Mercurial > repos > dereeper > blup_calculator
view blupcal.sh @ 1:c1c85170db1b draft default tip
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author | dereeper |
---|---|
date | Sun, 30 Dec 2018 01:39:11 -0500 |
parents | 45d215f2be74 |
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#!/bin/bash tool_directory=$1 galaxy_tabular_file=$2 galaxy_replication_vector_column_index=$3 galaxy_genotype_vector_column_index=$4 galaxy_first_y_vector_column_index=$5 galaxy_last_y_vector_column_index=$6 galaxy_design=$7 galaxy_summarize_by=$8 galaxy_summarize_by_vector_column_index=$9 galaxy_group_variable_1=${10} galaxy_group_variable_1_vector_column_index=${11} galaxy_group_variable_2=${12} galaxy_group_variable_2_vector_column_index=${13} galaxy_output_file_path=${14} block_vector_column_index=${15} directory=`dirname $0` mkdir tmpdir$$ counter=$galaxy_first_y_vector_column_index previous="tmpdir$$/output" echo '' >$previous while [ $counter -le $galaxy_last_y_vector_column_index ] do Rscript --vanilla $directory/blupcal_wrapper.R --tool_directory $tool_directory --tabular_file $galaxy_tabular_file --replication_vector_column_index $galaxy_replication_vector_column_index --genotype_vector_column_index $galaxy_genotype_vector_column_index --y_vector_column_index $counter --design $galaxy_design --summarize_by $galaxy_summarize_by --summarize_by_vector_column_index $galaxy_summarize_by_vector_column_index --group_variable_1 $galaxy_group_variable_1 --group_variable_1_vector_column_index $galaxy_group_variable_1_vector_column_index --group_variable_2 $galaxy_group_variable_2 --group_variable_2_vector_column_index $galaxy_group_variable_2_vector_column_index --output_file_path tmpdir$$/output.$counter --block_vector_column_index $block_vector_column_index #cat tmpdir$$/output.$counter >>$galaxy_output_file_path if [ "$counter" -gt "$galaxy_first_y_vector_column_index" ];then if [[ "$galaxy_summarize_by" == "true" ]];then cut -f 3-7 tmpdir$$/output.$counter >>tmpdir$$/output.$counter.cut fi if [[ "$galaxy_summarize_by" == "false" ]];then cut -f 2-6 tmpdir$$/output.$counter >>tmpdir$$/output.$counter.cut fi mv tmpdir$$/output.$counter.cut tmpdir$$/output.$counter fi if [ "$counter" -gt "$galaxy_first_y_vector_column_index" ];then paste $previous tmpdir$$/output.$counter >>tmpdir$$/output.$counter.$counter fi if [ "$counter" -eq "$galaxy_first_y_vector_column_index" ];then cp tmpdir$$/output.$counter tmpdir$$/output.$counter.$counter fi previous="tmpdir$$/output.$counter.$counter" cp -rf tmpdir$$/output.$counter.$counter $galaxy_output_file_path #paste $galaxy_output_file_path tmpdir$$/output.$counter >>$galaxy_output_file_path #cut -f 3-7 tmpdir$$/output.$counter >tmpdir$$/output.$counter.cut ((counter++)) done echo $galaxy_summarize_by