New upstream version 1.4.5+dfsg

.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

blib/

.build/

_build/

build/

cover_db/

inc/

Build

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"

# 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))

# 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