diff --git a/tools/ebi_tools/download_ebi_metagenomics_run_data b/deprecated/tools/ebi_tools/download_ebi_metagenomics_run_data
similarity index 100%
rename from tools/ebi_tools/download_ebi_metagenomics_run_data
rename to deprecated/tools/ebi_tools/download_ebi_metagenomics_run_data
diff --git a/tools/ebi_tools/ebi_metagenomics_run_downloader.xml b/deprecated/tools/ebi_tools/ebi_metagenomics_run_downloader.xml
similarity index 100%
rename from tools/ebi_tools/ebi_metagenomics_run_downloader.xml
rename to deprecated/tools/ebi_tools/ebi_metagenomics_run_downloader.xml
diff --git a/tools/ebi_tools/test-data/ERR675640_qc-stats_stats b/deprecated/tools/ebi_tools/test-data/ERR675640_qc-stats_stats
similarity index 100%
rename from tools/ebi_tools/test-data/ERR675640_qc-stats_stats
rename to deprecated/tools/ebi_tools/test-data/ERR675640_qc-stats_stats