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slideQuantify_v2_4_cellprofiler.sh
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slideQuantify_v2_4_cellprofiler.sh
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#!/bin/bash
#
# Description: Runs CellProfiler as part of a slideQuantify job-session.
#
# The MIT License (MIT)
# Copyright (c) 2014-2021, Bas G.L. Nelissen, Sander W. van der Laan,
# UMC Utrecht, Utrecht, the Netherlands.
#
# Permission is hereby granted, free of charge, to any person obtaining a
# copy of this software and associated documentation files (the
# "Software"), to deal in the Software without restriction, including
# without limitation the rights to use, copy, modify, merge, publish,
# distribute, sublicense, and/or sell copies of the Software, and to
# permit persons to whom the Software is furnished to do so, subject to
# the following conditions:
#
# The above copyright notice and this permission notice shall be included
# in all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
# OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
# MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
# IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY
# CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
# TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
# SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
#
### Creating display functions
### Setting colouring
NONE='\033[00m'
BOLD='\033[1m'
ITALIC='\033[3m'
OPAQUE='\033[2m'
FLASHING='\033[5m'
UNDERLINE='\033[4m'
RED='\033[01;31m'
GREEN='\033[01;32m'
YELLOW='\033[01;33m'
PURPLE='\033[01;35m'
CYAN='\033[01;36m'
WHITE='\033[01;37m'
### Regarding changing the 'type' of the things printed with 'echo'
### Refer to:
### - http://askubuntu.com/questions/528928/how-to-do-underline-bold-italic-strikethrough-color-background-and-size-i
### - http://misc.flogisoft.com/bash/tip_colors_and_formatting
### - http://unix.stackexchange.com/questions/37260/change-font-in-echo-command
### echo -e "\033[1mbold\033[0m"
### echo -e "\033[3mitalic\033[0m" ### THIS DOESN'T WORK ON MAC!
### echo -e "\033[4munderline\033[0m"
### echo -e "\033[9mstrikethrough\033[0m"
### echo -e "\033[31mHello World\033[0m"
### echo -e "\x1B[31mHello World\033[0m"
function echobold { #'echobold' is the function name
echo -e "${BOLD}${1}${NONE}" # this is whatever the function needs to execute, note ${1} is the text for echo
}
function echoitalic {
echo -e "${ITALIC}${1}${NONE}"
}
function echocyan {
echo -e "${CYAN}${1}${NONE}"
}
function echonooption {
echo -e "${OPAQUE}${RED}${1}${NONE}"
}
# errors
function echoerrorflash {
echo -e "${RED}${BOLD}${FLASHING}${1}${NONE}"
}
function echoerror {
echo -e "${RED}${1}${NONE}"
}
# errors no option
function echoerrornooption {
echo -e "${YELLOW}${1}${NONE}"
}
function echoerrorflashnooption {
echo -e "${YELLOW}${BOLD}${FLASHING}${1}${NONE}"
}
### MESSAGE FUNCTIONS
script_copyright_message() {
echo ""
THISYEAR=$(date +'%Y')
echo "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
echo "+ The MIT License (MIT) +"
echo "+ Copyright (c) 2016-${THISYEAR} Sander W. van der Laan +"
echo "+ +"
echo "+ Permission is hereby granted, free of charge, to any person obtaining a copy of this software and +"
echo "+ associated documentation files (the \"Software\"), to deal in the Software without restriction, +"
echo "+ including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, +"
echo "+ and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, +"
echo "+ subject to the following conditions: +"
echo "+ +"
echo "+ The above copyright notice and this permission notice shall be included in all copies or substantial +"
echo "+ portions of the Software. +"
echo "+ +"
echo "+ THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT +"
echo "+ NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND +"
echo "+ NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES +"
echo "+ OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN +"
echo "+ CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. +"
echo "+ +"
echo "+ Reference: http://opensource.org. +"
echo "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
}
script_arguments_error() {
echoerror "$1" # ERROR MESSAGE
echoerror "- Argument #1 -- path_to data directory"
echoerror "- Argument #2 -- path_to CellProfiler pipeline, e.g. FIBRIN.cppipe."
echoerror "- Argument #3 -- name of the stain as it appears in the filenames, e.g. FIBRIN."
echoerror "- Argument #4 -- slidenumber being processed (should contain no spaces)"
echoerror "- Argument #5 -- path to tiles directory."
echoerror ""
echoerror "An example command would be: slideQuantify_cellprofiler [arg1: path_to_dir] [arg2: path_to_cellprofiler_pipeline] [arg3: STAIN] [arg4: slide_number] [args5: /path/to/dir] "
echoerror ""
echoerror "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
# The wrong arguments are passed, so we'll exit the script now!
exit 1
}
echo "++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
echobold " slideQuantify: CellProfiler"
echo ""
echoitalic "* Written by : Sander W. van der Laan; Tim Bezemer; Tim van de Kerkhof"
echoitalic " Yipei Song, Tim Peters"
echoitalic "* E-mail : [email protected]"
echoitalic "* Last update : 2021-11-25"
echoitalic "* Version : 2.1.0"
echo ""
echoitalic "* Description : This script will start the quantification for a given stain"
echoitalic " in a given project directory using CellProfiler *after* "
echoitalic " processing with masking, tiling, and normalizing."
echoitalic " This is SLURM based."
echo ""
echo "++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
echo ""
### REQUIRED | GENERALS
DATADIR="$1"
PIPELINE="$2" # Depends on arg1
### OPTIONAL | GENERALS
### https://stackoverflow.com/questions/9332802/how-to-write-a-bash-script-that-takes-optional-input-arguments
STAIN="$3" # Depends on arg2
SLIDE_NUM="$4" # Depends on arg2
TILESDIR="$5"
### START of if-else statement for the number of command-line arguments passed ###
if [[ $# -lt 5 ]]; then
echo "Oh, computer says no! Number of arguments found \"$#\"."
script_arguments_error "You must supply correct (number of) arguments when running *** slideQuantify_4_cellprofiler ***!"
else
# Reference
# https://stackoverflow.com/questions/8903239/how-to-calculate-time-elapsed-in-bash-script
SECONDS=0
# do some work
# we check wether there is output already; if so, we exit
if [[ -d $DATADIR/cp_output/$SLIDE_NUM ]]; then
echo "..... CellProfiler was already run, or at least there is a cp_output-directory."
exit
# else
# creating necessary output directory
# echo "..... > making output directory..."
# mkdir -pv cp_output/$SLIDE_NUM
fi
echo "..... Starting CellProfiler run."
### Loading the CellProfiler-Anaconda3.8 environment
### You need to also have the conda init lines in your .bash_profile/.bashrc file
echo "..... > loading required anaconda environment containing the CellProfiler installation..."
eval "$(conda shell.bash hook)"
conda activate cp427
echo Loaded conda environment: $CONDA_PREFIX
echo ""
echo "..... > checking CellProfiler version..."
cellprofiler --version
# running cellprofiler
echo "..... Running CellProfiler using $PIPELINE for [ $SLIDE_NUM ] samples stained with [ $STAIN ]."
cellprofiler -c -r -p $PIPELINE --file-list $TILESDIR/files2cp.txt -o $DATADIR/cp_output/$SLIDE_NUM/;
echo "..... CellProfiler successfully finished."
duration=$SECONDS
echo "[ $(($duration / 60)) minutes and $(($duration % 60)) seconds elapsed ]"
### END of if-else statement for the number of command-line arguments passed ###
fi
script_copyright_message