# Tiger / Installing and Running Tiger

## Installing and updating Tiger

Tiger is hosted on bitbucket and can be downloaded and configured with the following commands:

git clone --depth 1 https://bitbucket.org/WegmannLab/Tiger.git
cd Tiger; git submodule update --init --recursive
git config --global submodule.recurse true


A makefile for Tiger is provided with the source code. Compile Tiger by typing

make


In order to always obtain the newest version of Tiger, make sure to update regularly using:

git fetch; git pull; make


If you are updating a tiger directory that you cloned before Oct. 15 2018 you might have to update the remote URL:

cd atlas; git remote set-url origin 'https://vlink@bitbucket.org/WegmannLab/tiger.git/'


## Running Tiger

The program Tiger is launched via the command line, preferentially with the name of an arguments file as the only argument. All necessary arguments are then specified in the argument file. Basically, an argument file is a simple collection of pairs of argument names and corresponding values (separated by one or several white space characters, i.e. blanks or tabs), enriched with comments. While each name-value pair has to be at the beginning of a new line, the order is of no importance. Comments may either be added after a name-value pair or given on a line on their own. Note that all comments must be proceeded with a double slash ''//''. Empty lines may be present anywhere within the file and are ignored.

For example, if the argument file is named example.arguments, the program has to be launched as follows:

./Tiger example.arguments


An example for a *.arguments file to run would be:

 task compareCalls vcf my.vcf.gz samplePairs samplePairs.txt verbose

Additionally, arguments may be passed on the command line. In that case, arguments that are also given in the input file will be overwritten. The required syntax is as follows:

./Tiger example.arguments name=value


where name is the name of an argument and value is the corresponding value. For instance,

./Tiger example.arguments vcf=other.vcf.gz


launches Tiger using teh vcf file other.vcf.gz instead of the file that might be specified in example.arguments.

Note that there is no restriction on the number of arguments to be passed that way and arguments can also be specified on the command line only. Note further that the order in which the arguments are given, both in the input file or on the command line, is of no importance.

Tiger is designed to perform multiple tasks. To specify the desired task, the mandatory argument task has to be specified either in the input file or on the command line. Each task requires/allows for specific parameters that can be found on its respective page of this manual. A list of all tasks can be found here.

## Progress Report & Log File

By default, Tiger writes a progress report to the screen. To get a only minimal information, simply add the argument silent either in the input file or on the command line. To save the progress report into a file (e.g. out.txt), simply redirect the output using

./Tiger example.arguments verbose > out.txt


Alternatively, Tiger can also write the progress report to a log file. To invoke this, simply use the argument logFile, followed by the name of the desired file. Note that this will overwrite any existing file with that name. Note further that verbose and logFile can both be used at the same time.

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