diff mothur/README @ 24:09740be2bc9c

Mothur - updates for Mothur version 1.24

--- a/mothur/README	Thu Jan 19 11:27:37 2012 -0600
+++ b/mothur/README	Wed Mar 28 15:45:03 2012 -0500
@@ -2,8 +2,8 @@
 
 (The environment variable MOTHUR_MAX_PROCESSORS can be used to limit the number of cpu processors used be mothur commands)
 
-Install mothur v.1.22.0 on your galaxy system so galaxy can execute the mothur command
-  ( This version of wrappers is designed for Mothur version 1.22 - it may work on later versions )
+Install mothur v.1.24.1 on your galaxy system so galaxy can execute the mothur command
+  ( This version of wrappers is designed for Mothur version 1.24 - it may work on later versions )
   http://www.mothur.org/wiki/Download_mothur
   http://www.mothur.org/wiki/Installation
   ( This Galaxy Mothur wrapper will invoke Mothur in command line mode: http://www.mothur.org/wiki/Command_line_mode )
@@ -15,6 +15,14 @@
   Install in galaxy:  tool-data/shared/jars/TreeVector.jar
 
 Install reference data from silva and greengenes
+ 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)
@@ -79,11 +87,19 @@
     /project/db/galaxy/mothur/Silva.eukarya.zip
     /project/db/galaxy/mothur/Gg_ss_map.zip
     /project/db/galaxy/mothur/core_set_aligned.imputed.fasta
+    /project/db/galaxy/mothur/RDP/FungiLSU_train_1400bp_8506_mod.fasta
+    /project/db/galaxy/mothur/RDP/FungiLSU_train_1400bp_8506_mod.tax
+    /project/db/galaxy/mothur/RDP/trainset6_032010.rdp.fasta
+    /project/db/galaxy/mothur/RDP/trainset6_032010.rdp.tax
+    /project/db/galaxy/mothur/RDP/trainset7_112011.pds.fasta
+    /project/db/galaxy/mothur/RDP/trainset7_112011.pds.tax
+    /project/db/galaxy/mothur/RDP/trainset7_112011.rdp.fasta
+    /project/db/galaxy/mothur/RDP/trainset7_112011.rdp.tax
 
 
-Add tool-data:  (contains  pointers to silva and greengenes reference data)
+
+Add tool-data:  (contains  pointers to silva, greengenes, and RDP reference data)
   tool-data/mothur_aligndb.loc
-  tool-data/mothur_calulators.loc
   tool-data/mothur_map.loc
   tool-data/mothur_taxonomy.loc
   tool-data/shared/jars/TreeVector.jar