Commit 16c83cb4 authored by TomKellyGenetics's avatar TomKellyGenetics
Browse files

update PATH in Docker container

parent fe37f6e5

.version

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1.2.4
 
1.2.5-dev

CHANGELOG

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### 1.2.5-dev



- updates PATH environment variable to call /universc/launch_universc.sh from any working directory



### 1.2.4



- enables unit testing via nextflow for nf-core module

CITATION.cff

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@@ -11,7 +11,7 @@ authors: 
  email: "kai.battenberg@riken.jp"

  affiliation: "Center for Sustainable Resource Science, RIKEN, Suehiro-cho-1-7-22, Tsurumi Ward, Yokohama, Japan"

  orcid: "http://orcid.org/0000-0001-7517-2657"

version: 1.2.4

version: 1.2.5-dev

doi: 10.1101/2021.01.19.427209

date-released: 2021-02-14

url: "https://github.com/minoda-lab/universc"

Dockerfile

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@@ -46,7 +46,7 @@ RUN mkdir -p /cellranger-3.0.2.9001/cellranger-tiny-ref \ 
 && ln -s /universc/test/cellranger_reference/cellranger-tiny-ref/1.2.0 /cellranger-3.0.2.9001/cellranger-tiny-ref \ 

 && ln -s /universc/test/cellranger_reference/cellranger-tiny-ref/3.0.0 /cellranger-3.0.2.9001/cellranger-tiny-ref



ENV PATH universc:$PATH

ENV PATH /universc:$PATH



RUN ln -s /universc/launch_universc.sh /cellranger-3.0.2.9001/cellranger-cs/3.0.2.9001/bin/universc

README.Rmd

+23 −23
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@@ -34,9 +34,9 @@ tags: 
![Docker Stars](https://img.shields.io/docker/stars/tomkellygenetics/universc)

![Docker Pulls](https://img.shields.io/docker/pulls/tomkellygenetics/universc)



![Docker Image Version (tag latest semver)](https://img.shields.io/docker/v/tomkellygenetics/universc/1.2.4)

![MicroBadger Layers (latest)](https://img.shields.io/microbadger/layers/tomkellygenetics/universc/latest?label="layers@1.2.4")

![Docker Image Size (v1.2.4)](https://img.shields.io/docker/image-size/tomkellygenetics/universc/1.2.4?label="image%20size@1.2.4)

![Docker Image Version (tag latest semver)](https://img.shields.io/docker/v/tomkellygenetics/universc/1.2.5-dev)

![MicroBadger Layers (latest)](https://img.shields.io/microbadger/layers/tomkellygenetics/universc/latest?label="layers@1.2.5-dev")

![Docker Image Size (v1.2.5-dev)](https://img.shields.io/docker/image-size/tomkellygenetics/universc/1.2.5-dev?label="image%20size@1.2.5-dev)

![Docker Image Version (latest by date)](https://img.shields.io/docker/v/tomkellygenetics/universc/latest)

![MicroBadger Layers (latest)](https://img.shields.io/microbadger/layers/tomkellygenetics/universc/latest)

![Docker Image Size (latest)](https://img.shields.io/docker/image-size/tomkellygenetics/universc/latest)
@@ -62,8 +62,8 @@ tags: 


![GitHub all releases](https://img.shields.io/github/downloads/minoda-lab/universc/total?label=GitHub%20downloads)

![GitHub release (latest by date)](https://img.shields.io/github/v/release/minoda-lab/universc?label=GitHub%20release)

![GitHub release (latest by date)](https://img.shields.io/github/downloads/minoda-lab/universc/1.2.4/total)

![GitHub release (by tag)](https://img.shields.io/github/downloads/minoda-lab/universc/1.2.4/total)

![GitHub release (latest by date)](https://img.shields.io/github/downloads/minoda-lab/universc/1.2.5-dev/total)

![GitHub release (by tag)](https://img.shields.io/github/downloads/minoda-lab/universc/1.2.5-dev/total)



![Docker CI](https://github.com/minoda-lab/universc/workflows/CI%20to%20Docker%20hub/badge.svg)

![Docker compose](https://github.com/minoda-lab/universc/workflows/Docker%20compose%20build/badge.svg)
@@ -94,7 +94,7 @@ and use this tool to process single-cell RNA-Seq data from FASTQ format. 


**Package**



UniverSC version 1.2.4

UniverSC version 1.2.5-dev



**Maintainers**
@@ -367,7 +367,7 @@ as follows: 
Kelly, S.T., Battenberg, Hetherington, N.A., K., Hayashi, K., and Minoda, A. (2021)

UniverSC: a flexible cross-platform single-cell data processing pipeline.

bioRxiv 2021.01.19.427209; doi: [https://doi.org/10.1101/2021.01.19.427209](https://doi.org/10.1101/2021.01.19.427209)

package version 1.2.4. [https://github.com/minoda-lab/universc](https://github.com/minoda-lab/universc)

package version 1.2.5-dev. [https://github.com/minoda-lab/universc](https://github.com/minoda-lab/universc)



```

@article {Kelly2021.01.19.427209,
@@ -380,7 +380,7 @@ package version 1.2.4. [https://github.com/minoda-lab/universc](https://github.c 
        abstract = {Single-cell RNA-sequencing analysis to quantify RNA molecules in individual cells has become popular owing to the large amount of information one can obtain from each experiment. We have developed UniverSC (https://github.com/minoda-lab/universc), a universal single-cell processing tool that supports any UMI-based platform. Our command-line tool enables consistent and comprehensive integration, comparison, and evaluation across data generated from a wide range of platforms.Competing Interest StatementThe authors have declared no competing interest.},

        eprint = {https://www.biorxiv.org/content/early/2021/01/19/2021.01.19.427209.full.pdf},

        journal = {{bioRxiv}},

        note = {package version 1.2.4},

        note = {package version 1.2.5-dev},

        URL = {https://github.com/minoda-lab/universc},

}
@@ -391,7 +391,7 @@ package version 1.2.4. [https://github.com/minoda-lab/universc](https://github.c 
    title = {{UniverSC}:  a flexible cross-platform single-cell data processing pipeline},

    author = {S. Thomas Kelly, Kai Battenberg, Nicola A. Hetherington, Makoto Hayashi, and Aki Minoda},

    year = {2022},

    note = {package version 1.2.4},

    note = {package version 1.2.5-dev},

    url = {https://github.com/minoda-lab/universc},

  }

```
@@ -844,7 +844,7 @@ your systems administrator. 


#### Pulling from remote DockerHub repository



We provide a docker image for UniverSC version 1.2.4.

We provide a docker image for UniverSC version 1.2.5-dev.



You can import it if you have docker installed.
@@ -952,14 +952,14 @@ 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/1.2.4/star/SA ]] && [[ -f $(dirname $cellrangerpath)/cellranger-tiny-ref/1.2.4/star/SA ]]; then

    rsync $(dirname $cellrangerpath)/cellranger-tiny-ref/1.2.4/star/SA test/cellranger_reference/cellranger-tiny-ref/1.2.4/star/SA

if [[ ! -f test/cellranger_reference/cellranger-tiny-ref/1.2.5-dev/star/SA ]] && [[ -f $(dirname $cellrangerpath)/cellranger-tiny-ref/1.2.5-dev/star/SA ]]; then

    rsync $(dirname $cellrangerpath)/cellranger-tiny-ref/1.2.5-dev/star/SA test/cellranger_reference/cellranger-tiny-ref/1.2.5-dev/star/SA

fi

```



This creates a reference for Cell Ranger here:



- test/cellranger_reference/cellranger-tiny-ref/1.2.4

- test/cellranger_reference/cellranger-tiny-ref/1.2.5-dev



- test/cellranger_reference/cellranger-tiny-ref/3.0.0
@@ -998,7 +998,7 @@ gffread test/cellranger_reference/cellranger-tiny-ref/genes-1.2.0.gff3 -T -o tes 
To generate new references we first remove the references imported.



```

rm -rf test/cellranger_reference/cellranger-tiny-ref/1.2.4 test/cellranger_reference/cellranger-tiny-ref/3.0.0

rm -rf test/cellranger_reference/cellranger-tiny-ref/1.2.5-dev test/cellranger_reference/cellranger-tiny-ref/3.0.0

```



We then generate references from the FASTA and GTF files as shown in the following examples:
@@ -1255,15 +1255,15 @@ Obtain DropSeq data from public database: 


```

wget https://www.ncbi.nlm.nih.gov/geo/download/\?acc\=GSM1629193\&format\=file\&file\=GSM1629193%5FPure%5FHumanMouse%2Ebam

mv index.html\?acc=GSM1629193\&format=file\&file=GSM1629193%5FPure%5FHumanMouse%2Ebam GSM1.2.49.bam

samtools sort -n GSM1.2.49.bam > GSM1.2.49.qsort

samtools view  GSM1.2.49.qsort  HUMAN_21:9825832-48085036 > GSM1.2.49.qsort2

samtools sort -O BAM GSM1.2.49.bam > GSM1.2.49.sort.bam

samtools index GSM1.2.49.sort.bam

samtools view  GSM1.2.49.sort.bam  HUMAN_21:9825832-48085036 > GSM1.2.49.chr21.bam

samtools view -O BAM  GSM1.2.49.sort.bam  HUMAN_21:9825832-48085036 > GSM1.2.49.chr21.sort.bam

samtools sort -n GSM1.2.49.chr21.sort.bam -o GSM1.2.49.chr21.qsort.bam

bedtools bamtofastq -i GSM1.2.49.chr21.qsort.bam -fq GSM1629193_chr21_R1.fastq

mv index.html\?acc=GSM1629193\&format=file\&file=GSM1629193%5FPure%5FHumanMouse%2Ebam GSM1.2.5-dev9.bam

samtools sort -n GSM1.2.5-dev9.bam > GSM1.2.5-dev9.qsort

samtools view  GSM1.2.5-dev9.qsort  HUMAN_21:9825832-48085036 > GSM1.2.5-dev9.qsort2

samtools sort -O BAM GSM1.2.5-dev9.bam > GSM1.2.5-dev9.sort.bam

samtools index GSM1.2.5-dev9.sort.bam

samtools view  GSM1.2.5-dev9.sort.bam  HUMAN_21:9825832-48085036 > GSM1.2.5-dev9.chr21.bam

samtools view -O BAM  GSM1.2.5-dev9.sort.bam  HUMAN_21:9825832-48085036 > GSM1.2.5-dev9.chr21.sort.bam

samtools sort -n GSM1.2.5-dev9.chr21.sort.bam -o GSM1.2.5-dev9.chr21.qsort.bam

bedtools bamtofastq -i GSM1.2.5-dev9.chr21.qsort.bam -fq GSM1629193_chr21_R1.fastq

mv GSM1629193_chr21_R1.fastq GSM1629193_chr21_R2.fastq

fastq-dump -F --split-files SRR1873277

fastq_pair GSM1629193_chr21_R2.fastq SRR1873277_1.fastq

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