project_NormalBreast/scRNAseq/LiteratureMarkers/Markers_SeuratNaming
topmarkerslist=/working/lab_julietF/m... |
c8de7a2520d3b623482aa197fa93cbe07cac7a6abac35b506ad67d08b5ae96c7 | Shell | 2,508 | 48 | #!/bin/bash
# pull in subject
subjectID=$1
echo "Preparing subject ${subjectID}, first session, for FEAT"
# directory containing raw nifti data
dataDir=/home/OBIWAN/DATA/STUDY/RAW/BIDS/sub-${subjectID}/
# output directory for preprocessed files
outDir=/home/OBIWAN/DATA/STUDY/DERIVED/ICA_ANTS/sub-${subjectID}/ses-fir... |
f757002828839b2502a48137d1aebe6a489ab810b678640d5074053434ad4610 | Shell | 2,566 | 81 | #!/bin/bash
# Makes an eroded white matter mask and an eroded ventricle mask.
# SESS should point to the MNINonLinear folder for a subject
# Expected inputs:
# In MNINonLinear folder: aparc+aseg.nii.gz and brainmask_fs.nii.gz
if [ ! $# -eq 2 ]
then
echo "Creates an eroded white matter mask and eroded ventricle ma... |
a48d67f0c093661851ab9358f273ea7e7a3e16ce89c0cff69e9adc91dde9c686 | Shell | 2,579 | 55 | #!/bin/sh
######################################################
# #
# ** DENTAL (de Novo Transcriptome Assembly Line) ** #
# #
######################################################
#################################... |
b816dd526148eb8c5793a9d947ea606eb14a5bd060e9eaa0eab0c2fe4874102e | Shell | 2,591 | 66 | #!/bin/bash
# This is an example of a script that will three post-processing ciftify functions using singularity exec
# The three functions are:
# ciftify_clean_img - to denoise and smooth the scans
# ciftify_PINT_vertices - to run PINT
# cifti_vis_PINT - to build PINT qc pages
# the inputs are:
# subject -> the s... |
0e049530ebc0a98298f2769a0fd07139602ad31959be5820c6e0e7da4261e5b7 | Shell | 2,838 | 86 | #!/bin/csh
# JHK
# C-shell script for Deep Detection model
# function selection
setenv op_train 'on' # train on/off
setenv op_test 'on' # test on/off
setenv op_ensmean 'on' # ensemble average on/off
setenv op_gpu 'off' # using GPU on/off
setenv exp_name 'dd_v01' # experiment name
# set outpu... |
0ccad9f46294e3a8b668e4e7e34c0b7f5eb4281cc195854eb8d31a9101f363f3 | Shell | 2,876 | 97 | #!/bin/bash
#SBATCH --job-name=bbduk_0210628_capture
#SBATCH --partition=comp06
#SBATCH --output=bbduk_0210628_capture_%j.txt
#SBATCH --error=bbduk_0210628_capture_%j.err
#SBATCH --mail-type=ALL
#SBATCH --mail-user=awijeratne.astate.edu
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=24
#SBATCH --time=04:00:00
########... |
347735d4d24522316a2b048462ab4b4e6e9d72e161a90c0de64d1e8aab6131a4 | Shell | 2,879 | 39 | #!/bin/bash
TITLE=Butyrate
FASTQ1_1=/srv/scratch/shared/surya/leepc12/data/bfremin/ATAC-SEQ/But-1-60K-CAGAGAGG_S3_R1_001.fastq.gz
FASTQ1_2=/srv/scratch/shared/surya/leepc12/data/bfremin/ATAC-SEQ/But-1-60K-CAGAGAGG_S3_R2_001.fastq.gz
FASTQ2_1=/srv/scratch/shared/surya/leepc12/data/bfremin/ATAC-SEQ/But-2-60K-AAGAGGCA_S4... |
da89167934414c36e012aab67153467c2a603018f561bcf7895a961e1387af7f | Shell | 2,926 | 55 | #!/bin/sh
######################################################
# #
# ** DENTAL (de Novo Transcriptome Assembly Line) ** #
# #
######################################################
#################################... |
b1cc0df83f5df487ad9080575704dee488bbf789d64c290c891be303e085286e | Shell | 2,991 | 65 | #!/bin/sh
######################################################
# #
# ** DENTAL (de Novo Transcriptome Assembly Line) ** #
# #
######################################################
#################################... |
6516f74cec9b37fa4f2a7c57bb4b992e2d82361066f870a5a2475fdf63ed8d10 | Shell | 3,055 | 24 | #!/bin/bash
python training.py -s GISLES2018 -n GFCNC -b 4 -c DCSsigmoid -O True -t True -N 10 --id DCSsigmoid4Ch -lr 1E-8 -g 100 --mod TMAX CBF CBV MTT --weight 5.5 -D experiment1_loss/ -X True --useful True > experiment1_loss/gfcnc_DCSsigmoid4Ch_eval.log
python training.py -s GISLES2018 -n GFCNC -b 4 -c DCSsigmoid... |
3e5a8958e90f2d66f3d191c4222251d45151bf2ae672182babede1e8280c30f7 | Shell | 3,193 | 129 | # Common code fragment for tests
#
srcdir=${srcdir:-.}
BUILDDIR=`pwd`
SRCDIR=`dirname $0`
SRCDIR=`cd $SRCDIR && pwd`
TOPSRCDIR=`cd $srcdir/.. && pwd`
TOOLS=`cd ../tools && pwd`
IMAGES="${SRCDIR}/images"
# Aliases for built tools
BMP2TIFF=${TOOLS}/bmp2tiff
FAX2PS=${TOOLS}/fax2ps
FAX2TIFF=${TOOLS}/fax2tiff
GIF2TIFF=${TO... |
d350ef5630a9710128fdce452b246e95e7b73e72aa4bd3ce159e84dde7d44fb9 | Shell | 3,292 | 86 |
#!/bin/sh
############################################
############################################
# #
# **GRADE in PBS Cluster** #
# General RNAseq Analysis for #
# Differential Expression #
# ... |
dfeeb091bcc5a3a405d3d1556d055401465243324a32a88512d6f0f56df68fad | Shell | 3,293 | 80 | #!/bin/sh
############################################
############################################
# #
# **GRADE in PBS Cluster** #
# General RNAseq Analysis for #
# Differential Expression #
# ... |
3faadf9f62f9bce99c341293e18c783cb2b1ddd3cb2eb95c22f14274d15cea3b | Shell | 3,297 | 63 | #!/bin/bash
channels=$1
fold=$2
tfold=$fold
if [[ $fold == "1" ]]
then
echo "WARNING: fold 1 is set to empty string!"
fold=""
fi
conda activate gfcn
if [[ $channels == "4ch" ]]
then
echo "running 4ch"
echo "Deleting files gendo_"
# rm data/gisles/processed/TRAINING/gendo_*.pt
tid="4Ch$fold"
echo "PointNe... |
9d9a324faa6595a50b01c75dee9b294b778c87b502677a31e9d761b00880e3e6 | Shell | 3,324 | 46 | #!/bin/bash
set -x -e -o pipefail
#For more verbosity, use verbose="-v"
verbose=""
#Gene name system as provided. Details see normalisr gocovt -h.
genefrom="symbol,alias"
#Gene name system of GO annotations. Details see normalisr gocovt -h.
geneto="uniprot.Swiss-Prot"
#Species for gene name conversion.
species="human... |
4682d7caa319e2b80980f3cda6c44a2a59b09dce95dd19585cd4ba1e1bafcf00 | Shell | 3,386 | 122 | #! /bin/sh
###############
#### Setup ####
###############
MODEL_MLCUBE_TEMPLATE=../../mlcube/model_mlcube/mlcube_medperf.yaml
METRICS_MLCUBE_TEMPLATE=../../mlcube/metrics_mlcube/mlcube_medperf.yaml
MODEL_MLCUBE_ENTRYPOINT=../../mlcube/model_mlcube/example_custom_entrypoint/getting_started_3d_rad_seg.py
METRICS_MLCU... |
8ef00a6167e20255daaabb2a89fb630e39fd5d6f0eaa7d978ee35c5f07de6d96 | Shell | 3,497 | 69 | #!/bin/bash
# pull in subject
subjectID=$1
# pull in session
sessionID=$2
# pull in task
taskID=$3
echo "Preparing subject ${subjectID} session ${sessionID} task ${taskID}"
# subject directory
subT2=/home/OBIWAN/DATA/STUDY/DERIVED/ICA_ANTS/sub-${subjectID}/ses-first/anat/sub-${subjectID}_ses-first_run-01_T2_reorie... |
2c0a8cabc678d9b9293988b42cb4e1706bd4254b8b1be364442feb528d50366d | Shell | 3,536 | 94 |
#!/bin/sh
############################################
############################################
# #
# **GRADE in PBS Cluster** #
# General RNAseq Analysis for #
# Differential Expression #
# ... |
a9a20fb6d482a2c2aabfb09c259845575140efbaa87d90a681640a098543f483 | Shell | 3,545 | 64 | #!/bin/sh
######################################################
# #
# ** DENTAL (de Novo Transcriptome Assembly Line) ** #
# #
######################################################
#################################... |
fb0cc287a4d8cf4a2edcf684d7460d86c990b9b5d00e3db1e47075fc58e79774 | Shell | 3,563 | 75 | #!/bin/bash
channels=$1
fold=$2
tfold=$fold
if [[ $fold == "1" ]]
then
echo "WARNING: fold 1 is set to empty string!"
fold=""
fi
conda activate gfcn
if [[ $channels == "4ch" ]]
then
echo "running 4ch"
echo " Deleting files gendo_"
# rm data/gisles2018/processed/TRAINING/gendo_*.pt
echo "Training upool pro... |
e258c285fb19a6080f06ff220b290917d793523659bf07cafd5efbbd6e6f3cb7 | Shell | 3,564 | 69 | #!/bin/sh
######################################################
# #
# ** DENTAL (de Novo Transcriptome Assembly Line) ** #
# #
######################################################
#################################... |
7026991755ad62124bd170035550a9e3b6067b9897bb9409f47e4495de4e47e8 | Shell | 3,568 | 178 | #!/usr/bin/env bash
set -euo pipefail
ensure_var () {
if [ ! -d "${CONDA_PREFIX}/var/mysql" ]; then
mkdir -p "${CONDA_PREFIX}/var/mysql"
fi
}
config_mysql_db () {
ensure_var
mysqld --initialize-insecure \
--user="$(whoami)" \
--datadir="${CONDA_PREFIX}/var/mysql"
}
destroy_mysql_db ()... |
42e66cc3e0e9d52edcc820fabc5b641c571eca27145b03b74827f3288bf94f9a | Shell | 3,579 | 69 | #!/bin/bash
channels=$1
fold=$2
tfold=$fold
if [[ $fold == "1" ]]
then
echo "WARNING: fold 1 is set to empty string!"
fold=""
fi
conda activate gfcn
if [[ $channels == "4ch" ]]
then
echo "running 4ch"
echo "Deleting files gendo_"
# rm data/gisles/processed/TRAINING/gendo_*.pt
tid="Pos4Ch$fold"
echo "GFCN... |
c9a9c9bcc67039a1ce1430917ec7580b6d6e5f9a38f971339adbc1f18973c16c | Shell | 3,698 | 62 | #!/bin/sh
######################################################
# #
# ** DENTAL (de Novo Transcriptome Assembly Line) ** #
# #
######################################################
#################################... |
6a9c09a3d58cd57b5693077791fd2e167c9dc22d2c19f18ac0b032f655ff7ebb | Shell | 3,713 | 75 | #!/bin/bash
channels=$1
fold=$2
tfold=$fold
if [[ $fold == "1" ]]
then
echo "WARNING: fold 1 is set to empty string!"
fold=""
fi
conda activate gfcn
if [[ $channels == "4ch" ]]
then
echo "running 4ch"
echo " Deleting files gendo_"
# rm data/gisles2018/processed/TRAINING/gendo_*.pt
echo "Training upool pro... |
3005e16728b9db59bbcc430c93f2cf93c60af97f3d9a17635156ffdc2a47da33 | Shell | 3,738 | 87 | #!/bin/sh
############################################
############################################
# #
# **GRADE in PBS Cluster** #
# General RNAseq Analysis for #
# Differential Expression #
# ... |
45ac9b9f0f4ec216c9266c215e42cb5ccedeb3258e41266acf293adadf7b7e04 | Shell | 3,758 | 69 | #!/bin/bash
channels=$1
fold=$2
tfold=$fold
if [[ $fold == "1" ]]
then
echo "WARNING: fold 1 is set to empty string!"
fold=""
fi
conda activate gfcn
if [[ $channels == "4ch" ]]
then
echo "running 4ch"
echo "Deleting files gendo_"
# rm data/gisles/processed/TRAINING/gendo_*.pt
tid="Pos4Ch$fold"
echo "GFCN... |
d5daee7b25913d410bb1277e3007abddb6ab69c0c550b874b55510a05033e2a6 | Shell | 3,782 | 69 | #!/bin/bash
channels=$1
fold=$2
tfold=$fold
if [[ $fold == "1" ]]
then
echo "WARNING: fold 1 is set to empty string!"
fold=""
fi
conda activate gfcn
if [[ $channels == "4ch" ]]
then
echo "running 4ch"
echo "Deleting files gendo_"
# rm data/gisles/processed/TRAINING/gendo_*.pt
tid="Pre4Ch$fold"
echo "GFCN... |
6f876ae2a98ad3ea4cf2a66ee566e16ee82fee5aa7e41cdca3f9ac911e4e250f | Shell | 3,795 | 88 | #!/bin/bash
# #############
# set this to the directory containing antsRegistration
ANTSPATH=/usr/local/ants/bin/
# ITK thread count
ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=1
export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS
# Check args
if [ $# -lt 1 ]; then
echo "USAGE: $0 <sbj>"
exit
fi
sbj=$1
echo Sbject: $sbj
# path... |
ff972fc0c9e1b7e8ac6fbddc526ba8b4cc84340876956f9f34cf3f1b70fd59ab | Shell | 3,943 | 142 | #!/bin/bash
## Script to test Python wheels, to be called from CI workflow
##
## Usage:
## ops/pipeline/test-python-wheel.sh --suite <suite> [--cuda-version <12|13>]
##
## --suite is required. --cuda-version is required for GPU suites but optional for CPU suites.
set -eo pipefail
suite=""
cuda_version=""
# Parse a... |
a4067dadda6a4a3fff5d9cc11794d64dd996d4119320771f29727df0d85cb65a | Shell | 3,965 | 69 | #!/bin/bash
channels=$1
fold=$2
tfold=$fold
if [[ $fold == "1" ]]
then
echo "WARNING: fold 1 is set to empty string!"
fold=""
fi
conda activate gfcn
if [[ $channels == "4ch" ]]
then
echo "running 4ch"
echo "Deleting files gendo_"
# rm data/gisles2018/processed/TRAINING/gendo_*.pt
tid="Pre4Ch$fold"
echo "... |
8763c475f8be2b6c1a91f71c8fdb91dc92f510bb48999038e5aa10eefda05c31 | Shell | 3,993 | 139 | #!/bin/bash
# Stop on error
set -e
## conda environment name
ENV_NAME=bds_atac
ENV_NAME_PY3=bds_atac_py3
INSTALL_GEM=0
INSTALL_PEAKSEQ=0
## install packages from official channels (bioconda and r)
conda create -n ${ENV_NAME} --file requirements.txt -y -c defaults -c bioconda -c r -c bcbio -c daler -c asmeurer
cond... |
6403a7efb26dfddf9e0822700f84c6031be45e587908708e47285fa1b49eb871 | Shell | 4,097 | 62 | #!/bin/sh
######################################################
# #
# ** DENTAL (de Novo Transcriptome Assembly Line) ** #
# #
######################################################
#################################... |
76f921349477e826e4a7262fc4e233ce440d1c464a984ff4d98782ddef7452e1 | Shell | 4,150 | 115 | #!/bin/bash
#
# Affine registration of different modalities from the same subject (eg T1 and T2) with
# slightly different geometry or head position (motion, etc)
#
# AUTHOR : Wolfgang Pauli
# PLACE : Caltech
# DATES : 01/08/2015
# ITK thread count
ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=1
export ITK_GLOBAL_DEFAULT_NUMBE... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.