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

### 1.1.3 (dev)

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

- bug fixes for subroutines (SmartSeq3 processing)

### 1.1.2

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 'convert' for processing all data from different

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.

docker pull tomkellygenetics/universc:latest

```

Then you can run convert with:

Then you can run UniverSC with:

```

run -it tomkellygenetics/universc:latest launch_universc.sh

docker run -it tomkellygenetics/universc:latest launch_universc.sh

```

You can open a shell in the docker image with:

```

run -it tomkellygenetics/universc:latest /bin/bash

docker run -it tomkellygenetics/universc:latest /bin/bash

```

```

run -it tomkellygenetics/universc:latest /bin/zsh 

docker run -it tomkellygenetics/universc:latest /bin/zsh 

```

Either of these shells are supported.

#### Running launch_universc.sh on 10x data

```

# call convert on 10x with multiple lanes

# call UniverSC on 10x with multiple lanes

bash /universc/launch_universc.sh --id "test-10x-v3" --technology "10x" \

 --reference "/universc/test/cellranger_reference/cellranger-tiny-ref/3.0.0" \

 --file "/universc/test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L001" \

rm ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/barcodes/.lock

```

When doing this *please ensure that no other instances are running* for Cell Ranger

convert.

When doing this *please ensure that no other instances are running* for UniverSC.

You can also see the current configuration of UniverSC for each Cell Ranger

install as follows:

<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 'convert' 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 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>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>

<p>We provide a docker image for UniverSC version 1.1.2.</p>

<p>You can import it if you have docker installed.</p>

<pre><code>docker pull tomkellygenetics/universc:latest</code></pre>

<p>Then you can run convert with:</p>

<pre><code>run -it tomkellygenetics/universc:latest launch_universc.sh</code></pre>

<p>Then you can run UniverSC with:</p>

<pre><code>docker run -it tomkellygenetics/universc:latest launch_universc.sh</code></pre>

<p>You can open a shell in the docker image with:</p>

<pre><code>run -it tomkellygenetics/universc:latest /bin/bash</code></pre>

<pre><code>run -it tomkellygenetics/universc:latest /bin/zsh </code></pre>

<pre><code>docker run -it tomkellygenetics/universc:latest /bin/bash</code></pre>

<pre><code>docker run -it tomkellygenetics/universc:latest /bin/zsh </code></pre>

<p>Either of these shells are supported.</p>

<h5 id="building-the-docker-image-locally">Building the Docker image locally</h5>

<p>The Dockerfile is provided in the repository so it can be built from source. This will build a Docker image with the latest version of universc provided that updates to dependencies on GitHub are still compatible.</p>

 --fastqs="cellranger-3.0.2.9001/cellranger-tiny-fastq/3.0.0/" --sample="tinygex" \

 --transcriptome=&quot;cellranger-3.0.2.9001/cellranger-tiny-ref/3.0.0&quot;</code></pre>

<h4 id="running-launch_universc.sh-on-10x-data">Running launch_universc.sh on 10x data</h4>

<pre><code># call convert on 10x with multiple lanes

<pre><code># call UniverSC on 10x with multiple lanes

bash /universc/launch_universc.sh --id "test-10x-v3" --technology "10x" \

 --reference "/universc/test/cellranger_reference/cellranger-tiny-ref/3.0.0" \

 --file "/universc/test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L001" \

<pre><code>cellrangerversion=`cellranger count --version | head -n 2 | tail -n 1 | cut -f2 -d&#39;(&#39; | cut -f1 -d&#39;)&#39;`

cellrangerpath=`which cellranger`

rm ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/barcodes/.lock</code></pre>

<p>When doing this <em>please ensure that no other instances are running</em> for Cell Ranger convert.</p>

<p>When doing this <em>please ensure that no other instances are running</em> for UniverSC.</p>

<p>You can also see the current configuration of UniverSC for each Cell Ranger install as follows:</p>

<pre><code>cellrangerversion=`cellranger count --version | head -n 2 | tail -n 1 | cut -f2 -d&#39;(&#39; | cut -f1 -d&#39;)&#39;`

cellrangerpath=`which cellranger`

   index: 1

 - name: "RIKEN Center for Sustainable Resource Sciences, Suehiro-cho-1-7-22, Tsurumi Ward, Yokohama, Kanagawa 230-0045, Japan"

   index: 2

date: "Friday 21 May 2021"

date: "Monday 07 June 2021"

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