--- a/bowtie_genome_wrapper/tool-data/bowtie_indices.loc.sample	Tue Mar 22 12:28:40 2022 +0000
+++ b/bowtie_genome_wrapper/tool-data/bowtie_indices.loc.sample	Tue Apr 05 12:51:03 2022 +0000
@@ -1,37 +1,9 @@
-#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.
-#
+homo_sapiens_hg19	hg19	Homo sapiens (hg19)	/data2/indices/bowtie/genome/homo_sapiens_hg19_genome
+homo_sapiens_hg38	hg38	Homo sapiens (hg38)	/data2/indices/bowtie/genome/homo_sapiens_hg38_genome
+mus_musculus_m28	m28	Mus musculus (m28)	/data2/indices/bowtie/genome/mus_musculus_m28/mus_musculus_m28_genome
+drosophila_melanogaster_dm3	dm3	Drosophila melanogaster (dm3)	/data2/indices/bowtie/genome/drosophila_melanogater_dm3_genome
+drosophila_melanogaster_dm6	dm6	Drosophila melanogaster (dm6)	/data2/indices/bowtie/genome/drosophila_melanogater_dm6_genome
+sacCer_9	sacCer9	Saccharomyces cerevisiae (v9)	/data2/indices/bowtie/genome/sacCer_9/sacCer_9_genome
+sarCer_3	sacCer3	Saccharomyces cerevisiae (v3)	/data2/indices/bowtie/genome/sacCer_3/sacCer_3_genome
+E_coli_K12_MG1655	e_coli	Escherichia coli (K12 MG1655)	/data2/indices/bowtie/genome/E_coli_K12_MG1655_genome
+Arabidopsis	araThal	Arabidopsis thaliana (TAIR10)	/data2/indices/bowtie/genome/Arabidopsis/Arabidopsis_genome

--- a/bowtie_genome_wrapper/tool_data_table_conf.xml.sample	Tue Mar 22 12:28:40 2022 +0000
+++ b/bowtie_genome_wrapper/tool_data_table_conf.xml.sample	Tue Apr 05 12:51:03 2022 +0000
@@ -3,6 +3,6 @@
     <!-- Locations of indexes in the Bowtie mapper format -->
     <table name="bowtie_indexes" comment_char="#">
         <columns>value, dbkey, name, path</columns>
-        <file path="/home/jack/projects/tools_for_Galaxy/ribogalaxy-toolshed/tools/bowtie_genome_wrapper/tool-data/bowtie_indices.loc.sample" />
+        <file path="tool-data/bowtie_indices.loc.sample" />
     </table>
 </tables>