--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bowtie_indices.loc.sample	Thu Nov 03 21:16:36 2011 -0400
@@ -0,0 +1,44 @@
+hg18	hg18	Human (Homo sapiens): hg18	/scratch/dongjun/galaxy/bowtie_indexes/hg18
+mm9	mm9	Mouse (Mus musculus): mm9	/p/keles/SOFTWARE/bowtie-0.12.5/indexes/mm9
+e_coli	eschColi_536	Escherichia coli (str. 536)	/p/keles/SOFTWARE/bowtie-0.12.5/indexes/e_coli
+e_coli_K12	eschColi_K12	Escherichia coli K12 (eschColi_K12)	/scratch/dongjun/galaxy/bowtie_indexes/e_coli_K12
+c_elegans_ws200	ce7	Caenorhabditis elegans (Feb 2009): WS200/ce7	/p/keles/SOFTWARE/bowtie-0.12.5/indexes/c_elegans_ws200	ce7
+a_thaliana	a_thaliana	Arabidopsis thaliana	/p/keles/SOFTWARE/bowtie-0.12.5/indexes/a_thaliana
+
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of Bowtie indexed sequences data files. You will
+#need to create these data files and then create a bowtie_indices.loc
+#file similar to this one (store it in this directory) that points to
+#the directories in which those files are stored. The bowtie_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 
+#/depot/data2/galaxy/bowtie/hg18/, 
+#then the bowtie_indices.loc entry would look like this:
+#
+#hg18   hg18   hg18   /depot/data2/galaxy/bowtie/hg18/hg18
+#
+#and your /depot/data2/galaxy/bowtie/hg18/ directory
+#would contain hg18.*.ebwt files:
+#
+#-rw-r--r--  1 james    universe 830134 2005-09-13 10:12 hg18.1.ebwt
+#-rw-r--r--  1 james    universe 527388 2005-09-13 10:12 hg18.2.ebwt
+#-rw-r--r--  1 james    universe 269808 2005-09-13 10:12 hg18.3.ebwt
+#...etc...
+#
+#Your bowtie_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   /depot/data2/galaxy/bowtie/hg18/hg18canon
+#hg18full           hg18   hg18 Full        /depot/data2/galaxy/bowtie/hg18/hg18full
+#/orig/path/hg19    hg19   hg19             /depot/data2/galaxy/bowtie/hg19/hg19
+#...etc...
+#
+#Note that for backwards compatibility with workflows, the unique ID of
+#an entry must be the path that was in the original loc file, because that
+#is the value stored in the workflow for that parameter. That is why the
+#hg19 entry above looks odd. New genomes can be better-looking.
+#