Mercurial > repos > bgruening > diamond

changeset 6:9a5e0e2c0713 draft

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Uploaded
author bgruening
date Sun, 08 Feb 2015 07:28:56 -0500
parents 47b17961c436
children 89f59d6c3344
files repository_dependencies.xml test-data/diamond_makedb_result1.dmnd test-data/diamond_result1.tabular test-data/protein.fasta tool-data/diamond_database.loc.sample tool_data_table_conf.xml.sample
diffstat 6 files changed, 4 insertions(+), 25 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/repository_dependencies.xml	Sun Feb 08 07:28:56 2015 -0500
@@ -0,0 +1,4 @@
+<?xml version="1.0"?>
+<repositories description="This requires the Diamond data manager.">
+    <repository changeset_revision="dbd491c28590" name="data_manager_diamond_database_builder" owner="bgruening" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+</repositories>
Binary file test-data/diamond_makedb_result1.dmnd has changed
--- a/test-data/diamond_result1.tabular	Sun Feb 08 04:14:15 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-gi|5524211|gb|AAD44166.1|	gi|5524211|gb|AAD44166.1|	90.85	284	26	0	1	284	1	284	7e-155	528.5
--- a/test-data/protein.fasta	Sun Feb 08 04:14:15 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
->gi|5524211|gb|AAD44166.1| cytochrome b [Elephas maximus maximus]
-LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFSAIPYIGTNLV
-EWIWGGFSVDKATLNRFFAFHFILPFTMVALAGVHLTFLHETGSNNPLGLTSDSDKIPFHPYYTIKDFLG
-LLILILLLLLLALLSPDMLGDPDNHMPADPLNTPLHIKPEWYFLFAYAILRSVPNKLGGVLALFLSIVIL
-GLMPFLHTSKHRSMMLRPLSQALFWTLTMDLLTLTWIGSQPVEYPYTIIGQMASILYFSIILAFLPIAGX
-IENY
--- a/tool-data/diamond_database.loc.sample	Sun Feb 08 04:14:15 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,10 +0,0 @@
-#This is a sample file that enables the diamind to find the protein databases
-#You will need to create these data files and then create 
-#a diamond_database.loc file similar to this one (store it in this directory) 
-#that points to the directories in which those files are stored. 
-#The diamond_database_indices.loc file has this format (longer white space characters are TAB characters):
-#
-#<unique_build_id>   <display_name>   <file_base_path>
-#
-#So, for example:
-#ncbi_nr	NCBI NR database (1-1-2015)	/data/db/diamond/1-1-2015/nr.dmnd
--- a/tool_data_table_conf.xml.sample	Sun Feb 08 04:14:15 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,8 +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 indexes in the Bowtie mapper format -->
-    <table name="diamond_database" comment_char="#">
-        <columns>value, name, db_path</columns>
-        <file path="tool-data/diamond_database.loc" />
-    </table>
-</tables>