+
+
+
diff -r 000000000000 -r 7e9e8da0522d tool-data/bowtie2_indices.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/bowtie2_indices.loc.sample Thu Mar 09 09:31:57 2017 -0500
@@ -0,0 +1,37 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of Bowtie2 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 bowtie2_indices.loc
+#file has this format (longer white space characters are TAB characters):
+#
+#
+#
+#So, for example, if you had hg18 indexed stored in
+#/depot/data2/galaxy/bowtie2/hg18/,
+#then the bowtie2_indices.loc entry would look like this:
+#
+#hg18 hg18 hg18 /depot/data2/galaxy/bowtie2/hg18/hg18
+#
+#and your /depot/data2/galaxy/bowtie2/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 bowtie2_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/bowtie2/hg18/hg18canon
+#hg18full hg18 hg18 Full /depot/data2/galaxy/bowtie2/hg18/hg18full
+#/orig/path/hg19 hg19 hg19 /depot/data2/galaxy/bowtie2/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.
+#
diff -r 000000000000 -r 7e9e8da0522d tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Thu Mar 09 09:31:57 2017 -0500
@@ -0,0 +1,8 @@
+
+
+
+