Commit 29cfd3ba authored by TomKellyGenetics's avatar TomKellyGenetics
Browse files

increment version to 1.1.4

parent bcdc458c

.gitattributes

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@@ -39,6 +39,7 @@ test/cellranger_reference/cellranger-tiny-ref/3.0.0/star/chrStart.txt filter=lfs 
/home/tom/repos/cellranger_convert/test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L002_R1_001.fastq.gz filter=lfs diff=lfs merge=lfs -text

/home/tom/repos/cellranger_convert/test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L002_R2_001.fastq.gz filter=lfs diff=lfs merge=lfs -text

/home/tom/repos/cellranger_convert/test/shared/cellranger-tiny-fastq/1.2.0/read-I1_si-TTTCATGA_lane-008-chunk-001.fastq.gz filter=lfs diff=lfs merge=lfs -text

/home/tom/repos/cellranger_convert/test/shared/cellranger-tiny-fastq/1.2.0/read-RA_si-TTTCATGA_lane-008-chunk-001.fastq.gz filter=lfs diff=lfs merge=lfs -text

/home/tom/repos/cellranger_convert/test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L001_I1_001.fastq.gz filter=lfs diff=lfs merge=lfs -text

/home/tom/repos/cellranger_convert/test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L001_R1_001.fastq.gz filter=lfs diff=lfs merge=lfs -text

/home/tom/repos/cellranger_convert/test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L001_R2_001.fastq.gz filter=lfs diff=lfs merge=lfs -text
@@ -59,6 +60,7 @@ test/shared/smartseq3-test/Smartseq3_diySpike_R2.fastq.gz filter=lfs diff=lfs me 
test/shared/sciseq-v3-test/SRR7827205_S1_R1.fastq.gz filter=lfs diff=lfs merge=lfs -text

test/shared/sciseq-v3-test/SRR7827205_S1_R2.fastq.gz filter=lfs diff=lfs merge=lfs -text

test/shared/icell8-test/72618_KU812_L002_R2_001.fastq.gz filter=lfs diff=lfs merge=lfs -text

test/shared/cellranger-tiny-fastq/1.2.0/read-RA_si-TTTCATGA_lane-008-chunk-001.fastq.gz filter=lfs diff=lfs merge=lfs -text

test/shared/icell8-test/72618_KU812_L001_R1_001.fastq.gz filter=lfs diff=lfs merge=lfs -text

test/shared/icell8-test/72618_KU812_L001_R2_001.fastq.gz filter=lfs diff=lfs merge=lfs -text

test/shared/icell8-test/72618_KU812_L002_R1_001.fastq.gz filter=lfs diff=lfs merge=lfs -text

.version

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1.1.3
 
1.1.4

CHANGELOG

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### 1.1.4



version in development



### 1.1.3



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

Dockerfile

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@@ -80,5 +80,3 @@ RUN wget https://github.com/alexdobin/STAR/archive/2.5.1b.tar.gz \ 
#  && tar -xvzf BBMap_38.87.tar.gz



# ENV PATH bbmap:$PATH
 


cp /cellranger-3.0.2.9001/cellranger-cs/3.0.2.9001/lib/python/cellranger/chemistry.py /cellranger-3.0.2.9001/cellranger-cs/3.0.2.9001/lib/python/cellranger/check.py

README.Rmd

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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/1.1.3)

![MicroBadger Layers (latest)](https://img.shields.io/microbadger/layers/tomkellygenetics/universc/latest?label="layers@1.1.3")

![Docker Image Size (v1.1.3)](https://img.shields.io/docker/image-size/tomkellygenetics/universc/1.1.3?label="image%20size@1.1.3)

![Docker Image Version (tag latest semver)](https://img.shields.io/docker/v/tomkellygenetics/universc/1.1.4)

![MicroBadger Layers (latest)](https://img.shields.io/microbadger/layers/tomkellygenetics/universc/latest?label="layers@1.1.4")

![Docker Image Size (v1.1.4)](https://img.shields.io/docker/image-size/tomkellygenetics/universc/1.1.4?label="image%20size@1.1.4)

![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)
@@ -61,8 +61,8 @@ 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/1.1.3/total)

![GitHub release (by tag)](https://img.shields.io/github/downloads/minoda-lab/universc/1.1.3/total)

![GitHub release (latest by date)](https://img.shields.io/github/downloads/minoda-lab/universc/1.1.4/total)

![GitHub release (by tag)](https://img.shields.io/github/downloads/minoda-lab/universc/1.1.4/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)
@@ -93,7 +93,7 @@ and use this tool to process single-cell RNA-Seq data from FASTQ format. 


**Package**



UniverSC version 1.1.3

UniverSC version 1.1.4



**Maintainers**
@@ -346,8 +346,8 @@ 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/10.11.1.3021.01.19.427209](https://doi.org/10.11.1.3021.01.19.427209)

package version 1.1.3. [https://github.com/minoda-lab/universc](https://github.com/minoda-lab/universc)

bioRxiv 2021.01.19.427209; doi: [https://doi.org/10.11.1.4021.01.19.427209](https://doi.org/10.11.1.4021.01.19.427209)

package version 1.1.4. [https://github.com/minoda-lab/universc](https://github.com/minoda-lab/universc)



```

@article {Kelly2021.01.19.427209,
@@ -355,12 +355,12 @@ package version 1.1.3. [https://github.com/minoda-lab/universc](https://github.c 
        title = {{UniverSC}: a flexible cross-platform single-cell data processing pipeline},

        elocation-id = {2021.01.19.427209},

        year = {2021},

        doi = {10.11.1.3021.01.19.427209},

        doi = {10.11.1.4021.01.19.427209},

        publisher = {Cold Spring Harbor Laboratory},

        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 1.1.3},

        note = {package version 1.1.4},

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

}
@@ -371,7 +371,7 @@ package version 1.1.3. [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 = {2021},

    note = {package version 1.1.3},

    note = {package version 1.1.4},

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

  }

```
@@ -824,7 +824,7 @@ your systems administrator. 


#### Pulling from remote DockerHub repository



We provide a docker image for UniverSC version 1.1.3.

We provide a docker image for UniverSC version 1.1.4.



You can import it if you have docker installed.

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