install guide preamble

We provide the following preset configurations for convenience based on published data and configurations used by other pipelines 

(e.g, DropSeqPipe and Kallisto/Bustools). To add further support for other technologies or troubleshoot problems, please submit an Issue

to the GitHub repository: https://github.com/TomKellyGenetics/universc/issues] as described in [Bug Reports](#Issues) below.

to the GitHub repository: [TomKellyGenetics/universc](https://github.com/TomKellyGenetics/universc/issues)

as described in [Bug Reports](#Issues) below.

Some changes to the cellranger install are required to run other technologies. Therefore we provide settings for 10x Genomics

which restores settings for the Chromium instrument. We therefore recommend using 'convert' for processing all data from different

#### Pre-set configurations

-  10x Genomics (version automatically detected): 10x, chromium

--  10x Genomics version 2 (16bp barcode, 10bp UMI): 10x-v2, chromium-v2

--  10x Genomics version 3 (16bp barcode, 12bp UMI): 10x-v3, chromium-v3

    -  10x Genomics version 2 (16bp barcode, 10bp UMI): 10x-v2, chromium-v2

    -  10x Genomics version 3 (16bp barcode, 12bp UMI): 10x-v3, chromium-v3

-  CEL-Seq (8bp barcode, 4bp UMI): celseq

-  CEL-Seq2 (6bp UMI, 6bp barcode): celseq2

-  Drop-Seq (12bp barcode, 8bp UMI): nadia, dropseq

-  iCell8 version 3 (11bp barcode, 14bp UMI): icell8 or custom

- inDrops

    -  inDrops version 1 (19bp barcode, 8bp UMI): indrops-v1, 1cellbio-v1

    -  inDrops version 2 (19bp barcode, 8bp UMI): indrops-v2, 1cellbio-v2

    -  inDrops version 3 (8bp barcode, 6bp UMI): indrops-v3, 1cellbio-v3

## Release

At the moment, we have not released the script publicly but we do intend to. We welcome any feedback on it. 

Hopefully it will save people time as make it easier to compare technologies.

This tool will be released open-source. We welcome any feedback on it.

We plan to make this open-source with the agreement of everyone in the project.

We have tested it on several technologies but we need users like you

to let us know how we can improve it. We hope that it will save you

time by handing tedious parts of data formatting so that you can

focus on the results.

### Citation <span id="Citation"><span>

To add further support for other technologies or troubleshoot problems, please submit an Issue 

to the GitHub repository: https://github.com/TomKellyGenetics/universc/issues

Please submit [issues](https://github.com/TomKellyGenetics/graphsim/issues) on GitHub to report

problems or suggest features. [Pull requests](https://github.com/TomKellyGenetics/graphsim/pulls)

to the `dev` branch on GitHub are also welcome to add features or correct problems. Please see

the [contributor guide](CONTRIBUTING.md) for more details.

### Requesting new technologies

Where possible, please provide an minimal example of the first few lines of each FASTQ file for testing purposes.

## Installation <span id="Install"><span>

This script requires cellranger to be installed and exported to the PATH (version 3.0.0 of higher recommended).

This script requires cellranger to be installed and exported to the PATH (version 3.0.0 or higher recommended).

The script itself is exectuable and does not require installation to run but you can put it in your PATH or

bin of your cellranger install if you wish to do so.

bin of your cellranger install if you wish to do so. We provide scripts to do this for your convenience.

### System Requirements

In principle, the script can run on any Unix systems with cellranger installed. You can check whether

cellranger is already availble by running:

```

whereis cellranger

```

You can see which cellranger installation will run as follows:

```

which cellranger

cellranger count --version

```

If cellranger is already installed on your system, you can add it to your $PATH as follows:

```

export PATH=/home/username/path/to/cellranger-x.x.x:$PATH    

```

#### Installing dependencies

If cellranger is not installed on your system, you must install it before running launch_universc.sh.

Please see the [manual for cellranger](https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)

on the 10x Genomics website for more details on how to use it. We provide support for

passing various options to cellranger and sensible defaults for each technology.

This script is compatible with the installation of cellranger that you can

[download](https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest)

from the 10x Genomics website and gives the same output formats.

However, we recommend to use the open-source release of cellranger on GitHub. This is

release on an MIT License and is not subject to the 10x Genomics End User

License Agreement.

We provide open-source repositories with minor updates for compatibility

with current versions of dependencies.

The code is available here:

[https://github.com/TomKellyGenetics/cellranger/releases](https://github.com/TomKellyGenetics/cellranger/releases)

We also provide Docker images for cellranger versions 2.0.2, 2.1.0, 2.1.1, and 3.0.2:

[https://github.com/TomKellyGenetics/cellranger_clean/packages](https://github.com/TomKellyGenetics/cellranger_clean/packages)

[https://hub.docker.com/r/tomkellygenetics/cellranger_clean/tags](https://hub.docker.com/r/tomkellygenetics/cellranger_clean/tags)

#### Cluster Mode configuration

#### Software Requirements

These have been pre-installed in the Docker image described above.

A full example of installation is available in the [GitHub repository](https://github.com/TomKellyGenetics/cellranger)

and on [DockerHub](https://hub.docker.com/r/tomkellygenetics/cellranger_clean/dockerfile).

- Python 2.7.13

- rust 1.28.0

- clang 6.0

- go 1.11

- node v8.11.4

#### Harware requirements

- 8-core Intel or AMD processor (16 cores recommended)

- 64GB RAM (128GB recommended)

- 1TB free disk space

- 64-bit CentOS/RedHat 6.0 or Ubuntu 12.04

#### Ensuring write-access to cellranger

The conversion process requires write-access to to the cellranger install directory so

an install on your user directory is recommended. 

with this configuration requires a lot of memory (40Gb) so running on server is recommended.

SGE job modes are supported to run cellranger with multiple threads.

- local install

- copy from root and add to PATH

#### Installing launch_universc.sh

##### Running the script

git clone

bash launch_universc.sh

####

```

make

```

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

```

### System Requirements

...Unix systems with cellranger installed.

### Docker image

...