use module only when available

marbl · Mar 24, 2020 · 99a7ad8 · 99a7ad8
1 parent 8a8cb1e
commit 99a7ad8
Show file tree

Hide file tree

Showing 8 changed files with 59 additions and 19 deletions.
diff --git a/eval/spectra-cn.sh b/eval/spectra-cn.sh
@@ -38,11 +38,13 @@ if [ -s $name ]; then
 fi
 
 
-## Comment this line if R is properly installed ##
-echo "Load R"
-module load R					#
-#################################################
-echo
+has_module=$(check_module)
+if [[ $has_module -gt 0 ]]; then
+	echo "No modules available.."
+else
+	module load R
+fi
+
 
 asm1=`echo $asm1_fa | sed 's/.fasta$//g' | sed 's/.fa$//g' | sed 's/.fasta.gz$//g' | sed 's/.fa.gz$//g'`
 

diff --git a/trio/block_n_stats.sh b/trio/block_n_stats.sh
@@ -31,9 +31,16 @@ else
     g_size=$4
 fi
 
-module load bedtools
-module load samtools
-module load R
+source $MERQURY/util/util.sh
+
+has_module=$(check_module)
+if [[ $has_module -gt 0 ]]; then
+        echo "No modules available.."
+else
+	module load bedtools
+	module load samtools
+	module load R
+fi
 
 for asm in $asm1 $asm2
 do

diff --git a/trio/hap_blob.sh b/trio/hap_blob.sh
@@ -67,7 +67,12 @@ done
 echo "
 Plot hap-mer blob plots"
 
-module load R
+has_module=$(check_module)
+if [[ $has_module -gt 0 ]]; then
+        echo "No modules available.."
+else
+	module load R
+fi
 
 echo "
 Rscript $MERQURY/plot/plot_blob.R -f $count -o $out.hapmers.blob"

diff --git a/trio/hapmers.sh b/trio/hapmers.sh
@@ -112,10 +112,14 @@ meryl histogram shrd.inherited.meryl | awk -v kmer="shared" '{print kmer"\t"$1"\
 echo
 
 echo "# Plot $hist"
-## Comment this line if R is properly installed ##
-echo "Load R"					 #
-module load R                                    #
-##################################################
+source $MERQURY/util/util.sh
+
+has_module=$(check_module)
+if [[ $has_module -gt 0 ]]; then
+        echo "No modules available.."
+else
+	module load R
+fi
 echo
 
 Rscript $MERQURY/plot/plot_spectra_cn.R -f $hist -o ${hist/.hist/} -l cutoffs.txt

diff --git a/trio/phase_block.sh b/trio/phase_block.sh
@@ -15,8 +15,13 @@ hap1=`link $2`
 hap2=`link $3`
 out=$4
 
-module load bedtools
-module load samtools
+has_module=$(check_module)
+if [[ $has_module -gt 0 ]]; then
+        echo "No modules available.."
+else
+        module load bedtools
+        module load samtools
+fi
 
 k=`meryl print $hap1 | head -n 2 | tail -n 1 | awk '{print length($1)}'`
 echo "Detected k-mer size: $k"

diff --git a/trio/spectra-hap.sh b/trio/spectra-hap.sh
@@ -33,9 +33,14 @@ k=`meryl print $read | head -n 2 | tail -n 1 | awk '{print length($1)}'`
 echo "Detected k-mer size $k"
 
 ## Remove this line if R is properly installed ##
-echo "Load R"
-module load R                                   #
-#################################################
+source $MERQURY/util/util.sh
+
+has_module=$(check_module)
+if [[ $has_module -gt 0 ]]; then
+        echo "No modules available.."
+else
+	module load R
+fi
 
 read=${read/.meryl/}		  # all read counts
 read_hap1=${read_hap1/.meryl/}    # pat specific mers with read counts

diff --git a/trio/switch_error.sh b/trio/switch_error.sh
@@ -48,7 +48,14 @@ echo "Count $hap1 and $hap2 hap-mers per block to $count"
 echo -e "Block\tRange\t$hap1\t$hap2\tSize" > $count
 awk -v hap1=$hap1 -v hap2=$hap2 '{ swi=$(NF-1); phase=$NF; {if ($4==hap1) { hap1_cnt=phase; hap2_cnt=swi; } else if ($4==hap2) { hap1_cnt=swi; hap2_cnt=phase; }} {print $4"\t"$1"_"$2"_"$3"\t"hap1_cnt"\t"hap2_cnt"\t"($3-$2)}}' $out.phased_block.bed >> $count
 
-module load R
+source $MERQURY/util/util.sh
+
+has_module=$(check_module)
+if [[ $has_module -gt 0 ]]; then
+        echo "No modules available.."
+else
+	module load R
+fi
 
 echo "
 Rscript $MERQURY/plot/plot_blob.R -f $count -o $out.phased_block.blob"

diff --git a/util/util.sh b/util/util.sh
@@ -9,3 +9,8 @@ function link()
         echo $db_name
 }
 
+function check_module()
+{
+	module -v 1> /dev/null 2> /dev/null
+	echo $?
+}