Commit f1d2c34b authored by TomKellyGenetics's avatar TomKellyGenetics
Browse files

update documentation for 1.2.2

parent 4e4a0317

README.Rmd

+6 −6
Original line number Diff line number Diff line
@@ -939,14 +939,14 @@ cellrangerpath=`which cellranger` 
if [[ ! -f test/cellranger_reference/cellranger-tiny-ref/3.0.0/star/SA ]] && [[ -f $(dirname $cellrangerpath)/cellranger-tiny-ref/3.0.0/star/SA ]]; then

    rsync $(dirname $cellrangerpath)/cellranger-tiny-ref/3.0.0/star/SA test/cellranger_reference/cellranger-tiny-ref/3.0.0/star/SA

fi

if [[ ! -f test/cellranger_reference/cellranger-tiny-ref/1.2.0/star/SA ]] && [[ -f $(dirname $cellrangerpath)/cellranger-tiny-ref/1.2.0/star/SA ]]; then

    rsync $(dirname $cellrangerpath)/cellranger-tiny-ref/1.2.0/star/SA test/cellranger_reference/cellranger-tiny-ref/1.2.0/star/SA

if [[ ! -f test/cellranger_reference/cellranger-tiny-ref/1.2.1/star/SA ]] && [[ -f $(dirname $cellrangerpath)/cellranger-tiny-ref/1.2.1/star/SA ]]; then

    rsync $(dirname $cellrangerpath)/cellranger-tiny-ref/1.2.1/star/SA test/cellranger_reference/cellranger-tiny-ref/1.2.1/star/SA

fi

```



This creates a reference for Cell Ranger here:



- test/cellranger_reference/cellranger-tiny-ref/1.2.0

- test/cellranger_reference/cellranger-tiny-ref/1.2.1



- test/cellranger_reference/cellranger-tiny-ref/3.0.0
@@ -979,7 +979,7 @@ The `gffread` function includes with the [cufflinks](http://cole-trapnell-lab.gi 
utility can convert to gtf. For example:



```

gffread test/cellranger_reference/cellranger-tiny-ref/genes-1.2.1.gff3 -T -o test/cellranger_reference/cellranger-tiny-ref/genes-1.2.1.gtf 

gffread test/cellranger_reference/cellranger-tiny-ref/genes-1.2.0.gff3 -T -o test/cellranger_reference/cellranger-tiny-ref/genes-1.2.0.gtf 

```



To generate new references we first remove the references imported.
@@ -992,8 +992,8 @@ We then generate references from the FASTA and GTF files as shown in the followi 


```

cellranger mkref --genome=test/cellranger_reference/cellranger-tiny-ref/1.2.0 \

        --fasta=test/cellranger_reference/cellranger-tiny-ref/genome-1.2.1.fa \

        --genes=test/cellranger_reference/cellranger-tiny-ref/ genes-1.2.1.gtf

        --fasta=test/cellranger_reference/cellranger-tiny-ref/genome-1.2.0.fa \

        --genes=test/cellranger_reference/cellranger-tiny-ref/ genes-1.2.0.gtf



cellranger mkref --genome=test/cellranger_reference/cellranger-tiny-ref/3.0.0 \

         --fasta=test/cellranger_reference/cellranger-tiny-ref/genome-3.0.0.fa \

README.html

+6 −6
Original line number Diff line number Diff line
@@ -435,12 +435,12 @@ cellrangerpath=`which cellranger` 
if [[ ! -f test/cellranger_reference/cellranger-tiny-ref/3.0.0/star/SA ]] && [[ -f $(dirname $cellrangerpath)/cellranger-tiny-ref/3.0.0/star/SA ]]; then

    rsync $(dirname $cellrangerpath)/cellranger-tiny-ref/3.0.0/star/SA test/cellranger_reference/cellranger-tiny-ref/3.0.0/star/SA

fi

if [[ ! -f test/cellranger_reference/cellranger-tiny-ref/1.2.0/star/SA ]] && [[ -f $(dirname $cellrangerpath)/cellranger-tiny-ref/1.2.0/star/SA ]]; then

    rsync $(dirname $cellrangerpath)/cellranger-tiny-ref/1.2.0/star/SA test/cellranger_reference/cellranger-tiny-ref/1.2.0/star/SA

if [[ ! -f test/cellranger_reference/cellranger-tiny-ref/1.2.1/star/SA ]] && [[ -f $(dirname $cellrangerpath)/cellranger-tiny-ref/1.2.1/star/SA ]]; then

    rsync $(dirname $cellrangerpath)/cellranger-tiny-ref/1.2.1/star/SA test/cellranger_reference/cellranger-tiny-ref/1.2.1/star/SA

fi</code></pre>

<p>This creates a reference for Cell Ranger here:</p>

<ul>

<li><p>test/cellranger_reference/cellranger-tiny-ref/1.2.0</p></li>

<li><p>test/cellranger_reference/cellranger-tiny-ref/1.2.1</p></li>

<li><p>test/cellranger_reference/cellranger-tiny-ref/3.0.0</p></li>

</ul>

<h4 id="automated-references">Automated references</h4>
@@ -455,13 +455,13 @@ cd ../../..</code></pre> 
<h4 id="custom-cell-ranger-references">Custom Cell Ranger references</h4>

<p>It is also possible to generate a custom reference for any genome provided you have a FASTQ genome reference file and a GTF/GFF3 annotation file. Please ensure that the chromosomes match between the FASTA headers and the chromosome column (1st) of the GTF/GFF3 file.</p>

<p>The <code>gffread</code> function includes with the <a href="http://cole-trapnell-lab.github.io/cufflinks/file_formats/#the-gffread-utility">cufflinks</a> utility can convert to gtf. For example:</p>

<pre><code>gffread test/cellranger_reference/cellranger-tiny-ref/genes-1.2.1.gff3 -T -o test/cellranger_reference/cellranger-tiny-ref/genes-1.2.1.gtf </code></pre>

<pre><code>gffread test/cellranger_reference/cellranger-tiny-ref/genes-1.2.0.gff3 -T -o test/cellranger_reference/cellranger-tiny-ref/genes-1.2.0.gtf </code></pre>

<p>To generate new references we first remove the references imported.</p>

<pre><code>rm -rf test/cellranger_reference/cellranger-tiny-ref/1.2.0 test/cellranger_reference/cellranger-tiny-ref/3.0.0</code></pre>

<p>We then generate references from the FASTA and GTF files as shown in the following examples:</p>

<pre><code>cellranger mkref --genome=test/cellranger_reference/cellranger-tiny-ref/1.2.0 \

        --fasta=test/cellranger_reference/cellranger-tiny-ref/genome-1.2.1.fa \

        --genes=test/cellranger_reference/cellranger-tiny-ref/ genes-1.2.1.gtf

        --fasta=test/cellranger_reference/cellranger-tiny-ref/genome-1.2.0.fa \

        --genes=test/cellranger_reference/cellranger-tiny-ref/ genes-1.2.0.gtf



cellranger mkref --genome=test/cellranger_reference/cellranger-tiny-ref/3.0.0 \

         --fasta=test/cellranger_reference/cellranger-tiny-ref/genome-3.0.0.fa \

README.md

+6 −6
Original line number Diff line number Diff line
@@ -939,14 +939,14 @@ cellrangerpath=`which cellranger` 
if [[ ! -f test/cellranger_reference/cellranger-tiny-ref/3.0.0/star/SA ]] && [[ -f $(dirname $cellrangerpath)/cellranger-tiny-ref/3.0.0/star/SA ]]; then

    rsync $(dirname $cellrangerpath)/cellranger-tiny-ref/3.0.0/star/SA test/cellranger_reference/cellranger-tiny-ref/3.0.0/star/SA

fi

if [[ ! -f test/cellranger_reference/cellranger-tiny-ref/1.2.0/star/SA ]] && [[ -f $(dirname $cellrangerpath)/cellranger-tiny-ref/1.2.0/star/SA ]]; then

    rsync $(dirname $cellrangerpath)/cellranger-tiny-ref/1.2.0/star/SA test/cellranger_reference/cellranger-tiny-ref/1.2.0/star/SA

if [[ ! -f test/cellranger_reference/cellranger-tiny-ref/1.2.1/star/SA ]] && [[ -f $(dirname $cellrangerpath)/cellranger-tiny-ref/1.2.1/star/SA ]]; then

    rsync $(dirname $cellrangerpath)/cellranger-tiny-ref/1.2.1/star/SA test/cellranger_reference/cellranger-tiny-ref/1.2.1/star/SA

fi

```



This creates a reference for Cell Ranger here:



- test/cellranger_reference/cellranger-tiny-ref/1.2.0

- test/cellranger_reference/cellranger-tiny-ref/1.2.1



- test/cellranger_reference/cellranger-tiny-ref/3.0.0
@@ -979,7 +979,7 @@ The `gffread` function includes with the [cufflinks](http://cole-trapnell-lab.gi 
utility can convert to gtf. For example:



```

gffread test/cellranger_reference/cellranger-tiny-ref/genes-1.2.1.gff3 -T -o test/cellranger_reference/cellranger-tiny-ref/genes-1.2.1.gtf 

gffread test/cellranger_reference/cellranger-tiny-ref/genes-1.2.0.gff3 -T -o test/cellranger_reference/cellranger-tiny-ref/genes-1.2.0.gtf 

```



To generate new references we first remove the references imported.
@@ -992,8 +992,8 @@ We then generate references from the FASTA and GTF files as shown in the followi 


```

cellranger mkref --genome=test/cellranger_reference/cellranger-tiny-ref/1.2.0 \

        --fasta=test/cellranger_reference/cellranger-tiny-ref/genome-1.2.1.fa \

        --genes=test/cellranger_reference/cellranger-tiny-ref/ genes-1.2.1.gtf

        --fasta=test/cellranger_reference/cellranger-tiny-ref/genome-1.2.0.fa \

        --genes=test/cellranger_reference/cellranger-tiny-ref/ genes-1.2.0.gtf



cellranger mkref --genome=test/cellranger_reference/cellranger-tiny-ref/3.0.0 \

         --fasta=test/cellranger_reference/cellranger-tiny-ref/genome-3.0.0.fa \

docker_build.sh

+2 −2
Original line number Diff line number Diff line 
version=1.2.1

old_version=1.2.0

version=1.2.2

old_version=1.2.1

sed -i "s/$old_version/$version/g"  *md *html launch_universc.sh .version man/*sh inst/*

R -e "knitr::knit('README.Rmd')"; pandoc -f markdown -t html README.md > README.html

echo "updating GitHub version $version"

podman_build.sh

+2 −2
Original line number Diff line number Diff line 
version=1.2.1

old_version=1.2.0

version=1.2.2

old_version=1.2.1

sed -i "s/$old_version/$version/g"  *md *html  launch_universc.sh .version man/*sh inst/*

R -e "knitr::knit('README.Rmd')"; pandoc -f markdown -t html README.md > README.html

echo "updating GitHub version $version"

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