Mercurial > repos > gdroc > scaffhunter

changeset 1:b1807ab520a1 draft

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Uploaded
author gdroc
date Mon, 14 Nov 2016 08:01:49 -0500
parents 9c61692acd7b
children ec31e4883c99
files scaffhunter/locOnRef.xml scaffhunter/tool-data/scaffhunter.loc scaffhunter/tool_data_table_conf.xml.sample scaffhunter/tool_dependencies.xml
diffstat 4 files changed, 23 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- a/scaffhunter/locOnRef.xml	Mon Nov 14 07:39:42 2016 -0500
+++ b/scaffhunter/locOnRef.xml	Mon Nov 14 08:01:49 2016 -0500
@@ -1,9 +1,9 @@
 <tool id="locOnRef" name="locOnRef" version="0.1"> 
     <description> : Locate markers having uniq position on a reference </description> 
 	<requirements>
-        <requirement type="binary">blastn</requirement>
-        <requirement type="binary">bwa</requirement> 
-        <requirement type="binary">bowtie2</requirement>
+		<requirement type="package" version="0.7.7">bwa</requirement>
+        <requirement type="package" version="2.2.6">bowtie2</requirement>
+		<requirement type="package" version="2.2.31">blast+</requirement>
     </requirements> 
     <stdio>
         <exit_code range="1:" />
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scaffhunter/tool-data/scaffhunter.loc	Mon Nov 14 08:01:49 2016 -0500
@@ -0,0 +1,1 @@
+sample_sh	Sample for Scaffhunter	/bank/musa_acuminata/sample/scaffolds.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scaffhunter/tool_data_table_conf.xml.sample	Mon Nov 14 08:01:49 2016 -0500
@@ -0,0 +1,7 @@
+<tables>
+    <!-- Locations of scaffhunter file -->
+    <table name="scaffhunter" comment_char="#">
+        <columns>value, dbkey, path</columns>
+        <file path="tool-data/scaffhunter.loc" />
+    </table> 
+</tables>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scaffhunter/tool_dependencies.xml	Mon Nov 14 08:01:49 2016 -0500
@@ -0,0 +1,12 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="bwa" version="0.7.7">
+        <repository changeset_revision="def70e393020" name="package_bwa_0_7_7" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="blast+" version="2.2.31">
+        <repository changeset_revision="e36f75574aec" name="package_blast_plus_2_2_31" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="bowtie2" version="2.2.6">
+        <repository changeset_revision="0d9cd7487cc9" name="package_bowtie_2_2_6" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+</tool_dependency>