Merge branch 'hotfix/5.0.1'

cancerit · Feb 19, 2020 · 9898bc7 · 9898bc7
2 parents 9c476d3 + 1dd84c7
commit 9898bc7
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Showing 4 changed files with 9 additions and 4 deletions.
diff --git a/CHANGES.md b/CHANGES.md
@@ -1,5 +1,9 @@
 # CHANGES
 
+## 5.0.1
+
+* Fix for pushing data for threaded item to stdout/err on failure
+
 ## 5.0.0
 
 * Adds basic `merge_or_mark.pl` script

diff --git a/Dockerfile b/Dockerfile
@@ -58,7 +58,7 @@ FROM  ubuntu:16.04
 
 LABEL maintainer="[email protected]"\
       uk.ac.sanger.cgp="Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute" \
-      version="5.0.0" \
+      version="5.0.1" \
       description="pcap-core"
 
 ENV OPT /opt/wtsi-cgp

diff --git a/lib/PCAP.pm b/lib/PCAP.pm
@@ -28,7 +28,7 @@ use FindBin qw($Bin);
 use File::Which qw(which);
 # don't use autodie, only core perl in here
 
-our $VERSION = '5.0.0';
+our $VERSION = '5.0.1';
 our @EXPORT = qw($VERSION _which);
 
 const my $LICENSE =>

diff --git a/lib/PCAP/Threaded.pm b/lib/PCAP/Threaded.pm
@@ -235,10 +235,11 @@ sub external_process_handler {
       system("/usr/bin/time bash $script 1> $out 2> $err");
     }
     catch {
+      sleep 5; # give files time to close
       warn "\nTHREAD_EXITED: General output can be found in this file, last 10 lines below: $out\n";
-      system(sprintf 'tail -n 10 %s | xargs -I {} echo STDOUT: {}', $out);
+      system(sprintf q(tail -n 10 %s | perl -ne 'print qq{STDOUT: $_};'), $out);
       warn "\nTHREAD_EXITED: Errors can be found in this file, output below: $err\n\n";
-      system(sprintf 'cat %s | xargs -I {} echo STDERR: {}', $err);
+      system(sprintf q(perl -ne 'print qq{STDERR: $_};' %s), $err);
       die "\nTHREAD_EXITED: Wrapper script message:\n".$_;
     };