--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/segemehl_indices.loc.sample	Thu Oct 17 04:07:29 2013 -0400
@@ -0,0 +1,30 @@
+#This is a sample file that enables the segemehl mapper to find genome indices
+#and database files. You will need to create these data files and then create 
+#a segemehl_indices.loc file similar to this one (store it in this directory) 
+#that points to the directories in which those files are stored. 
+#The segemehl_indices.loc file has this format (longer white space characters are TAB characters):
+#
+#<unique_build_id>   <dbkey>   <display_name>   <file_base_path>
+#
+#So, for example, if you had hg18 indexed stored in 
+#/data/0/galaxy/segemehl/hg18/, 
+#then the segemehl_indices.loc entry would look like this:
+#
+#hg18   hg18   hg18   /data/0/galaxy/segemehl/hg18/chromosomes.fa   /data/0/galaxy/segemehl/hg18/chromosomes.idx
+#
+#and your /data/0/galaxy/segemehl/hg18/ directory
+#would contain hg18.*.ebwt files:
+#
+#-rw-r--r--  1 bag    bag 539833 2013-10-13 10:12 chromosomes.idx
+#-rw-r--r--  1 bag    bag 342562 2013-10-13 10:12 chromosomes.fa
+#...etc...
+#
+#Your segemehl_indices.loc file should include an entry per line for each
+#index set you have stored. The "file" in the path does not actually
+#exist, but it is the prefix for the actual index files. For example:
+#
+#hg18canon          hg18   hg18 Canonical   /data/0/galaxy/segemehl/hg18/chromosomes_can.fa   /data/0/galaxy/segemehl/hg18/chromosomes_can.idx
+#hg18full           hg18   hg18 Full        /data/0/galaxy/segemehl/hg18/chromosomes_full.fa   /data/0/galaxy/segemehl/hg18/chromosomes_full.idx
+#/orig/path/hg19    hg19   hg19             /data/0/galaxy/segemehl/hg19/chromosomes.fa   /data/0/galaxy/segemehl/hg19/chromosomes.idx
+#...etc...
+#