--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tophat_indexes.loc	Thu Feb 11 08:45:06 2016 -0500
@@ -0,0 +1,78 @@
+#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...
+#
+
+#Banques temporaires mises en place au debut de l installation de Galaxy
+#AthalianaAllChr	AthalianaAllChr	AthalianaAllChr	/path/to/bank/bowtiedb/AthalianaAllChr
+#Drosophila_melanogaster_AllChr	Drosophila_melanogaster_AllChr	Drosophila melanogaster All Chr	/path/to/bank/bowtiedb/Drosophila_melanogaster_AllChr
+#Homo_sapiens_AllChr	Homo_sapiens_AllChr	Homo_sapiens_AllChr	/path/to/bank/bowtiedb/Homo_sapiens_AllChr
+#yeast.nt	yeast.nt	yeast nt	/path/to/bank/bowtiedb/yeast.nt
+
+#Banques definitives transmises par l administrateur system sur /path/to/bank/bowtiedb
+Arabidopsis_thaliana	Arabidopsis_thaliana	Arabidopsis thaliana	/path/to/bank/bowtie2db/Arabidopsis_thaliana
+Assembly_Bacteria_2014-06-24-Mycoplasma_agalactiae_GCF_000089865	Assembly_Bacteria_2014-06-24-Mycoplasma_agalactiae_GCF_000089865	Assembly_Bacteria_2014-06-24-Mycoplasma_agalactiae_GCF_000089865	
+Capra_hircus	Capra_hircus	Capra_hircus	/path/to/bank/bowtie2db/Capra_hircus
+Danio_rerio_Zv9_62_chr_22	Danio_rerio_Zv9_62_chr_22	Danio rerio Zv9 62 chr 22	/path/to/bank/bowtie2db/Danio_rerio.Zv9.62
+Drosophila_melanogaster_AllChr	Drosophila_melanogaster_AllChr	Drosophila melanogaster AllChr	/path/to/bank/bowtie2db/Drosophila_melanogaster_AllChr
+ensembl_bos_taurus_genome	ensembl_bos_taurus_genome	ensembl bos taurus genome	/path/to/bank/bowtie2db/ensembl_bos_taurus_genome
+ensembl_danio_rerio_genome	ensembl_danio_rerio_genome	ensembl danio rerio genome	/path/to/bank/bowtie2db/ensembl_danio_rerio_genome
+ensembl_equus_caballus_genome	ensembl_equus_caballus_genome	ensembl equus caballus genome	/path/to/bank/bowtie2db/ensembl_equus_caballus_genome
+ensembl_gallus_gallus_genome	ensembl_gallus_gallus_genome	ensembl gallus gallus genome	/path/to/bank/bowtie2db/ensembl_gallus_gallus_genome
+ensembl_homo_sapiens_genome	ensembl_homo_sapiens_genome	ensembl homo sapiens genome	/path/to/bank/bowtie2db/ensembl_homo_sapiens_genome
+ensembl_mus_musculus_genome	ensembl_mus_musculus_genome	ensembl mus musculus genome	/path/to/bank/bowtie2db/ensembl_mus_musculus_genome
+ensembl_oreochromis_niloticus_genome	ensembl_oreochromis_niloticus_genome	ensembl oreochromis niloticus genome	/path/to/bank/bowtie2db/ensembl_oreochromis_niloticus_genome
+ensembl_ovis_aries_genome	ensembl_ovis_aries_genome	ensembl ovis aries genome v3	/path/to/bank/bowtie2db/ensembl_ovis_aries_genome
+ensembl_rattus_norvegicus_genome	ensembl_rattus_norvegicus_genome	ensembl rattus norvegicus genome	/path/to/bank/bowtie2db/ensembl_rattus_norvegicus_genome
+ensembl_sus_scrofa_genome	susScr3	ensembl sus scrofa genome	/path/to/bank/bowtie2db/ensembl_sus_scrofa_genome
+ensembl_gadus_morhua_genome	ensembl_gadus_morhua_genome	ensembl gadus morhua gadMor1 (Jan 2010)	/path/to/bank/bowtie2db/ensembl_gadus_morhua_genome
+ensembl_oryzias_latipes_genome	ensembl_oryzias_latipes_genome	ensembl oryzias latipes HdrR Oct 2005	/path/to/bank/bowtie2db/ensembl_oryzias_latipes_genome
+Mycoplasma_agalactiae_GCF_000089865	Mycoplasma_agalactiae_GCF_000089865	Mycoplasma_agalactiae_GCF_000089865	/path/to/bank/ncbi/genomes/Assembly_Bacteria/Assembly_Bacteria_2014-06-24/bowtie2/Mycoplasma_agalactiae_GCF_000089865
+Mycoplasma_agalactiae_PG2_uid61619	Mycoplasma_agalactiae_PG2_uid61619	Mycoplasma_agalactiae_PG2_uid61619	/path/to/bank/bowtie2db/Mycoplasma_agalactiae_PG2_uid61619_test
+Mycoplasma_agalactiae_uid46679	Mycoplasma_agalactiae_uid46679	Mycoplasma_agalactiae_uid46679	/path/to/bank/bowtie2db/Mycoplasma_agalactiae_uid46679_test
+Mycoplasma_bovis_HB0801_uid168665	Mycoplasma_bovis_HB0801_uid168665	Mycoplasma_bovis_HB0801_uid168665	/path/to/bank/bowtie2db/Mycoplasma_bovis_HB0801_uid168665_test
+Mycoplasma_bovis_Hubei_1_uid68691	Mycoplasma_bovis_Hubei_1_uid68691	Mycoplasma_bovis_Hubei_1_uid68691	/path/to/bank/bowtie2db/Mycoplasma_bovis_Hubei_1_uid68691_test
+Mycoplasma_bovis_PG45_uid60859	Mycoplasma_bovis_PG45_uid60859	Mycoplasma_bovis_PG45_uid60859	/path/to/bank/bowtie2db/Mycoplasma_bovis_PG45_uid60859_test
+Mycoplasma_capricolum_ATCC_27343_uid58525	Mycoplasma_capricolum_ATCC_27343_uid58525	Mycoplasma_capricolum_ATCC_27343_uid58525	/path/to/bank/bowtie2db/Mycoplasma_capricolum_ATCC_27343_uid58525_test
+Mycoplasma_hominis_ATCC_23114_uid41875	Mycoplasma_hominis_ATCC_23114_uid41875	Mycoplasma_hominis_ATCC_23114_uid41875	/path/to/bank/bowtie2db/Mycoplasma_hominis_ATCC_23114_uid41875_test
+Mycoplasma_mycoides_capri_LC_95010_uid66189	Mycoplasma_mycoides_capri_LC_95010_uid66189	Mycoplasma_mycoides_capri_LC_95010_uid66189	/path/to/bank/bowtie2db/Mycoplasma_mycoides_capri_LC_95010_uid66189_test
+Mycoplasma_mycoides_SC_Gladysdale_uid197153	Mycoplasma_mycoides_SC_Gladysdale_uid197153	Mycoplasma_mycoides_SC_Gladysdale_uid197153	/path/to/bank/bowtie2db/Mycoplasma_mycoides_SC_Gladysdale_uid197153_test
+Mycoplasma_mycoides_SC_PG1_uid58031	Mycoplasma_mycoides_SC_PG1_uid58031	Mycoplasma_mycoides_SC_PG1_uid58031	/path/to/bank/bowtie2db/Mycoplasma_mycoides_SC_PG1_uid58031_test
+Mycoplasma_pneumoniae_309_uid85495	Mycoplasma_pneumoniae_309_uid85495	Mycoplasma_pneumoniae_309_uid85495	/path/to/bank/bowtie2db/Mycoplasma_pneumoniae_309_uid85495_test
+Mycoplasma_pneumoniae_FH_uid162027	Mycoplasma_pneumoniae_FH_uid162027	Mycoplasma_pneumoniae_FH_uid162027	/path/to/bank/bowtie2db/Mycoplasma_pneumoniae_FH_uid162027_test
+Mycoplasma_pneumoniae_M129_B7_uid185759	Mycoplasma_pneumoniae_M129_B7_uid185759	Mycoplasma_pneumoniae_M129_B7_uid185759	/path/to/bank/bowtie2db/Mycoplasma_pneumoniae_M129_B7_uid185759_test
+Mycoplasma_pneumoniae_M129_uid57709	Mycoplasma_pneumoniae_M129_uid57709	Mycoplasma_pneumoniae_M129_uid57709	/path/to/bank/bowtie2db/Mycoplasma_pneumoniae_M129_uid57709_test
+oryCun2_ucsc	oryCun2_ucsc	oryCun2 ucsc	/path/to/bank/bowtie2db/oryCun2_ucsc
+#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.
+#