Update samtools from 1.6 to 1.9. Auto Adjust bwa alignment score by r…

…eads length for PanGIA pipeline.
LANL-Bioinformatics · Aug 29, 2018 · 5425692 · 5425692
1 parent ba69daf
commit 5425692
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Showing 3 changed files with 5 additions and 4 deletions.
diff --git a/INSTALL.sh b/INSTALL.sh
@@ -965,13 +965,13 @@ echo "
 
 install_samtools()
 {
-local VER=1.6
+local VER=1.9
 echo "------------------------------------------------------------------------------
                            Compiling samtools-$VER
 ------------------------------------------------------------------------------
 "
 tar xvzf samtools-$VER.tar.gz
-cd samtools-1.6
+cd samtools-$VER
 #make CFLAGS='-g -fPIC -Wall -O2'
 ./configure --prefix=$rootdir
 make
@@ -1962,7 +1962,7 @@ then
   then
       samtools_installed_VER=`samtools 2>&1| grep 'Version'|perl -nle 'print $1 if m{Version: (\d+\.\d+)}'`; 
   fi
-  if  ( echo $samtools_installed_VER | awk '{if($1>=1.3) exit 0; else exit 1}' )
+  if  ( echo $samtools_installed_VER | awk '{if($1>=1.7) exit 0; else exit 1}' )
   then
       echo "samtools is found"
   else

diff --git a/scripts/microbial_profiling/microbial_profiling.pl b/scripts/microbial_profiling/microbial_profiling.pl
@@ -228,6 +228,7 @@
 			$cmd = &param_replace( $cmd, $file_info, $tools, $idx, $tool );
 			$qsub_cmd = &param_replace( $qsub_cmd, $file_info, $tools, $idx, $tool );
 			if ($tools->{system}->{RUN_TOOL_AS_JOB}){
+				unlink $log;
 				&_notify("[RUN_TOOL] [$tool] COMMAND: $qsub_cmd\n");
 				&_notify("[RUN_TOOL] [$tool] Logfile: $log\n");
 				#&_notify("$qsub_cmd -v EDGE_HOME=$ENV{EDGE_HOME} $script_dirname/script/$cmd\n");

diff --git a/scripts/microbial_profiling/microbial_profiling.settings.tmpl b/scripts/microbial_profiling/microbial_profiling.settings.tmpl
@@ -131,7 +131,7 @@ OUTPUT_DIR=%OUTDIR%/%SERIAL%_%PREFIX%/%TOOL%
 
 <TMPL_IF NAME="pangia">
 [pangia]
-COMMAND=uge-pangia.sh -i %FASTQ% -p %PREFIX% -o %OUTPUT_DIR% -t %THREADS% -d "<TMPL_VAR NAME=pangia-db>" -c <TMPL_VAR NAME=pangia-rc> -a <TMPL_VAR NAME=pangia-opts DEFAULT="'-sb -se'"> -r <TMPL_VAR NAME=pangia-ra> -S <TMPL_VAR NAME=pangia-ms> -R <TMPL_VAR NAME=pangia-mr> -B <TMPL_VAR NAME=pangia-mb> -L <TMPL_VAR NAME=pangia-ml> <TMPL_VAR NAME=pangia-bg>
+COMMAND=uge-pangia.sh -i %FASTQ% -p %PREFIX% -o %OUTPUT_DIR% -t %THREADS% -d "<TMPL_VAR NAME=pangia-db>" -c <TMPL_VAR NAME=pangia-rc> -a '-ams <TMPL_VAR NAME=bwaScoreCut DEFAULT=30> <TMPL_VAR NAME=pangia-opts DEFAULT="-sb -se">' -r <TMPL_VAR NAME=pangia-ra> -S <TMPL_VAR NAME=pangia-ms> -R <TMPL_VAR NAME=pangia-mr> -B <TMPL_VAR NAME=pangia-mb> -L <TMPL_VAR NAME=pangia-ml> <TMPL_VAR NAME=pangia-bg|>
 OUTPUT_DIR=%OUTDIR%/%SERIAL%_%PREFIX%/%TOOL%
 </TMPL_IF>