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From: Milot Mirdita <milot@mirdita.de>
Date: Tue, 1 Sep 2020 22:23:03 +0200
Subject: Make test script work without MPI
Origin: upstream, https://github.com/soedinglab/hh-suite/commit/c296b369410900b193a6b74f0554ac90ccfd7d08
Forwarded: not-needed
--- a/data/test.sh
+++ b/data/test.sh
@@ -2,36 +2,51 @@
rm -f single* search_* blits_*
-hhalign -i query.a3m -t query.a3m
+if $(command -v "ffindex_apply_mpi" >/dev/null 2>&1); then
+ MPI=1
+fi
+
+hhalign -i query.a3m -o result.hhr -t query.a3m
ffindex_build -s single.ffdata single.ffindex query.a3m
-mpirun -np 2 \
- ffindex_apply_mpi single.ffdata single.ffindex -d single_a3m_cons.ffdata -i single_a3m_cons.ffindex \
+APPLY="ffindex_apply"
+if [ -n "$MPI" ]; then
+ APPLY="mpirun -np 2 ffindex_apply_mpi"
+fi
+
+$APPLY single.ffdata single.ffindex -d single_a3m_cons.ffdata -i single_a3m_cons.ffindex \
-- hhconsensus -i stdin -oa3m stdout -M a3m -v 0
-mpirun -np 2 \
- ffindex_apply_mpi single_a3m_cons.ffdata single_a3m_cons.ffindex -d single_a3m.ffdata -i single_a3m.ffindex \
+$APPLY single_a3m_cons.ffdata single_a3m_cons.ffindex -d single_a3m.ffdata -i single_a3m.ffindex \
-- hhfilter -i stdin -o stdout -diff 1000 -v 0
-mpirun -np 2 \
- ffindex_apply_mpi single_a3m.ffdata single_a3m.ffindex -d single_hhm.ffdata -i single_hhm.ffindex \
+$APPLY single_a3m.ffdata single_a3m.ffindex -d single_hhm.ffdata -i single_hhm.ffindex \
-- hhmake -i stdin -o stdout -v 0
-mpirun -np 2 cstranslate_mpi -i single -o single_cs219 -b -x 0.3 -c 4 -I a3m
+if [ -n "$MPI" ]; then
+ mpirun -np 2 cstranslate_mpi -i single -o single_cs219 -b -x 0.3 -c 4 -I a3m
+else
+ cstranslate -i single -o single_cs219 -b -x 0.3 -c 4 -I a3m -f
+fi
-hhblits -i query.a3m -d single -blasttab blits_app_res -n 1
+hhblits -i query.a3m -o result.hhr -d single -blasttab blits_app_res -n 1
hhblits_omp -i single -d single -blasttab blits_omp_res -n 1
-mpirun -np 2 hhblits_mpi -i single -d single -blasttab blits_mpi_res -n 1
-
diff <(tr -d '\000' < blits_omp_res.ffdata) blits_app_res
-diff <(tr -d '\000' < blits_mpi_res.ffdata) blits_app_res
+if [ -n "$MPI" ]; then
+ mpirun -np 2 hhblits_mpi -i single -d single -blasttab blits_mpi_res -n 1
+ diff <(tr -d '\000' < blits_mpi_res.ffdata) blits_app_res
+fi
-hhsearch -i query.a3m -d single -blasttab search_app_res
+hhsearch -i query.a3m -o result.hhr -d single -blasttab search_app_res
hhsearch_omp -i single -d single -blasttab search_omp_res
-mpirun -np 2 hhsearch_mpi -i single -d single -blasttab search_mpi_res
-
diff <(tr -d '\000' < search_omp_res.ffdata) search_app_res
-diff <(tr -d '\000' < search_mpi_res.ffdata) search_app_res
+
+if [ -n "$MPI" ]; then
+ mpirun -np 2 hhsearch_mpi -i single -d single -blasttab search_mpi_res
+ diff <(tr -d '\000' < search_mpi_res.ffdata) search_app_res
+fi
diff <(cut -f 1-10,12 blits_app_res) <(cut -f 1-10,12 search_app_res)
+
+rm -f result.hhr
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