-
Notifications
You must be signed in to change notification settings - Fork 1
/
Copy pathmain2.sh
executable file
·172 lines (163 loc) · 7.68 KB
/
main2.sh
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
#!/bin/sh
if [ $# != 6 ]
then
MSG="Parameter mismatch."
echo -e "jobid:${PBS_JOBID}\nprogram=$0 stopped at line=$LINENO. Reason=$MSG" | ssh iforge "mailx -s '[Support #200] Mayo variant identification pipeline' "$redmine""
exit 1;
else
set -x
echo `date`
scriptfile=$0
runfile=$1
runmode=$2
elog=$3
olog=$4
email=$5
qsubfile=$6
LOGS="jobid:${PBS_JOBID}\nqsubfile=$qsubfile\nerrorlog=$elog\noutputlog=$olog"
if [ ! -s $runfile ]
then
MSG="$runfile configuration file not found"
echo -e "program=$scriptfile stopped at line=$LINENO.\nReason=$MSG\n$LOGS" | ssh iforge "mailx -s '[Support #200] Mayo variant identification pipeline' "$redmine,$email""
exit 1;
fi
scriptdir=$( cat $runfile | grep -w SCRIPTDIR | cut -d '=' -f2 )
outputdir=$( cat $runfile | grep -w OUTPUTDIR | cut -d '=' -f2 )
pbsprj=$( cat $runfile | grep -w PBSPROJECTID | cut -d '=' -f2 )
thr=$( cat $runfile | grep -w PBSTHREADS | cut -d '=' -f2 )
analysis=$( cat $runfile | grep -w ANALYSIS | cut -d '=' -f2 | tr '[a-z]' '[A-Z]' )
resortbam=$( cat $runfile | grep -w RESORTBAM | cut -d '=' -f2 )
bam2fqflag=$( cat $runfile | grep -w BAM2FASTQFLAG | cut -d '=' -f2 )
epilogue=$( cat $runfile | grep -w EPILOGUE | cut -d '=' -f2 )
type=$( cat $runfile | grep -w TYPE | cut -d '=' -f2 | tr '[a-z]' '[A-Z]' )
if [ $type == "GENOME" -o $type == "WHOLE_GENOME" -o $type == "WHOLEGENOME" -o $type == "WGS" ]
then
pbscpu=$( cat $runfile | grep -w PBSCPUOTHERWGEN | cut -d '=' -f2 )
pbsqueue=$( cat $runfile | grep -w PBSQUEUEWGEN | cut -d '=' -f2 )
else
if [ $type == "EXOME" -o $type == "WHOLE_EXOME" -o $type == "WHOLEEXOME" -o $type == "WES" ]
then
pbscpu=$( cat $runfile | grep -w PBSCPUOTHEREXOME | cut -d '=' -f2 )
pbsqueue=$( cat $runfile | grep -w PBSQUEUEEXOME | cut -d '=' -f2 )
else
MSG="Invalid value for TYPE=$type in configuration file."
echo -e "program=$0 stopped at line=$LINENO.\nReason=$MSG\n$LOGS" | ssh iforge "mailx -s '[Support #200] Mayo variant identification pipeline' "$redmine,$email""
exit 1;
fi
fi
if [ -z $thr -o -z $outputdir -o -z $pbsprj -o -z $epilogue ]
then
MSG="Invalid value specified for any of these paramaters in configuration file:\nPBSTHREADS=$thr\nOUTPUTDIR=$outputdir\nPBSPROJECTID=$pbsprj\nEPILOGUE=$epilogue"
echo -e "program=$0 stopped at line=$LINENO.\nReason=$MSG\n$LOGS" | ssh iforge "mailx -s '[Support #200] Mayo variant identification pipeline' "$redmine,$email""
exit 1;
fi
if [ $resortbam == "YES" -a $bam2fqflag == "YES" ]
then
MSG="Invalid values for parameters RESORTBAM=$resortbam and BAM2FASTQFLAG=$bam2fqflag in the configuration file."
echo -e "program=$scriptfile stopped at line=$LINENO.\nReason=$MSG\n$LOGS" | ssh iforge "mailx -s '[Support #200] Mayo variant identification pipeline' "$redmine,$email""
exit 1;
fi
if [ ! -d $scriptdir ]
then
MSG="SCRIPTDIR=$scriptdir directory not found"
echo -e "program=$scriptfile stopped at line=$LINENO.\nReason=$MSG\n$LOGS" | ssh iforge "mailx -s '[Support #200] Mayo variant identification pipeline' "$redmine,$email""
exit 1;
fi
if [ ! -d $outputdir ]
then
mkdir -p $outputdir
mkdir -p $outputdir/logs
elif [ $runmode != "batch" ]
then
echo "resetting logs"
`rm -r $outputdir/logs/*`
fi
`chmod -R 770 $outputdir`
`chmod 750 $epilogue`
outputlogs=$outputdir/logs
if [ $analysis == "ALIGN" -o $analysis == "ALIGNMENT" ]
then
echo "Type of analysis to run: ALIGNMENT only"
qsub1=$outputlogs/qsub.main.aln
echo "#PBS -V" > $qsub1
echo "#PBS -A $pbsprj" >> $qsub1
echo "#PBS -N MAINaln" >> $qsub1
echo "#pbs -l epilogue=$epligue" >> $qsub1
echo "#PBS -l walltime=$pbscpu" >> $qsub1
echo "#PBS -l nodes=1:ppn=1" >> $qsub1
echo "#PBS -o $outputlogs/MAINaln.ou" >> $qsub1
echo "#PBS -e $outputlogs/MAINaln.in" >> $qsub1
echo "#PBS -q $pbsqueue" >> $qsub1
echo "#PBS -m ae" >> $qsub1
echo "#PBS -M $email" >> $qsub1
echo "$scriptdir/alignew2.sh $runfile $outputlogs/MAINaln.in $outputlogs/MAINaln.ou $email $outputlogs/qsub.main.aln" >> $qsub1
`chmod a+r $qsub1`
`qsub $qsub1 >> $outputlogs/MAINALNpbs`
echo `date`
else
if [ $resortbam == "YES" -a [ $analysis == "REALIGN" -o $analysis == "REALIGNMENT" ] ]
then
echo "Type of analysis to run: REALIGNMENT only. bams provided"
qsub2=$outputlogs/qsub.main.realn
echo "#PBS -V" > $qsub2
echo "#PBS -A $pbsprj" >> $qsub2
echo "#PBS -N MAINrealn" >> $qsub2
echo "#pbs -l epilogue=$epligue" >> $qsub2
echo "#PBS -l walltime=$pbscpu" >> $qsub2
echo "#PBS -l nodes=1:ppn=1" >> $qsub2
echo "#PBS -o $outputlogs/MAINrealn.ou" >> $qsub2
echo "#PBS -e $outputlogs/MAINrealn.in" >> $qsub2
echo "#PBS -q $pbsqueue" >> $qsub2
echo "#PBS -m ae" >> $qsub2
echo "#PBS -M $email" >> $qsub2
echo "$scriptdir/realign.sh $runfile $outputlogs/MAINrealn.in $outputlogs/MAINrealn.ou $email $outputlogs/qsub.main.realn" >> $qsub2
`chmod a+r $qsub2`
`qsub $qsub2 >> $outputlogs/MAINREALNpbs`
echo `date`
else
if [ $analysis == "REALIGN" -o $analysis == "REALIGNMENT" ]
then
echo "Type of analysis to run: ALIGNMENT and REALIGNMENT"
qsub1=$outputlogs/qsub.main.aln
echo "#PBS -V" > $qsub1
echo "#PBS -A $pbsprj" >> $qsub1
echo "#PBS -N MAINaln" >> $qsub1
echo "#pbs -l epilogue=$epligue" >> $qsub1
echo "#PBS -l walltime=$pbscpu" >> $qsub1
echo "#PBS -l nodes=1:ppn=1" >> $qsub1
echo "#PBS -o $outputlogs/MAINaln.ou" >> $qsub1
echo "#PBS -e $outputlogs/MAINaln.in" >> $qsub1
echo "#PBS -q $pbsqueue" >> $qsub1
echo "#PBS -m ae" >> $qsub1
echo "#PBS -M $email" >> $qsub1
echo "$scriptdir/alignew2.sh $runfile $outputlogs/MAINaln.in $outputlogs/MAINaln.ou $email $outputlogs/qsub.main.aln" >> $qsub1
`chmod a+r $qsub1`
`qsub $qsub1 >> $outputlogs/MAINALNpbs`
echo `date`
jobid=$( cat $outputlogs/MAINALNpbs | sed "s/\.[a-z]*//" | tr "\n" ":" )
qsub2=$outputlogs/qsub.main.realn
echo "#PBS -V" > $qsub2
echo "#PBS -A $pbsprj" >> $qsub2
echo "#PBS -N MAINrealn" >> $qsub2
echo "#pbs -l epilogue=$epligue" >> $qsub2
echo "#PBS -l walltime=$pbscpu" >> $qsub2
echo "#PBS -l nodes=1:ppn=1" >> $qsub2
echo "#PBS -o $outputlogs/MAINrealn.ou" >> $qsub2
echo "#PBS -e $outputlogs/MAINrealn.in" >> $qsub2
echo "#PBS -q $pbsqueue" >> $qsub2
echo "#PBS -m ae" >> $qsub2
echo "#PBS -M $email" >> $qsub2
echo "#PBS -W depend=afterok:$jobid" >> $qsub2
echo "$scriptdir/realign.sh $runfile $outputlogs/MAINrealn.in $outputlogs/MAINrealn.ou $email $outputlogs/qsub.main.realn" >> $qsub2
`chmod a+r $qsub2`
`qsub $qsub2 >> $outputlogs/MAINREALNpbs`
echo `date`
else
MSG="Invalid value for parameter ANALYSIS=$analysis in configuration file."
echo -e "program=$scriptfile stopped at line=$LINENO.\nReason=$MSG\n$LOGS" | ssh iforge "mailx -s '[Support #200] Mayo variant identification pipeline' "$redmine,$email""
exit 1;
fi
fi
fi
fi