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Release/docker 1.2.1 #51

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Release/docker 1.2.1 #51

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ac11ac8
Merge pull request #2 from DongqingSun96/feat/cicd-1
DongqingSun96 Jul 21, 2020
56d53b2
Merge pull request #3 from liulab-dfci/master
DongqingSun96 Aug 4, 2020
86f0cd6
Merge pull request #4 from liulab-dfci/master
DongqingSun96 Aug 11, 2020
f9db9f4
Release docker 1.2.1
DongqingSun Aug 12, 2020
6998572
Update user name in example
DongqingSun Aug 12, 2020
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4 changes: 2 additions & 2 deletions docker/Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -34,8 +34,8 @@ ENV PATH=/root/miniconda3/bin:${PATH}

# add conda channels and install softwares
RUN conda config --add channels defaults && conda config --add channels conda-forge && \
conda config --add channels bioconda && conda install -c liulab-dfci maestro=1.2.1 && \
conda install mamba -c conda-forge && mamba create -n lisa -c qinqian lisa=1.0
conda config --add channels bioconda && conda create -n MAESTRO -c liulab-dfci maestro=1.2.1 && \
conda install mamba -c conda-forge && mamba create -n lisa -y -c qinqian lisa=1.0


# install giggle and rabit
Expand Down
50 changes: 29 additions & 21 deletions docker/README.md
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
# MAESTRO v1.1.0 docker
# MAESTRO v1.2.1 docker

If it is difficult to install MAESTRO because of the system configuration, users can adopt an alternative way to get MAESTRO running through a docker container.

Expand All @@ -19,70 +19,79 @@ The docker distribution includes the latest MAESTRO conda package, as well as RA
Please use the following commands to the pull the MAESTRO docker image.

``` bash
$ sudo docker pull winterdongqing/maestro:1.1.0
$ sudo docker pull winterdongqing/maestro:1.2.1
$ sudo docker image list
REPOSITORY TAG IMAGE ID CREATED SIZE
winterdongqing/maestro 1.1.0 831bfd245e63 3 hours ago 8.7GB
winterdongqing/maestro 1.2.1 57f41ffbe200 4 hours ago 9.6GB
```

### Run in the container

To run the MAESTRO container, please use the following commands. The ```-v``` flag mounts the current directory ```/home1/wangchenfei``` into ```/root/MAESTRO``` in the container.
To run the MAESTRO container, please use the following commands. The ```-v``` flag mounts the current directory ```/home1/user``` into ```/root/MAESTRO``` in the container.

```bash
$ pwd
/home1/wangchenfei
/home1/user
$ ls
annotations docker miniconda3 ncbi Project R tmp Tool
$ sudo docker run -v /home1/wangchenfei:/root/MAESTRO -it winterdongqing/maestro:1.1.0
$ sudo docker run -v /home1/user:/root/MAESTRO -it winterdongqing/maestro:1.2.1
```

```#``` means that users have been in the container. There are four folders in the ```root``` directory of the container. The ```Annotation``` directory stores the RABIT index and GIGGLE index. Users can access local data and locally installed softwares through the ```MAESTRO```.

```bash
root@45c5df8b6635:~# ls
root@c561fe9a9410:~# ls
MAESTRO miniconda3
root@45c5df8b6635:~# conda env list
root@c561fe9a9410:~# conda env list
# conda environments:
#
base * /root/miniconda3
MAESTRO /root/miniconda3/envs/MAESTRO
lisa /root/miniconda3/envs/lisa

root@45c5df8b6635:~# cd MAESTRO/ && ls
root@c561fe9a9410:~# cd MAESTRO/ && ls
Project R Tool annotations docker miniconda3 ncbi tmp
```

Then users can run MAESTRO following the [tutorial](../example/ATAC_infrastructure_10x/ATAC_infrastructure_10x.md).
```bash
root@45c5df8b6635:~/MAESTRO# cd ~/MAESTRO/Project/SingleCell/scATAC/Analysis/
root@45c5df8b6635:~/MAESTRO/Project/SingleCell/scATAC/Analysis# MAESTRO scatac-init -d 10X_PBMC_1k_MAESTRO_V110_docker \
root@c561fe9a9410:~# source activate MAESTRO
(MAESTRO) root@c561fe9a9410:~# cd ~/MAESTRO/Project/SingleCell/scATAC/Analysis/
(MAESTRO) root@c561fe9a9410:~/MAESTRO/Project/SingleCell/scATAC/Analysis# MAESTRO scatac-init -d 10X_PBMC_1k_MAESTRO_V121_docker \
--fastq-dir /root/MAESTRO/Project/SingleCell/scATAC/Analysis/10X_PBMC_1k/Data/atac_pbmc_1k_v1_fastqs --fastq-prefix atac_pbmc_1k_v1 \
--outprefix 10X_PBMC_1k_MAESTRO_V110 \
--outprefix 10X_PBMC_1k_MAESTRO \
--whitelist /root/MAESTRO/Tool/cellranger-atac-1.1.0/cellranger-atac-cs/1.1.0/lib/python/barcodes/737K-cratac-v1.txt \
--giggleannotation /root/MAESTRO/Project/SingleCell/scATAC/Code/MAESTRO_V110/MAESTRO/annotations/giggle \
--fasta /root/MAESTRO/annotations/MAESTRO/Refdata_scATAC_MAESTRO_GRCh38_1.1.0/GRCh38_genome.fa
root@45c5df8b6635:~/MAESTRO/Project/SingleCell/scATAC/Analysis# cd 10X_PBMC_1k_MAESTRO_V110_docker
root@45c5df8b6635:~/MAESTRO/Project/SingleCell/scATAC/Analysis# ls
--giggleannotation /root/MAESTRO/annotations/MAESTRO/giggle.all \
--fasta /root/MAESTRO/annotations/MAESTRO/Refdata_scATAC_MAESTRO_GRCh38_1.1.0/GRCh38_genome.fa \
--annotation --method RP-based --signature human.immune.CIBERSORT --clusterpeak --rpmodel Enhanced
(MAESTRO) root@c561fe9a9410:~/MAESTRO/Project/SingleCell/scATAC/Analysis# cd 10X_PBMC_1k_MAESTRO_V121_docker
(MAESTRO) root@c561fe9a9410:~/MAESTRO/Project/SingleCell/scATAC/Analysis/10X_PBMC_1k_MAESTRO_V121_docker# ls
Snakefile config.yaml
```

Once configured, users can use snakemake to run the workflow as they do in their local system.

```bash
root@45c5df8b6635:~/MAESTRO/Project/SingleCell/scATAC/Analysis/10X_PBMC_1k_MAESTRO_V110_docker# snakemake -np
(MAESTRO) root@c561fe9a9410:~/MAESTRO/Project/SingleCell/scATAC/Analysis/10X_PBMC_1k_MAESTRO_V121_docker# snakemake -np
Building DAG of jobs...
Job counts:
count jobs
1 all
1 scatac_allpeakcall
1 scatac_analysis
1 scatac_bamaddCB
1 scatac_bamcluster
1 scatac_bamindex
1 scatac_barcodecorrect
1 scatac_countpeak
1 scatac_fqaddbarcode
1 scatac_fragmentcorrect
1 scatac_fragmentgenerate
1 scatac_fragmentindex
1 scatac_genescore
1 scatac_map
1 scatac_mergepeak
1 scatac_preprocess
1 scatac_qcfilter
1 scatac_qcplot
1 scatac_qcstat_bulk
Expand All @@ -91,17 +100,16 @@ Job counts:
1 scatac_qcstat_singlecell
1 scatac_report
1 scatac_rmdp
18

24
...
...
...

This was a dry-run (flag -n). The order of jobs does not reflect the order of execution.
root@45c5df8b6635:~/MAESTRO/Project/SingleCell/scATAC/Analysis/10X_PBMC_1k_MAESTRO_V110_docker# nohup snakemake --cores 10 > 10X_PBMC_1k_MAESTRO_V110_docker.out &
(MAESTRO) root@c561fe9a9410:~/MAESTRO/Project/SingleCell/scATAC/Analysis/10X_PBMC_1k_MAESTRO_V121_docker# nohup snakemake --cores 10 > 10X_PBMC_1k_MAESTRO_V121_docker.out &
```

## Built with
* Ubuntu 18.04 docker image
* miniconda3
* R 3.6.2
* R 4.0.2