#!/bin/sh
-# Last updated: Jul/31/2008 By Rami
+# Last updated: Aug/11/2008 By Rami
# ---------------------------------
# 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).
################################################################################
-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 [ $2 ] && [ $2 == 'init' ]
- then
+if [ $3 ] && [ $3 == 'init' ]
+ then
rm -r ExpTrackLog
echo "==== Starting from scratch ====\n"
fi
+
if [ -d ExpTrackLog ]
then echo ""
else mkdir ExpTrackLog
exptrackmainsc="exp_track_main.py"
# -- Check Image folders and find out cycle number
#tocycle=`$HOME/EXPTRACK/CheckImageFolders`
-tocycle=`CheckImageFolders`
+#tocycle=`CheckImageFolders`
## Uncomment this if you want to force a cycle number:
tocycle=36
## PRINT PRE CHECK REPORT
echo "=================================== PRELIMINARY CHECKS ================================"
-echo "Full current path: $fullpath"
+echo "Full path: $fullpath"
echo "Run Folder: $runfolder"
echo "FlowcellId: $fcid"
echo "------------------------------------------------------"
echo "ERROR: config.txt not found."
exit
fi
-cat config.txt
+#cat config.txt
+
echo ""
echo "------------------------------------------------------"
echo "LaneNames.xml file generation: "
echo "ERROR: LaneNames.xml not found."
exit
fi
-cat LaneNames.xml
+#cat LaneNames.xml
echo ""
echo "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
echo "Will run Cycles: 1 to $tocycle"
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 "====================================================================================="
+
confirm="GO";
-if [ $2 ] && [ $2 == 'GO' ]
+if [ $3 ] && [ $3 == 'GO' ]
then
echo "Autostarting";
else
read confirm
fi
-
+
#######################
if [ $confirm ] && [ $confirm == "GO" ]
-then echo "Proceeding .."
+then echo ""
else echo "Response: "$confirm; exit
fi
+
###### START PROCESS
## First check if this is a run from scratch or from Bustard or Gerald ~~~~~
-firecrestdir=`ls Data | grep "^C1-$tocycle.*_Firecrest.*"`
-firecrestfinished=Data/$firecrestdir/finished.txt
-bustfinished=Data/$firecrestdir/Bustard*_*/finished.txt
-gerfinished=Data/$firecrestdir/Bustard*_*/GERALD_*/finished.txt
+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)'
+ 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]] (Enter [Any Key] to Start from scratch)'
+ 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='It seems like Solexa pipeline has completed (found all 3 finished.txt files). Procees to next steps (CollectReads etc..)? [Yes/[Any Key]] (Enter [Any Key] to Start from scratch)'
- nextDo='next'
+ phaseMsg='It seems like Solexa pipeline has completed (found all 3 finished.txt files). Procees to next steps (CollectReads etc..)'
+ #? [Yes/[Any Key]] (Any Key = Start from scratch)'
+ nextDo='CollectReads'
+ echo " and Gerald finished.txt found."
fi
fi
else
- echo "Finished.txt not found: $firecrestfinished"
+ echo "Run from start"
fi
echo $phaseMsg
+
+
+
if [ $nextDo == "all" ]
then
- echo ""
+ echo "Run from start"
else
confirm=''
- read confirm
+ # Can't read from prompt yet using the Jabber api
+ # read confirm
+ confirm="Yes"
if [ $confirm == "Yes" ]
- then
+ then
#Launch MPListener in the background
- #$HOME/EXPTRACK/MPListener $fcid $runfolder $tocycle &
- MPListener $fcid $runfolder $tocycle &
- if [ $nextDxo == "Bustard" ]
+ echo " ..... supposed to run MPListener in the background here ...."
+ ##NOT READY YET MPListener $fcid $runfolder $tocycle &
+ if [ $nextDo == "Bustard" ]
then
- #Change dir down to Bustard run folder
- echo "Changing dir to Data/$firecrestdir/Bustard*_*/"
- cd Data/$firecrestdir/Bustard*_*
- echo "Starting Solexa data process (`date`) FROM BUSTARD ..."
- python $exptrackmainsc updsts $fcid $runfolder 1 From_BUSTARD
- make -j 8 recursive
- ## MPListner takes care of the rest
+ #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 [ $nextDxo == "Gerald" ]
+ if [ $nextDo == "Gerald" ]
then
#Change dir down to Bustard run folder
- echo "Changing dir to Data/$firecrestdir/Bustard*_*/Gerald..."
- cd Data/$firecrestdir/Bustard*_*/GERALD_*
- echo "Starting Solexa data process (`date`) FROM GERALD ..."
- python $exptrackmainsc updsts $fcid $runfolder 1 From_GERALD
- make -j 8
- ## MPListner takes care of the rest
+ 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
- $makefilescmd
+ ##NOT READY YET $makefilescmd
else
echo "FAILED: get_check_config_file."
python $exptrackmainsc updsts $fcid $runfolder 0 Check_ConfigFile_Failed
exit
fi
-## Make sure we find the Firecrest folder, then check "Makefile" in the 3 directories
-# firecrestdir=`ls Data | grep C1.*_Firecrest.*_encode`
-firecrestdir=`ls Data | grep "^C1-$tocycle.*_Firecrest.*"`
-countdirs=`ls Data | grep -c "^C1-$tocycle.*_Firecrest.*"`
+
+
+## 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"
fi
fi
-firemakefile=Data/$firecrestdir/Makefile
-bustmakefile=Data/$firecrestdir/Bustard*_*/Makefile
-germakefile=Data/$firecrestdir/Bustard*_*/GERALD_*/Makefile
+firemakefile=$fullpath/Data/$firecrestdir/Makefile
+bustmakefile=$fullpath/Data/$firecrestdir/Bustard*_*/Makefile
+germakefile=$fullpath/Data/$firecrestdir/Bustard*_*/GERALD_*/Makefile
if [ -f $firemakefile ] && [ -f $bustmakefile ] && [ -f $germakefile ]
then
#Launch MPListener in the background
#$HOME/EXPTRACK/MPListener $fcid $runfolder $tocycle &
MPListener $fcid $runfolder $tocycle &
#Change dir down 2 folders to the Firecrest folder
- echo "Changing dir to Data/$firecrestdir"
- cd Data/$firecrestdir
- echo "Starting Solexa data process at `date`. This would be a good time for a short ski 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 ... ;) ..."
make -j 8 recursive
else
echo "FAILED: can't find 3 Makefile. Looked for: $firemakefile, $bustmakefile, $germakefile"
projects / htsworkflow.git / commitdiff