Merge branch 'JABAWS_Release_2_5' into develop

[jabaws.git] / binaries / src / jpred / tests / todo.bash

diff --git a/binaries/src/jpred/tests/todo.bash b/binaries/src/jpred/tests/todo.bash
new file mode 100755 (executable)
index 0000000..030ea8a
--- /dev/null
+++ b/binaries/src/jpred/tests/todo.bash
@@ -0,0 +1,29 @@
+#define path to BLOSUM files
+setenv BLASTMAT /home/asherstnev/Projects/Jpred.project/jpred/branches/portable/data/blast
+ln -s /data/UNIREFdb databases
+
+####################################################################################################
+#  test of main binaries
+#
+# 1 core PHIBLAST check ()
+# 1 core PHIBLAST check ()
+../bin/blastpgp -e0.05 -h0.01 -m6 -b10000 -v10000 -j3 -d /home/asherstnev/Projects/Jpred.project/jpred/branches/portable/tests/databases/uniref90.filt -i d16vpa_.fasta -Q test.test.profile -o test.test.blas
+# multi-core (-a3) PHIBLAST check
+../bin/blastpgp -a4 -e0.05 -h0.01 -m6 -b10000 -v10000 -j3 -d /home/asherstnev/Projects/Jpred.project/jpred/branches/portable/tests/databases/uniref90.filt -i d16vpa_.fasta -Q test.test.profile -o test.test.blas
+
+####################################################################################################
+#  test of x86_64 binaries
+#
+# 1 core PHIBLAST check ()
+../x86_64/blastpgp -e0.05 -h0.01 -m6 -b10000 -v10000 -j3 -d /home/asherstnev/Projects/Jpred.project/jpred/branches/portable/tests/databases/uniref90.filt -i d16vpa_.fasta -Q test.test.profile -o test.test.blas
+# multi-core (-a3) PHIBLAST check
+../x86_64/blastpgp -a4 -e0.05 -h0.01 -m6 -b10000 -v10000 -j3 -d /home/asherstnev/Projects/Jpred.project/jpred/branches/portable/tests/databases/uniref90.filt -i d16vpa_.fasta -Q test.test.profile -o test.test.blas
+
+
+####################################################################################################
+../jpred.pl -seq d16vpa_.fas -o res_d16vpa_ -dbname ported_db -dbpath /data/UNIREFdb/ -ncpu 4 -debug
+../jpred.pl -seq SCOP175B_nr.seq -o res_SCOP175B_nr -dbname ported_db -dbpath /data/UNIREFdb/ -ncpu 4 -debug
+../jpred.pl -seq T-state1.fas    -o res_T-state1.res -dbname ported_db -dbpath /data/UNIREFdb/ -ncpu 4 -debug
+../jpred.pl -seq T-state2.fas    -o res_T-state2.res -dbname ported_db -dbpath /data/UNIREFdb/ -ncpu 4 -debug
+
+./webscripts/fasta2concise < d16vpa_.res.align > d16vpa_.res.align.csv