Merge branch 'hotfix/5.7.3'

cancerit · Nov 27, 2024 · d9d382a · d9d382a
2 parents 9ef1b2a + 9ebd2db
commit d9d382a
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Showing 6 changed files with 15 additions and 1,005 deletions.
diff --git a/CHANGES.md b/CHANGES.md
@@ -1,5 +1,10 @@
 # CHANGES
 
+## 5.7.3
+
+* Exit with a clearer error message when file does not pass the minimum read threshold
+* Update Dockerfile and setup.sh
+
 ## 5.7.2
 
 * OS and Bio::DB::HTS updates

diff --git a/Dockerfile b/Dockerfile
@@ -1,4 +1,4 @@
-FROM ubuntu:20.04 as builder
+FROM ubuntu:24.04 as builder
 
 USER  root
 
@@ -28,6 +28,9 @@ RUN apt-get install -yq --no-install-recommends libgnutls28-dev
 RUN apt-get install -yq --no-install-recommends libgd-dev
 RUN apt-get install -yq --no-install-recommends libdb-dev
 RUN apt-get install -yq --no-install-recommends g++
+RUN apt-get install -yq --no-install-recommends libssl-dev
+RUN apt-get install -yq --no-install-recommends xz-utils
+RUN apt-get install -yq --no-install-recommends libxml2
 
 RUN locale-gen en_US.UTF-8
 RUN update-locale LANG=en_US.UTF-8

diff --git a/perl/bin/cpanm b/perl/bin/cpanm
diff --git a/perl/lib/Sanger/CGP/Vaf.pm b/perl/lib/Sanger/CGP/Vaf.pm
@@ -2,7 +2,7 @@ package Sanger::CGP::Vaf;
 use strict;
 use Const::Fast qw(const);
 
-our $VERSION = '5.7.2';
+our $VERSION = '5.7.3';
 
 const my $LICENSE =>
 "#################

diff --git a/perl/lib/Sanger/CGP/Vaf/Data/ReadVcf.pm b/perl/lib/Sanger/CGP/Vaf/Data/ReadVcf.pm
@@ -942,6 +942,9 @@ sub _get_read_length {
                 }
             }
          }
+
+    die "A minimum of " . $Sanger::CGP::Vaf::VafConstants::NO_READS_READLEN
+        . " reads is expected, but the input file only has $read_counter.\n";
 }
 
 

diff --git a/setup.sh b/setup.sh
@@ -134,7 +134,7 @@ else
   for i in "${perlmods[@]}" ; do
     echo "Installing build prerequisite $i..."
       set -x
-      $INIT_DIR/perl/bin/cpanm -v --mirror http://cpan.metacpan.org --notest -l $INST_PATH $i
+      cpanm -v --mirror http://cpan.metacpan.org --notest -l $INST_PATH $i
       set +x
       echo; echo
   done
@@ -268,7 +268,7 @@ if ! ( perl -MExtUtils::MakeMaker -e 1 >/dev/null 2>&1); then
 fi
 
 set -x
-perl $INIT_DIR/perl/bin/cpanm -v --mirror http://cpan.metacpan.org --notest -l $INST_PATH --installdeps . < /dev/null
+cpanm -v --mirror http://cpan.metacpan.org --notest -l $INST_PATH --installdeps . < /dev/null
 set +x
 
 echo -n "Installing cgpVaf ..."
-Original file line number
+Diff line change
@@ Expand Up / @@ -942,6 +942,9 @@ sub _get_read_length { @@
                     }
                 }
              }
+        die "A minimum of " . $Sanger::CGP::Vaf::VafConstants::NO_READS_READLEN
+            . " reads is expected, but the input file only has $read_counter.\n";
     }
@@ Expand Down @@