--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README	Tue Mar 20 21:54:35 2018 -0400
@@ -0,0 +1,57 @@
+Galaxy wrappers for the Mothur metagenomics tools (http://www.mothur.org/wiki/Main_Page)
+
+The Mothur Tool Suite repository:
+	- Provides Mothur wrappers for the Mothur tools
+	- Downloads and builds Mothur and all its dependencies on the Linux or Mac operating system
+
+Installing Tools via the API:
+This is a rather large tool suite, if you are having problems installing via the toolshed, try using the API instead
+    - Install ephemeris: pip install ephemeris -U
+    - Use ephemeris to install tools: shed_install -a <your admin API key> -t tools.yaml
+    - (You can find a tools.yaml you can use in this repo as well)
+
+Installing reference data from silva and greengenes:
+    - There is a Galaxy datamanager for available for Mothur
+
+ RDP reference file (modified for mothur):
+  http://www.mothur.org/wiki/RDP_reference_files
+   - 16S rRNA reference (RDP): A collection of 9,662 bacterial and 384 archaeal 16S rRNA gene sequences with an improved taxonomy compared to version 6.
+     http://www.mothur.org/w/images/2/29/Trainset7_112011.rdp.zip
+   - 16S rRNA reference (PDS): The RDP reference with three sequences reversed and 119 mitochondrial 16S rRNA gene sequences added as members of the Rickettsiales
+     http://www.mothur.org/w/images/4/4a/Trainset7_112011.pds.zip
+   - 28S rRNA reference (RDP): A collection of 8506 reference 28S rRNA gene sequences from the Fungi that were curated by the Kuske lab
+     http://www.mothur.org/w/images/3/36/FungiLSU_train_v7.zip
+ Silva reference:
+  http://www.mothur.org/wiki/Silva_reference_files
+  - Bacterial references (14,956 sequences)
+    http://www.mothur.org/w/images/9/98/Silva.bacteria.zip
+  - Archaeal references (2,297 sequences)
+    http://www.mothur.org/w/images/3/3c/Silva.archaea.zip
+  - Eukaryotic references (1,238 sequences)
+    http://www.mothur.org/w/images/1/1a/Silva.eukarya.zip
+  - Silva-based alignment of template file for chimera.slayer (5,181 sequences)
+    http://www.mothur.org/w/images/f/f1/Silva.gold.bacteria.zip
+ Alignment database rRNA gene sequences:
+  http://www.mothur.org/wiki/Alignment_database
+  - greengenes reference alignment
+    http://www.mothur.org/w/images/7/72/Greengenes.alignment.zip
+  - SILVA (Silva reference)
+    http://www.mothur.org/w/images/f/f1/Silva.gold.bacteria.zip
+ Secondary structure mapping files:
+  http://www.mothur.org/wiki/Secondary_structure_map
+    http://www.mothur.org/w/images/6/6d/Silva_ss_map.zip
+    http://www.mothur.org/w/images/4/4b/Gg_ss_map.zip
+ Lane masks:
+  http://www.mothur.org/wiki/Lane_mask
+  greengenes-compatible mask:
+     - lane1241.gg.filter - A Lane Masks that comes with the greengenes arb database
+       http://www.mothur.org/w/images/2/2a/Lane1241.gg.filter
+     - lane1287.gg.filter - A Lane Masks that comes with the greengenes arb database
+       http://www.mothur.org/w/images/a/a0/Lane1287.gg.filter
+     - lane1349.gg.filter - Pat Schloss's transcription of the mask from the Lane paper
+       http://www.mothur.org/w/images/3/3d/Lane1349.gg.filter
+  SILVA-compatible mask:
+     - lane1349.silva.filter - Pat Schloss's transcription of the mask from the Lane paper
+       http://www.mothur.org/w/images/6/6d/Lane1349.silva.filter
+ Lookup Files for sff flow analysis using shhh.flows:
+  http://www.mothur.org/wiki/Alignment_database