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Commit 14be1720 authored by Anne-Sophie Denommé-Pichon's avatar Anne-Sophie Denommé-Pichon
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launch_ehdn.sh
View file @ 14be1720
#! /bin/sh #! /bin/sh
### ASDP PIPELINE ### ### ASDP PIPELINE ###
## launch_wrapper_ehdn.sh ## Version: 0.0.1
## Version : 0.0.1 ## Licence: AGPLv3
## Licence : FIXME ## Author: anne-sophie.denomme-pichon@u-bourgogne.fr
## Description : script to launch the wrapper for qsubing ExpansionHunter denovo script for STR detection ## Description: script to launch the wrapper for qsubing ExpansionHunter denovo script for STR detection
## Usage :
## Output : FIXME
## Requirements : FIXME
## Author : anne-sophie.denomme-pichon@u-bourgogne.fr
## Creation Date : 20191102
## last revision date : 20191126
## Known bugs : None
INPUTFILE=/work/gad/shared/analyse/STR/pipeline/dijen073/dijen073.bam INPUTFILE=/work/gad/shared/analyse/STR/pipeline/dijen073/dijen073.bam
DATE="$(date +"%F_%H-%M-%S")" DATE="$(date +"%F_%H-%M-%S")"
......
launch_ehdn_outlier.sh
View file @ 14be1720
...@@ -2,16 +2,10 @@ ...@@ -2,16 +2,10 @@
### ASDP PIPELINE ### ### ASDP PIPELINE ###
## Version: 0.0.1 ## Version: 0.0.1
## Licence: FIXME ## Licence: AGPLv3
## Author: anne-sophie.denomme-pichon@u-bourgogne.fr
## Description: script to launch the wrapper for qsubing outlier analysis by ExpansionHunter denovo script for STR detection ## Description: script to launch the wrapper for qsubing outlier analysis by ExpansionHunter denovo script for STR detection
## Usage: FIXME
## Output: FIXME
## Requirements: FIXME
## Author: anne-sophie.denomme-pichon@u-bourgogne.fr
## Creation Date: 20200215
## Last revision date: 20200215
## Known bugs: None
CASE="$1" CASE="$1"
DATE="$(date +"%F_%H-%M-%S")" DATE="$(date +"%F_%H-%M-%S")"
......
launch_expansionhunter.sh
View file @ 14be1720
#! /bin/sh #! /bin/sh
### ASDP PIPELINE ### ### ASDP PIPELINE ###
## launch_wrapper_expansionhunter.sh ## Version: 0.0.1
## Version : 0.0.1 ## Licence: AGPLv3
## Licence : FIXME ## Author: anne-sophie.denomme-pichon@u-bourgogne.fr
## Description : script to launch the wrapper for qsubing ExpansionHunter script for STR detection ## Description: script to launch the wrapper for qsubing ExpansionHunter script for STR detection
## Usage :
## Output : FIXME
## Requirements : FIXME
## Author : anne-sophie.denomme-pichon@u-bourgogne.fr
## Creation Date : 20191102
## last revision date : 20191126
## Known bugs : None
INPUTFILE=/work/gad/shared/analyse/STR/Data/dijen561.bam INPUTFILE=/work/gad/shared/analyse/STR/Data/dijen561.bam
DATE="$(date +"%F_%H-%M-%S")" DATE="$(date +"%F_%H-%M-%S")"
......
launch_gangstr.sh
View file @ 14be1720
#! /bin/sh #! /bin/sh
### ASDP PIPELINE ### ### ASDP PIPELINE ###
## launch_wrapper_gangstr.sh ## Version: 0.0.1
## Version : 0.0.1 ## Licence: AGPLv3
## Licence : FIXME ## Author: anne-sophie.denomme-pichon@u-bourgogne.fr
## Description : script to launch the wrapper for qsubing GangSTR script for STR detection ## Description: script to launch the wrapper for qsubing GangSTR script for STR detection
## Usage : FIXME
## Output : FIXME
## Requirements : FIXME
## Author : anne-sophie.denomme-pichon@u-bourgogne.fr
## Creation Date : 20191104
## last revision date : 20191126
## Known bugs : None
INPUTFILE=/work/gad/shared/analyse/STR/Data/dijen017/offtargetdijen017/dijen017.offtarget.bam INPUTFILE=/work/gad/shared/analyse/STR/Data/dijen017/offtargetdijen017/dijen017.offtarget.bam
DATE="$(date +"%F_%H-%M-%S")" DATE="$(date +"%F_%H-%M-%S")"
......
launch_pipeline_ehdn.sh
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...@@ -2,16 +2,10 @@ ...@@ -2,16 +2,10 @@
### ASDP PIPELINE ### ### ASDP PIPELINE ###
## Version: 0.0.1 ## Version: 0.0.1
## Licence: FIXME ## Licence: AGPLv3
## Author : anne-sophie.denomme-pichon@u-bourgogne.fr
## Description : script to launch the pipeline for STR detection with EHDN outlier ## Description : script to launch the pipeline for STR detection with EHDN outlier
## Usage :
## Output : FIXME
## Requirements : FIXME
## Author : anne-sophie.denomme-pichon@u-bourgogne.fr
## Creation Date : 20200215
## last revision date : 20200215
## Known bugs : None
LAUNCHER="$(readlink -f "$(dirname "$0")/launch_ehdn_outlier.sh")" LAUNCHER="$(readlink -f "$(dirname "$0")/launch_ehdn_outlier.sh")"
......
launch_transfer.sh
View file @ 14be1720
#! /bin/sh #! /bin/sh
### ASDP PIPELINE ### ### ASDP PIPELINE ###
## launch_wrapper_transfer.sh ## Version: 0.0.1
## Version : 0.0.1 ## Licence: AGPLv3
## Licence : FIXME
## Description : script to launch the wrapper for qsubing ExpansionHunter denovo script for STR detection
## Usage :
## Output : FIXME
## Requirements : FIXME
## Author : anne-sophie.denomme-pichon@u-bourgogne.fr ## Author : anne-sophie.denomme-pichon@u-bourgogne.fr
## Creation Date : 20191102 ## Description: script to launch the wrapper for qsubing ExpansionHunter denovo script for STR detection
## last revision date : 20191126
## Known bugs : None
INPUTFILE="/archive/gad/shared/bam_new_genome_temp/dijen016.bam" INPUTFILE="/archive/gad/shared/bam_new_genome_temp/dijen016.bam"
DATE="$(date +"%F_%H-%M-%S")" DATE="$(date +"%F_%H-%M-%S")"
......
launch_tredparse.sh
View file @ 14be1720
#! /bin/sh #! /bin/sh
### ASDP PIPELINE ### ### ASDP PIPELINE ###
## launch_wrapper_tredparse.sh ## Version: 0.0.1
## Version : 0.0.1 ## Licence: AGPLv3
## Licence : FIXME
## Description : script to launch the wrapper for qsubing Tredparse script for STR detection
## Usage : FIXME
## Output : FIXME
## Requirements : FIXME
## Author : anne-sophie.denomme-pichon@u-bourgogne.fr ## Author : anne-sophie.denomme-pichon@u-bourgogne.fr
## Creation Date : 20191103 ## Description: script to launch the wrapper for qsubing Tredparse script for STR detection
## last revision date : 20191126
## Known bugs : None
INPUTFILE=/work/gad/shared/analyse/STR/Data/dijen561.bam INPUTFILE=/work/gad/shared/analyse/STR/Data/dijen561.bam
DATE="$(date +"%F_%H-%M-%S")" DATE="$(date +"%F_%H-%M-%S")"
......
pipeline.sh
View file @ 14be1720
#! /bin/sh #! /bin/sh
### ASDP PIPELINE ### ### ASDP PIPELINE ###
## Version : 0.0.1 ## Version: 0.0.1
## Licence : FIXME ## Licence: AGPLV3
## Description : script to launch the pipeline for STR detection ## Author: anne-sophie.denomme-pichon@u-bourgogne.fr
## Usage : ## Description: script to launch the pipeline for STR detection
## Author : anne-sophie.denomme-pichon@u-bourgogne.fr
## Creation Date : 20191208
## last revision date : 20200606
# $1 : first argument in the command line : the input file # $1 : first argument in the command line : the input file
SAMPLE="$1" SAMPLE="$1"
......
wrapper_delete.sh
View file @ 14be1720
#! /bin/sh #! /bin/sh
### ASDP PIPELINE ### ### ASDP PIPELINE ###
## wrapper_delete.sh ## Version: 0.0.1
## Version : 0.0.1 ## Licence: AGPLV3
## Licence : FIXME ## Author: anne-sophie.denomme-pichon@u-bourgogne.fr
## Description : a wrapper for qsubing bam deletion for STR pipeline ## Description: a wrapper for qsubing bam deletion for STR pipeline
## Usage : qsub -pe smp 1 -v SAMPLE=<sample>,[LOGFILE=<path to the log file>] wrapper_delete.sh ## Usage: qsub -pe smp 1 -v SAMPLE=<sample>,[LOGFILE=<path to the log file>] wrapper_delete.sh
## Output : FIXME
## Requirements : FIXME
## Author : anne-sophie.denomme-pichon@u-bourgogne.fr
## Creation Date : 20191208
## last revision date : 20191208
## Known bugs : None
# Log file path option # Log file path option
......
wrapper_ehdn.sh
View file @ 14be1720
#! /bin/sh #! /bin/sh
### ASDP PIPELINE ### ### ASDP PIPELINE ###
## wrapper_ehdn.sh ## Version: 0.0.1
## Version : 0.0.1 ## Licence: AGPLv3
## Licence : FIXME ## Author: anne-sophie.denomme-pichon@u-bourgogne.fr
## Description : a wrapper for qsubing ExpansionHunter denovo script for STR detection ## Description: a wrapper for qsubing ExpansionHunter denovo script for STR detection
## Usage : qsub -pe smp 1 -v INPUTFILE=<path to the bam file>,OUTPUTPREFIX=<output prefix>,[LOGFILE=<path to the log file>] wrapper_ehdn.sh ## Usage: qsub -pe smp 1 -v INPUTFILE=<path to the bam file>,OUTPUTPREFIX=<output prefix>,[LOGFILE=<path to the log file>] wrapper_ehdn.sh
## Output : FIXME
## Requirements : FIXME
## Author : anne-sophie.denomme-pichon@u-bourgogne.fr
## Creation Date : 20191208
## last revision date : 20191208
## Known bugs : None
# Log file path option # Log file path option
......
wrapper_ehdn_outlier.sh
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...@@ -2,16 +2,10 @@ ...@@ -2,16 +2,10 @@
### ASDP PIPELINE ### ### ASDP PIPELINE ###
## Version: 0.0.1 ## Version: 0.0.1
## Licence: FIXME ## Licence: AGPLv3
## Author: anne-sophie.denomme-pichon@u-bourgogne.fr
## Description: script to generate automatically a manifest and multisampleprofile in a tsv format, then do outlier analyses for a single patient ## Description: script to generate automatically a manifest and multisampleprofile in a tsv format, then do outlier analyses for a single patient
## Usage: FIXME
## Output: FIXME
## Requirements: FIXME
## Author: anne-sophie.denomme-pichon@u-bourgogne.fr
## Creation Date: 20200215
## Last revision date: 20200215
## Known bugs: None
EHDN="/work/gad/shared/bin/expansionhunterdenovo/ExpansionHunterDenovo-v0.8.0-linux_x86_64/bin/ExpansionHunterDenovo-v0.8.0" EHDN="/work/gad/shared/bin/expansionhunterdenovo/ExpansionHunterDenovo-v0.8.0-linux_x86_64/bin/ExpansionHunterDenovo-v0.8.0"
EHDN_OUTLIER="/work/gad/shared/bin/expansionhunterdenovo/ExpansionHunterDenovo-v0.8.0-linux_x86_64/scripts/outlier.py" EHDN_OUTLIER="/work/gad/shared/bin/expansionhunterdenovo/ExpansionHunterDenovo-v0.8.0-linux_x86_64/scripts/outlier.py"
......
wrapper_expansionhunter.sh
View file @ 14be1720
#! /bin/sh #! /bin/sh
### ASDP PIPELINE ### ### ASDP PIPELINE ###
## wrapper_expansionhunter.sh ## Version: 0.0.1
## Version : 0.0.1 ## Licence: AGPLv3
## Licence : FIXME ## Author: anne-sophie.denomme-pichon@u-bourgogne.fr
## Description : a wrapper for qsubing ExpansionHunter script for STR detection ## Description: a wrapper for qsubing ExpansionHunter script for STR detection
## Usage : qsub -pe smp 1 -v INPUTFILE=<path to the bam file>,OUTPUTPREFIX=<output prefix>,[LOGFILE=<path to the log file>] wrapper_expansionhunter.sh ## Usage: qsub -pe smp 1 -v INPUTFILE=<path to the bam file>,OUTPUTPREFIX=<output prefix>,[LOGFILE=<path to the log file>] wrapper_expansionhunter.sh
## Output : FIXME
## Requirements : FIXME
## Author : anne-sophie.denomme-pichon@u-bourgogne.fr
## Creation Date : 20191102
## last revision date : 20191102
## Known bugs : None
# Log file path option # Log file path option
......
wrapper_gangstr.sh
View file @ 14be1720
#! /bin/sh #! /bin/sh
### ASDP PIPELINE ### ### ASDP PIPELINE ###
## wrapper_gangstr.sh ## Version: 0.0.1
## Version : 0.0.1 ## Licence: AGPLv3
## Licence : FIXME ## Author: anne-sophie.denomme-pichon@u-bourgogne.fr
## Description : a wrapper for qsubing GangSTR script for STR detection ## Description: a wrapper for qsubing GangSTR script for STR detection
## Usage : qsub -pe smp 1 -v INPUTFILE=<path to the bam file>,OUTPUTPREFIX=<output prefix>,[LOGFILE=<path to the log file>] wrapper_gangstr.sh ## Usage: qsub -pe smp 1 -v INPUTFILE=<path to the bam file>,OUTPUTPREFIX=<output prefix>,[LOGFILE=<path to the log file>] wrapper_gangstr.sh
## Output : FIXME
## Requirements : FIXME
## Author : anne-sophie.denomme-pichon@u-bourgogne.fr
## Creation Date : 20191104
## last revision date : 20191127
## Known bugs : None
# Log file path option # Log file path option
if [ -z "$LOGFILE" ] if [ -z "$LOGFILE" ]
......
wrapper_stretch.sh
View file @ 14be1720
#! /bin/sh #! /bin/sh
### ASDP PIPELINE ### ### ASDP PIPELINE ###
## wrapper_stretch.sh ## Version: 0.0.1
## Version : 0.0.1 ## Licence: AGPLv3
## Licence : FIXME ## Author: anne-sophie.denomme-pichon@u-bourgogne.fr
## Description : a wrapper for qsubing STRetch script for STR detection ## Description: a wrapper for qsubing STRetch script for STR detection
## Usage : qsub -pe smp 1 -v INPUTFILE=<path to the bam file>,OUTPUTPREFIX=<output prefix>,[LOGFILE=<path to the log file>] wrapper_stretch.sh ## Usage: qsub -pe smp 1 -v INPUTFILE=<path to the bam file>,OUTPUTPREFIX=<output prefix>,[LOGFILE=<path to the log file>] wrapper_stretch.sh
## Output : FIXME
## Requirements : FIXME
## Author : anne-sophie.denomme-pichon@u-bourgogne.fr
## Creation Date : 20191118
## last revision date : 20191118
## Known bugs : None
# Log file path option # Log file path option
......
wrapper_transfer.sh
View file @ 14be1720
#! /bin/sh #! /bin/sh
### ASDP PIPELINE ### ### ASDP PIPELINE ###
## wrapper_transfer.sh ## Version: 0.0.1
## Version : 0.0.1 ## Licence: AGPLv3
## Licence : FIXME ## Author: anne-sophie.denomme-pichon@u-bourgogne.fr
## Description : a wrapper for qsubing bam transfer for STR pipeline ## Description: a wrapper for qsubing bam transfer for STR pipeline
## Usage : qsub -pe smp 1 -v INPUTFILE=<path to the bam file>,OUTPUTDIR=<output directory>,[LOGFILE=<path to the log file>] wrapper_transfer.sh ## Usage: qsub -pe smp 1 -v INPUTFILE=<path to the bam file>,OUTPUTDIR=<output directory>,[LOGFILE=<path to the log file>] wrapper_transfer.sh
## Output : FIXME
## Requirements : FIXME
## Author : anne-sophie.denomme-pichon@u-bourgogne.fr
## Creation Date : 20191208
## last revision date : 20191208
## Known bugs : None
# Log file path option # Log file path option
......
wrapper_tredparse.sh
View file @ 14be1720
#! /bin/sh #! /bin/sh
### ASDP PIPELINE ### ### ASDP PIPELINE ###
## wrapper_tredparse.sh ## Version: 0.0.1
## Version : 0.0.1 ## Licence: AGPLv3
## Licence : FIXME ## Author: anne-sophie.denomme-pichon@u-bourgogne.fr
## Description : a wrapper for qsubing Tredparse script for STR detection ## Description: a wrapper for qsubing Tredparse script for STR detection
## Usage : qsub -pe smp 1 -v INPUTFILE=<path to the bam file>,OUTPUTDIR=<output directory>,[LOGFILE=<path to the log file>] wrapper_tredparse.sh ## Usage: qsub -pe smp 1 -v INPUTFILE=<path to the bam file>,OUTPUTDIR=<output directory>,[LOGFILE=<path to the log file>] wrapper_tredparse.sh
## Output : FIXME
## Requirements : FIXME
## Author : anne-sophie.denomme-pichon@u-bourgogne.fr
## Creation Date : 20191103
## last revision date : 20191103
## Known bugs : None
# Log file path option # Log file path option
......
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