... | ... | @@ -17,18 +17,18 @@ conda config --add channels conda-forge ? |
|
|
|
|
|
**Create conda environment and export it in .yml file**
|
|
|
```
|
|
|
conda create -n env_pipeline_diamond -c conda-forge -c bioconda cutadapt sickle-trim bwa samtools bedtools spades megahit kaiju cd-hit krona subread fastqc prokka bcbio-gff multiqc diamond
|
|
|
conda create -n env_pipeline_diamond_pandas -c conda-forge -c bioconda cutadapt sickle-trim bwa samtools bedtools spades megahit kaiju cd-hit krona subread fastqc prokka bcbio-gff multiqc diamond pandas
|
|
|
|
|
|
conda activate env_pipeline_diamond
|
|
|
conda activate env_pipeline_diamond_pandas
|
|
|
|
|
|
conda deactivate
|
|
|
|
|
|
conda env export -n env_pipeline_diamond > env_pipeline_diamond.yml
|
|
|
conda env export -n env_pipeline_diamond_pandas > env_pipeline_diamond_pandas.yml
|
|
|
```
|
|
|
|
|
|
**Create Singularity recipe**
|
|
|
|
|
|
In Singularity_recipe_env_pipeline_diamond file write:
|
|
|
In Singularity_recipe_env_pipeline_diamond_pandas file write:
|
|
|
|
|
|
```
|
|
|
Bootstrap: docker
|
... | ... | @@ -36,14 +36,14 @@ From: continuumio/miniconda3 |
|
|
IncludeCmd: yes
|
|
|
|
|
|
%files
|
|
|
env_pipeline_diamond.yml /
|
|
|
env_pipeline_diamond_pandas.yml /
|
|
|
|
|
|
%post
|
|
|
apt-get update && apt-get install -y procps && apt-get clean -y
|
|
|
/opt/conda/bin/conda env create -f /env_pipeline_diamond.yml && /opt/conda/bin/conda clean -a
|
|
|
/opt/conda/bin/conda env create -f /env_pipeline_diamond_pandas.yml && /opt/conda/bin/conda clean -a
|
|
|
|
|
|
%environment
|
|
|
export PATH=/opt/conda/envs/env_pipeline_diamond/bin:$PATH
|
|
|
export PATH=/opt/conda/envs/env_pipeline_diamond_pandas/bin:$PATH
|
|
|
|
|
|
%runscript
|
|
|
"$@"
|
... | ... | @@ -51,6 +51,6 @@ export PATH=/opt/conda/envs/env_pipeline_diamond/bin:$PATH |
|
|
|
|
|
**Build Singularity container**
|
|
|
```
|
|
|
sudo singularity build Singularity_container_diamond.img Singularity_recipe_env_pipeline_diamond
|
|
|
sudo singularity build Singularity_container_diamond_pandas.img Singularity_recipe_env_pipeline_diamond_pandas
|
|
|
```
|
|
|
|