# HG changeset patch
# User Lance Parsons <lparsons@princeton.edu>
# Date 1314211529 14400
# Node ID 3112c78841c5d3d409a95967e779cb485260a71d
# Parent  b8525303b945b00f861db283b91a7c53919c2f12
Another attempt to organize files to appease Galaxy Tools Shed

diff -r b8525303b945 -r 3112c78841c5 sam_fa_indices.loc.sample
--- a/sam_fa_indices.loc.sample	Wed Aug 24 14:43:09 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,28 +0,0 @@
-#This is a sample file distributed with Galaxy that enables tools
-#to use a directory of Samtools indexed sequences data files.  You will need
-#to create these data files and then create a sam_fa_indices.loc file 
-#similar to this one (store it in this directory) that points to 
-#the directories in which those files are stored. The sam_fa_indices.loc 
-#file has this format (white space characters are TAB characters):
-#
-#index	<seq>	<location>
-#
-#So, for example, if you had hg18 indexed stored in 
-#/depot/data2/galaxy/sam/, 
-#then the sam_fa_indices.loc entry would look like this:
-#
-#index	hg18	/depot/data2/galaxy/sam/hg18.fa
-#
-#and your /depot/data2/galaxy/sam/ directory
-#would contain hg18.fa and hg18.fa.fai files:
-#
-#-rw-r--r--  1 james    universe 830134 2005-09-13 10:12 hg18.fa
-#-rw-r--r--  1 james    universe 527388 2005-09-13 10:12 hg18.fa.fai
-#
-#Your sam_fa_indices.loc file should include an entry per line for 
-#each index set you have stored.  The file in the path does actually
-#exist, but it should never be directly used. Instead, the name serves
-#as a prefix for the index file.  For example:
-#
-#index	hg18	/depot/data2/galaxy/sam/hg18.fa
-#index	hg19	/depot/data2/galaxy/sam/hg19.fa
diff -r b8525303b945 -r 3112c78841c5 tool-data/sam_fa_indices.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/sam_fa_indices.loc.sample	Wed Aug 24 14:45:29 2011 -0400
@@ -0,0 +1,28 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of Samtools indexed sequences data files.  You will need
+#to create these data files and then create a sam_fa_indices.loc file 
+#similar to this one (store it in this directory) that points to 
+#the directories in which those files are stored. The sam_fa_indices.loc 
+#file has this format (white space characters are TAB characters):
+#
+#index	<seq>	<location>
+#
+#So, for example, if you had hg18 indexed stored in 
+#/depot/data2/galaxy/sam/, 
+#then the sam_fa_indices.loc entry would look like this:
+#
+#index	hg18	/depot/data2/galaxy/sam/hg18.fa
+#
+#and your /depot/data2/galaxy/sam/ directory
+#would contain hg18.fa and hg18.fa.fai files:
+#
+#-rw-r--r--  1 james    universe 830134 2005-09-13 10:12 hg18.fa
+#-rw-r--r--  1 james    universe 527388 2005-09-13 10:12 hg18.fa.fai
+#
+#Your sam_fa_indices.loc file should include an entry per line for 
+#each index set you have stored.  The file in the path does actually
+#exist, but it should never be directly used. Instead, the name serves
+#as a prefix for the index file.  For example:
+#
+#index	hg18	/depot/data2/galaxy/sam/hg18.fa
+#index	hg19	/depot/data2/galaxy/sam/hg19.fa