diff --git a/CHANGES.md b/CHANGES.md index 7a0de97..ca5c57a 100644 --- a/CHANGES.md +++ b/CHANGES.md @@ -1,4 +1,8 @@ +### 3.1.0 +* Adds travis testing +* Cleansup install script and adds multi versioned paths to options + ### 3.0.0 * Removed use of legacy Tabix codebase and switches to samtools 1.2+ * Switches to gihub version of vcftools and makes several patches unnecessary -* Several bugfixes \ No newline at end of file +* Several bugfixes diff --git a/MANIFEST b/MANIFEST index 5a611cc..d4c37f6 100644 --- a/MANIFEST +++ b/MANIFEST @@ -1,3 +1,4 @@ +.travis.yml bin/Admin_EnsemblGtf2CacheConverter.pl bin/Admin_EnsemblReferenceFileGenerator.pl bin/Admin_EnsemblTranscriptFastaFilter.pl diff --git a/README.md b/README.md index bec60e4..7d65f1e 100644 --- a/README.md +++ b/README.md @@ -9,6 +9,10 @@ each variation/transcript combination and describes the effects in the mRNA, CDS contexts. It provides details of the sequence and position of the change within the transcript/protein as well as Sequence Ontology terms to classify its consequences. +| Master | Dev | +|---|---| +| [![Build Status](https://travis-ci.org/cancerit/VAGrENT.svg?branch=master)](https://travis-ci.org/cancerit/VAGrENT) | [![Build Status](https://travis-ci.org/cancerit/VAGrENT.svg?branch=dev)](https://travis-ci.org/cancerit/VAGrENT) | + --- ###Dependencies/Install @@ -70,4 +74,4 @@ them. For example, a copyright statement that reads ‘Copyright (c) 2005, 2007- reads ‘Copyright (c) 2005, 2007, 2008, 2009, 2011, 2012’ and a copyright statement that reads ‘Copyright (c) 2005-2012’ should be interpreted as being identical to a statement that reads ‘Copyright (c) 2005, 2006, 2007, 2008, -2009, 2010, 2011, 2012’." \ No newline at end of file +2009, 2010, 2011, 2012’." diff --git a/docs.tar.gz b/docs.tar.gz index ce048d9..e32ae94 100644 Binary files a/docs.tar.gz and b/docs.tar.gz differ diff --git a/lib/Sanger/CGP/Vagrent.pm b/lib/Sanger/CGP/Vagrent.pm index ede2dfd..031c6a1 100644 --- a/lib/Sanger/CGP/Vagrent.pm +++ b/lib/Sanger/CGP/Vagrent.pm @@ -26,7 +26,7 @@ use strict; use Const::Fast qw(const); use base 'Exporter'; -our $VERSION = '3.0.2'; +our $VERSION = '3.1.0'; our @EXPORT = qw($VERSION); 1; diff --git a/prerelease.sh b/prerelease.sh index e7599eb..bd1e009 100755 --- a/prerelease.sh +++ b/prerelease.sh @@ -46,7 +46,7 @@ echo '########## Running perl tests ##########' export HARNESS_PERL_SWITCHES=-MDevel::Cover=-db,reports,-select='^lib/*\.pm$',-ignore,'^t/' rm -rf docs mkdir -p docs/reports_text -prove -w -I lib t +prove -j 4 -w -I lib t echo '### Generating test/pod coverage reports ###' # removed 'condition' from coverage as '||' 'or' doesn't work properly