Installation¶

Requirements¶

capC-MAP requires a C++ compiler and Python; also the following software should be installed and visible on the system path:

cutadapt (>=1.11)
bowtie (>=1.1.1 - note that capC-MAP is not compatible with bowtie2)
samtools (>=1.3.1)

and the following python packages should be installed:

BioPython

Version numbers are those which have been tested, and other versions may also work.

Installation¶

There are several ways to install capC-MAP. One of the easiest is if the bioconda/conda packaging system is available on your system (see https://bioconda.github.io/#install-bioconda for details on how to get it). In this case capC-MAP and all of its requirements can be installed with the single command.

conda install capc-map

If you do not have conda on your system, you will need to install the requirements listed above separately. Then install capC-MAP perform the following steps:

Download the software and unzip into a directory in your home directory. Or clone from git using the command:
```
git clone https://git.ecdf.ed.ac.uk/cbrackle/capC-MAP.git
```
capC-MAP consists of a set of programs written in C++ and a Python package, which both need to be installed on your system. If you have root privileges on your system you can compile and install the C++ programs by running the following commands in the capC-MAP root directory
```
./configure
make
make install
```
and you can install the Python package using pip with the command
```
pip install .
```
when in the capC-MAP package directory.

Alternatively, if you do not have root privileges, you can install a local copy of capC-MAP in your home directory using, for example, the commands
```
./configure --prefix=${HOME}/.local/
make
make install
```
and
```
pip install --user .
```
If you do not have pip available on your system you can instead install the python package using the command
```
python setup.py install
```
or without root privileges
```
python setup.py install --user
```
If you have installed capC-MAP in your home directory, you will need to ensure the binaries directory is present on the system PATH. For example, by adding the following line to your ~/.bashrc file
```
export PATH=$PATH:~/.local/bin
```