-
Notifications
You must be signed in to change notification settings - Fork 1
/
.gitlab-ci.yml
391 lines (371 loc) · 19.1 KB
/
.gitlab-ci.yml
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
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
workflow:
rules:
- if: $CI_COMMIT_BRANCH =~ /-WIP$/
when: never
- when: always
variables:
GIT_STRATEGY: fetch
REGISTRY: registry.gitlab.com
APPLICATION: mhm2
TEST_IMAGE: $REGISTRY/$REGISTRY_USER/$APPLICATION:latest
RELEASE_IMAGE: $REGISTRY/$REGISTRY_USER/$APPLICATION:$CI_BUILD_REF_NAME
HULK_UPCXX_VER: 2021.3.0
stages:
- build
- validation
- accuracy
#
# cori
#
Cori:build:
stage: build
tags:
- Cori
script:
- set -e
- set -x
- git submodule init
- git submodule sync
- git submodule update
- uname -a
- pwd
- date
- echo "Establishing variables"
- export MHM2_SOURCE=$(pwd)
- export BASE=${SCRATCH}/tmp/gitlab-runner-scratch-Cori-mhm2-${USER}
- export SCRATCH=${BASE}/mhm2-${CI_COMMIT_SHORT_SHA}-${CI_COMMIT_REF_NAME}-${CI_COMMIT_TAG}
- export INSTALL_PREFIX=${SCRATCH}/install
- export BUILD_PREFIX=${SCRATCH}/build
- export RUN_PREFIX=${SCRATCH}/runs
- echo "BASE=${BASE} SCRATCH=${SCRATCH}"
- mkdir -p ${BASE}
- rm -rf ${SCRATCH}
- echo "Cleaning out old installs"
- find ${BASE} -maxdepth 1 -name 'mhm*' -mtime +4 -type d -exec rm -rf '{}' ';' || /bin/true
- mkdir -p ${SCRATCH} ${RUN_PREFIX}
- exec > >(tee -ia ${SCRATCH}/build.log)
- exec 2> >(tee -ia ${SCRATCH}/build.err >&2)
- echo "Logging to ${SCRATCH}/build.log and .err at $(date) on $(uname -n) in $(pwd)"
- lmstat -a -c $INTEL_LICENSE_FILE || /bin/true
- echo "Loading Haswell modules for upcxx GNU"
- source ${MHM2_SOURCE}/contrib/environments/cori-haswell/gnu.sh
- module list
- export MHM2_BUILD=${BUILD_PREFIX}-haswell-dbg
- mkdir -p ${MHM2_BUILD}
- cd $MHM2_BUILD
- echo "Building Haswell GNU Debug"
- CXX=CC cmake -DCMAKE_INSTALL_PREFIX=${INSTALL_PREFIX}-haswell -DCMAKE_BUILD_TYPE=Debug ${MHM2_SOURCE}
- make -j 12 all check install
- export MHM2_BUILD=${BUILD_PREFIX}-haswell
- mkdir -p ${MHM2_BUILD}
- cd $MHM2_BUILD
- echo "Building Haswell GNU Release"
- CXX=CC cmake -DCMAKE_INSTALL_PREFIX=${INSTALL_PREFIX}-haswell -DCMAKE_BUILD_TYPE=Release ${MHM2_SOURCE}
- make -j 12 all check install
- echo "Loading KNL modules for upcxx on cori GNU"
- source ${MHM2_SOURCE}/contrib/environments/cori-knl/gnu.sh
- module list
- export MHM2_BUILD=${BUILD_PREFIX}-knl-dbg
- mkdir -p ${MHM2_BUILD}
- cd $MHM2_BUILD
- echo "Building KNL GNU Debug"
- CXX=CC cmake -DCMAKE_INSTALL_PREFIX=${INSTALL_PREFIX}-knl-dbg -DCMAKE_BUILD_TYPE=Debug ${MHM2_SOURCE}
- make -j 12 all install # cannot check knl build on haswell
- export MHM2_BUILD=${BUILD_PREFIX}-knl-rwdi
- mkdir -p ${MHM2_BUILD}
- cd $MHM2_BUILD
- echo "Building KNL GNU RelWithDebInfo"
- CXX=CC cmake -DCMAKE_INSTALL_PREFIX=${INSTALL_PREFIX}-knl-rwdi -DCMAKE_BUILD_TYPE=RelWithDebInfo ${MHM2_SOURCE}
- make -j 12 all install # cannot check knl build on haswell
- export MHM2_BUILD=${BUILD_PREFIX}-knl
- mkdir -p ${MHM2_BUILD}
- cd $MHM2_BUILD
- echo "Building KNL GNU Release"
- CXX=CC cmake -DCMAKE_INSTALL_PREFIX=${INSTALL_PREFIX}-knl -DCMAKE_BUILD_TYPE=Release ${MHM2_SOURCE}
- make -j 12 all install # cannot check knl build on haswell
- echo "Done building"
Cori:validation:
stage: validation
tags:
- Cori
script:
- set -e
- set -x
- uname -a
- pwd
- date
- export GASNET_BACKTRACE=1
- echo "Establishing variables"
- export MHM2_SOURCE=$(pwd)
- export BASE=${SCRATCH}/tmp/gitlab-runner-scratch-Cori-mhm2-${USER}
- export SCRATCH=${BASE}/mhm2-${CI_COMMIT_SHORT_SHA}-${CI_COMMIT_REF_NAME}-${CI_COMMIT_TAG}
- export INSTALL_PREFIX=${SCRATCH}/install
- export BUILD_PREFIX=${SCRATCH}/build
- export RUN_PREFIX=${SCRATCH}/runs
- echo "BASE=${BASE} SCRATCH=${SCRATCH}"
- echo "Loading KNL modules for upcxx on cori"
- source ${MHM2_SOURCE}/contrib/environments/cori-knl/gnu.sh
- module list
- cd $SCRATCH
- exec > >(tee -ia ${SCRATCH}/validation.log)
- exec 2> >(tee -ia ${SCRATCH}/validation.err >&2)
- echo "Logging to ${SCRATCH}/validation.log and .err at $(date) on $(uname -n) in $(pwd)"
- FAILED=""
- inst=${INSTALL_PREFIX}-knl
- echo "Testing builds on KNL - $inst"
- export RWDI=${INSTALL_PREFIX}-knl-rwdi/bin/
- export DBG=${INSTALL_PREFIX}-knl-dbg/bin/
- export REL=${INSTALL_PREFIX}-knl/bin/
- export ARCTIC=/global/cscratch1/sd/regan/GitlabCIData/
- export OPTS="-r ${ARCTIC}/arctic_sample_0.fq -v --checkpoint=yes"
- export GASNET_BACKTRACE=1
- echo "Submitting job on 3 nodes - on 2 nodes roughly RWDI=400s, DBG --kmer-lens 63 =456s ...REL=170s"
- knl_job=$(sbatch --parsable --job-name="CImhv-${CI_COMMIT_SHORT_SHA}" --account=mp215 -C knl --nodes=3 --qos=debug --time=30:00 --wrap="${RWDI}/mhm2.py $OPTS -o ${RUN_PREFIX}/rwdi && ${DBG}/mhm2.py ${OPTS} --kmer-lens 63 -o ${RUN_PREFIX}/dbg && echo Good")
- echo "Waiting for knl job $knl_job"
- date
- while /bin/true ; do sleep 120 ; date ; sacct=$(sacct -j $knl_job -o state -X -n 2>/dev/null || true) ; if [ -n "${sacct}" -a -z "$(echo "${sacct}" | grep ING)" ] ; then break ; fi ; done
- echo "sacct $sacct"
- sacct=$(sacct -j $knl_job -X -n)
- echo "sacct $sacct"
- cat slurm-${knl_job}.out
- wasgood=$(echo "${sacct}" | grep -v '0:0' || true)
- if [ -z "$wasgood" ] ; then true ; else echo "knl job ${knl_job} failed somehow - ${wasgood}"; false ; fi
- if [ ! -f ${RUN_PREFIX}/rwdi/final_assembly.fasta ] ; then FAILED="${FAILED} Did not find final_assembly.fasta on rwdi" ; fi
- ${RWDI}/check_asm_quality.py --asm-dir ${RUN_PREFIX}/rwdi --expected-quals ${RWDI}/../share/good-arctic-sample0.txt --refs ${ARCTIC}/arcticsynth-refs.fa || FAILED="${FAILED} Did not pass check_asm_quality.py on rwdi"
- if [ ! -f ${RUN_PREFIX}/dbg/final_assembly.fasta ] ; then FAILED="${FAILED} Did not find final_assembly.fasta on dbg" ; fi
- ${RWDI}/check_asm_quality.py --asm-dir ${RUN_PREFIX}/dbg --expected-quals ${RWDI}/../share/good-arctic-sample0-k63.txt --refs ${ARCTIC}/arcticsynth-refs.fa || echo "WARN Did not pass check_asm_quality.py on dbg with reduced workflow k63"
- if [ -z "$FAILED" ] ; then true ; else echo "Something failed somehow - ${FAILED}"; false ; fi
- echo "Completed"
Cori:accuracy:
stage: accuracy
tags:
- Cori
script:
- set -e
- set -x
- uname -a
- pwd
- date
- export GASNET_BACKTRACE=1
- echo "Establishing variables"
- export MHM2_SOURCE=$(pwd)
- export BASE=${SCRATCH}/tmp/gitlab-runner-scratch-Cori-mhm2-${USER}
- export SCRATCH=${BASE}/mhm2-${CI_COMMIT_SHORT_SHA}-${CI_COMMIT_REF_NAME}-${CI_COMMIT_TAG}
- export INSTALL_PREFIX=${SCRATCH}/install
- export BUILD_PREFIX=${SCRATCH}/build
- export RUN_PREFIX=${SCRATCH}/runs
- echo "BASE=${BASE} SCRATCH=${SCRATCH}"
- echo "Loading KNL modules for upcxx on cori"
- source ${MHM2_SOURCE}/contrib/environments/cori-knl/gnu.sh
- exec > >(tee -ia ${SCRATCH}/accuracy.log)
- exec 2> >(tee -ia ${SCRATCH}/accuracy.err >&2)
- echo "Logging to ${SCRATCH}/accuracy.log and .err at $(date) on $(uname -n) in $(pwd)"
- module list
- cd $SCRATCH
- FAILED=""
- echo "Testing accuracy"
- export REL=${INSTALL_PREFIX}-knl/bin/
- export ARCTIC=/global/cscratch1/sd/regan/GitlabCIData/
- export OPTS="-r ${ARCTIC}/arctic_sample_0.fq --checkpoint=no"
- echo "Submitting job on 5 nodes... on 2 nodes is is roughly REL=170s"
- knl_job=$(sbatch --parsable --job-name="CImha-${CI_COMMIT_SHORT_SHA}" --account=mp215 -C knl --nodes=5 --qos=debug --time=10:00 --wrap="${REL}/mhm2.py $OPTS -o ${RUN_PREFIX}/rel && echo Good")
- echo "Submitting full arctic job on 15 nodes"
- export OPTS2="-r ${ARCTIC}/arctic_samples.fq --checkpoint=no"
- knl_job2=$(sbatch --parsable --job-name="CI-mhm2-${CI_COMMIT_SHORT_SHA}" --account=mp215 -C knl --nodes=15 --qos=debug --time=30:00 --wrap="${REL}/mhm2.py $OPTS2 -o ${RUN_PREFIX}/rel-full && echo Good")
- echo "Waiting for knl job $knl_job"
- date
- while /bin/true ; do sleep 120 ; date ; sacct=$(sacct -j $knl_job -o state -X -n 2>/dev/null || true) ; if [ -n "${sacct}" -a -z "$(echo "${sacct}" | grep ING)" ] ; then break ; fi ; done
- echo "sacct $sacct"
- sacct=$(sacct -j $knl_job -X -n)
- echo "sacct $sacct"
- cat slurm-${knl_job}.out
- wasgood=$(echo "${sacct}" | grep -v '0:0' || true)
- if [ -z "$wasgood" ] ; then true ; else echo "knl job ${knl_job} failed somehow - ${wasgood}"; false ; fi
- if [ ! -f ${RUN_PREFIX}/rel/final_assembly.fasta ] ; then FAILED="${FAILED} Did not find final_assembly.fasta on rel" ; fi
- ${REL}/check_asm_quality.py --asm-dir ${RUN_PREFIX}/rel --expected-quals ${REL}/../share/good-arctic-sample0.txt --refs ${ARCTIC}/arcticsynth-refs.fa || FAILED="${FAILED} Did not pass check_asm_quality.py"
- echo "Waiting for second (full) job to finish ${knl_job2}"
- while /bin/true ; do sleep 120 ; date ; sacct=$(sacct -j $knl_job2 -o state -X -n 2>/dev/null || true) ; if [ -n "${sacct}" -a -z "$(echo "${sacct}" | grep ING)" ] ; then break ; fi ; done
- echo "sacct $sacct"
- sacct=$(sacct -j $knl_job2 -X -n)
- echo "sacct $sacct"
- cat slurm-${knl_job2}.out
- wasgood=$(echo "${sacct}" | grep -v '0:0' || true)
- if [ -z "$wasgood" ] ; then true ; else echo "knl job ${knl_job2} failed somehow - ${wasgood}"; false ; fi
- if [ ! -f ${RUN_PREFIX}/rel-full/final_assembly.fasta ] ; then FAILED="${FAILED} Did not find final_assembly.fasta on rel-full" ; fi
- ${REL}/check_asm_quality.py --thres 0.015 --rna --asm-dir ${RUN_PREFIX}/rel-full --expected-quals ${REL}/../share/good-arcticsynth.txt --refs ${ARCTIC}/arcticsynth-refs.fa || FAILED="${FAILED} Did not pass check_asm_quality.py (full)"
- if [ -z "$FAILED" ] ; then true ; else echo "Something failed somehow - ${FAILED}" ; false ; fi
- echo "Completed"
#
# hulk
#
HULK:build:
stage: build
tags:
- HULK
script:
- set -e
- set -x
- git submodule init
- git submodule sync
- git submodule update
- BASE=/work/gitlab-ci
- CI_INSTALL=$BASE/ci-install-mhm2-upcxx-${HULK_UPCXX_VER}
- export PATH=$CI_INSTALL/bin:/bin:/usr/bin:/usr/local/bin
- export HIPMER_DATA=${BASE}/scratch/
- mkdir -p ${HIPMER_DATA}
- export SCRATCH=${BASE}/scratch/mhm2-${CI_COMMIT_SHORT_SHA}-${CI_COMMIT_REF_NAME}-${CI_COMMIT_TAG}
- export RUN_PREFIX=${SCRATCH}/runs
- export GASNET_BACKTRACE=1
- echo "Verifing and/or downloading test arctic data set"
- export ARCTIC_URL=https://portal.nersc.gov/project/hipmer/MetaHipMer_datasets_12_2019/ArcticSynth/samples/
- bash -c "[ -f ${HIPMER_DATA}/arcticsynth-refs.fa ] || ( curl -LO ${ARCTIC_URL}/arcticsynth-refs.fa.gz && gunzip arcticsynth-refs.fa.gz && mv arcticsynth-refs.fa ${HIPMER_DATA}/arcticsynth-refs.fa )"
- bash -c "for i in 0 1 2 3 4 5 6 7 8 9 10 11 ; do [ -f ${HIPMER_DATA}/arctic_sample_\$i.fq ] || ( curl -LO ${ARCTIC_URL}/arctic_sample_\$i.fq.gz && gunzip arctic_sample_\$i.fq.gz && mv arctic_sample_\$i.fq ${HIPMER_DATA}/arctic_sample_\$i.fq ) ; done"
- echo "Establishing all tests under BASE=$BASE and SCRATCH=$SCRATCH"
- rm -rf ${SCRATCH}
- mkdir -p ${SCRATCH}
- chmod a+rx ${SCRATCH}
- chmod g+s ${SCRATCH}
- mkdir -p ${RUN_PREFIX}
- exec > >(tee -ia ${SCRATCH}/build.log)
- exec 2> >(tee -ia ${SCRATCH}/build.err >&2)
- echo "Logging to ${SCRATCH}/build.log and .err at $(date) on $(uname -n) in $(pwd)"
- export MHM2_SOURCE=$(pwd)
- env
- uname -a
- pwd
- find * -type d -ls
- date
- echo "Purging any old tests"
- find ${BASE}/scratch -maxdepth 1 -name 'mhm*' -mtime +4 -type d -exec rm -rf '{}' ';' || /bin/true
- df -h
- FAILED=""
- echo "Checking for cmake, Berkeley UPC and UPC++"
- which cmake && cmake --version || FAILED="${FAILED} cmake not found"
- echo "Checking or building upcxx"
- which upcxx || UPCXXVER=${HULK_UPCXX_VER} ./upcxx-utils/contrib/install_upcxx.sh $CI_INSTALL || FAILED="${FAILED} could not install upcxx"
- upcxx --version || FAILED="${FAILED} no upcxx was found"
- echo "Building all flavors"
- mkdir -p ${RUN_PREFIX}
- export GASNET_BACKTRACE=1
- export INSTALL_PREFIX=${SCRATCH}
- rm -rf $SCRATCH/build
- mkdir -p $SCRATCH/build
- cd $SCRATCH/build
- echo "Building Debug"
- cmake -DCMAKE_INSTALL_PREFIX=${INSTALL_PREFIX}/mhm2-dbg -DCMAKE_BUILD_TYPE=Debug ${MHM2_SOURCE} || FAILED="${FAILED} Could not configure Debug"
- make -j 16 all check install || FAILED="${FAILED} Could not build Debug"
- make clean
- export UPCXX_CODEMODE=debug
- echo "Building RelWithDebInfo with UPCXX_CODEMODE=$UPCXX_CODEMODE"
- cmake -DCMAKE_INSTALL_PREFIX=${INSTALL_PREFIX}/mhm2-rwdi -DCMAKE_BUILD_TYPE=RelWithDebInfo ${MHM2_SOURCE} || FAILED="${FAILED} could not configure RelWithDebInfo"
- make -j 16 all check install || FAILED="${FAILED} Cuold not build RelWithDebInfo"
- make clean
- unset UPCXX_CODEMODE
- echo "Building Release"
- cmake -DCMAKE_INSTALL_PREFIX=${INSTALL_PREFIX}/mhm2-rel -DCMAKE_BUILD_TYPE=Release ${MHM2_SOURCE} || FAILED="${FAILED} could not configure Release"
- make -j 16 all check install || FAILED="${FAILED} Could not build Release"
- echo "${FAILED}"
- if [ -z "$FAILED" ] ; then true ; else echo "Something failed somehow - ${FAILED}"; false ; fi
- cd -
- rm -rf $SCRATCH/build
- echo "Completed"
HULK:validation:
stage: validation
tags:
- HULK
script:
- set -e
- set -x
- BASE=/work/gitlab-ci
- CI_INSTALL=$BASE/ci-install-mhm2-upcxx-${HULK_UPCXX_VER}
- export PATH=$CI_INSTALL/bin:/bin:/usr/bin:/usr/local/bin
- export HIPMER_DATA=${BASE}/scratch/
- export SCRATCH=${BASE}/scratch/mhm2-${CI_COMMIT_SHORT_SHA}-${CI_COMMIT_REF_NAME}-${CI_COMMIT_TAG}
- export RUN_PREFIX=${SCRATCH}/runs
- export INSTALL_PREFIX=${SCRATCH}
- export GASNET_BACKTRACE=1
- exec > >(tee -ia ${SCRATCH}/validation.log)
- exec 2> >(tee -ia ${SCRATCH}/validation.err >&2)
- echo "Logging to ${SCRATCH}/validation.log and .err at $(date) on $(uname -n) in $(pwd)"
- echo "Validating all tests under BASE=$BASE and SCRATCH=$SCRATCH"
- env
- df -h
- uname -a
- pwd
- date
- upcxx --version
- cd ${SCRATCH}
- FAILED=""
- reads=${HIPMER_DATA}/arctic_sample_0.fq
- export DBG=${INSTALL_PREFIX}/mhm2-dbg/bin/
- export RWDI=${INSTALL_PREFIX}/mhm2-rwdi/bin/
- export REL=${INSTALL_PREFIX}/mhm2-rel/bin/
- echo "Starting RelWithDebInfo mhm2 on Arctic $reads"
- if [ ! -f arctic_sample_0.fq -a -f $reads ] ; then ln -s $reads ; fi
- if [ ! -f arcticsynth-refs.fa -a -f ${HIPMER_DATA}/arcticsynth-refs.fa ] ; then ln -s ${HIPMER_DATA}/arcticsynth-refs.fa ; fi
- ${RWDI}/ci_asm_qual_test.sh || FAILED="${FAILED} Could not run ci_asm_qual_test"
- if [ ! -f ./test-arctic-sample0/final_assembly.fasta ] ; then FAILED="${FAILED} Did not find final_assembly.fasta for rwdi in test-arctic-sample0" ; fi
- mv test-arctic-sample0 ${RUN_PREFIX}/rwdi-test-arctic-sample0
- echo "Starting debug run on with reduced workflow"
- ${DBG}/mhm2.py -r $reads -o ${RUN_PREFIX}/dbg --kmer-lens 31,63 --checkpoint=no -v || FAILED="${FAILED} Could not run dbg"
- echo "verify dbg results $(ls -la ${RUN_PREFIX}/dbg)"
- if [ ! -f ${RUN_PREFIX}/dbg/final_assembly.fasta ] ; then FAILED="${FAILED} Did not find final_assembly.fasta on dbg" ; fi
- ${DBG}/check_asm_quality.py --asm-dir ${RUN_PREFIX}/dbg --expected-quals ${DBG}/../share/good-arctic-sample0-k31k63.txt --refs ${HIPMER_DATA}/arcticsynth-refs.fa || echo "WARN did not pass check_asm_quality.py for dbg with reduced workflow k31k63"
- if [ -z "$FAILED" ] ; then true ; else echo "Something failed somehow - ${FAILED}"; false ; fi
- echo "Completed"
HULK:accuracy:
stage: accuracy
tags:
- HULK
script:
- set -e
- set -x
- git submodule init
- git submodule sync
- git submodule update
- BASE=/work/gitlab-ci
- CI_INSTALL=$BASE/ci-install-mhm2-upcxx-${HULK_UPCXX_VER}
- export PATH=$CI_INSTALL/bin:/bin:/usr/bin:/usr/local/bin
- export HIPMER_DATA=${BASE}/scratch/
- export SCRATCH=${BASE}/scratch/mhm2-${CI_COMMIT_SHORT_SHA}-${CI_COMMIT_REF_NAME}-${CI_COMMIT_TAG}
- export RUN_PREFIX=${SCRATCH}/runs
- export INSTALL_PREFIX=${SCRATCH}
- export GASNET_BACKTRACE=1
- exec > >(tee -ia ${SCRATCH}/accuracy.log)
- exec 2> >(tee -ia ${SCRATCH}/accuracy.err >&2)
- echo "Logging to ${SCRATCH}/accuracy.log and .err at $(date) on $(uname -n) in $(pwd)"
- echo "Running accuracy tests under BASE=$BASE and SCRATCH=$SCRATCH"
- env
- df -h
- uname -a
- pwd
- date
- upcxx --version
- cd ${SCRATCH}
- FAILED=""
- export REL=${INSTALL_PREFIX}/mhm2-rel/bin/
- echo "Starting Release mhm2 on Arctic"
- if [ ! -f arctic_sample_0.fq -a -f ${HIPMER_DATA}/arctic_sample_0.fq ] ; then ln -s ${HIPMER_DATA}/arctic_sample_0.fq ; fi
- if [ ! -f arctic_sample_1.fq -a -f ${HIPMER_DATA}/arctic_sample_1.fq ] ; then ln -s ${HIPMER_DATA}/arctic_sample_1.fq ; fi
- if [ ! -f arctic_sample_2.fq -a -f ${HIPMER_DATA}/arctic_sample_2.fq ] ; then ln -s ${HIPMER_DATA}/arctic_sample_2.fq ; fi
- if [ ! -f arctic_sample_3.fq -a -f ${HIPMER_DATA}/arctic_sample_3.fq ] ; then ln -s ${HIPMER_DATA}/arctic_sample_3.fq ; fi
- if [ ! -f arctic_sample_4.fq -a -f ${HIPMER_DATA}/arctic_sample_4.fq ] ; then ln -s ${HIPMER_DATA}/arctic_sample_4.fq ; fi
- if [ ! -f arctic_sample_5.fq -a -f ${HIPMER_DATA}/arctic_sample_5.fq ] ; then ln -s ${HIPMER_DATA}/arctic_sample_5.fq ; fi
- if [ ! -f arctic_sample_6.fq -a -f ${HIPMER_DATA}/arctic_sample_6.fq ] ; then ln -s ${HIPMER_DATA}/arctic_sample_6.fq ; fi
- if [ ! -f arctic_sample_7.fq -a -f ${HIPMER_DATA}/arctic_sample_7.fq ] ; then ln -s ${HIPMER_DATA}/arctic_sample_7.fq ; fi
- if [ ! -f arctic_sample_8.fq -a -f ${HIPMER_DATA}/arctic_sample_8.fq ] ; then ln -s ${HIPMER_DATA}/arctic_sample_8.fq ; fi
- if [ ! -f arctic_sample_9.fq -a -f ${HIPMER_DATA}/arctic_sample_9.fq ] ; then ln -s ${HIPMER_DATA}/arctic_sample_9.fq ; fi
- if [ ! -f arctic_sample_10.fq -a -f ${HIPMER_DATA}/arctic_sample_10.fq ] ; then ln -s ${HIPMER_DATA}/arctic_sample_10.fq ; fi
- if [ ! -f arctic_sample_11.fq -a -f ${HIPMER_DATA}/arctic_sample_11.fq ] ; then ln -s ${HIPMER_DATA}/arctic_sample_11.fq ; fi
- if [ ! -f arcticsynth-refs.fa -a -f ${HIPMER_DATA}/arcticsynth-refs.fa ] ; then ln -s ${HIPMER_DATA}/arcticsynth-refs.fa ; fi
- ${REL}/ci_asm_qual_test.sh || FAILED="${FAILED} Could not run ci_asm_qual_test"
- if [ ! -f ./test-arctic-sample0/final_assembly.fasta ] ; then FAILED="${FAILED} Did not find final_assembly.fasta on rel" ; fi
- mv test-arctic-sample0 ${RUN_PREFIX}/rel-test-arctic-sample0
- ${REL}/ci_asm_qual_test-full.sh || FAILED="${FAILED} Could not run ci_asm_qual_test-full"
- if [ ! -f ./test-arctic-samples/final_assembly.fasta ] ; then FAILED="${FAILED} Did not find final_assembly.fasta on rel" ; fi
- mv test-arctic-samples ${RUN_PREFIX}/rel-test-arctic-samples
- if [ -z "$FAILED" ] ; then true ; else echo "Something failed somehow - ${FAILED}"; false ; fi
- echo "Completed"
after_script:
- date
- echo "Done"