diff --git a/README.md b/README.md index 44a22ef7..7596a84d 100644 --- a/README.md +++ b/README.md @@ -268,19 +268,32 @@ cd AlphaPulldownSnakemake >If you want to use the latest version from GitHub replace `--tag X.X.X` to `--branch main` **Install CCP4 package**: -To install the software needed for [the anaysis step](https://github.com/KosinskiLab/AlphaPulldown?tab=readme-ov-file#3-analysis-and-visualization), please follow these instructions: +To install the software needed for [the analysis step](https://github.com/KosinskiLab/AlphaPulldown?tab=readme-ov-file#3-analysis-and-visualization), please follow these instructions: +Download so-called Singularity image with our analysis software package ```bash singularity pull docker://kosinskilab/fold_analysis:latest singularity build --sandbox fold_analysis_latest.sif -# Download the top one from https://www.ccp4.ac.uk/download/#os=linux +``` + can be any temporary directory and can be deleted later. + +Download CCP4 from https://www.ccp4.ac.uk/download/#os=linux and copy to your server +```bash tar xvzf ccp4-9.0.003-linux64.tar.gz cd ccp4-9 cp bin/pisa bin/sc /software/ cp /lib/* /software/lib64/ -singularity build ``` +Create a new Singularity with CCP4 included +```bash +cd +singularity build fold_analysis_latest_withCCP4.sif +``` +It should create `fold_analysis_latest_withCCP4.sif` file. + +You can delete the now. + ## 2. Configuration Adjust `config/config.yaml` for your particular use case. @@ -288,7 +301,7 @@ Adjust `config/config.yaml` for your particular use case. If you want to use CCP4 for analysis, open `config/config.yaml` in a text editor and change the path to the analysis container to: ```yaml -analysis_container : "/path/to/new_image.sif" +analysis_container : "/path/to/fold_analysis_latest_withCCP4.sif" ``` **input_files**