bowtie2: do not use pipes

fixes galaxyproject#5983

by using a pipe bowtie2 and samtools run in parallel. since already
bowtie2 alone uses more CPU than the assigned ones (less that 1 core)
we should not do this, but run them serially.

also properly redirects stderr.

tools/bowtie2/bowtie2_wrapper.xml

@@ -12,8 +12,6 @@
     </requirements>
     <version_command>bowtie2 --version</version_command>
     <command detect_errors="exit_code"><![CDATA[
-## Use pipefail if available to quit with first non-zero exit code
-set -o | grep -q pipefail && set -o pipefail;
 ## prepare bowtie2 index
 #set index_path = ''
 #if str($reference_genome.source) == "history":
@@ -303,14 +301,16 @@ bowtie2
 
 ## mapping stats (i.e. stderr from bowtie2)
 #if $save_mapping_stats
-    2> '$mapping_stats'
+    2> >(tee '$mapping_stats' >&2) 
 #end if
 
 ## output file
 #if str( $sam_options.sam_options_selector ) == "no" or (str( $sam_options.sam_opt ) == "false" and str($sam_options.reorder) == ''):
-    | samtools sort --no-PG -@\${GALAXY_SLOTS:-2} -T "\${TMPDIR:-.}" -O bam -o '$output'
+    > alignment.sam
+    && samtools sort --no-PG -@\${GALAXY_SLOTS:-2} -T "\${TMPDIR:-.}" -O bam -o '$output' alignment.sam
 #else if $sam_options.reorder:
-    | samtools view --no-PG -bS - -o '$output'
+    > alignment.sam
+    && samtools view --no-PG -b -o '$output' alignment.sam
 #else:
     > '$output'
 #end if