@@ -47,16 +47,19 @@ Use the following command to run the docker image:
```
$ docker run
-v `pwd`/data/modules:/modules
-v `pwd`/data/fasta:/biorseo/data/fasta
-v `pwd`/BayesPairing/bayespairing:/byp
-v `pwd`/results:/biorseo/results
biorseo
persalteas/biorseo
yourexamplejobcommandhere
```
You can replace \`pwd\` by the full path of the biorseo/ root folder. Here we launch the biorseo image with 3 volumes : A first to give BiORSEO access to the module files, a second to give it access to your trained BayesPairing, and a third for it to output the result files of your job. An example job command can be ` ./biorseo.py -i /biorseo/data/fasta/applications.fa --rna3dmotifs --patternmatch --func B`, so the full run command would be
You can replace \`pwd\` by the full path of the biorseo/ root folder. Here we launch the biorseo image with 4 volumes : A first to give BiORSEO access to the module files, a second to give it access to your input file(s), a third for your trained BayesPairing, and a last for it to output the result files of your job. An example job command can be ` ./biorseo.py -i /biorseo/data/fasta/applications.fa --rna3dmotifs --patternmatch --func B`, so the full run command would be
```
$ docker run -v `pwd`/data/modules:/modules -v `pwd`/BayesPairing/bayespairing:/byp -v `pwd`/results:/biorseo/results biorseo ./biorseo.py -i /biorseo/data/fasta/applications.fa --rna3dmotifs --patternmatch --func B
$ docker run -v `pwd`/data/modules:/modules -v `pwd`/data/fasta:/biorseo/data/fasta -v `pwd`/BayesPairing/bayespairing:/byp -v `pwd`/results:/biorseo/results persalteas/biorseo ./biorseo.py -i /biorseo/data/fasta/applications.fa --rna3dmotifs --patternmatch --func B
```
Note that the paths to the input and output files are paths *inside the Docker container*, and those paths are mounted to folders of the host machine with -v options.
Option 2 : Compile and Install from source (without docker, Linux only)
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@@ -139,7 +142,7 @@ This is a quite long step, but the bayesian networks will be ready for all the f
Now you can run biorseo.py, but, as you are not into the Docker environment, you MUST provide the options to tell it the jar3d or BayesPairing locations, for example: