# HG changeset patch
# User jasper
# Date 1492919238 14400
# Node ID 94d7100ad5d02f5abdbd3b8182f6c9775b5b4b55
Uploaded
diff -r 000000000000 -r 94d7100ad5d0 PathoMap.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/PathoMap.xml Sat Apr 22 23:47:18 2017 -0400
@@ -0,0 +1,77 @@
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+ Pathoscope Map
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+ pathoscope
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+ &1
+ && mv outalign.sam "$outalign"
+ && mv pathomap-appendAlign.fq "$pathomap_appendAlign"
+ ]]>
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+ IMPORTANT: The name and the path of the reference database (with bowtie indexed)
+ should be added to the pathoscope.loc entry.
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+ 10.1101/gr.150151.112
+ 10.1186/2049-2618-2-33
+ 10.1186/1471-2105-15-262
+ 10.4137/CIN.S13890
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diff -r 000000000000 -r 94d7100ad5d0 tool-data/pathoscope.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/pathoscope.loc.sample Sat Apr 22 23:47:18 2017 -0400
@@ -0,0 +1,34 @@
+# pathoscope.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 Pathoscope_Map.
+# 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.
+#
+# The path points to the "basename" for the set, not a specific file.
+# It has four text columns seperated by TABS.
+#
+#
+# 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:
+#
+#hg19 hg19 Human (hg19) /depot/data2/galaxy/hg19/bowtie2/hg19canon
+#
+#Important: put all reference bowtie index into same directory (including both
+#target and filter reference botwie index)
+#
+#More examples:
+#ref_prok_rep_genomes prok /depot/data/ref
+#ce11 ce /depot/data/ref
diff -r 000000000000 -r 94d7100ad5d0 tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Sat Apr 22 23:47:18 2017 -0400
@@ -0,0 +1,6 @@
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