Steffen Möller · Steffen Möller · Steffen Möller · Steffen Möller · Steffen Möller · Steffen Möller
--- a/.gitattributes
+++ b/.gitattributes
+.bam filter=lfs diff=lfs merge=lfs -text
+samples/sample_lg_tr.bam filter=lfs diff=lfs merge=lfs -text
+sample_lg_tr.bam filter=lfs diff=lfs merge=lfs -text
--- a/.gitignore
+++ b/.gitignore
 blib/
 .build/
 _build/
+build/
 cover_db/
 inc/
 Build

--- a/.travis.yml
+++ b/.travis.yml
-language: perl
-addons:
-  apt:
-    packages:
-    - zlib1g-dev
-perl:
-  - "5.14"
-sudo: false
+sudo: required
+services:
+  - docker
 install:
-  - "source ./install_dependencies.sh"
-before_script:
-  - cpanm --quiet --notest Dist::Zilla::App::Command::cover
-  - cpanm --quiet --notest --skip-satisfied Devel::Cover::Report::Codecov
-script: "dzil test"
-after_success:
-  - dzil cover -test -report codecov
\ No newline at end of file
+  - docker pull sangerpathogens/bio-tradis
+script:
+  - docker run --rm -it sangerpathogens/bio-tradis /bin/bash -c "git clone https://github.com/sanger-pathogens/Bio-Tradis.git && cd Bio-Tradis && dzil test"
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
+# Change Log
+
+## [Unreleased](https://github.com/sanger-pathogens/Bio-Tradis/tree/HEAD)
+
+[Full Changelog](https://github.com/sanger-pathogens/Bio-Tradis/compare/v1.4.1...HEAD)
+
+**Merged pull requests:**
+
+- Include tests in README [\#97](https://github.com/sanger-pathogens/Bio-Tradis/pull/97) ([ssjunnebo](https://github.com/ssjunnebo))
+
+## [v1.4.1](https://github.com/sanger-pathogens/Bio-Tradis/tree/v1.4.1) (2018-09-20)
+[Full Changelog](https://github.com/sanger-pathogens/Bio-Tradis/compare/1.4.1...v1.4.1)
+
+**Merged pull requests:**
+
+- update version for cpan [\#96](https://github.com/sanger-pathogens/Bio-Tradis/pull/96) ([ssjunnebo](https://github.com/ssjunnebo))
+- Add to codecov [\#95](https://github.com/sanger-pathogens/Bio-Tradis/pull/95) ([ssjunnebo](https://github.com/ssjunnebo))
+
+## [1.4.1](https://github.com/sanger-pathogens/Bio-Tradis/tree/1.4.1) (2018-07-19)
+[Full Changelog](https://github.com/sanger-pathogens/Bio-Tradis/compare/1.4.0...1.4.1)
+
+**Closed issues:**
+
+- Installation on Ubuntu 17.10 fails [\#84](https://github.com/sanger-pathogens/Bio-Tradis/issues/84)
+- Port 18 volume discrepancy? [\#83](https://github.com/sanger-pathogens/Bio-Tradis/issues/83)
+
+**Merged pull requests:**
+
+- Change TryCatch to Try::Tiny [\#94](https://github.com/sanger-pathogens/Bio-Tradis/pull/94) ([ssjunnebo](https://github.com/ssjunnebo))
+- fix typo in badge [\#93](https://github.com/sanger-pathogens/Bio-Tradis/pull/93) ([ssjunnebo](https://github.com/ssjunnebo))
+- Include TOC [\#92](https://github.com/sanger-pathogens/Bio-Tradis/pull/92) ([ssjunnebo](https://github.com/ssjunnebo))
+- 621538 docker [\#91](https://github.com/sanger-pathogens/Bio-Tradis/pull/91) ([ssjunnebo](https://github.com/ssjunnebo))
+- 621538 docker [\#90](https://github.com/sanger-pathogens/Bio-Tradis/pull/90) ([ssjunnebo](https://github.com/ssjunnebo))
+- include reference genome for cram [\#89](https://github.com/sanger-pathogens/Bio-Tradis/pull/89) ([ssjunnebo](https://github.com/ssjunnebo))
+- Revert "Replace cram file without reads" [\#88](https://github.com/sanger-pathogens/Bio-Tradis/pull/88) ([ssjunnebo](https://github.com/ssjunnebo))
+- Replace cram file without reads [\#87](https://github.com/sanger-pathogens/Bio-Tradis/pull/87) ([ssjunnebo](https://github.com/ssjunnebo))
+- update tutorial for ENA switch to https \(from http\) [\#85](https://github.com/sanger-pathogens/Bio-Tradis/pull/85) ([lbarquist](https://github.com/lbarquist))
+
+## [1.4.0](https://github.com/sanger-pathogens/Bio-Tradis/tree/1.4.0) (2017-11-28)
+[Full Changelog](https://github.com/sanger-pathogens/Bio-Tradis/compare/v1.3.3...1.4.0)
+
+**Closed issues:**
+
+- Duplicate genes [\#81](https://github.com/sanger-pathogens/Bio-Tradis/issues/81)
+- Installing Bio-Tradis Fail  [\#80](https://github.com/sanger-pathogens/Bio-Tradis/issues/80)
+
+**Merged pull requests:**
+
+- include last base of annotation in insertion count [\#82](https://github.com/sanger-pathogens/Bio-Tradis/pull/82) ([lbarquist](https://github.com/lbarquist))
+- Rename license file' [\#79](https://github.com/sanger-pathogens/Bio-Tradis/pull/79) ([ssjunnebo](https://github.com/ssjunnebo))
+- update AUTHORS and rename LICENSE [\#78](https://github.com/sanger-pathogens/Bio-Tradis/pull/78) ([ssjunnebo](https://github.com/ssjunnebo))
+- Tmp file time stamp [\#77](https://github.com/sanger-pathogens/Bio-Tradis/pull/77) ([ssjunnebo](https://github.com/ssjunnebo))
+
+## [v1.3.3](https://github.com/sanger-pathogens/Bio-Tradis/tree/v1.3.3) (2017-05-08)
+[Full Changelog](https://github.com/sanger-pathogens/Bio-Tradis/compare/v1.3.2...v1.3.3)
+
+**Merged pull requests:**
+
+- try localtime for tmp file timestamp [\#76](https://github.com/sanger-pathogens/Bio-Tradis/pull/76) ([ssjunnebo](https://github.com/ssjunnebo))
+
+## [v1.3.2](https://github.com/sanger-pathogens/Bio-Tradis/tree/v1.3.2) (2017-05-08)
+[Full Changelog](https://github.com/sanger-pathogens/Bio-Tradis/compare/v1.3.1...v1.3.2)
+
+**Closed issues:**
+
+- cpan update? [\#75](https://github.com/sanger-pathogens/Bio-Tradis/issues/75)
+- tradis\_comparison.R error [\#71](https://github.com/sanger-pathogens/Bio-Tradis/issues/71)
+
+**Merged pull requests:**
+
+- modified ranges to accommodate higher density insertion data [\#74](https://github.com/sanger-pathogens/Bio-Tradis/pull/74) ([lbarquist](https://github.com/lbarquist))
+- removed File::Slurp [\#73](https://github.com/sanger-pathogens/Bio-Tradis/pull/73) ([vaofford](https://github.com/vaofford))
+- dont add POD to R scripts [\#72](https://github.com/sanger-pathogens/Bio-Tradis/pull/72) ([andrewjpage](https://github.com/andrewjpage))
+
+## [v1.3.1](https://github.com/sanger-pathogens/Bio-Tradis/tree/v1.3.1) (2016-09-23)
+[Full Changelog](https://github.com/sanger-pathogens/Bio-Tradis/compare/v1.3.0...v1.3.1)
+
+**Closed issues:**
+
+- Mapping score always set to 1 if -m option used with plot\_tradis [\#66](https://github.com/sanger-pathogens/Bio-Tradis/issues/66)
+- Error in step 3.5 of bacteria\_tradis, using samtools 1.3 [\#63](https://github.com/sanger-pathogens/Bio-Tradis/issues/63)
+
+**Merged pull requests:**
+
+- change to dist zilla starter bundle [\#70](https://github.com/sanger-pathogens/Bio-Tradis/pull/70) ([nds](https://github.com/nds))
+- switch PCR primers [\#69](https://github.com/sanger-pathogens/Bio-Tradis/pull/69) ([andrewjpage](https://github.com/andrewjpage))
+- updated readme [\#68](https://github.com/sanger-pathogens/Bio-Tradis/pull/68) ([lbarquist](https://github.com/lbarquist))
+- Fix for bug \#66, change mapping\_score option spec in B::T::CL::PlotTradis [\#67](https://github.com/sanger-pathogens/Bio-Tradis/pull/67) ([RoyChaudhuri](https://github.com/RoyChaudhuri))
+
+## [v1.3.0](https://github.com/sanger-pathogens/Bio-Tradis/tree/v1.3.0) (2016-04-13)
+[Full Changelog](https://github.com/sanger-pathogens/Bio-Tradis/compare/v1.2.4...v1.3.0)
+
+**Merged pull requests:**
+
+- Merge Roys changes [\#65](https://github.com/sanger-pathogens/Bio-Tradis/pull/65) ([andrewjpage](https://github.com/andrewjpage))
+- added recipes \(again\) [\#62](https://github.com/sanger-pathogens/Bio-Tradis/pull/62) ([lbarquist](https://github.com/lbarquist))
+
+## [v1.2.4](https://github.com/sanger-pathogens/Bio-Tradis/tree/v1.2.4) (2015-12-11)
+[Full Changelog](https://github.com/sanger-pathogens/Bio-Tradis/compare/v1.2.3...v1.2.4)
+
+**Closed issues:**
+
+- tradis\_essentiality.R [\#28](https://github.com/sanger-pathogens/Bio-Tradis/issues/28)
+
+**Merged pull requests:**
+
+- fixes for revision [\#61](https://github.com/sanger-pathogens/Bio-Tradis/pull/61) ([lbarquist](https://github.com/lbarquist))
+- bugfix to tradis\_essentiality.R [\#60](https://github.com/sanger-pathogens/Bio-Tradis/pull/60) ([lbarquist](https://github.com/lbarquist))
+
+## [v1.2.3](https://github.com/sanger-pathogens/Bio-Tradis/tree/v1.2.3) (2015-11-03)
+[Full Changelog](https://github.com/sanger-pathogens/Bio-Tradis/compare/v1.2.2...v1.2.3)
+
+**Merged pull requests:**
+
+- Bump the version number [\#59](https://github.com/sanger-pathogens/Bio-Tradis/pull/59) ([bewt85](https://github.com/bewt85))
+- Ticket 463867: What if a tag isn't found? [\#58](https://github.com/sanger-pathogens/Bio-Tradis/pull/58) ([bewt85](https://github.com/bewt85))
+- updated bacteria\_tradis help messages [\#57](https://github.com/sanger-pathogens/Bio-Tradis/pull/57) ([lbarquist](https://github.com/lbarquist))
+- Add package version module to dist zilla [\#56](https://github.com/sanger-pathogens/Bio-Tradis/pull/56) ([andrewjpage](https://github.com/andrewjpage))
+
+## [v1.2.2](https://github.com/sanger-pathogens/Bio-Tradis/tree/v1.2.2) (2015-09-14)
+[Full Changelog](https://github.com/sanger-pathogens/Bio-Tradis/compare/v1.2.1...v1.2.2)
+
+**Merged pull requests:**
+
+- Added sequencing recipes [\#55](https://github.com/sanger-pathogens/Bio-Tradis/pull/55) ([lbarquist](https://github.com/lbarquist))
+- updated help messages for R scripts [\#54](https://github.com/sanger-pathogens/Bio-Tradis/pull/54) ([lbarquist](https://github.com/lbarquist))
+- POD formatting [\#53](https://github.com/sanger-pathogens/Bio-Tradis/pull/53) ([andrewjpage](https://github.com/andrewjpage))
+
+## [v1.2.1](https://github.com/sanger-pathogens/Bio-Tradis/tree/v1.2.1) (2015-09-10)
+[Full Changelog](https://github.com/sanger-pathogens/Bio-Tradis/compare/v1.2...v1.2.1)
+
+**Merged pull requests:**
+
+- Simplify installation [\#52](https://github.com/sanger-pathogens/Bio-Tradis/pull/52) ([andrewjpage](https://github.com/andrewjpage))
+
+## [v1.2](https://github.com/sanger-pathogens/Bio-Tradis/tree/v1.2) (2015-09-08)
+[Full Changelog](https://github.com/sanger-pathogens/Bio-Tradis/compare/v1.132190...v1.2)
+
+**Merged pull requests:**
+
+- Ticket 473325: Install two different versions of SAMTOOLS [\#51](https://github.com/sanger-pathogens/Bio-Tradis/pull/51) ([bewt85](https://github.com/bewt85))
+- Add TravisCI support [\#50](https://github.com/sanger-pathogens/Bio-Tradis/pull/50) ([bewt85](https://github.com/bewt85))
+- fixed filtering bug [\#49](https://github.com/sanger-pathogens/Bio-Tradis/pull/49) ([lbarquist](https://github.com/lbarquist))
+- Updated shebang line in R scripts for portability [\#48](https://github.com/sanger-pathogens/Bio-Tradis/pull/48) ([carlacummins](https://github.com/carlacummins))
+- added installation notes [\#47](https://github.com/sanger-pathogens/Bio-Tradis/pull/47) ([lbarquist](https://github.com/lbarquist))
+- only require 2 command line args, not 3 [\#46](https://github.com/sanger-pathogens/Bio-Tradis/pull/46) ([lbarquist](https://github.com/lbarquist))
+- Bug fixes and added features [\#45](https://github.com/sanger-pathogens/Bio-Tradis/pull/45) ([carlacummins](https://github.com/carlacummins))
+- Adding tabix a prerequisite [\#44](https://github.com/sanger-pathogens/Bio-Tradis/pull/44) ([js21](https://github.com/js21))
+- Cram file output [\#43](https://github.com/sanger-pathogens/Bio-Tradis/pull/43) ([andrewjpage](https://github.com/andrewjpage))
+- Code is now cross-platform [\#42](https://github.com/sanger-pathogens/Bio-Tradis/pull/42) ([js21](https://github.com/js21))
+- Pass through samtools exec and verbose mode [\#41](https://github.com/sanger-pathogens/Bio-Tradis/pull/41) ([andrewjpage](https://github.com/andrewjpage))
+- Cram support [\#40](https://github.com/sanger-pathogens/Bio-Tradis/pull/40) ([andrewjpage](https://github.com/andrewjpage))
+- added the missing test files [\#39](https://github.com/sanger-pathogens/Bio-Tradis/pull/39) ([js21](https://github.com/js21))
+- suppressed uninitialised warnings when importing PE data [\#38](https://github.com/sanger-pathogens/Bio-Tradis/pull/38) ([carlacummins](https://github.com/carlacummins))
+- Tabix indexed plot files in place [\#37](https://github.com/sanger-pathogens/Bio-Tradis/pull/37) ([js21](https://github.com/js21))
+- added filtering option, so default is old behavior. -f now enables read ... [\#36](https://github.com/sanger-pathogens/Bio-Tradis/pull/36) ([lbarquist](https://github.com/lbarquist))
+- fixed typo [\#35](https://github.com/sanger-pathogens/Bio-Tradis/pull/35) ([lbarquist](https://github.com/lbarquist))
+- feature addition to tradis\_comparison, bugfix tradis\_essentiality [\#34](https://github.com/sanger-pathogens/Bio-Tradis/pull/34) ([lbarquist](https://github.com/lbarquist))
+- Added AUTHORS file [\#33](https://github.com/sanger-pathogens/Bio-Tradis/pull/33) ([aslett1](https://github.com/aslett1))
+- Fixed problem with opening combined plots in Artemis [\#32](https://github.com/sanger-pathogens/Bio-Tradis/pull/32) ([carlacummins](https://github.com/carlacummins))
+- Fixed problem with unusual characters in filenames [\#31](https://github.com/sanger-pathogens/Bio-Tradis/pull/31) ([carlacummins](https://github.com/carlacummins))
+- Updates [\#30](https://github.com/sanger-pathogens/Bio-Tradis/pull/30) ([carlacummins](https://github.com/carlacummins))
+- index needs to be offset by 2 [\#29](https://github.com/sanger-pathogens/Bio-Tradis/pull/29) ([raeece](https://github.com/raeece))
+- Fixed issue with exposed -y smalt param [\#27](https://github.com/sanger-pathogens/Bio-Tradis/pull/27) ([carlacummins](https://github.com/carlacummins))
+- Exposed -y smalt parameter [\#26](https://github.com/sanger-pathogens/Bio-Tradis/pull/26) ([carlacummins](https://github.com/carlacummins))
+- Added GPL-LICENCE [\#25](https://github.com/sanger-pathogens/Bio-Tradis/pull/25) ([carlacummins](https://github.com/carlacummins))
+- Fixed problems with merging plots [\#24](https://github.com/sanger-pathogens/Bio-Tradis/pull/24) ([carlacummins](https://github.com/carlacummins))
+- Updates to help text [\#23](https://github.com/sanger-pathogens/Bio-Tradis/pull/23) ([carlacummins](https://github.com/carlacummins))
+- Added R scripts [\#22](https://github.com/sanger-pathogens/Bio-Tradis/pull/22) ([carlacummins](https://github.com/carlacummins))
+- Removed leftover debugging statement [\#21](https://github.com/sanger-pathogens/Bio-Tradis/pull/21) ([carlacummins](https://github.com/carlacummins))
+- Exposed SMALT indexing parameters [\#20](https://github.com/sanger-pathogens/Bio-Tradis/pull/20) ([carlacummins](https://github.com/carlacummins))
+- Bug fix [\#19](https://github.com/sanger-pathogens/Bio-Tradis/pull/19) ([carlacummins](https://github.com/carlacummins))
+- Fix for combined plots not reading in Artemis [\#18](https://github.com/sanger-pathogens/Bio-Tradis/pull/18) ([carlacummins](https://github.com/carlacummins))
+- gzip no prompt for overwrite [\#17](https://github.com/sanger-pathogens/Bio-Tradis/pull/17) ([carlacummins](https://github.com/carlacummins))
+- Fixed problem with blank lines [\#16](https://github.com/sanger-pathogens/Bio-Tradis/pull/16) ([carlacummins](https://github.com/carlacummins))
+- Fixed combine\_tradis\_plots [\#15](https://github.com/sanger-pathogens/Bio-Tradis/pull/15) ([carlacummins](https://github.com/carlacummins))
+- Plot update [\#14](https://github.com/sanger-pathogens/Bio-Tradis/pull/14) ([carlacummins](https://github.com/carlacummins))
+- Updated help text for combine\_tradis\_plots [\#13](https://github.com/sanger-pathogens/Bio-Tradis/pull/13) ([carlacummins](https://github.com/carlacummins))
+- Added module to combine plot files [\#12](https://github.com/sanger-pathogens/Bio-Tradis/pull/12) ([carlacummins](https://github.com/carlacummins))
+- Further file checking updates [\#11](https://github.com/sanger-pathogens/Bio-Tradis/pull/11) ([carlacummins](https://github.com/carlacummins))
+- Bug fix in file existance check [\#10](https://github.com/sanger-pathogens/Bio-Tradis/pull/10) ([carlacummins](https://github.com/carlacummins))
+- Updates [\#9](https://github.com/sanger-pathogens/Bio-Tradis/pull/9) ([carlacummins](https://github.com/carlacummins))
+- Updated bacteria\_tradis help [\#8](https://github.com/sanger-pathogens/Bio-Tradis/pull/8) ([carlacummins](https://github.com/carlacummins))
+- Distribution ready [\#7](https://github.com/sanger-pathogens/Bio-Tradis/pull/7) ([carlacummins](https://github.com/carlacummins))
+
+## [v1.132190](https://github.com/sanger-pathogens/Bio-Tradis/tree/v1.132190) (2013-08-07)
+[Full Changelog](https://github.com/sanger-pathogens/Bio-Tradis/compare/v1.132140...v1.132190)
+
+## [v1.132140](https://github.com/sanger-pathogens/Bio-Tradis/tree/v1.132140) (2013-08-02)
+**Merged pull requests:**
+
+- Complete package v1 [\#6](https://github.com/sanger-pathogens/Bio-Tradis/pull/6) ([carlacummins](https://github.com/carlacummins))
+- fix cigar string [\#5](https://github.com/sanger-pathogens/Bio-Tradis/pull/5) ([andrewjpage](https://github.com/andrewjpage))
+- Reverse complement fix [\#4](https://github.com/sanger-pathogens/Bio-Tradis/pull/4) ([andrewjpage](https://github.com/andrewjpage))
+- die if the number of reads outputted differs [\#3](https://github.com/sanger-pathogens/Bio-Tradis/pull/3) ([andrewjpage](https://github.com/andrewjpage))
+- Executables in bin [\#2](https://github.com/sanger-pathogens/Bio-Tradis/pull/2) ([carlacummins](https://github.com/carlacummins))
+- Bio-Tradis [\#1](https://github.com/sanger-pathogens/Bio-Tradis/pull/1) ([carlacummins](https://github.com/carlacummins))
+
--- a/Dockerfile
+++ b/Dockerfile
 # This container will install Bio-Tradis from master
 #
-FROM debian:testing
+FROM debian:bullseye-slim

 # Install the dependancies
-RUN apt-get update -qq && apt-get install -y sudo make wget unzip zlib1g-dev cpanminus gcc bzip2 libncurses5-dev libncursesw5-dev libssl-dev r-base git
-RUN cpanm IPC::System::Simple DateTime::Locale DateTime
-RUN sudo Rscript -e "source('http://bioconductor.org/biocLite.R')" -e "biocLite(c('edgeR','getopt', 'MASS'))"
-RUN git clone https://github.com/sanger-pathogens/Bio-Tradis.git
-RUN cd Bio-Tradis && ./install_dependencies.sh
-ENV PATH /Bio-Tradis/bin:/Bio-Tradis/build/smalt-0.7.6-bin:/Bio-Tradis/build/tabix-master:/Bio-Tradis/build/samtools-1.3:$PATH
-RUN export PATH
+RUN apt-get update -qq && apt-get install -y sudo make wget unzip zlib1g-dev cpanminus gcc bzip2 libncurses5-dev libncursesw5-dev libssl-dev r-base git libxml-libxml-perl libgd-gd2-perl bioperl bwa smalt tabix samtools
+RUN wget https://github.com/lh3/minimap2/releases/download/v2.17/minimap2-2.17_x64-linux.tar.bz2
+RUN tar xjfv minimap2-2.17_x64-linux.tar.bz2
+
+# Install R dependencies
+RUN Rscript -e "install.packages('BiocManager')" -e "BiocManager::install()" -e "BiocManager::install(c('edgeR','getopt', 'MASS'))"
+
+# Install some perl dependencies (will probably install more later after adding source code).
+# It seems like we have to force installation of Xpath because the tests fail for some reason.  
+# This in turn means we need to force install BioPerl as well
+RUN cpanm IPC::System::Simple DateTime::Locale DateTime Dist::Zilla Moose Text::CSV ExtUtils::MakeMaker Getopt::Long Try::Tiny Exception::Class
+RUN cpanm Dist::Zilla::Plugin::AutoPrereqs Dist::Zilla::Plugin::Encoding Dist::Zilla::Plugin::FileFinder::ByName Dist::Zilla::Plugin::MetaResources Dist::Zilla::Plugin::PkgVersion Dist::Zilla::Plugin::PodWeaver Dist::Zilla::Plugin::RequiresExternal Dist::Zilla::Plugin::RunExtraTests Dist::Zilla::PluginBundle::Git Dist::Zilla::PluginBundle::Starter
+RUN cpanm --force XML::DOM::XPath
+RUN cpanm --force Bio::Seq Bio::SeqIO
+
+# Add source code
+ADD . Bio-Tradis
+
+# Install missing dependencies gathered from source code
+# This can take a while and slow down building the docker image if we install everything this way.  
+# Some known dependencies are installed earlier in the dockerfile (before adding source code) to speed up build time
+WORKDIR /Bio-Tradis
+RUN dzil authordeps --missing | cpanm 
+RUN dzil listdeps --missing | cpanm
+
+# Set environment
+ENV PATH /Bio-Tradis/bin:/minimap2-2.17_x64-linux:$PATH
 ENV PERL5LIB=/Bio-Tradis/lib:$PERL5LIB
-RUN export PERL5LIB
\ No newline at end of file
+WORKDIR /work
--- a/README.md
+++ b/README.md
@@ -4,6 +4,8 @@ A set of tools to analyse the output from TraDIS analyses
 [![Build Status](https://travis-ci.org/sanger-pathogens/Bio-Tradis.svg?branch=master)](https://travis-ci.org/sanger-pathogens/Bio-Tradis)  
 [![License: GPL v3](https://img.shields.io/badge/License-GPL%20v3-brightgreen.svg)](https://github.com/sanger-pathogens/Bio-Tradis/blob/master/software_license)  
 [![status](https://img.shields.io/badge/Bioinformatics-10.1093-brightgreen.svg)](https://doi.org/10.1093/bioinformatics/btw022)  
+[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/biotradis/README.html)   
+[![Container ready](https://img.shields.io/badge/container-ready-brightgreen.svg)](https://quay.io/repository/biocontainers/biotradis)  
 [![Docker Build Status](https://img.shields.io/docker/build/sangerpathogens/bio-tradis.svg)](https://hub.docker.com/r/sangerpathogens/bio-tradis)  
 [![Docker Pulls](https://img.shields.io/docker/pulls/sangerpathogens/bio-tradis.svg)](https://hub.docker.com/r/sangerpathogens/bio-tradis)  
 [![codecov](https://codecov.io/gh/sanger-pathogens/bio-tradis/branch/master/graph/badge.svg)](https://codecov.io/gh/sanger-pathogens/bio-tradis)
@@ -14,6 +16,7 @@ A set of tools to analyse the output from TraDIS analyses
    * [Required dependencies](#required-dependencies)
    * [Bioconda](#bioconda)
    * [Docker](#docker)
+    * [Running the tests](#running-the-tests)
  * [Usage](#usage)
    * [Scripts](#scripts)
    * [Analysis Scripts](#analysis-scripts)
@@ -32,6 +35,7 @@ For more information on the TraDIS method, see http://bioinformatics.oxfordjourn
 Bio-Tradis has the following dependencies:

 ### Required dependencies
+* bwa
 * smalt
 * samtools
 * tabix
@@ -44,17 +48,8 @@ There are a number of ways to install Bio-Tradis and details are provided below.
 Install conda and enable the bioconda channel.

 ```
-conda config --add channels r
-conda config --add channels defaults
-conda config --add channels conda-forge
-conda config --add channels bioconda
-conda install r smalt samtools perl-app-cpanminus
-
-sudo cpanm -f Bio::Tradis
-R 
-source("http://bioconductor.org/biocLite.R")
-biocLite()
-biocLite(c("edgeR","getopt", "MASS"))
+conda install-c bioconda biotradis=1.4.1.dev
+
 ```

 ### Docker
@@ -66,6 +61,11 @@ To use Bio-Tradis use a command like this (substituting in your directories), wh

    docker run --rm -it -v /home/ubuntu/data:/data sangerpathogens/bio-tradis bacteria_tradis -h

+### Running the tests
+The test can be run with dzil from the top level directory:  
+  
+`dzil test`  
+
 ## Usage

 For command-line usage instructions, please see the tutorial in the file "BioTraDISTutorial.pdf". Note that default parameters are for comparative experiments, and will need to be modified for gene essentiality studies.
@@ -88,7 +88,7 @@ Executable scripts to carry out most of the listed functions are available in th
 * `filter_tradis_tags` - Create a fastq file containing reads that match the supplied tag
 * `remove_tradis_tags` - Creates a fastq file containing reads with the supplied tag removed from the sequences
 * `tradis_plot` - Creates an gzipped insertion site plot
-* `bacteria_tradis` - Runs complete analysis, starting with a fastq file and produces mapped BAM files and plot files for each file in the given file list and a statistical summary of all files. Note that the -f option expects a text file containing a list of fastq files, one per line.
+* `bacteria_tradis` - Runs complete analysis, starting with a fastq file and produces mapped BAM files and plot files for each file in the given file list and a statistical summary of all files. Note that the -f option expects a text file containing a list of fastq files, one per line. This script can be run with or without supplying tags. 

 A help menu for each script can be accessed by running the script with no parameters.

@@ -155,15 +155,16 @@ __Bio::Tradis::Map__
 * Methods:
 	* `index_ref` - create index files of the reference genome. These are required
 				for the mapping step. Only skip this step if index files already
-				exist. -k and -s options for referencing are calculated based
+				exist. If SMALT is used as the aligner -sk and -ss options for referencing are calculated based
 				on the length of the reads being mapped:
-		* <70 : `-k 13 -s 4`
-		* >70 & <100 : `-k 13 -s 6`
-		* >100 : `-k 20 -s 13`
+		* <70 : `-sk 13 -ss 4`
+		* >70 & <100 : `-sk 13 -ss 6`
+		* >100 : `-sk 20 -ss 13`
 	* `do_mapping` - map `fastqfile` to `reference`. Options used for mapping are:
-				 `-r -1, -x and -y 0.96`
+				 `-k the min seed length for BWA`
+				 `-s (for using SMALT as alternative aligner) -r -1, -x and -y 0.96 for SMALT (see SMALT manual)`
 				
-	For more information on the mapping and indexing options discussed here, see the SMALT manual (ftp://ftp.sanger.ac.uk/pub4/resources/software/smalt/smalt-manual-0.7.4.pdf)
+	For more information on the mapping and indexing options discussed here, see the BWA manual (http://rothlab.ucdavis.edu/howto/attachments/bwa_manpage.pdf) and/or SMALT manual (ftp://ftp.sanger.ac.uk/pub4/resources/software/smalt/smalt-manual-0.7.4.pdf)
 				
 __Bio::Tradis::TradisPlot__  
 * Required parameters:

--- a/bcinstall.log
+++ b/bcinstall.log
+--> Working on Bio::Tradis
+Fetching http://www.cpan.org/authors/id/S/SS/SSJUNNEBO/Bio-Tradis-1.4.1.tar.gz ... OK
+Configuring Bio-Tradis-1.4.1 ... OK
+==> Found dependencies: Moose
+--> Working on Moose
+Fetching http://www.cpan.org/authors/id/E/ET/ETHER/Moose-2.2011.tar.gz ... OK
+Configuring Moose-2.2011 ... N/A
--- a/bin/add_tradis_tags
+++ b/bin/add_tradis_tags
 #!/usr/bin/env perl

 package Bio::Tradis::Bin::DetectTags;
+use FindBin qw($Bin); 

 # ABSTRACT: check if tr tag is present
 # PODNAME: check_tags
@@ -13,7 +14,8 @@ Checks the presence of tr/tq tags in a given BAM file

 BEGIN { unshift( @INC, '../lib' ) }
 BEGIN { unshift( @INC, './lib' ) }
-BEGIN { unshift( @INC, '/software/pathogen/internal/prod/lib/' ) }
+# BEGIN { unshift( @INC, '/software/pathogen/internal/prod/lib/' ) }
+BEGIN { unshift( @INC, "$Bin/../lib/" ) }

 use Bio::Tradis::CommandLine::AddTags;


--- a/bin/bacteria_tradis
+++ b/bin/bacteria_tradis
@@ -2,6 +2,9 @@

 package Bio::Tradis::Bin::RunTradis;

+use FindBin qw($Bin);
+
+
 # ABSTRACT: Perform full tradis analysis
 # PODNAME: run_tradis

@@ -14,7 +17,8 @@ site plots for use in Artemis

 BEGIN { unshift( @INC, '../lib' ) }
 BEGIN { unshift( @INC, './lib' ) }
-BEGIN { unshift( @INC, '/software/pathogen/internal/prod/lib/' ) }
+# BEGIN { unshift( @INC, '/software/pathogen/internal/prod/lib/' ) }
+BEGIN { unshift( @INC, "$Bin/../lib/" ) }

 use Bio::Tradis::CommandLine::TradisAnalysis;


--- a/bin/check_tradis_tags
+++ b/bin/check_tradis_tags
 #!/usr/bin/env perl

 package Bio::Tradis::Bin::DetectTags;
+use FindBin qw($Bin); 

 # ABSTRACT: check if tr tag is present
 # PODNAME: check_tags
@@ -13,7 +14,8 @@ Checks the presence of tr/tq tags in a given BAM file

 BEGIN { unshift( @INC, '../lib' ) }
 BEGIN { unshift( @INC, './lib' ) }
-BEGIN { unshift( @INC, '/software/pathogen/internal/prod/lib/' ) }
+# BEGIN { unshift( @INC, '/software/pathogen/internal/prod/lib/' ) }
+BEGIN { unshift( @INC, "$Bin/../lib/" ) }

 use Bio::Tradis::CommandLine::CheckTags;


--- a/bin/combine_tradis_plots
+++ b/bin/combine_tradis_plots
 #!/usr/bin/env perl

 package Bio::Tradis::Bin::CombineTradisPlots;
+use FindBin qw($Bin); 

 # ABSTRACT: Combine multiple plotfiles and generate updated statistics for the combined files

@@ -16,7 +17,8 @@ plotfile and as an identifier in the stats file, so ensure these are unique.

 BEGIN { unshift( @INC, '../lib' ) }
 BEGIN { unshift( @INC, './lib' ) }
-BEGIN { unshift( @INC, '/software/pathogen/internal/prod/lib/' ) }
+# BEGIN { unshift( @INC, '/software/pathogen/internal/prod/lib/' ) }
+BEGIN { unshift( @INC, "$Bin/../lib/" ) }

 use Bio::Tradis::CommandLine::PlotCombine;


--- a/bin/filter_tradis_tags
+++ b/bin/filter_tradis_tags
 #!/usr/bin/env perl

 package Bio::Tradis::Bin::FilterTags;
+use FindBin qw($Bin); 

 # ABSTRACT: filter tags at start of fastq sequences
 # PODNAME: filter_tags
@@ -14,7 +15,8 @@ match the tag provided

 BEGIN { unshift( @INC, '../lib' ) }
 BEGIN { unshift( @INC, './lib' ) }
-BEGIN { unshift( @INC, '/software/pathogen/internal/prod/lib/' ) }
+# BEGIN { unshift( @INC, '/software/pathogen/internal/prod/lib/' ) }
+BEGIN { unshift( @INC, "$Bin/../lib/" ) }

 use Bio::Tradis::CommandLine::FilterFastqTags;


--- a/bin/remove_tradis_tags
+++ b/bin/remove_tradis_tags
 #!/usr/bin/env perl

 package Bio::Tradis::Bin::RemoveTags;
+use FindBin qw($Bin); 

 # ABSTRACT: remove user specified tags from start of fastq sequences
 # PODNAME: remove_tags
@@ -14,6 +15,7 @@ Removes tags from the sequence and quality strings based on user input
 BEGIN { unshift( @INC, '../lib' ) }
 BEGIN { unshift( @INC, './lib' ) }
 BEGIN { unshift( @INC, '/software/pathogen/internal/prod/lib/' ) }
+BEGIN { unshift( @INC, "$Bin/../lib/" ) }

 use Bio::Tradis::CommandLine::RemoveFastqTags;


--- a/bin/tradis_comparison.R
+++ b/bin/tradis_comparison.R
@@ -3,7 +3,7 @@
 # PODNAME: tradis_comparison.R
 # ABSTRACT: tradis_comparison.R

-library("edgeR")
+if(!require(edgeR)){install.packages("edgeR", repos = "http://cran.us.r-project.org")}
 library("getopt")

 options(width=80)

--- a/bin/tradis_gene_insert_sites
+++ b/bin/tradis_gene_insert_sites
 #!/usr/bin/env perl

 package Bio::Tradis::Bin::GeneInsertSites;
+use FindBin qw($Bin); 

 # ABSTRACT: Generate insertion site details from TraDIS pipeline plots


--- a/bin/tradis_merge_plots
+++ b/bin/tradis_merge_plots
 #!/usr/bin/env perl

 package Bio::Tradis::Bin::MergePlots;
+use FindBin qw($Bin); 

 # ABSTRACT: 


--- a/bin/tradis_plot
+++ b/bin/tradis_plot
 #!/usr/bin/env perl

 package Bio::Tradis::Bin::TradisPlot;
+use FindBin qw($Bin); 

 # ABSTRACT: Generate plots as part of a tradis analysis
 # PODNAME: tradis_plot
@@ -15,6 +16,7 @@ a reference in GFF format
 BEGIN { unshift( @INC, '../lib' ) }
 BEGIN { unshift( @INC, './lib' ) }
 BEGIN { unshift( @INC, '/software/pathogen/internal/prod/lib/' ) }
+BEGIN { unshift( @INC, "$Bin/../lib/" ) }

 use Bio::Tradis::CommandLine::PlotTradis;


--- a/build/bwa-0.7.17.tbz
+++ b/build/bwa-0.7.17.tbz
--- a/build/samtools-1.3.tbz
+++ b/build/samtools-1.3.tbz
--- a/build/smalt-0.7.6.tgz
+++ b/build/smalt-0.7.6.tgz