Merge branch 'master' of github.com:minoda-lab/universc into dev

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### 1.1.3 (dev)

### 1.1.3

- update paths for compatibility with Red Hat Linux (Fedora and CentOS)

- bug fixes for subroutines (SmartSeq3 processing)

- bug fixes for arithmetic operations

- updated documentation

### 1.1.2

- bug fixes for aligent parameters

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

RUN cd universc/test/cellranger_reference/cellranger-tiny-ref/ \

 && git lfs pull \

# && git lfs pull \

 && rm -rf 3.0.0 1.2.0 \ 

 && cellranger mkref --genome=3.0.0 --fasta=genome-3.0.0.fa --genes=genes-3.0.0.gtf \

 && cellranger mkref --genome=1.2.0 --fasta=genome-1.2.0.fa --genes=genes-1.2.0.gtf 

COPY .version universc/.version

COPY CHANGELOG universc/CHANGELOG

COPY README.Rmd universc/README.Rmd

COPY README.md universc/README.md

COPY README.html universc/README.html

COPY inst/CITATION universc/inst/CITATION

COPY launch_universc.sh universc/launch_universc.sh

COPY sub/FilterSmartSeqReadUMI.pl universc/sub/FilterSmartSeqReadUMI.pl

RUN cd universc \

 && make reference \

 && cd .. 

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

Some changes to the Cell Ranger 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 UnicerSC for processing all data from different

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

technologies as the tool manages these changes. Please note that on a single install of Cell Ranger, multiple technologies or multiple samples 

of the same technology with different whitelist barcodes cannot be run cannot be run simultaneousely (the tool will also check for this to

avoid causing problems with existing runs). Multiple samples of the same technology with the same barcode whitelist can be run simultaneously.

<p>In principle, any technology with a cell barcode and unique molecular identifier (UMI) can be supported.</p>

<p>The following technologies have been tested to ensure that they give the expected results: 10x Genomics, Nadia (DropSeq), ICELL8 version 3</p>

<p>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: <a href="https://github.com/minoda-lab/universc/issues">minoda-lab/universc</a> as described in <a href="#Issues">Bug Reports</a> below.</p>

<p>Some changes to the Cell Ranger 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 UnicerSC for processing all data from different technologies as the tool manages these changes. Please note that on a single install of Cell Ranger, multiple technologies or multiple samples of the same technology with different whitelist barcodes cannot be run cannot be run simultaneousely (the tool will also check for this to avoid causing problems with existing runs). Multiple samples of the same technology with the same barcode whitelist can be run simultaneously.</p>

<p>Some changes to the Cell Ranger 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 UniverSC for processing all data from different technologies as the tool manages these changes. Please note that on a single install of Cell Ranger, multiple technologies or multiple samples of the same technology with different whitelist barcodes cannot be run cannot be run simultaneousely (the tool will also check for this to avoid causing problems with existing runs). Multiple samples of the same technology with the same barcode whitelist can be run simultaneously.</p>

<p>If you are using <code>UniverSC</code> you should also do so to run 10x Genomics data. If you wish to restore Cell Ranger to default settings, see the <a href="#Uninstalling">installation</a> or <a href="#Debugging">troubleshooting</a> sections below.</p>

<h4 id="pre-set-configurations">Pre-set configurations</h4>

<ul>