if error=$( perl -e 'use 5.8.0;' 2>&1 ); then
echo_green "OK"
+ log "OK"
else
echo $error | sed "s/, stopped.*//"
echo_red "FAIL"
exit
else
echo_green "OK"
+ log "OK"
fi
}
if error=$( ruby -e 'raise "Ruby version 1.9 required--this is only #{RUBY_VERSION}" if RUBY_VERSION < "1.9"' 2>&1 ); then
echo_green "OK"
+ log "OK"
else
echo $error | sed "s/.*: //"
echo_red "FAIL"
if error=$( gem list --local | grep $gem ); then
echo_green "OK"
+ log "OK"
else
echo_red "FAIL"
echo " Try: gem install $gem"
fi
}
+function test_aux_program
+{
+ local program=$1
+
+ echo -n "Checking auxillary program - \"$program\": "
+
+ if command -v $program >/dev/null; then
+ echo_green "OK"
+ log "OK"
+ else
+ echo_yellow "WARNING"
+ log "WARNING"
+ fi
+}
test_ruby
test_ruby_gem "gnuplot"
test_ruby_gem "narray"
+test_aux_program "blastall"
+test_aux_program "blat"
+test_aux_program "bwa"
+test_aux_program "bowtie"
+test_aux_program "formatdb"
+test_aux_program "gnuplot"
+test_aux_program "idba"
+test_aux_program "muscle"
+test_aux_program "mummer"
+test_aux_program "mysql"
+test_aux_program "prodigal"
+test_aux_program "ray"
+test_aux_program "scan_for_matches"
+test_aux_program "uclust"
+test_aux_program "velveth"
+test_aux_program "velvetg"
+test_aux_program "vmatch"
count=0
time0=`date +%s`
test_count=`cat $log_file | wc -l | sed "s/ //g"`
test_ok=`grep -c "OK" $log_file`
+test_fail=`grep -c "FAIL" $log_file`
+test_warn=`grep -c "WARNING" $log_file`
-test_fail=$[ $test_count - $test_ok ]
+report="Biopieces tested: $count Tests run: $test_count OK: $test_ok FAIL: $test_fail WARNING: $test_warn Time: $time secs"
-report="Biopieces tested: $count Tests run: $test_count OK: $test_ok FAIL: $test_fail Time: $time secs"
-
-if [ $test_fail = 0 ]; then
- echo_green "$report"
-else
+if (($test_fail > 0)); then
echo_red "$report"
+elif (($test_warn > 0)); then
+ echo_yellow "$report"
+else
+ echo_green "$report"
fi