install and update guide with GNU Make

bash launch_universc.sh

```

##### Manual configuration

##### Automated configuration

You can manually add the script here to the PATH, for example:

We provide a Makefile with all necessary configurations to automatically

check whether launch_universc.sh is installed correctly.

You can specify any directory to install as a "prefix". This will

create a directory "$HOME/local/universc-0.3" where

the files needed will be stored.

```

PATH=$HOME/Downloads/universc:$PATH

cd $HOME/Downloads

git clone https://github.com/TomKellyGenetics/universc.git

make

make install prefix=$HOME/local

```

This means that the directory where the script is can be found

from the shell.

It is also possible to add the current working directory as 

the installed directory.

```

echo $PATH

cd ~

launch_universc.sh

make install prefix="."

```

Add the following line to the `~/.bashrc` file and use `source ~/.bashrc`

to load a new session. This means that you do not need to add the

sript to the PATH in future sessions.

In this case *do not* delete the installed directory after you

install it or the script will fail to run.

By default it will be installed in a root directory with

read-only access. This requires administrator priviledges.

Note that the manual can onlly be installed with root

priviledges.

```

export PATH=$HOME/Downloads/universc:$PATH 

sudo make install

sudo make manual

```

You can verify that launch_universc.sh has been added to the PATH.

```

echo $PATH

which launch_universc.sh

```

You can then run `launch_universc.sh` from any working directory.

##### Updating

If launch_universc.sh is already installed and you wish to update it,

first you need to pull the changes from GitHub from the

universc directory.

####

```

cd universc

git pull origin master

make

```

Then you can update to the directory of your choice using

the same options for `--prefix` as to install.

```

sudo make install manual

make install prefix=$HOME/local

```

This is remove previous versions of launch_universc.sh and install

the latest version.

The manual can be updated with:

```

make install prefix=$HOME/local

sudo make manual

```

##### Uninstalling

We provide an automated script to reverse these changes.

```

make uninstall

```

This is will automatically detect the installation of launch_universc.sh.

If multiple versions of cellranger are present, you can

specify which to remove with.

-> migrate to Makefile?

```

make remove prefix=$HOME/local

```

#### Custom shell

Make will install the script with `bash` by default but

alternative shells are supported. You will need to run the

install script or run it with your shell of choice.

```

sh launch_universc.sh

sh inst/INSTALL --prefix $HOME/local

launch_universc.sh

```

```

ksh launch_universc.sh

ksh inst/INSTALL --prefix $HOME/local

launch_universc.sh

```

```

zsh launch_universc.sh

zsh inst/INSTALL --prefix $HOME/local

launch_universc.sh

```

```

bash inst/UPGRADE --prefix "/home/tom/local"

fish launch_universc.sh

fish inst/INSTALL --prefix $HOME/local

launch_universc.sh

```

The help menu should reflect the shell used to run it.

To update, similarly run the `inst/UPGRADE` script with

your chosen shell.

### Docker image <span id="Docker"><span>

...

##### Manual configuration

You can manually add the script here to the PATH, for example:

```

PATH=$HOME/Downloads/universc:$PATH

```

This means that the directory where the script is can be found

from the shell.

```

echo $PATH

cd ~

launch_universc.sh

```

Add the following line to the `~/.bashrc` file and use `source ~/.bashrc`

to load a new session. This means that you do not need to add the

sript to the PATH in future sessions.

```

export PATH=$HOME/Downloads/universc:$PATH

```

## Usage <span id="Usage"><span>

### Manual <span id="Help"><span>

#### Locally instaleld manual

#### Locally install manual

You can display a manual from the locally installed universc directory with:

#### Installing the manual with root priviliges:

##### Automated Configuration

We provide an automated script to install the manual.

```

sudo make manual

```

You can remove the manual with:

```

sudo make manual-clean

```

##### Configuration

The manual can be installed as follows on Mac and Linux.

```

```

man launch_universc.sh

```

`

-> change to make?

#### Help menu