--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/eggnog_mapper.loc.sample	Tue Oct 31 14:17:50 2017 -0400
@@ -0,0 +1,30 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of eggnog_mapper data files. 
+#
+# eggnog-mapper requires the following files to be installed in the data directory:
+#  https://github.com/jhcepas/eggnog-mapper/blob/master/data/og2level.tsv.gz
+#  http://eggnogdb.embl.de/download/eggnog_4.5/eggnog-mapper-data/eggnog.db.gz
+#  http://eggnogdb.embl.de/download/eggnog_4.5/eggnog-mapper-data/OG_fasta.tar.gz
+# In addition individual HMM DBs can be installed from:
+#  http://eggnogdb.embl.de/download/eggnog_4.5/eggnog-mapper-data/hmmdb_levels/
+# A complete diamond database is available from:
+#  http://eggnogdb.embl.de/download/eggnog_4.5/eggnog-mapper-data/eggnog_proteins.dmnd.gz
+#
+# The python script download_eggnog_data.py, 
+# included with eggnog_mapper, can be used to download the files to the correct directory
+#
+# The near-equivalence of columns "value" and "db" is needed for the tests to work,
+# and for the setting of --data_dir to the parent directory of eggnog.db
+# The complicated eggNOG database structure makes passing custom HMM databases somewhat tricky. 
+# See test-data/cached_locally/eggnog_mapper.loc for how this was done with the included test databases
+# In all other cases, when the appropriate HMM database (for example, "thaNOG") was downloaded from eggnogdb.embl.de, 
+# value and db should be the same (in the example, both should be "thaNOG")
+#
+#
+#name	value	type	db	
+#eggnog_4.5	eggnog_4.5 data	/path/to/directory/that/contains/eggnog.db
+#Full eggNOG database	NOG	hmmer	NOG
+#Eukaryotes	euk	hmmer	euk
+#Bacteria	bact	hmmer	bact
+#Archaea	arch	hmmer	arch
+#dmnd	diamond	diamond	dmnd