Merge pull request #103 from kantale/master

Removed Process Substitution

compute5/Imputation_impute2/protocols/alignWithReference.sh

@@ -10,13 +10,15 @@
 #string genotypeAlignerJar
 #string vcf
 #string refType
+#string javaExecutable
 
 echo "chr: ${chr}"
 echo "outputFolder: ${outputFolder}"
 echo "knownHapsG: ${knownHapsG}"
 echo "genotypeAlignerJar: ${genotypeAlignerJar}"
 echo "vcf: ${vcf}"
 echo "refType: ${refType}"
+echo "javaExecutable: $(javaExecutable)"
 
 haps_input=${knownHapsG}
 sample_input="${knownHapsG%.haps}.sample"
@@ -41,7 +43,7 @@ getFile ${sample_input}
 inputs ${sample_input}
 
 #Do the alignment
-if java -jar ${genotypeAlignerJar} \
+if ${javaExecutable} -jar ${genotypeAlignerJar} \
 	--input ${basename_input} \
 	--inputType SHAPEIT2 \
 	--ref ${vcf} \

compute5/Imputation_impute2/protocols/concatImpute2ChrResults_samples.sh

@@ -60,15 +60,29 @@ rm -f ${imputationIntermediatesFolder}/chr${chr}_${fromChrPos}-${toChrPos}_info
 
 #Merging chunks
 toExecute="paste <(cut -d ' ' -f 1-5 ${imputation__has__impute2ChunkOutput[0]})"
+concatCommandColumns="cut -d ' ' -f 1-5 ${imputation__has__impute2ChunkOutput[0]} > ${imputationIntermediatesFolder}/~chr${chr}_${fromChrPos}-${toChrPos}.columns"
+concatCommand="paste ${imputationIntermediatesFolder}/~chr${chr}_${fromChrPos}-${toChrPos}.columns "
+echo "Running: ${concatCommandColumns}"
+eval ${concatCommandColumns}
+indexVar=0
 for element in ${imputation__has__impute2ChunkOutput[@]}
 do
+	indexVar=`expr $indexVar + 1`
 	toExecute="${toExecute} <( cut -d ' ' -f 6- ${element} )"
+	concatCommandColumns="cut -d ' ' -f 6- ${element} > ${imputationIntermediatesFolder}/~chr${chr}_${fromChrPos}-${toChrPos}.${indexVar}"
+	echo "Running: ${concatCommandColumns}"
+	eval ${concatCommandColumns}
+	concatCommand="${concatCommand} ${imputationIntermediatesFolder}/~chr${chr}_${fromChrPos}-${toChrPos}.${indexVar} "
 done
 toExecute="${toExecute} > ${imputationIntermediatesFolder}/~chr${chr}_${fromChrPos}-${toChrPos}"
+concatCommand="${concatCommand} > ${imputationIntermediatesFolder}/~chr${chr}_${fromChrPos}-${toChrPos}"
 
-echo "Executing: $toExecute"
-eval ${toExecute}
+# Process substitution is not available in all Unix shells
+#echo "Executing: $toExecute"
+#eval ${toExecute}
 
+echo "Executing: ${concatCommand}"
+eval ${concatCommand}
 
 returnCode=$?
 if [ $returnCode -eq 0 ]

compute5/Imputation_impute2/protocols/impute2Imputation.sh

@@ -126,8 +126,14 @@ mkdir -p ${imputationIntermediatesFolder}
 #Create subset of samples to exclude 
 sample_subset_to_exclude=${tmpOutput}.toExclude
 echo "Samples excluded from this run: ${sample_subset_to_exclude}"
-cat <(cat ${genotype_aligner_output_sample} | tail -n +3 | head -n `expr ${fromSample} - 1`) <(cat ${genotype_aligner_output_sample} | tail -n +3 | tail -n +`expr ${toSample} + 1`) | cut -f 2 -d ' ' > ${sample_subset_to_exclude}
 
+# Process substitution is not supported from all shells : http://www.gnu.org/software/bash/manual/bashref.html#Process-Substitution so it's better to avoid it.
+# This is the way to implement the following three lines in a single command with process substitution:
+# cat <(cat ${genotype_aligner_output_sample} | tail -n +3 | head -n `expr ${fromSample} - 1`) <(cat ${genotype_aligner_output_sample} | tail -n +3 | tail -n +`expr ${toSample} + 1`) | cut -f 2 -d ' ' > ${sample_subset_to_exclude}
+
+cat ${genotype_aligner_output_sample} | tail -n +3 | head -n `expr ${fromSample} - 1` > ${sample_subset_to_exclude}.part1
+cat ${genotype_aligner_output_sample} | tail -n +3 | tail -n +`expr ${toSample} + 1` > ${sample_subset_to_exclude}.part2
+cat ${sample_subset_to_exclude}.part1 ${sample_subset_to_exclude}.part2 | cut -f 2 -d ' ' > ${sample_subset_to_exclude}
 
 #From http://mathgen.stats.ox.ac.uk/impute/impute_v2.html
 #To use pre-phased study data in this example, you would replace the -g file with a -known_haps_g file and add the -use_prephased_g flag to your IMPUTE2 command.