.travis.yml

@@ -8,4 +8,9 @@ perl:
 sudo: false
 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

AUTHORS

-Carla Cummins (cc21@sanger.ac.uk)
+Carla Cummins (path-help@sanger.ac.uk)
 Andrew J. Page (ap13@sanger.ac.uk)
 Lars Barquist (lars.barquist@uni-wuerzburg.de)

Dockerfile

+# This container will install Bio-Tradis from master
+#
+FROM debian:testing
+
+# 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:$PATH
+RUN export PATH
+ENV PERL5LIB=/Bio-Tradis/lib:$PERL5LIB
+RUN export PERL5LIB
\ No newline at end of file

README.md

-Bio-Tradis
-==========
-Bio-Tradis contains a set of tools to analyse the output from TraDIS analyses. 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.
- 
-For more information on the TraDIS method, see http://bioinformatics.oxfordjournals.org/content/32/7/1109 and http://genome.cshlp.org/content/19/12/2308
+# Bio-Tradis
+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)  
+[![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)
 
-Bio-Tradis provides functionality to:
-* detect TraDIS tags in a BAM file
-* add the tags to the reads
-* filter reads in a FastQ file containing a user defined tag
-* remove tags
-* map to a reference genome
-* create an insertion site plot file
-available as standalone scripts or as perl modules.
+## Contents
+  * [Introduction](#introduction)
+  * [Installation](#installation)
+    * [Required dependencies](#required-dependencies)
+    * [Bioconda](#bioconda)
+    * [Docker](#docker)
+  * [Usage](#usage)
+    * [Scripts](#scripts)
+    * [Analysis Scripts](#analysis-scripts)
+    * [Internal Objects and Methods](#internal-objects-and-methods)
+    * [Perl Programming Examples](#perl-programming-examples)
+  * [License](#license)
+  * [Feedback/Issues](#feedbackissues)
+  * [Citation](#citation)
 
-Installation
-=======
+## Introduction 
+The Bio::TraDIS pipeline provides software utilities for the processing, mapping, and analysis of transposon insertion sequencing data. The pipeline was designed with the data from the TraDIS sequencing protocol in mind, but should work with a variety of transposon insertion sequencing protocols as long as they produce data in the expected format.
 
-####HomeBrew/LinuxBrew
-To install the dependancies, the easiest way is through [HomeBrew](http://brew.sh/) (OSX) or [LinuxBrew](http://brew.sh/linuxbrew/) (Linux).
-```
-brew tap homebrew/science
-brew install r smalt samtools cpanm 
-sudo cpanm -f Bio::Tradis
+For more information on the TraDIS method, see http://bioinformatics.oxfordjournals.org/content/32/7/1109 and http://genome.cshlp.org/content/19/12/2308.
 
-R 
-source("http://bioconductor.org/biocLite.R")
-biocLite()
-biocLite(c("edgeR","getopt", "MASS"))
-````
+## Installation
+Bio-Tradis has the following dependencies:
 
-####Without Homebrew
-Install [SMALT](https://www.sanger.ac.uk/resources/software/smalt/) version 0.7.6 or greater, [Samtools](http://www.htslib.org/) version 1.3 or greater and [R](https://cran.r-project.org/) version 3.2 or greater. Ensure they are in your PATH.
+### Required dependencies
+* smalt
+* samtools
+* tabix
+* R
+* Bioconductor
+
+There are a number of ways to install Bio-Tradis and details are provided below. If you encounter an issue when installing Bio-Tradis please contact your local system administrator. If you encounter a bug please log it [here](https://github.com/sanger-pathogens/Bio-Tradis/issues) or email us at path-help@sanger.ac.uk.
+
+### Bioconda
+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")
@@ -42,11 +57,30 @@ biocLite()
 biocLite(c("edgeR","getopt", "MASS"))
 ```
 
-####Windows
-Install Linux.
+### Docker
+Bio-Tradis can be run in a Docker container. First install Docker, then install Bio-Tradis:
+
+    docker pull sangerpathogens/bio-tradis
 
-Scripts
-=======
+To use Bio-Tradis use a command like this (substituting in your directories), where your files are assumed to be stored in /home/ubuntu/data:
+
+    docker run --rm -it -v /home/ubuntu/data:/data sangerpathogens/bio-tradis bacteria_tradis -h
+
+## 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.
+
+Bio-Tradis provides functionality to:
+* detect TraDIS tags in a BAM file
+* add the tags to the reads
+* filter reads in a FastQ file containing a user defined tag
+* remove tags
+* map to a reference genome
+* create an insertion site plot file
+  
+The functions are avalable as standalone scripts or as perl modules.
+
+### Scripts
 Executable scripts to carry out most of the listed functions are available in the `bin`:
 
 * `check_tradis_tags` - Prints 1 if tags are present, prints 0 if not.
@@ -56,10 +90,9 @@ Executable scripts to carry out most of the listed functions are available in th
 * `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.
 
-A help menu for each script can be accessed by running the script with no parameters
+A help menu for each script can be accessed by running the script with no parameters.
 
-Analysis Scripts
-================
+### Analysis Scripts
 Three scripts are provided to perform basic analysis of TraDIS results in `bin`:
 
 * `tradis_gene_insert_sites` - Takes genome annotation in embl format along with plot files produced by bacteria_tradis and generates tab-delimited files containing gene-wise annotations of insert sites and read counts.
@@ -67,15 +100,14 @@ Three scripts are provided to perform basic analysis of TraDIS results in `bin`:
 * `tradis_comparison.R` - Takes tab files to compare two growth conditions using edgeR. This analysis requires experimental replicates.
 
 
-Internal Objects and Methods
-===================
-####Bio::Tradis::DetectTags
+### Internal Objects and Methods
+__Bio::Tradis::DetectTags__  
 * Required parameters:
 	* `bamfile` - path to/name of file to check
 * Methods:
 	* `tags_present` - returns true if TraDIS tags are detected in `bamfile`
 	
-####Bio::Tradis::AddTagsToSeq
+__Bio::Tradis::AddTagsToSeq__  
 * Required parameters:
 	* `bamfile` - path to/name of file containing reads and tags
 * Optional parameters:
@@ -92,7 +124,7 @@ Internal Objects and Methods
 					  in the correct orientation at the start of the sequences
 					  in the resulting FastQ file.
 
-####Bio::Tradis::FilterTags
+__Bio::Tradis::FilterTags__  
 * Required parameters:
 	* `fastqfile` - path to/name of file to filter. This may be a gzipped fastq file, in which case a temporary unzipped version is used and removed on completion.
 	* `tag`       - TraDIS tag to match
@@ -102,7 +134,7 @@ Internal Objects and Methods
 * Methods:
 	* `filter_tags` - output all reads containing the tag to `outfile`
 	
-####Bio::Tradis::RemoveTags
+__Bio::Tradis::RemoveTags__  
 * Required parameters:
 	* `fastqfile` - path to/name of file to filter.
 	* `tag`       - TraDIS tag to remove
@@ -113,7 +145,7 @@ Internal Objects and Methods
 	* `remove_tags` - output all reads with the tags removed from both sequence and
 				  quality strings to `outfile`
 				
-####Bio::Tradis::Map
+__Bio::Tradis::Map__  
 * Required parameters:
 	* `fastqfile` - path to/name of file to map to the reference
 	* `reference` - path to/name of reference genome in fasta format (.fa)
@@ -133,7 +165,7 @@ Internal Objects and Methods
 				
 	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)
 				
-####Bio::Tradis::TradisPlot
+__Bio::Tradis::TradisPlot__  
 * Required parameters:
 	* `mappedfile` - mapped and sorted BAM file
 * Optional parameters:
@@ -142,7 +174,7 @@ Internal Objects and Methods
 * Methods:
 	* `plot` - create insertion site plots for reads in `mappedfile`. This file will be readable by the Artemis genome browser (http://www.sanger.ac.uk/resources/software/artemis/)
 	 
-####Bio::Tradis::RunTradis
+__Bio::Tradis::RunTradis__  
 * Required parameters:
 	* `fastqfile` - file containing a list of fastqs (gzipped or raw) to run the 
 				complete analysis on. This includes all (including 
@@ -158,8 +190,7 @@ Internal Objects and Methods
 * Methods:
 	* `run_tradis` - run complete analysis
 
-Perl Programming Examples
-========
+### Perl Programming Examples
 You can reuse the Perl modules as part of other Perl scripts. This section provides example Perl code.
 Check whether `file.bam` contains TraDIS tag fields and, if so, adds the tags
 to the reads' sequence and quality strings.
@@ -212,3 +243,14 @@ Bio::Tradis::RunTradis(
 	mismatch => 1
 )->run_tradis;
 ```
+## License
+Bio-Tradis is free software, licensed under [GPLv3](https://github.com/sanger-pathogens/Bio-Tradis/blob/master/software_license).
+
+## Feedback/Issues
+Please report any issues to the [issues page](https://github.com/sanger-pathogens/bio-tradis/issues) or email path-help@sanger.ac.uk
+
+## Citation
+If you use this software please cite:
+
+
+"The TraDIS toolkit: sequencing and analysis for dense transposon mutant libraries", Barquist L, Mayho M, Cummins C, Cain AK, Boinett CJ, Page AJ, Langridge G, Quail MA, Keane JA, Parkhill J. Bioinformatics. 2016 Apr 1;32(7):1109-11. doi: [10.1093/bioinformatics/btw022](https://doi.org/10.1093/bioinformatics/btw022). Epub 2016 Jan 21.
\ No newline at end of file

_config.yml

+theme: jekyll-theme-cayman
\ No newline at end of file

bin/tradis_gene_insert_sites

@@ -132,7 +132,7 @@ for my $insert_sites ( @ins_list ){
 
         my $count = 0;
         my $inserts = 0;
-        for(my $j=$read_start;$j < $read_end; $j++){
+        for(my $j=$read_start;$j <= $read_end; $j++){
             $count += $insert_sites->[$j];
             $inserts += 1 if $insert_sites->[$j] > 0;
         }

debian/changelog

+bio-tradis (1.4.1+dfsg-1) unstable; urgency=medium
+
+  * New upstream version
+  * Point Vcs fields to salsa.debian.org
+  * Standards-Version: 4.2.1
+  * Fix perl interpreter
+
+ -- Andreas Tille <tille@debian.org>  Wed, 17 Oct 2018 11:56:52 +0200
+
 bio-tradis (1.3.3+dfsg-3) unstable; urgency=medium
 
   * Standards-Version: 4.1.3

debian/control

@@ -9,9 +9,9 @@ Build-Depends: debhelper (>= 11~),
                libtest-most-perl,
                libtest-files-perl,
                libbio-perl-perl
-Standards-Version: 4.1.3
-Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/bio-tradis.git
-Vcs-Git: https://anonscm.debian.org/git/debian-med/bio-tradis.git
+Standards-Version: 4.2.1
+Vcs-Browser: https://salsa.debian.org/med-team/bio-tradis
+Vcs-Git: https://salsa.debian.org/med-team/bio-tradis.git
 Homepage: https://github.com/sanger-pathogens/Bio-Tradis
 
 Package: bio-tradis
@@ -25,7 +25,7 @@ Depends: ${perl:Depends},
          r-cran-getopt,
          r-cran-mass
 Suggests: artemis,
-          r-bioc-edger,
+          r-bioc-edger
 Description: analyse the output from TraDIS analyses of genomic sequences
  Bio-Tradis contains a set of tools to analyse the output from
  TraDIS analyses.

debian/rules

@@ -11,6 +11,10 @@ TEST_FILES = $(shell find t -name "*.t")
 override_dh_install:
 	dh_install
 	find debian/*/usr/bin -name "*.R" -exec sh -c 'mv {} `echo {} | sed "s/\.R$$//"`' \;
+	dh_install
+	for pl in `grep -Rl '#!/usr/bin/env[[:space:]]\+perl' debian/*/usr/*` ; do \
+	    sed -i '1s?^#!/usr/bin/env[[:space:]]\+perl?#!/usr/bin/perl?' $${pl} ; \
+	done
 
 override_dh_auto_test:
 	dh_auto_test -- TEST_FILES="$(TEST_FILES)"

dist.ini

@@ -3,7 +3,7 @@ author  = Carla Cummins <path-help@sanger.ac.uk>
 license = GPL_3
 copyright_holder = Wellcome Trust Sanger Institute
 copyright_year   = 2013
-version = 1.3.3
+version = 1.4.1
 
 [MetaResources]
 homepage        = http://www.sanger.ac.uk/
@@ -53,6 +53,8 @@ filename = t/data/TradisPlot/expected.plot.gz
 filename = t/data/TradisPlot/test.mapped.bam
 filename = t/data/AddTags/expected_tradis.cram
 filename = t/data/DetectTags/sample_sm_tr.cram
+filename = t/data/DetectTags/AE004091.fasta
+filename = t/data/DetectTags/AE004091.fasta.fai
 filename = t/data/AddTags/sample_sm_tr.cram
 filename = t/data/CombinePlots/tabix_sorted.insert_site_plot.gz.tbi
 filename = t/data/CombinePlots/tabix_sorted.insert_site_plot.gz

lib/Bio/Tradis/CommandLine/TradisAnalysis.pm

@@ -13,7 +13,7 @@ use Moose;
 use Getopt::Long qw(GetOptionsFromArray);
 use Cwd qw(abs_path cwd);
 use Bio::Tradis::RunTradis;
-use TryCatch;
+use Try::Tiny;
 
 has 'args'        => ( is => 'ro', isa => 'ArrayRef', required => 1 );
 has 'script_name' => ( is => 'ro', isa => 'Str',      required => 1 );
@@ -161,10 +161,10 @@ sub run {
             $analysis->run_tradis;
             $at_least_one_good_fastq = 1;
         }
-	catch (Bio::Tradis::Exception::TagFilterError $e) {
+	catch {
 		my $tag = $self->tag;
 		warn "There was a problem filtering '$full_path' by '$tag'; it looks like the tag was not found in any read\n";
-	}
+	};
     }
     if ( ! $at_least_one_good_fastq ) {
         Bio::Tradis::Exception::TagFilterError->throw( error => "None of the input files contained the specified tag.  Please check that your inputs are valid fastq files and that at least one read in one of them starts with the specified tag\n" );

t/data/DetectTags/AE004091.fasta.fai

+ENA|AE004091|AE004091.2	6264404	71	60	61