#!/bin/sh
-# Last updated: Aug/11/2008 By Rami
-# ---------------------------------
+#Last updated: May/14/2009 By Rami
+#----------Standard / IPAR-----------------------
# Main Desc: Top level wrapper script for the whole Data pipeline after sequencing is done until data analysis.
# Start: Read current folder as input Run Folder (ex: 080220_HWI-FC2057U).
# This scripts assumes that:
# 1 - Sequence reading has finished and all data are in Run Folder.
-# 2 - DataRun record saved with apropriate cnfig params in the FcTracker online DB (http://myerslab.stanford.edu/admin)
-# 3 - Curren directory, from were this script is ran, is the Run Folder ( = DataRun.RunFolder field in the Fctracker DB).
+# 2 - DataRun record saved with apropriate cnfig params in the FcTracker online DB (http://htsw.stanford.edu/admin)
+# 3 - Curren directory, from were this script is ran, is the Run Folder
# ----
# START: (checks in ExpTrackLog dir if OKfiles exist before executing scripts)
# Get Input: <FlowCellId> ["init" (to start from scatch, otherwise starts after the last successful step)]
# Aks the user to check if the retrieved parameters are OK. If Yes, enter "GO", otherwise <ENTER> and fix ..
# ---- <GO>:
# Runs the PipelineListener & for the rest of the process flow
-# Goes down 2 dirs to C1-X_Firecrest_...etc .
+# Goes down 2 dirs to Firecrest...etc .
# Runs the make -j ect ...
# FINISH
################################################################################
+fullpath=`pwd`
+runfolder=`pwd | sed -e 's/^.*\///'`
+
if [ $1 ]
then echo ""
else
echo "Missing argument: FlowcellId. Try again. Example: ./MainPipelineScript FC99999 <enter>"
exit
fi
-fcid=$1
-echo "fcid is $fcid"
-
-#fullpath=`pwd`
-#runfolder=`pwd | sed -e 's/^.*\///'`
-#changed for the HTSW merged
-fullpath=$2
-echo "fullpath is $fullpath"
-runfolder=`echo $fullpath | sed -e 's/^.*\///'`
-echo "runfolder is $runfolder"
+fcid=$1
-if [ $3 ] && [ $3 == 'init' ]
- then
+if [ $2 ] && [ $2 == 'init' ]
+ then
rm -r ExpTrackLog
- echo "==== Starting from scratch ====\n"
+ echo "==== Starting from scratch at `date` ===="
+ else
+ echo "=== Starting at `date` ===";
fi
+echo "=== Retrieving Information - Please wait ... ===";
if [ -d ExpTrackLog ]
then echo ""
else mkdir ExpTrackLog
fi
-#exptrackmainsc="$HOME/EXPTRACK/exp_track_main.py"
-exptrackmainsc="exp_track_main.py"
+exptrackmainsc="$EXPTRACKDIR/exp_track_main.py"
# -- Check Image folders and find out cycle number
-#tocycle=`$HOME/EXPTRACK/CheckImageFolders`
-echo "calling CheckImageFolders"
-tocycle=`./CheckImageFolders $fullpath`
+tocycle=`$EXPTRACKDIR/CheckImageFolders`
## Uncomment this if you want to force a cycle number:
-#tocycle=36
+##tocycle=36
if [ $tocycle -gt 0 ] && [ $tocycle -lt 37 ]
-then echo ""
+then echo "Cheked Imag Folders -> cycle set to: $tocycle"
else
- echo "PROBLEM: CheckImagefolders failed to return a cycle number between 0 and 36. Returned: '$tocycle'"
+ echo "PROBLEM: Check Image folders failed to a cycle between 0 and 36. Found: $tocycle"
echo "Note: to input cycle number edit the MainP..Script un-comment ##tocycle=36"
echo " --- tocycle SET to 0 --- "
echo "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!"
exit
fi
+analysis_mode='standard'
+pipeline_version='1.3'
## The Command that runs the making of the "make" files
-makefilescmd="/Applications/GAPipeline-0.3.0/Goat/goat_pipeline.py --cycles=1-$tocycle --GERALD=config.txt --matrix=auto5 --phasing=auto5 $fullpath/Images/ --make"
+if [ -d Data/IPAR_$pipeline_version ]
+then
+ datadir=Data/IPAR_$pipeline_version
+ analysis_mode='IPAR'
+else
+ datadir=Data
+fi
+
+# control lane by default 4
+makefilescmd="/Applications/SolexaPipeline/Goat/goat_pipeline.py --cycles=1-$tocycle --matrix=auto --phasing=auto --control-lane=4 --GERALD=config.txt $fullpath/$datadir --make"
+if [ $analysis_mode == 'IPAR' ]
+then
+ # For IPAR we can't use the goat. we use the bustard.py (see user man for Pipeline Version 1.3 page 22 at the bottom)
+ makefilescmd="/usr/local/src/GAPipeline-$pipeline_version.2/bin/bustard.py $fullpath/$datadir --make --cycles=1-$tocycle --matrix=auto --phasing=auto --control-lane=4 --GERALD=config.txt"
+fi
+
## PRINT PRE CHECK REPORT
echo "=================================== PRELIMINARY CHECKS ================================"
-echo "Full path: $fullpath"
-echo "Run Folder: $runfolder"
-echo "FlowcellId: $fcid"
-echo "------------------------------------------------------"
+
echo "Config File generation"
rm config.txt
python $exptrackmainsc getconfile $fcid $runfolder
exit
fi
cat config.txt
-
echo ""
echo "------------------------------------------------------"
echo "LaneNames.xml file generation: "
fi
cat LaneNames.xml
echo ""
-echo "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
-echo "Will run Cycles: 1 to $tocycle"
-echo "Command for Make files generation step:"
-echo "--------------------------------------"
-echo $makefilescmd
+
+echo "----------------Analysis Params:----------------------"
+echo "Analysis Mode: $analysis_mode"
+echo "Pipeline Software Version: $pipeline_version"
+echo "Cycles: 1 to $tocycle"
+echo "Will run this to generate Make files: $makefilescmd"
+echo "Full current path: $fullpath"
+echo "Run Folder: $runfolder"
+echo "FlowcellId: $fcid"
+echo "------------------------------------------------------"
echo ""
echo "NOTE!!: To change any of the above parameters just quit and modify this script according to your current needs."
echo ""
echo ""
-echo "If these are the correct parameters for your Data Pipeline Run type GO to proceed\n Otherwise type anything else to quit."
+echo "If these are the correct parameters for your Data Pipeline Run type GO to proceed"
+echo ""
+echo "Otherwise type anything else to quit"
echo "====================================================================================="
-
confirm="GO";
-if [ $3 ] && [ $3 == 'GO' ]
+if [ $2 ] && [ $2 == 'GO' ]
then
echo "Autostarting";
else
read confirm
fi
-
-
#######################
if [ $confirm ] && [ $confirm == "GO" ]
-then echo ""
+then echo "Proceeding .."
else echo "Response: "$confirm; exit
fi
-
###### START PROCESS
-
-## First check if this is a run from scratch or from Bustard or Gerald ~~~~~
-firecrestdir=`ls $fullpath/Data | grep "^C1-$tocycle.*_Firecrest.*"`
-#echo "tocycle is $tocycle. fullpath is $fullpath"
-#echo "firecrestdir is $firecrestdir"
-firecrestfinished=$fullpath/Data/$firecrestdir/finished.txt
-bustfinished=$fullpath/Data/$firecrestdir/Bustard*_*/finished.txt
-gerfinished=$fullpath/Data/$firecrestdir/Bustard*_*/GERALD_*/finished.txt
-
-phaseMsg=''
-nextDo='all'
-
-if [ -f $firecrestfinished ]
-then
- phaseMsg='Firecrest Finished (found finished.txt). Start from BUSTARD'
- #? [Yes/[Any Key]] (Enter [Any Key] to Start from scratch)'
- nextDo='Bustard'
- echo "Firecrest finished.txt found."
- if [ -f $bustfinished ]
- then
- phaseMsg='Bustard Finished (found finished.txt). Start from GERALD'
- # ? [Yes/[Any Key]] (Any Key = Start from scratch)'
- nextDo='Gerald'
- echo " and Bustard finished.txt found."
- if [ -f $gerfinished ]
- then
- phaseMsg='Looks like Solexa pipeline has completed (found all 3 finished.txt files).'
- #? [Yes/[Any Key]] (Any Key = Start from scratch)'
- nextDo='CollectReads'
- echo " and Gerald finished.txt found."
- fi
- fi
-else
- echo "Run from start"
-fi
-
-echo $phaseMsg
-
-
-
-if [ $nextDo == "all" ]
-then
- echo "Run from start"
-else
- confirm=''
- # Can't read from prompt yet using the Jabber api
- # read confirm
- confirm="Yes"
- if [ $confirm == "Yes" ]
- then
- #Launch MPListener in the background
- echo " ... starting MPListener in the background ..."
- #./MPListener $fcid $runfolder $tocycle &
- ./MPListener $fcid $fullpath $tocycle &
- if [ $nextDo == "Bustard" ]
- then
- #Change dir down to Bustard run folder
- #echo "Starting Solexa data process (`date`) FROM BUSTARD ..."
- python $exptrackmainsc updsts $fcid $runfolder 1 Start_from_BUSTARD
- echo "Changing dir to $fullpath/Data/$firecrestdir/Bustard*_*/"
- cd $fullpath/Data/$firecrestdir/Bustard*_*
- echo " ..... supposed to run make -j 8 recursive here ...."
- ##NOT READY YET make -j 8 recursive
- else
- if [ $nextDo == "Gerald" ]
- then
- #Change dir down to Bustard run folder
- python $exptrackmainsc updsts $fcid $runfolder 1 Start_from_GERALD
- #echo "Starting Solexa data process (`date`) FROM GERALD ..."
- echo "Changing dir to $fullpath/Data/$firecrestdir/Bustard*_*/Gerald..."
- cd $fullpath/Data/$firecrestdir/Bustard*_*/GERALD_*
- echo " ..... supposed to run make -j 8 here ...."
- ##NOT READY YET make -j 8
- fi
- fi
- ## MPListner takes care of the rest
- exit
- fi
-fi
-### ~~~~~~~~
-
-
if [ -f ExpTrackLog/OK_get_check_config_file ]
then
echo "Ready for Make file generation step"
#run Make files generation step
python $exptrackmainsc updsts $fcid $runfolder 0 Generating_Make_files
- ##NOT READY YET $makefilescmd
+ $makefilescmd
else
echo "FAILED: get_check_config_file."
python $exptrackmainsc updsts $fcid $runfolder 0 Check_ConfigFile_Failed
exit
fi
+######################
+## Make sure we find the ONE specific Start folder (Firecrest or Standard / Bustard for IPAR), then check existance of "Makefile" these directories
+if [ $analysis_mode == 'IPAR' ]
+then
+ #firecrestdir=`ls $datadir | grep "Firecrest"`
+ #countdirs=`ls $datadir | grep -c Firecrest`
+ #Rami
+ startdir=`ls $datadir | grep Bustard$pipeline_version`
+ countdirs=`ls $datadir | grep -c Bustard$pipeline_version`
+else
+ startdir=`ls $datadir | grep C1-[0-9][0-9]_Firecrest`
+ countdirs=`ls $datadir | grep -c C1-[0-9][0-9]_Firecrest`
+fi
-## CHECKING OF THE MAKE FILE. Checks presence of the Firecrest folder, then check "Makefile" in the 3 directories
-firecrestdir=`ls $fullpath/Data | grep "^C1-$tocycle.*_Firecrest.*"`
-countdirs=`ls $fullpath/Data | grep -c "^C1-$tocycle.*_Firecrest.*"`
if [ $countdirs == 1 ]
then
- echo "ok. firecrest folder '$firecrestdir' found"
+ echo "ok. start folder '$startdir' found"
else
if [ $countdirs -gt 1 ]
then
- echo "ERROR: Found too many ($countdirs) firecrest directories. You need to be more specific. Found:"
+ echo "ERROR: Found too many ($countdirs) start directories (firecrest/bustard(for IPAR)). You need to specify ONE folder or REMOVE duplicates. Found:"
echo ""
- echo $firecrestdir
- python $exptrackmainsc updsts $fcid $runfolder 0 ERROR:_Need_Specific_Firecrest_Dir
+ echo $startdir
+ python $exptrackmainsc updsts $fcid $runfolder 0 ERROR:_Need_Specific_Start_Dir
exit
else
- echo "ERROR: Firecrest directory NOT FOUND. Looked for /^C1-$tocycle.*_Firecrest.*/"
- python $exptrackmainsc updsts $fcid $runfolder 0 ERROR:_Firecrest_Dir_Not_Found
+ echo "ERROR: Start (firecrest/bustard(for IPAR)) directory NOT FOUND."
+ python $exptrackmainsc updsts $fcid $runfolder 0 ERROR:_Start_Dir_Not_Found
exit
fi
fi
-firemakefile=$fullpath/Data/$firecrestdir/Makefile
-bustmakefile=$fullpath/Data/$firecrestdir/Bustard*_*/Makefile
-germakefile=$fullpath/Data/$firecrestdir/Bustard*_*/GERALD_*/Makefile
+
+if [ $analysis_mode == 'IPAR' ]
+then
+ firemakefile=$datadir/$startdir/Makefile # dummy check, since there's no need to check this one in IPAR
+ bustmakefile=$datadir/$startdir/Makefile
+ germakefile=$datadir/$startdir/GERALD_*/Makefile
+else
+ firemakefile=$datadir/$startdir/Makefile
+ bustmakefile=$datadir/$startdir/Bustard*_*/Makefile
+ germakefile=$datadir/$startdir/Bustard*_*/GERALD_*/Makefile
+fi
+
+#####################
+
+
if [ -f $firemakefile ] && [ -f $bustmakefile ] && [ -f $germakefile ]
then
#Launch MPListener in the background
- #$HOME/EXPTRACK/MPListener $fcid $runfolder $tocycle &
- MPListener $fcid $runfolder $tocycle &
+ $EXPTRACKDIR/MPListener_IPAR $fcid $runfolder $tocycle &
#Change dir down 2 folders to the Firecrest folder
+ echo "Changing dir to $datadir"
+
+ cd $datadir/$startdir
+
+ echo "Starting Solexa data process at `date`. This would be a good time for a climbing escapade at Lake Tahoe ... ;) ..."
python $exptrackmainsc updsts $fcid $runfolder 1
- python $exptrackmainsc updsts $fcid $runfolder 1 Firecrest_Dir:_$firecrestdir
- echo "Changing dir to $fullpath/Data/$firecrestdir"
- cd $fullpath/Data/$firecrestdir
- echo "Starting Solexa data process at `date`. This would be a good time for a short ski escapade at Lake Tahoe ... ;) ..."
+ msgtext="Mode:$analysis_mode$pipeline_version"
+ python $exptrackmainsc updsts $fcid $runfolder 1 $msgtext
make -j 8 recursive
+
+#BNP Changes
+ cp Bustard*/GERALD*/Summary.htm /Volumes/EncodeDisk4/$fcid_Summary.htm
+#end BNP Changes
+
else
echo "FAILED: can't find 3 Makefile. Looked for: $firemakefile, $bustmakefile, $germakefile"
projects / htsworkflow.git / commitdiff