# HG changeset patch
# User glogobyte
# Date 1602874136 0
# Node ID 456fefe9cc6401e2083ebbe040304a33d9c56a62
# Parent  668af099b77f1e0ddf122a28b5c0ffef704062df
Deleted selected files

diff -r 668af099b77f -r 456fefe9cc64 mirbase.loc
--- a/mirbase.loc	Fri Oct 16 18:48:16 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,35 +0,0 @@
-# bowtie2_indices.loc.sample
-# This is a *.loc.sample file distributed with Galaxy that enables tools
-# to use a directory of indexed data files. This one is for Bowtie2 and Tophat2.
-# See the wiki: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup
-# First create these data files and save them in your own data directory structure.
-# Then, create a bowtie_indices.loc file to use those indexes with tools.
-# Copy this file, save it with the same name (minus the .sample),
-# follow the format examples, and store the result in this directory.
-# The file should include an one line entry for each index set.
-# The path points to the "basename" for the set, not a specific file.
-# It has four text columns seperated by TABS.
-#
-# <unique_build_id>     <dbkey> <display_name>  <file_base_path>
-#
-# So, for example, if you had hg18 indexes stored in:
-#
-#    /depot/data2/galaxy/hg19/bowtie2/
-#
-# containing hg19 genome and hg19.*.bt2 files, such as:
-#    -rw-rw-r-- 1 james   james   914M Feb 10 18:56 hg19canon.fa
-#    -rw-rw-r-- 1 james   james   914M Feb 10 18:56 hg19canon.1.bt2
-#    -rw-rw-r-- 1 james   james   683M Feb 10 18:56 hg19canon.2.bt2
-#    -rw-rw-r-- 1 james   james   3.3K Feb 10 16:54 hg19canon.3.bt2
-#    -rw-rw-r-- 1 james   james   683M Feb 10 16:54 hg19canon.4.bt2
-#    -rw-rw-r-- 1 james   james   914M Feb 10 20:45 hg19canon.rev.1.bt2
-#    -rw-rw-r-- 1 james   james   683M Feb 10 20:45 hg19canon.rev.2.bt2
-#
-# then the bowtie2_indices.loc entry could look like this:
-#
-#
-hg38	homo sapiens	hsa.gff3	hsa
-#
-#
-#
-#
diff -r 668af099b77f -r 456fefe9cc64 mirgene.loc
--- a/mirgene.loc	Fri Oct 16 18:48:16 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,36 +0,0 @@
-# bowtie2_indices.loc.sample
-# This is a *.loc.sample file distributed with Galaxy that enables tools
-# to use a directory of indexed data files. This one is for Bowtie2 and Tophat2.
-# See the wiki: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup
-# First create these data files and save them in your own data directory structure.
-# Then, create a bowtie_indices.loc file to use those indexes with tools.
-# Copy this file, save it with the same name (minus the .sample),
-# follow the format examples, and store the result in this directory.
-# The file should include an one line entry for each index set.
-# The path points to the "basename" for the set, not a specific file.
-# It has four text columns seperated by TABS.
-#
-# <unique_build_id>     <dbkey> <display_name>  <file_base_path>
-#
-# So, for example, if you had hg18 indexes stored in:
-#
-#    /depot/data2/galaxy/hg19/bowtie2/
-#
-# containing hg19 genome and hg19.*.bt2 files, such as:
-#    -rw-rw-r-- 1 james   james   914M Feb 10 18:56 hg19canon.fa
-#    -rw-rw-r-- 1 james   james   914M Feb 10 18:56 hg19canon.1.bt2
-#    -rw-rw-r-- 1 james   james   683M Feb 10 18:56 hg19canon.2.bt2
-#    -rw-rw-r-- 1 james   james   3.3K Feb 10 16:54 hg19canon.3.bt2
-#    -rw-rw-r-- 1 james   james   683M Feb 10 16:54 hg19canon.4.bt2
-#    -rw-rw-r-- 1 james   james   914M Feb 10 20:45 hg19canon.rev.1.bt2
-#    -rw-rw-r-- 1 james   james   683M Feb 10 20:45 hg19canon.rev.2.bt2
-#
-# then the bowtie2_indices.loc entry could look like this:
-#
-#
-Hsa	Human (Homo sapiens)
-#
-#
-#
-#
-#
diff -r 668af099b77f -r 456fefe9cc64 tool_data_table_conf.xml
--- a/tool_data_table_conf.xml	Fri Oct 16 18:48:16 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,128 +0,0 @@
-<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc-->
-<tables>
-    <!-- Locations of all fasta files under genome directory -->
-    <table name="all_fasta" comment_char="#" allow_duplicate_entries="False">
-        <columns>value, dbkey, name, path</columns>
-        <file path="tool-data/all_fasta.loc" />
-    </table>
-    <!-- Locations of indexes in the BFAST mapper format -->
-    <table name="bfast_indexes" comment_char="#" allow_duplicate_entries="False">
-        <columns>value, dbkey, formats, name, path</columns>
-        <file path="tool-data/bfast_indexes.loc" />
-    </table>
-    <!-- Locations of nucleotide BLAST databases -->
-    <table name="blastdb" comment_char="#" allow_duplicate_entries="False">
-        <columns>value, name, path</columns>
-        <file path="tool-data/blastdb.loc" />
-    </table>
-    <!-- Locations of protein BLAST databases -->
-    <table name="blastdb_p" comment_char="#" allow_duplicate_entries="False">
-        <columns>value, name, path</columns>
-        <file path="tool-data/blastdb_p.loc" />
-    </table>
-    <!-- Locations of protein domain BLAST databases -->
-    <table name="blastdb_d" comment_char="#" allow_duplicate_entries="False">
-        <columns>value, name, path</columns>
-        <file path="tool-data/blastdb_d.loc" />
-    </table>
-    <!-- Locations of indexes in the BWA mapper format -->
-    <table name="bwa_indexes" comment_char="#" allow_duplicate_entries="False">
-        <columns>value, dbkey, name, path</columns>
-        <file path="tool-data/bwa_index.loc" />
-    </table>
-    <!-- Locations of indexes in the BWA color-space mapper format -->
-    <table name="bwa_indexes_color" comment_char="#" allow_duplicate_entries="False">
-        <columns>value, dbkey, name, path</columns>
-        <file path="tool-data/bwa_index_color.loc" />
-    </table>
-    <!-- Locations of MAF files that have been indexed with bx-python -->
-    <table name="indexed_maf_files">
-        <columns>name, value, dbkey, species</columns>
-        <file path="tool-data/maf_index.loc" />
-    </table>
-    <!-- Locations of fasta files appropriate for NGS simulation -->
-    <table name="ngs_sim_fasta" comment_char="#" allow_duplicate_entries="False">
-        <columns>value, dbkey, name, path</columns>
-        <file path="tool-data/ngs_sim_fasta.loc" />
-    </table>
-    <!-- Locations of PerM base index files -->
-    <table name="perm_base_indexes" comment_char="#" allow_duplicate_entries="False">
-        <columns>value, name, path</columns>
-        <file path="tool-data/perm_base_index.loc" />
-    </table>
-    <!-- Locations of PerM color-space index files -->
-    <table name="perm_color_indexes" comment_char="#" allow_duplicate_entries="False">
-        <columns>value, name, path</columns>
-        <file path="tool-data/perm_color_index.loc" />
-    </table>
-    <!-- Location of Picard dict file and other files -->
-    <table name="picard_indexes" comment_char="#" allow_duplicate_entries="False">
-        <columns>value, dbkey, name, path</columns>
-        <file path="tool-data/picard_index.loc" />
-    </table>
-    <!-- Location of SRMA dict file and other files -->
-    <table name="srma_indexes" comment_char="#" allow_duplicate_entries="False">
-        <columns>value, dbkey, name, path</columns>
-        <file path="tool-data/picard_index.loc" />
-    </table>
-    <!-- Location of Mosaik files -->
-    <table name="mosaik_indexes" comment_char="#" allow_duplicate_entries="False">
-        <columns>value, dbkey, name, path</columns>
-        <file path="tool-data/mosaik_index.loc" />
-    </table>
-    <!-- Locations of indexes in the 2bit format -->
-    <table name="twobit" comment_char="#" allow_duplicate_entries="False">
-        <columns>value, path</columns>
-        <file path="tool-data/twobit.loc" />
-    </table>
-    <!-- Available IGV builds, loaded from URL -->
-    <table name="igv_broad_genomes" comment_char="#" allow_duplicate_entries="False">
-        <columns>name, url, value</columns>
-        <file url="http://igv.broadinstitute.org/genomes/genomes.txt" />
-    </table>
-    <!-- Available liftOver chain file -->
-    <table name="liftOver" comment_char="#" allow_duplicate_entries="False">
-        <columns>dbkey, name, value</columns>
-        <file path="tool-data/liftOver.loc" />
-    </table>
-    <!-- iobio bam servers -->
-    <table name="bam_iobio" comment_char="#" allow_duplicate_entries="False">
-        <columns>value, name, url</columns>
-        <file path="tool-data/bam_iobio.loc" />
-    </table>
-    <!-- iobio vcf servers -->
-    <table name="vcf_iobio" comment_char="#" allow_duplicate_entries="False">
-        <columns>value, name, url</columns>
-        <file path="tool-data/vcf_iobio.loc" />
-    </table>
-    <!-- simple biom servers -->
-    <table name="biom_simple_display" comment_char="#" allow_duplicate_entries="False">
-        <columns>value, name, url</columns>
-        <file path="tool-data/biom_simple_display.loc" />
-    </table>
-    <!-- simple intermine servers -->
-    <table name="intermine_simple_display" comment_char="#" allow_duplicate_entries="False">
-        <columns>value, name, url</columns>
-        <file path="tool-data/intermine_simple_display.loc" />
-    </table>
-    <!-- Locations of 2bit sequence files for use in Lastz -->
-    <table name="n_spiecies" comment_char="#">
-        <columns>value, name, path</columns>
-        <file path="tool-data/n_spiecies.loc" />
-    </table>
-    <!-- Locations of 2bit sequence files for use in Lastz -->
-    <table name="mirbase" comment_char="#">
-        <columns>value, name, dbkey, path</columns>
-        <file path="tool-data/mirbase.loc" />
-    </table>
-    <!-- Locations of 2bit sequence files for use in Lastz -->
-    <table name="mirgene" comment_char="#">
-        <columns>value, name</columns>
-        <file path="tool-data/mirgene.loc" />
-    </table>
-    <table name="Mirbase_v22" comment_char="#">
-        <columns>value, name, id</columns>
-        <file path="tool-data/Mirbase_v22.loc" />
-    </table>
-</tables>
-