Mercurial > repos > glogobyte > armdb

changeset 5:9c727a08f980 draft

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Uploaded
author glogobyte
date Fri, 16 Oct 2020 18:45:54 +0000
parents 7c9e524a3d1a
children 668af099b77f
files tool_data_table_conf.xml
diffstat 1 files changed, 128 insertions(+), 0 deletions(-) [+]
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line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml	Fri Oct 16 18:45:54 2020 +0000
@@ -0,0 +1,128 @@
+<!-- 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>
+