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https://github.com/stolarczyk/saarpipeline
Origin mechanisms of SAARs – use case of L-SAARs in signal peptides among higher Eukaryotes
https://github.com/stolarczyk/saarpipeline
evolution l-saars low-complexity-regions perl signal-peptides snakemake-workflows
Last synced: about 1 month ago
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Origin mechanisms of SAARs – use case of L-SAARs in signal peptides among higher Eukaryotes
- Host: GitHub
- URL: https://github.com/stolarczyk/saarpipeline
- Owner: stolarczyk
- Created: 2018-02-13T02:06:45.000Z (almost 7 years ago)
- Default Branch: master
- Last Pushed: 2018-11-10T18:21:53.000Z (about 6 years ago)
- Last Synced: 2024-11-06T08:47:00.581Z (3 months ago)
- Topics: evolution, l-saars, low-complexity-regions, perl, signal-peptides, snakemake-workflows
- Language: R
- Homepage:
- Size: 141 MB
- Stars: 0
- Watchers: 0
- Forks: 0
- Open Issues: 4
-
Metadata Files:
- Readme: README.md
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README
# Single amino acid repeats (SAAR) evolutionary analysis pipeline
This repository consists of a suite of R and Perl scripts performing the evolutionary SAAR analysis. The workflow is automatized and maintained by [Snakemake](https://snakemake.readthedocs.io/en/stable/) software.
For the convenience of the portability and ease of use it is also distributed as a [Docker](https://www.docker.com/) container, which can be accessed at [DockerHub repository](https://hub.docker.com/r/mstolarczyk/saarpipeline/).
## Usage
**1. Install the Docker software**
The Docker installation guide can be found [here](https://docs.docker.com/install/)
**2. Downolad the container with the pipeline setup and all dependencies installed**
`(sudo) docker pull mstolarczyk/saarpipeline`
**3. Make sure the image is available**
`(sudo) docker images`
The line above should output similar to the one presented below
```
REPOSITORY TAG IMAGE ID CREATED SIZE
mstolarczyk/saarpipeline latest 1142d796e7ad 3 minutes ago 6.27GB
```
**4. Run the image**
`(sudo) docker run -it mstolarczyk/saarpipeline `
**5. Perform the analysis**
The commands that will run the analysis are `Snakemake` commands:
`snakemake `
To test the part of workflow to be executed run
`snakemake -np `
The line above will show the execution plan instead of actually perform the steps. The `-p` flag instructs Snakemake to also print the resulting shell command for illustration
_More details regarding the usage will be provided soon_
After completion of the analysis exit the container
`exit`
**6. Save the docker container state and copy the results**
In order to pick up when you have left save the state of the container
`(sudo) docker commit `
e.g. `sudo docker commit 1bf3b5f36b94 mstolarczyk/saarpipeline_changed`
`(sudo)`
To copy the results of the analysis use the Docker `docker cp` command, for more details see the [website](https://docs.docker.com/engine/reference/commandline/cp/#description)
```
docker cp [OPTIONS] CONTAINER:SRC_PATH DEST_PATH|-
docker cp [OPTIONS] SRC_PATH|- CONTAINER:DEST_PATH
```