Update documentation and module list to include edirect - Githubissues

NAL-i5K / NAL_RNA_seq_annotation_pipeline

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Update documentation and module list to include edirect #51

Closed mpoelchau closed 2 years ago

mpoelchau commented 2 years ago

The documentation for edirect (also called entrez-direct) installation in the readme is confusing.

Add edirect to the prerequisites list: https://dataguide.nlm.nih.gov/edirect/install.html#edirect-installation
Add edirect to the 'module load' line in the example sbatch file: https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/blob/master/rnannot/sbatch.sh
In the 'Run on Ceres (by conda virtual environment)' section, remove the information on entrez-direct

Also - we may run into the same problem with pysam.