https://github.com/bartoszbartmanski/singularitycarnival
Repository for CARNIVAL singularity images based on Ubuntu 20.04.
https://github.com/bartoszbartmanski/singularitycarnival
singularity-container
Last synced: about 1 month ago
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Repository for CARNIVAL singularity images based on Ubuntu 20.04.
- Host: GitHub
- URL: https://github.com/bartoszbartmanski/singularitycarnival
- Owner: BartoszBartmanski
- License: gpl-3.0
- Created: 2021-08-08T10:13:12.000Z (almost 5 years ago)
- Default Branch: main
- Last Pushed: 2021-10-12T14:19:12.000Z (over 4 years ago)
- Last Synced: 2025-12-26T09:14:51.544Z (6 months ago)
- Topics: singularity-container
- Language: R
- Homepage:
- Size: 31.3 KB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# SingularityCARNIVAL
Repository for [CARNIVAL](https://github.com/saezlab/CARNIVAL/)
singularity images based on Ubuntu 20.04.
## Download
To download an image from sylabs library:
```
singularity pull library://bartosz_bartmanski/default/carnival:
```
For example:
```
singularity pull library://bartosz_bartmanski/default/carnival:2.2.0
```
## Usage
To run the example script that uses lpSolve contained in `/example/` directory
within the container, execute the following:
```
./carnival_2.2.0.sif
```
which will produce `example_output.Rds` amongst other intermediate files.
To use [CPLEX](https://www.ibm.com/analytics/cplex-optimizer) ILP solver
```
singularity exec -B :,./:/data/ carnival_2.2.0.sif /example/other_solvers.R cplex /cplex /data/cplex_example.Rds
```
where `` is the cplex installation path e.g.
`/opt/ibm/ILOG/CPLEX_Studio201/cplex/bin/x86-64_linux/`.
To use [Gurobi](https://www.gurobi.com/) ILP solver:
```
singularity exec -B :,./:/data/ --env "LD_LIBRARY_PATH=/linux64/lib" carnival_2.2.0.sif /example/other_solvers.R gurobi /linux64/bin/gurobi_cl /data/gurobi_example.Rds
```
where `` is the gurobi installation path e.g.
`/opt/gurobi911/`
## Build
To create a new image:
```
sudo singularity build carnival_.sif carnival.def
```
For example:
```
sudo singularity build carnival_2.2.0.sif carnival.def
```