Mercurial > repos > nick > dunovo

changeset 18:075ef42d1ce5 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Bugfix in kalign for very diverse read lengths.
author nick
date Thu, 02 Nov 2017 15:46:18 -0400
parents a34e074e4818
children e5d1d90c099b
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 12:39:26 2017 -0400
+++ b/align_families.xml	Thu Nov 02 15:46:18 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 12:39:26 2017 -0400
+++ b/correct_barcodes.xml	Thu Nov 02 15:46:18 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 12:39:26 2017 -0400
+++ b/dunovo.xml	Thu Nov 02 15:46:18 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 12:39:26 2017 -0400
+++ b/make_families.xml	Thu Nov 02 15:46:18 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 12:39:26 2017 -0400
+++ b/tool_dependencies.xml	Thu Nov 02 15:46:18 2017 -0400
@@ -9,13 +9,13 @@
   <package name="mafft" version="7.221">
     <repository changeset_revision="dd4a533a0e3c" name="mafft" owner="rnateam" toolshed="https://testtoolshed.g2.bx.psu.edu" />
   </package>
-  <package name="networkx" version="1.11">
+  <package name="networkx" version="1.10">
     <repository changeset_revision="3469a6858fd4" name="package_networkx_1_10" owner="iuc" toolshed="https://testtoolshed.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>