Commit 7b59c0fc authored by mirachirkova's avatar mirachirkova
Browse files

fix Dockerfile

parent daea506c
FROM docker.io/bioconductor/bioconductor_docker:RELEASE_3_13
COPY install.R .
RUN Rscript install.R
COPY source/ .
COPY hobotnica/ .
COPY run.R .
RUN mkdir source
COPY source/ /source
RUN mkdir hobotnica
COPY hobotnica/ /hobotnica
RUN mkdir data
RUN Rscript install.R
#RUN cd hobotnica && R CMD INSTALL --no-multiarch --with-keep.source .
......@@ -69,14 +69,41 @@ subsets. File name is **'venn_diagram.pdf'**.
Quick start
------------
Type in command line this two commands:
Download repository and change to the directory where this repository
is stored. There are to ways to run program.
- **From your computer**
>**Rscript install.R**
Type in command line this commands:
> **$ Rscript install.R**
>
> **Rscript run.R countmatrix annotation**
> **$ Rscript run.R countmatrix annotation**
Where **countmatrix** is matrix of un-normalized counts file name and
**annotation** is table of annotation file name
**annotation** is table of annotation file name.
- **From Docker**
Create an image **diffexprimage** and start container **de_container**
(it automatically uses Dockerfile from repository):
> **$ docker build -t diffexprimage .**
>
> **$ docker run --name de_container diffexprimage echo "hello from docker"**
>
Copy your input data to container. **countmatrix.txt** is matrix of un-normalized counts file name and
**annotation.txt** is table of annotation file name.
>
> **$ docker cp countmatrix.txt de_container:data/countmatrix.txt**
>
> **$ docker cp annotation.txt de_container:data/annotation.txt**
>
Start work in container.
> **$ docker start de_container**
>
> **$ docker exec -it de_container /bin/bash**
>
Start work with program from Docker container.
> **/# Rscript run.R data/countmatrix.txt data/annotation.txt**
-------------------------------------
......@@ -187,8 +214,7 @@ Current problems
----------------
- A lot of unuseful information in output.
- ***filtered_signature*** signature is unrepresentative. Perhaps every
tool has their own sensitiveness for logFC, p-value etc.
- Dockerfile need to be updated
tool has their own sensitiveness for logFC, p-value etc.
......
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