# HG changeset patch
# User greg
# Date 1700764583 0
# Node ID 85e400e1f2dd57c9e355ae2dd7519bb72112dea9
# Parent e589aadb5a8057006ae0b3e280de1098975826b9
Uploaded
diff -r e589aadb5a80 -r 85e400e1f2dd tool-data/bowtie2_indices.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/bowtie2_indices.loc.sample Thu Nov 23 18:36:23 2023 +0000
@@ -0,0 +1,54 @@
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+ value, dbkey, name, path
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+(base) o1-3s4vnf2:bowtie2 gvk$ cd ttol-da
+-bash: cd: ttol-da: No such file or directory
+(base) o1-3s4vnf2:bowtie2 gvk$ cd tool-data/
+(base) o1-3s4vnf2:tool-data gvk$ ll
+total 8
+drwxr-xr-x 3 gvk staff 96 Jan 31 2018 .
+drwxr-xr-x 8 gvk staff 256 Nov 23 13:26 ..
+-rw-r--r-- 1 gvk staff 1713 Jan 31 2018 bowtie2_indices.loc.sample
+(base) o1-3s4vnf2:tool-data gvk$ cat bowtie2_indices.loc.sample
+# 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.
+#
+#
+#
+# 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
+#
+#More examples:
+#
+#mm10 mm10 Mouse (mm10) /depot/data2/galaxy/mm10/bowtie2/mm10
+#dm3 dm3 D. melanogaster (dm3) /depot/data2/galaxy/mm10/bowtie2/dm3
+#
+#
diff -r e589aadb5a80 -r 85e400e1f2dd tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Thu Nov 23 18:36:23 2023 +0000
@@ -0,0 +1,8 @@
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+ value, dbkey, name, path
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diff -r e589aadb5a80 -r 85e400e1f2dd tool_data_table_conf.xml.test
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test Thu Nov 23 18:36:23 2023 +0000
@@ -0,0 +1,8 @@
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+ value, dbkey, name, path
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