The script is intended only as an example. Hopefully it will be possible for you to modify it to fit your purposes.
You can download the script including data from
http://www.clcbio.com/files/CLCServerCommandLineTools/1.6/example-workflow.zip.
This is a shell script that will run on Linux and Mac OS.
#!/bin/bash ################################################################################################### ## Example workflow script for CLC Server Command Line Tools 1.6 ## CLC bio, June 2012 ## ## For full documentation please visit: http://clcbio.com/usermanuals ################################################################################################### ### SETTINGS (Edit before use) #################################################################### # 1. Configure your server connection parameters SERVER="localhost" PORT="7777" USER="root" PASSWORD="default" # 2. Configure the path to the CLC Server Command Line tools SERVERCMDPATH="/home/user/clcservercmdline/clcserver" PARSECMDPATH="/home/user/clcservercmdline/clcresultparser" # 3. Configure High-throughput sequencing data import location for import data # - Use the server web-interface to setup a data import location # - Copy the example files from the data directory to this location # - Edit the IMPORTPATH variable below to a CLC URL point to this location # # For more info please visit: # http://www.clcbio.com/index.php?id=1484&manual=Direct_import_high_throughput_sequencing_data.html # # For information about CLC URLs please visit: # http://www.clcbio.com/index.php?id=1641&manual=Referring_files_CLC_URL.html IMPORTPATH="clc://serverfile/tmp/cmdline" # 4. Configure data paths for saving results # - Use the server web-interface to configure a file system location for data storage # - Edit the DATAPATH variable below to a CLC URL pointing to this location # # For more info please visit: # http://www.clcbio.com/index.php?id=1484&manual=Adding_file_system_location.html # # For information about CLC URLs please visit: # http://www.clcbio.com/index.php?id=1641&manual=Referring_files_CLC_URL.html DATAPATH="clc://server/test" DIR="clc-example" SUBDIR="workflow-example" ### FUNCTIONS ##################################################################################### function check_return_code { return_code=$? cmdname=$1 #echo Return code: $return_code if [ $return_code -ne 0 ] then echo "" echo "### Error during: $cmdname ###" echo "Terminating script" exit 1 fi } ### COMMANDS ###################################################################################### SERVERCMD="$SERVERCMDPATH -S $SERVER -P $PORT -U $USER -W $PASSWORD" PARSECMD=$PARSECMDPATH ### WORKFLOW SCRIPT ############################################################################### # Make a directory for DIR echo "" echo "Make a directory: $DIR" $SERVERCMD -A mkdir -t ${DATAPATH} -n ${DIR} -O tmpdir_result.txt check_return_code "make dir" tmpdir=`$PARSECMD -f "tmpdir_result.txt" -c "clc-example"` check_return_code "make dir result parsing" rm tmpdir_result.txt # Make subdirectory in DIR folder for result and data echo "" echo "Make subdirectory: $SUBDIR" $SERVERCMD -A mkdir -t ${tmpdir} -n ${SUBDIR} -O mkdir_result.txt check_return_code "Make sub dir" destdir=`$PARSECMD -f mkdir_result.txt -p "-d" -c $SUBDIR` check_return_code "Make sub dir result parsing" rm mkdir_result.txt # Import solid data echo "" echo "Import solid data" $SERVERCMD -A ngs_import_solid -f "$IMPORTPATH/solid_matepair_F3.csfasta" -f "$IMPORTPATH/solid_matepair_F3._QV.qual" -f "$IMPORTPATH/solid_matepair_R3.csfasta" -f "$IMPORTPATH/solid_matepair_R3._QV.qual" --paired-reads true --read-orientation FORWARD_FORWARD ${destdir} -O ngs_import_solid_result.txt --min-distance 100 --max-distance 25000 check_return_code "Import solid data" soliddata=`$PARSECMD -f ngs_import_solid_result.txt -p "-i" -c "solid" --ignorelog true` check_return_code "Import solid data result parsing" rm ngs_import_solid_result.txt # Import genome echo "" echo "Import genome" $SERVERCMD -A import -f automaticimport -s "$IMPORTPATH/reference.fa" ${destdir} -O import_result.txt check_return_code "Import genome" refdata=`$PARSECMD -f import_result.txt -p "--references" -c "reference"` check_return_code "Import genome result parsing" rm import_result.txt # Do readmapping echo "" echo "Read Mapping" $SERVERCMD -A read_mapping ${soliddata} ${destdir} ${refdata} -O read_mapping_result.txt check_return_code "Read Mapping" echo $PARSECMD -f read_mapping_result.txt -p "-i" -c "mapping" readmap=`$PARSECMD -f read_mapping_result.txt -p "-i" -c "Reads"` check_return_code "Read Mapping result parsing" rm read_mapping_result.txt # Quality-based Variant Detection echo "" echo "Quality-based Variant Detection" $SERVERCMD -A quality-based_variant_detection --create-table true --min-coverage 1 --variant-in-forward-reverse-reads false ${readmap} ${destdir} -O quality_result.txt check_return_code "Quality-based Variation Detection" table=`$PARSECMD -f quality_result.txt -p "-s" -c "(Reads)"` check_return_code "Quality-based Variation Detection result parsing" rm quality_result.txt # Export variant table to excel echo "" echo "Export variant table to excel" $SERVERCMD -A export -e excel_2010_exporter -d . ${table} -O table_export_result.txt check_return_code "Export variant table to excel" file=`$PARSECMD -f table_export_result.txt -O File` check_return_code "Export variant table to excel result parsing" rm table_export_result.txt # Workflow completed echo "" echo "Workflow completed succesfully" echo "Variant table: ${file}"