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Instructions for overriding config files in the conda env. #7

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Instructions for overriding config files in the conda env. #7

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33 changes: 33 additions & 0 deletions README.md
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# Atlas in house perl modules

Repository includes internal perl modules that is used for processing studies in atlas data production pipeline particularly handling MAGE-TABs, baseline and differential analysis, zooma mappings, release data exports.

# Changing config files for local setup

Execution of certain scripts when using the conda installation might fail because certain configuration files won't be found. Currently the main work-around for this (sorry, yes, this is a work-around) is to replace the AtlasSiteConfig.yaml and ArrayExpressSiteConfig.yaml for files that point to the necessary content in the machine where this runs. For this, follow these steps (which assume that a conda environment with perl-atlas-modules is installed):

1.- Find the path to your conda env that contains perl-atlas-modules:

```
PERL_ATLAS_ENV=$(conda env list | grep perl-atlas | awk '{ print $2 }')
echo $PERL_ATLAS_ENV
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This command didn't work. It assumes that the conda env is called "perl-atlas", right? But mine is called "atlas_curation". I had to set up the PERL_ATLAS_ENV variable manually to proceed.

```

2.- Copy the AtlasSite and ArrayExpressSite config files to a safe editable location

```
mkdir ~/atlas-config
cp $PERL_ATLAS_ENV/atlasprod/supporting_files/ArrayExpressSiteConfig.yml ~/atlas-config/
cp $PERL_ATLAS_ENV/atlasprod/supporting_files/AtlasSiteConfig.yml ~/atlas-config/
```

3.- Replace contents on `atlasprod/supporting_files/` with links to the copied files

```
cd $PERL_ATLAS_ENV/atlasprod/supporting_files
rm ArrayExpressSiteConfig.yml && ln -s ~/atlas-config/ArrayExpressSiteConfig.yml ArrayExpressSiteConfig.yml
rm AtlasSiteConfig.yml && ln -s ~/atlas-config/AtlasSiteConfig.yml AtlasSiteConfig.yml
```

4.- Edit files in `~/atlas-config/` to reflect local setup.

These links (step 3) will be deleted if the conda package is re-installed in the same environment. We will provide a better way of dealing with this soon.