<commit_before>![](https://github.com/NCBI-Hackathons/RNA_mapping/blob/master/images/RNAmappermatchup.png)

* Do you want to learn how to align RNA-sequences to a reference genome? 

* Do you want to bypass the process of installing alignment software and get a preview into a panel of different alignment strategies?

* Do you want to compare how popular mapping algorithms perform on your data?

#### Then this is the tutorial for you!  [Please proceed to our wiki](https://github.com/NCBI-Hackathons/RNA_mapping/wiki)

#### *Just interested in comparing two or more .bam files?  Check out [bamdiff](https://github.com/NCBI-Hackathons/RNA_mapping/tree/master/build/bamdiff)*

#### Docker
A Docker image is available for this project.  For a detailed description of docker, please refer to this [overview.](https://www.docker.com/what-docker)

##### Install Docker
Follow [instructions](https://www.docker.com/docker-mac) to install Docker for your environment.

##### Get a pre-built image from DockerHub and run the server
```
docker pull stevetsa/rna_mapping
docker run -it stevetsa/rna_mapping

At the root prompt inside the container - 
/RNA_mapping/build/doAll.sh
```<commit_msg>added singularity description<commit_after>![](https://github.com/NCBI-Hackathons/RNA_mapping/blob/master/images/RNAmappermatchup.png)

* Do you want to learn how to align RNA-sequences to a reference genome? 

* Do you want to bypass the process of installing alignment software and get a preview into a panel of different alignment strategies?

* Do you want to compare how popular mapping algorithms perform on your data?

#### Then this is the tutorial for you!  [Please proceed to our wiki](https://github.com/NCBI-Hackathons/RNA_mapping/wiki)

#### *Just interested in comparing two or more .bam files?  Check out [bamdiff](https://github.com/NCBI-Hackathons/RNA_mapping/tree/master/build/bamdiff)*

#### Docker
A Docker image is available for this project.  For a detailed description of docker, please refer to this [overview.](https://www.docker.com/what-docker)

##### Install Docker
Follow [instructions](https://www.docker.com/docker-mac) to install Docker for your environment.

##### Get a pre-built image from DockerHub and run the server
```
docker pull stevetsa/rna_mapping
docker run -it stevetsa/rna_mapping

At the root prompt inside the container, execute the script - 
/RNA_mapping/build/doAll.sh
```
#### Singularity
Run this image on the NIH biowulf cluster

```
sinteractive --cpus-per-task=16 --mem=10g
singularity shell docker://stevetsa/rna_mapping
 
inside Singularity container, execute the script - 
/RNA_mapping/build/doAll.sh

```
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{'dir': 'git-commits-cleaned', 'id': '845547', 'n_tokens_mistral': 831, 'n_tokens_neox': 756, 'n_words': 283}