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Organize repo and split off pipelines to its own directory.

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1 parent 9263f38 commit 5ea071a5a8276ae42456b7181d4f8ff94a653b6d @trvrb trvrb committed Jan 7, 2017
Showing with 67 additions and 63 deletions.
  1. +8 −63 README.md
  2. 0 data-schema.md → data/README.md
  3. +59 −0 pipelines/README.md
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# Experimental protocols and bioinformatic pipelines for Zika genome sequencing
-#### Allison Black<sup>1,2</sup>, Barney Potter<sup>2</sup>, Nicholas J. Loman<sup>3</sup>, Trevor Bedford<sup>2</sup>
+#### Allison Black<sup>1,2</sup>, Barney Potter<sup>2</sup>, Josh Quick<sup>3</sup>, Nicholas J. Loman<sup>3</sup>, Nathan D Grubaugh<sup>4</sup>, Kristian G Andersen<sup>4</sup>, Trevor Bedford<sup>2</sup>
-<sup>1</sup>Department of Epidemiology, University of Washington, Seattle, WA, USA, <sup>2</sup>Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA, <sup>3</sup>Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
+<sup>1</sup>Department of Epidemiology, University of Washington, Seattle, WA, USA, <sup>2</sup>Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA, <sup>3</sup>Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, UK, <sup>4</sup>The Scripps Research Institute, La Jolla, CA, USA.
-## Data sync
-
-Primary sequencing data lives on the Rhino FHCRC cluster at:
-
- /fh/fast/bedford_t/zika-seq/data/
-
-And locally on the Meristem drive at:
-
- /Volumes/Meristem/data/
-
-To sync Meristem to Rhino, run:
-
- rsync -azP <username>@rhino.fhcrc.org:/fh/fast/bedford_t/zika-seq/data/ /Volumes/Meristem/data/
-
-Replacing `<username>` with your username. This `data/` directory is assumed to follow [a particular schema](data-schema.md).
-
-## Bioinformatic pipeline
-
-Here, we use the ZiBRA project bioinformatic pipeline at [zibraproject/zika-pipeline](https://github.com/zibraproject/zika-pipeline/). This pipeline is instantiated in the Docker image [zibra/zibra](https://hub.docker.com/r/zibra/zibra/). Data processing is done entirely using Docker.
-
-### Data volume
-
-Create a named data volume that mirrors local `data/` to `data/` within container:
-
- docker create --name zibra-data -v /Volumes/Meristem/data:/data zibra/zibra
-
-This is to get data into the Docker container. Note that the path to local directory has to be an absolute path.
-
-### Samples volume
-
-Create a named data volume that mirrors local sample metadata `samples/` to `samples/` within container:
-
- docker create --name zibra-samples -v /Volumes/Meristem/samples:/samples zibra/zibra
-
-This is to get sample metadata into the Docker container. Note that the path to local directory has to be an absolute path. [Notes on metadata schema are here](samples/).
-
-### Build volume
-
-Create a named data volume that mirrors local `build/` to `build/` within container:
-
- docker create --name zibra-build -v /Volumes/Meristem/build:/build zibra/zibra
-
-This is to get data out of the Docker container. Note that the path to local directory has to be an absolute path.
-
-### Start
-
-Enter docker image:
-
- docker run -t -i --volumes-from zibra-data --volumes-from zibra-samples --volumes-from zibra-build zibra/zibra /bin/bash
-
-Run script:
-
- python scripts/pipeline.py
-
-## Validation
-
- * [Initial coverage results](depth-coverage/)
-
-## Consensus genomes
-
- * [Consensus genomes](consensus-genomes/)
+* [Data schema](data/)
+* [Sample metadata](samples/)
+* [Experimental protocols](protocols/)
+* [Bioinformatic pipelines](pipelines/)
+* [Validation and coverage](depth-coverage/)
+* [Consensus genomes](consensus-genomes/)
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+# Pipelines for Zika sequencing
+
+#### Trevor Bedford<sup>1</sup>
+
+<sup>1</sup>Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
+
+## Data sync
+
+Primary sequencing data lives on the Rhino FHCRC cluster at:
+
+ /fh/fast/bedford_t/zika-seq/data/
+
+And locally on the Meristem drive at:
+
+ /Volumes/Meristem/data/
+
+To sync Meristem to Rhino, run:
+
+ rsync -azP <username>@rhino.fhcrc.org:/fh/fast/bedford_t/zika-seq/data/ /Volumes/Meristem/data/
+
+Replacing `<username>` with your username. This `data/` directory is assumed to follow [a particular schema](../data/).
+
+## Bioinformatic pipeline
+
+Here, we use the ZiBRA project bioinformatic pipeline at [zibraproject/zika-pipeline](https://github.com/zibraproject/zika-pipeline/). This pipeline is instantiated in the Docker image [zibra/zibra](https://hub.docker.com/r/zibra/zibra/). Data processing is done entirely using Docker.
+
+### Data volume
+
+Create a named data volume that mirrors local `data/` to `data/` within container:
+
+ docker create --name zibra-data -v /Volumes/Meristem/data:/data zibra/zibra
+
+This is to get data into the Docker container. Note that the path to local directory has to be an absolute path. [Notes on data schema are here](../data/).
+
+### Samples volume
+
+Create a named data volume that mirrors local sample metadata `samples/` to `samples/` within container:
+
+ docker create --name zibra-samples -v /Volumes/Meristem/samples:/samples zibra/zibra
+
+This is to get sample metadata into the Docker container. Note that the path to local directory has to be an absolute path. [Notes on metadata schema are here](../samples/).
+
+### Build volume
+
+Create a named data volume that mirrors local `build/` to `build/` within container:
+
+ docker create --name zibra-build -v /Volumes/Meristem/build:/build zibra/zibra
+
+This is to get data out of the Docker container. Note that the path to local directory has to be an absolute path.
+
+### Start
+
+Enter docker image:
+
+ docker run -t -i --volumes-from zibra-data --volumes-from zibra-samples --volumes-from zibra-build zibra/zibra /bin/bash
+
+Run script:
+
+ python scripts/pipeline.py

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