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changeset 3:f19e18ab01b1 draft

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Uploaded v2.0.2 (use conda for dependency resolution)
author pjbriggs
date Mon, 05 Mar 2018 10:19:50 -0500
parents 3c5f10f7dd40
children 89315bdc1a8c
files README.rst tool_dependencies.xml weeder2_macros.xml weeder2_wrapper.xml
diffstat 4 files changed, 15 insertions(+), 42 deletions(-) [+]
line wrap: on
line diff
--- a/README.rst	Fri Nov 27 11:06:28 2015 -0500
+++ b/README.rst	Mon Mar 05 10:19:50 2018 -0500
@@ -79,6 +79,7 @@
 ========== ======================================================================
 Version    Changes
 ---------- ----------------------------------------------------------------------
+2.0.2      - Drop ``tool_dependencies.xml`` & use conda to resolve dependencies
 2.0.1      - Explicitly specify frequency files in ``weeder2.loc``.
 2.0.0      - Initial version
 ========== ======================================================================
--- a/tool_dependencies.xml	Fri Nov 27 11:06:28 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,39 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-  <package name="weeder" version="2.0">
-    <install version="1.0">
-      <actions>
-	<action type="download_by_url">http://159.149.160.51/modtools/downloads/weeder2.0.tar.gz</action>
-	<action type="shell_command">
-	  g++ weeder2.cpp -o weeder2 -O3
-	</action>
-	<!-- Move weeder2 executable -->
-	<action type="move_file">
-	  <source>weeder2</source>
-	  <destination>$INSTALL_DIR/bin</destination>
-	</action>
-	<!-- Move data files -->
-        <action type="move_directory_files">
-          <source_directory>FreqFiles</source_directory>
-          <destination_directory>$INSTALL_DIR/FreqFiles</destination_directory>
-        </action>
-	<!-- Set environment variables -->
-	<action type="set_environment">
-	  <environment_variable name="WEEDER_DIR" action="set_to">$INSTALL_DIR</environment_variable>
-	</action>
-	<action type="set_environment">
-	  <environment_variable name="WEEDER_FREQFILES_DIR" action="set_to">$INSTALL_DIR/FreqFiles</environment_variable>
-        </action>
-        <action type="set_environment">
-          <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
-        </action>
-      </actions>
-    </install>
-    <readme>Installs Weeder 2.0
-
-      See http://159.149.160.51/modtools/downloads/weeder2.html
-      and http://159.149.160.51/modtools/
-    </readme>
-  </package>
-</tool_dependency>
-
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/weeder2_macros.xml	Mon Mar 05 10:19:50 2018 -0500
@@ -0,0 +1,6 @@
+<macros>
+  <!--
+       Set the path for the weeder2 data files
+  -->
+  <token name="@CONDA_WEEDER2_FREQFILES_PATH@">if [ -z "\$WEEDER_FREQFILES_DIR" ]; then export WEEDER_FREQFILES_DIR=\$(dirname \$(readlink -e \$(which weeder2)))/FreqFiles; fi</token>
+</macros>
--- a/weeder2_wrapper.xml	Fri Nov 27 11:06:28 2015 -0500
+++ b/weeder2_wrapper.xml	Mon Mar 05 10:19:50 2018 -0500
@@ -1,9 +1,14 @@
-<tool id="motiffinding_weeder2" name="Weeder2" version="2.0.1">
+<tool id="motiffinding_weeder2" name="Weeder2" version="2.0.2">
   <description>Motif discovery in sequences from coregulated genes of a single species</description>
+  <macros>
+    <import>weeder2_macros.xml</import>
+  </macros>
   <requirements>
     <requirement type="package" version="2.0">weeder</requirement>
   </requirements>
-  <command interpreter="bash">weeder2_wrapper.sh
+  <command><![CDATA[
+  @CONDA_WEEDER2_FREQFILES_PATH@ &&
+  bash $__tool_directory__/weeder2_wrapper.sh
   $sequence_file $species_code ${species_code.fields.path}
   $output_motifs_file $output_matrix_file
   $strands
@@ -16,7 +21,7 @@
      -sim $advanced_options.sim_threshold
      -em $advanced_options.em_cycles
   #end if
-  </command>
+  ]]></command>
   <inputs>
     <param name="sequence_file" type="data" format="fasta" label="Input sequence" />
     <param name="species_code" type="select" label="Species to use for background comparison">