-
Notifications
You must be signed in to change notification settings - Fork 26
/
test-snippets-debian7-64bits-gcc-4.7.sh
executable file
·205 lines (173 loc) · 8.23 KB
/
test-snippets-debian7-64bits-gcc-4.7.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
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
#!/bin/bash
#--------------------------------------------------------------#
# Continuous integration script for Jenkins #
#--------------------------------------------------------------#
set +xv
echo "
-----------------------------------------
Miscellaneous information·
-----------------------------------------
date : `date`
hostname : `hostname`
pwd : `pwd`
-----------------------------------------
Jenkins build parameters (user defined)
-----------------------------------------
BRANCH_TO_BUILD : ${BRANCH_TO_BUILD}
RELEASE_TO_BUILD : ${RELEASE_TO_BUILD}
-----------------------------------------
Jenkins build parameters (built in)
-----------------------------------------
BUILD_NUMBER : ${BUILD_NUMBER}
"
set -xv
# quick look at resources
#---------------------------------------------------------------
free -h
#---------------------------------------------------------------
lstopo
#---------------------------------------------------------------
df -kh
#---------------------------------------------------------------
################################################################
# COMPILATION #
################################################################
gcc --version
g++ --version
cmake --version
[ `gcc -dumpversion` = 4.7 ] && { echo "GCC 4.7"; } || { echo "GCC version is not 4.7, we exit"; exit 1; }
JENKINS_TASK=test-snippets-debian7-64bits-gcc-4.7
GIT_DIR=/builds/workspace/$JENKINS_TASK/gatb-core
BUILD_DIR=/scratchdir/$JENKINS_TASK/gatb-core/build
#>>>>>>>>>>>>>>>>>>>>>
#if false; then
#>>>>>>>>>>>>>>>>>>>>>
rm -rf $BUILD_DIR
mkdir -p $BUILD_DIR
cd $BUILD_DIR
#---------------------------------------------------------------
cmake -DGATB_CORE_INCLUDE_EXAMPLES=True -Wno-dev $GIT_DIR
#---------------------------------------------------------------
make -j2 examples
#>>>>>>>>>>>>>>>>>>>>>
#fi
#>>>>>>>>>>>>>>>>>>>>>
################################################################
# RUN SNIPPETS #
################################################################
cd $BUILD_DIR/bin/
# list all compiled snippets
ls -l
# prepare environment
DB_DIR=${GIT_DIR}/test/db
TMP_DIR=${BUILD_DIR}/tmp
[ ! -d ${TMP_DIR} ] && { mkdir ${TMP_DIR}; }
# Note:
# we redirect stderr and stdout to dev/null to avoir poluting log
# with lots of data. In case of an error on a snippet:
# 1. un-comment above 'if-then' to avoid compiling code
# 2. remove stream redirection on the snippet of interest
###################### iterator snippets ###########################
./iterators1 > /dev/null 2>&1 # no args expected
./iterators2 > /dev/null 2>&1 # no args expected
./iterators3 > /dev/null 2>&1 # no args expected
./iterators4 > /dev/null 2>&1 # no args expected
./iterators5 > /dev/null 2>&1 # no args expected
./iterators6 > /dev/null 2>&1 # no args expected
./iterators7 > /dev/null 2>&1 # no args expected
./iterators8 > /dev/null 2>&1 # no args expected
./iterators9 > /dev/null 2>&1 # no args expected
###################### bank snippets ###########################
./bank1 ${DB_DIR}/reads1.fa > /dev/null 2>&1
./bank2 ${DB_DIR}/reads1.fa > /dev/null 2>&1
./bank3 ${DB_DIR}/reads1.fa > /dev/null 2>&1
./bank4 ${DB_DIR}/reads1.fa > /dev/null 2>&1
./bank5 ${DB_DIR}/reads1.fa > /dev/null 2>&1
./bank6 ${DB_DIR}/reads1.fa > /dev/null 2>&1
./bank7 ${DB_DIR}/reads1.fa 500 > /dev/null 2>&1
./bank8 ${DB_DIR}/reads1.fa ${TMP_DIR}/reads1.fa.bin > /dev/null 2>&1
./bank9 ${DB_DIR}/reads1.fa ${TMP_DIR}/reads1_filtered.fa 5 > /dev/null 2>&1
./bank10 -in ${DB_DIR}/reads1.fa -out-dir ${TMP_DIR} -max-size 5000 > /dev/null 2>&1
./bank11 -kmer-size 4 -out ${TMP_DIR}/kmer.fa > /dev/null 2>&1
./bank12 -in ${DB_DIR}/reads1.fa -seq-ids ${DB_DIR}/reads1_list_ids.txt
./bank13 -in ${DB_DIR}/reads1.fa -filter-ratio 0.8 > /dev/null 2>&1
./bank14 -in ${DB_DIR}/reads1.fa > /dev/null 2>&1
./bank15 ${DB_DIR}/reads1.fa > /dev/null 2>&1
./bank16 -in ${DB_DIR}/reads1.fa > /dev/null 2>&1
./bank17 -in ${DB_DIR}/album.txt > /dev/null 2>&1
./bank18 -one ${DB_DIR}/reads1.fa -two ${DB_DIR}/reads2.fa > /dev/null 2>&1
./bank19 -in ${DB_DIR}/reads1.fa > /dev/null 2>&1
./bank20 -in ${DB_DIR}/reads1.fa > /dev/null 2>&1
###################### kmer snippets ###########################
./kmer1 > /dev/null 2>&1 # no args expected
./kmer2 > /dev/null 2>&1 # no args expected
./kmer3 > /dev/null 2>&1 # no args expected
./kmer4 -in ${DB_DIR}/reads1.fa -kmer-size 11 > /dev/null 2>&1
./kmer5 -in ${DB_DIR}/reads1.fa -kmer-size 11 -minimizer-size 11 > /dev/null 2>&1
# kmer6 will report an EXCEPTION: this is the expected behavior
./kmer6 > /dev/null 2>&1 # no args expected
./kmer7 -in ${DB_DIR}/reads1.fa -kmer-size 11 > /dev/null 2>&1
./kmer8 -in ${DB_DIR}/reads1.fa -kmer-size 11 -minimizer-size 11 > /dev/null 2>&1
./kmer9 -in ${DB_DIR}/reads1.fa > /dev/null 2>&1
./kmer10 -in ${DB_DIR}/reads1.fa > /dev/null 2>&1
./kmer11 -in ${DB_DIR}/reads1.fa > /dev/null 2>&1
./kmer12 -in "${DB_DIR}/reads1.fa,${DB_DIR}/reads2.fa" > /dev/null 2>&1
./kmer13 -in "${DB_DIR}/reads1.fa,${DB_DIR}/reads2.fa" > /dev/null 2>&1
./kmer14 -in ${DB_DIR}/reads1.fa > /dev/null 2>&1
./kmer15 -in ${DB_DIR}/reads1.fa > /dev/null 2>&1
./kmer16 -in ${DB_DIR}/reads1.fa > /dev/null 2>&1
./kmer17 -in ${DB_DIR}/reads1.fa -kmer-size 11 -minimizer-size 11 > /dev/null 2>&1
###################### debruijn snippets #######################
./debruijn1 -in ${DB_DIR}/reads1.fa > /dev/null 2>&1
./debruijn2 ${DB_DIR}/reads1.fa > /dev/null 2>&1
./debruijn3 ${DB_DIR}/reads1.fa > /dev/null 2>&1
./debruijn4 > /dev/null 2>&1 # no args expected
./debruijn5 ${DB_DIR}/celegans_reads.h5 > /dev/null 2>&1
./debruijn6 ${DB_DIR}/celegans_reads.h5 > /dev/null 2>&1
./debruijn7 ${DB_DIR}/celegans_reads.h5 > /dev/null 2>&1
./debruijn8 ${DB_DIR}/celegans_reads.h5 > /dev/null 2>&1
./debruijn9 > /dev/null 2>&1 # no args expected
./debruijn10 > /dev/null 2>&1 # no args expected
./debruijn11 > /dev/null 2>&1 # no args expected
./debruijn12 > /dev/null 2>&1 # no args expected
./debruijn13 > /dev/null 2>&1 # no args expected
./debruijn14 > /dev/null 2>&1 # no args expected
./debruijn15 > /dev/null 2>&1 # no args expected
./debruijn16 > /dev/null 2>&1 # no args expected
./debruijn17 > /dev/null 2>&1 # no args expected
./debruijn18 -graph ${DB_DIR}/celegans_reads.h5 > /dev/null 2>&1
./debruijn19 -graph ${DB_DIR}/celegans_reads.h5 > /dev/null 2>&1
./debruijn20 -graph ${DB_DIR}/celegans_reads.h5 > /dev/null 2>&1
./debruijn21 -graph ${DB_DIR}/celegans_reads.h5 > /dev/null 2>&1
./debruijn22 -graph ${DB_DIR}/celegans_reads.h5 -out ${TMP_DIR}/data.h5 > /dev/null 2>&1
./debruijn23 > /dev/null 2>&1 # no args expected
./debruijn24 -graph ${DB_DIR}/celegans_reads.h5 > /dev/null 2>&1
./debruijn25 -in ${DB_DIR}/reads1.fa > /dev/null 2>&1
./debruijn26 > /dev/null 2>&1 # no args expected
./debruijn27 ${DB_DIR}/celegans_reads.h5 "TTTGCCCATTTCCTGCCATTTGTC" > /dev/null 2>&1
./traversal1 -graph ${DB_DIR}/celegans_reads.h5 > /dev/null 2>&1
./traversal2 -traversal unitig > /dev/null 2>&1
./traversal2 -traversal contig > /dev/null 2>&1
###################### storage snippets ########################
./storage1 > /dev/null 2>&1 # no args expected
./storage2 > /dev/null 2>&1 # no args expected
./storage3 > /dev/null 2>&1 # no args expected
./storage4 > /dev/null 2>&1 # no args expected
./storage5 > /dev/null 2>&1 # no args expected
./storage6 -graph ${DB_DIR}/celegans_reads.h5 > /dev/null 2>&1
./storage7 > /dev/null 2>&1 # no args expected
./storage8 > /dev/null 2>&1 # no args expected
./storage9 ${DB_DIR}/celegans_reads.h5 > /dev/null 2>&1
###################### tools snippets ##########################
./ToyTool > /dev/null 2>&1 # no args expected
./multithreading1 > /dev/null 2>&1 # no args expected
./multithreading2 > /dev/null 2>&1 # no args expected
./multithreading3 > /dev/null 2>&1 # no args expected
./multithreading4 > /dev/null 2>&1 # no args expected
./multithreading5 > /dev/null 2>&1 # no args expected
./multithreading6 ${DB_DIR}/reads1.fa > /dev/null 2>&1
./observer1 > /dev/null 2>&1 # no args expected
./optionsparser1 > /dev/null 2>&1 # no args expected
./optionsparser2 > /dev/null 2>&1 # no args expected
###################### protos snippets #########################
./MicroSNP -in ${DB_DIR}/microsnp.fa -kmer-size 7 -abundance-min 1 > /dev/null 2>&1