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changeset 26:db602e459536 draft

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planemo upload for repository https://github.com/galaxyproject/dunovo commit b'7f9e80fb8da2f00b75ac3ba8bd4e11017cabc08c\n'-dirty
author nick
date Fri, 05 Jan 2018 04:54:42 -0500
parents 78b1544fba8c
children 06e47132b979
files align_families.xml correct_barcodes.xml dunovo.xml make_families.xml tool_dependencies.xml
diffstat 5 files changed, 17 insertions(+), 25 deletions(-) [+]
line wrap: on
line diff
--- a/align_families.xml	Fri Jan 05 03:40:33 2018 -0500
+++ b/align_families.xml	Fri Jan 05 04:54:42 2018 -0500
@@ -1,9 +1,9 @@
 <?xml version="1.0"?>
-<tool id="align_families" name="Du Novo: Align families" version="2.0.10">
+<tool id="align_families" name="Du Novo: Align families" version="2.0.11">
   <description>of duplex sequencing reads</description>
   <requirements>
     <requirement type="package" version="7.221">mafft</requirement>
-    <requirement type="package" version="2.0.10">dunovo</requirement>
+    <requirement type="package" version="2.0.11">dunovo</requirement>
     <!-- TODO: require Python 2.7 -->
   </requirements>
   <version_command>align-families.py --version</version_command>
--- a/correct_barcodes.xml	Fri Jan 05 03:40:33 2018 -0500
+++ b/correct_barcodes.xml	Fri Jan 05 04:54:42 2018 -0500
@@ -1,20 +1,20 @@
 <?xml version="1.0"?>
-<tool id="correct_barcodes" name="Du Novo: Correct barcodes" version="2.0.10">
+<tool id="correct_barcodes" name="Du Novo: Correct barcodes" version="2.0.11">
   <description>of duplex sequencing reads</description>
   <requirements>
     <requirement type="package" version="1.1.2">bowtie</requirement>
     <requirement type="package" version="1.10">networkx</requirement>
-    <requirement type="package" version="2.0.10">dunovo</requirement>
+    <requirement type="package" version="2.0.11">dunovo</requirement>
     <!-- TODO: require Python 2.7 -->
   </requirements>
   <version_command>correct.py --version</version_command>
   <command detect_errors="exit_code"><![CDATA[
     baralign.sh -c $advanced.chunkmbs -t \${GALAXY_SLOTS:-1} '$input' refdir correct.sam
     && correct.py --galaxy $phone --dist $dist --mapq $mapq --pos $pos
-         '$input' refdir/barcodes.fa correct.sam
-         > families.corrected.tsv
+      '$input' refdir/barcodes.fa correct.sam
+      > families.corrected.tsv
     && sort families.corrected.tsv
-         > '$output'
+      > '$output'
   ]]>
   </command>
   <inputs>
--- a/dunovo.xml	Fri Jan 05 03:40:33 2018 -0500
+++ b/dunovo.xml	Fri Jan 05 04:54:42 2018 -0500
@@ -1,8 +1,8 @@
 <?xml version="1.0"?>
-<tool id="dunovo" name="Du Novo: Make consensus reads" version="2.0.10">
+<tool id="dunovo" name="Du Novo: Make consensus reads" version="2.0.11">
   <description>from duplex sequencing alignments</description>
   <requirements>
-    <requirement type="package" version="2.0.10">dunovo</requirement>
+    <requirement type="package" version="2.0.11">dunovo</requirement>
     <!-- TODO: require Python 2.7 -->
   </requirements>
   <version_command>make-consensi.py --version</version_command>
--- a/make_families.xml	Fri Jan 05 03:40:33 2018 -0500
+++ b/make_families.xml	Fri Jan 05 04:54:42 2018 -0500
@@ -1,8 +1,8 @@
 <?xml version="1.0"?>
-<tool id="make_families" name="Du Novo: Make families" version="2.0.10">
+<tool id="make_families" name="Du Novo: Make families" version="2.0.11">
   <description>of duplex sequencing reads</description>
   <requirements>
-    <requirement type="package" version="2.0.10">dunovo</requirement>
+    <requirement type="package" version="2.0.11">dunovo</requirement>
   </requirements>
   <!-- TODO: Add dependency on coreutils to get paste? -->
   <version_command>make-consensi.py --version</version_command>
--- a/tool_dependencies.xml	Fri Jan 05 03:40:33 2018 -0500
+++ b/tool_dependencies.xml	Fri Jan 05 04:54:42 2018 -0500
@@ -9,34 +9,28 @@
   <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="2.0.10">
+  <package name="dunovo" version="2.0.11">
     <install version="1.0">
       <actions>
         <!-- download the main dunovo package files -->
-        <action sha256sum="81ef826b54746f4335f400b0ec5580bf04b5edfd8051682a684717fb32246227" type="download_by_url">https://github.com/galaxyproject/dunovo/archive/v2.0.10.tar.gz</action>
+        <action sha256sum="45d67ec4559880aacc228cb1a8be40dc4821ecf41699ea76efd62222a5e4deab" type="download_by_url">https://github.com/galaxyproject/dunovo/archive/v2.0.11.tar.gz</action>
+        <!-- TODO: Store dunovo version number in variable instead of hardcoding it everywhere. -->
         <action type="shell_command">rmdir kalign utillib ET</action>
         <!-- download the utillib submodule -->
         <action type="download_file">https://github.com/NickSto/utillib/archive/v0.1.0.tar.gz</action>
         <action type="shell_command">tar -zxvpf v0.1.0.tar.gz</action>
         <action type="shell_command">rm v0.1.0.tar.gz</action>
-        <action type="shell_command">echo DEBUG $TMP_WORK_DIR</action>
-        <action type="shell_command">pwd</action>
-        <action type="shell_command">ls -lFhAb &gt; /home/me/tmp/galaxy/install.ls1.log</action>
-        <action type="shell_command">ls -lFhAb utillib-0.1.0 &gt; /home/me/tmp/galaxy/install.ls2.log</action>
         <action rename_to="utillib" type="move_file">
           <source>utillib-0.1.0</source>
-          <destination>$TMP_WORK_DIR/dunovo-2.0.10</destination>
+          <destination>$TMP_WORK_DIR/dunovo-2.0.11</destination>
         </action>
-        <action type="shell_command">ls -lFhAb &gt; /home/me/tmp/galaxy/install.ls3.log</action>
-        <action type="shell_command">ls -lFhAb $TMP_WORK_DIR &gt; /home/me/tmp/galaxy/install.ls4.log</action>
-        <action type="shell_command">ls -lFhAb utillib &gt; /home/me/tmp/galaxy/install.ls5.log</action>
         <!-- download the kalign submodule -->
         <action type="download_file">https://github.com/makrutenko/kalign-dunovo/archive/v0.2.0.tar.gz</action>
         <action type="shell_command">tar -zxvpf v0.2.0.tar.gz</action>
         <action type="shell_command">rm v0.2.0.tar.gz</action>
         <action rename_to="kalign" type="move_file">
           <source>kalign-dunovo-0.2.0</source>
-          <destination>$TMP_WORK_DIR/dunovo-2.0.10</destination>
+          <destination>$TMP_WORK_DIR/dunovo-2.0.11</destination>
         </action>
         <!-- download the ET submodule -->
         <action type="download_file">https://github.com/NickSto/ET/archive/v0.2.2.tar.gz</action>
@@ -44,17 +38,15 @@
         <action type="shell_command">rm v0.2.2.tar.gz</action>
         <action rename_to="ET" type="move_file">
           <source>ET-0.2.2</source>
-          <destination>$TMP_WORK_DIR/dunovo-2.0.10</destination>
+          <destination>$TMP_WORK_DIR/dunovo-2.0.11</destination>
         </action>
         <!-- make and install -->
         <action type="shell_command">make clean</action>
         <action type="shell_command">make</action>
-        <action type="shell_command">ls -lFhAb &gt; /home/me/tmp/galaxy/install.ls6.log</action>
         <action type="move_directory_files">
           <source_directory>.</source_directory>
           <destination_directory>$INSTALL_DIR</destination_directory>
         </action>
-        <action type="shell_command">ls -lFhAb $INSTALL_DIR &gt; /home/me/tmp/galaxy/install.ls7.log</action>
         <action type="set_environment">
           <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable>
         </action>