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changeset 6:23f5d9316694 draft

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Bugfix in kalign for very diverse read lengths.
author nick
date Thu, 02 Nov 2017 16:24:48 -0400
parents 000969829a5d
children e7b88ffb8294
files align_families.xml correct_barcodes.xml dunovo.xml make_families.xml tool_dependencies.xml
diffstat 5 files changed, 12 insertions(+), 12 deletions(-) [+]
line wrap: on
line diff
--- a/align_families.xml	Fri Oct 27 12:50:39 2017 -0400
+++ b/align_families.xml	Thu Nov 02 16:24:48 2017 -0400
@@ -1,9 +1,9 @@
 <?xml version="1.0"?>
-<tool id="align_families" name="Du Novo: Align families" version="2.0.6">
+<tool id="align_families" name="Du Novo: Align families" version="2.0.8">
   <description>of duplex sequencing reads</description>
   <requirements>
     <requirement type="package" version="7.221">mafft</requirement>
-    <requirement type="package" version="2.0.6">dunovo</requirement>
+    <requirement type="package" version="2.0.8">dunovo</requirement>
     <!-- TODO: require Python 2.7 -->
   </requirements>
   <version_command>align_families.py --version</version_command>
--- a/correct_barcodes.xml	Fri Oct 27 12:50:39 2017 -0400
+++ b/correct_barcodes.xml	Thu Nov 02 16:24:48 2017 -0400
@@ -1,11 +1,11 @@
 <?xml version="1.0"?>
-<tool id="correct_barcodes" name="Du Novo: Correct barcodes" version="2.0.6.1">
+<tool id="correct_barcodes" name="Du Novo: Correct barcodes" version="2.0.8">
   <description>of duplex sequencing reads</description>
   <requirements>
     <requirement type="package" version="2.2.5">bowtie2</requirement>
     <requirement type="package" version="0.1.18">samtools</requirement>
-    <requirement type="package" version="1.11">networkx</requirement>
-    <requirement type="package" version="2.0.6">dunovo</requirement>
+    <requirement type="package" version="1.10">networkx</requirement>
+    <requirement type="package" version="2.0.8">dunovo</requirement>
     <!-- TODO: require Python 2.7 -->
   </requirements>
   <version_command>correct.py --version</version_command>
--- a/dunovo.xml	Fri Oct 27 12:50:39 2017 -0400
+++ b/dunovo.xml	Thu Nov 02 16:24:48 2017 -0400
@@ -1,8 +1,8 @@
 <?xml version="1.0"?>
-<tool id="dunovo" name="Du Novo: Make consensus reads" version="2.0.6">
+<tool id="dunovo" name="Du Novo: Make consensus reads" version="2.0.8">
   <description>from duplex sequencing alignments</description>
   <requirements>
-    <requirement type="package" version="2.0.6">dunovo</requirement>
+    <requirement type="package" version="2.0.8">dunovo</requirement>
     <!-- TODO: require Python 2.7 -->
   </requirements>
   <version_command>dunovo.py --version</version_command>
--- a/make_families.xml	Fri Oct 27 12:50:39 2017 -0400
+++ b/make_families.xml	Thu Nov 02 16:24:48 2017 -0400
@@ -1,8 +1,8 @@
 <?xml version="1.0"?>
-<tool id="make_families" name="Du Novo: Make families" version="2.0.6">
+<tool id="make_families" name="Du Novo: Make families" version="2.0.8">
   <description>of duplex sequencing reads</description>
   <requirements>
-    <requirement type="package" version="2.0.6">dunovo</requirement>
+    <requirement type="package" version="2.0.8">dunovo</requirement>
   </requirements>
   <!-- TODO: Add dependency on coreutils to get paste? -->
   <version_command>dunovo.py --version</version_command>
--- a/tool_dependencies.xml	Fri Oct 27 12:50:39 2017 -0400
+++ b/tool_dependencies.xml	Thu Nov 02 16:24:48 2017 -0400
@@ -9,13 +9,13 @@
   <package name="mafft" version="7.221">
     <repository changeset_revision="15974dd17515" name="mafft" owner="rnateam" toolshed="https://toolshed.g2.bx.psu.edu" />
   </package>
-  <package name="networkx" version="1.11">
+  <package name="networkx" version="1.10">
     <repository changeset_revision="e761775277c1" name="package_networkx_1_10" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
   </package>
-  <package name="dunovo" version="2.0.6">
+  <package name="dunovo" version="2.0.8">
     <install version="1.0">
       <actions>
-        <action sha256sum="3d628d297767f9836ab57ef738b2b29f588c36df8c43ec6814ea97e29da1d5ec" type="download_by_url">https://github.com/galaxyproject/dunovo/archive/v2.0.6.tar.gz</action>
+        <action sha256sum="4c105e29eff271b9e32f12c5d2862b717ba960981f4820dae26e159e2a0ed33d" type="download_by_url">https://github.com/galaxyproject/dunovo/archive/v2.0.8.tar.gz</action>
         <action type="shell_command">make</action>
         <action type="move_directory_files">
           <source_directory>.</source_directory>