Mercurial > repos > pjbriggs > macs21

changeset 19:51303ba3fbbe draft

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Uploaded version 2.1.1.0 (update Macs2 version and switch to conda dependency resolution).
author pjbriggs
date Fri, 09 Mar 2018 09:21:56 -0500
parents 4e85d68a2347
children 4d41e5cda4e6
files README.rst macs21_wrapper.xml tool_dependencies.xml
diffstat 3 files changed, 17 insertions(+), 86 deletions(-) [+]
line wrap: on
line diff
--- a/README.rst	Wed Mar 22 11:24:52 2017 -0400
+++ b/README.rst	Fri Mar 09 09:21:56 2018 -0500
@@ -1,7 +1,7 @@
-MACS21: Model-based Analysis of ChIP-Seq (MACS 2.1.0) peak calling
-==================================================================
+MACS21: Model-based Analysis of ChIP-Seq (MACS 2.1) peak calling
+================================================================
 
-Galaxy tool wrapper for the peak calling function of MACS 2.1.0. MACS has been
+Galaxy tool wrapper for the peak calling function of MACS 2.1. MACS has been
 developed by Tao Lui
 https://github.com/taoliu/MACS/
 
@@ -15,7 +15,7 @@
 ======================
 
 Installation via the Galaxy Tool Shed will take of installing the tool wrapper and
-the MACS 2.1.0 program.
+the MACS 2.1 program.
 
 Manual Installation
 ===================
@@ -31,7 +31,7 @@
 
     <tool file="macs21/macs21_wrapper.xml" />
 
-You will also need to install MACS 2.1.0 and its dependencies:
+You will also need to install MACS 2.1 and its dependencies:
 
 - https://pypi.python.org/pypi/MACS2
 
@@ -52,13 +52,14 @@
 
 - http://toolshed.g2.bx.psu.edu/view/modencode-dcc/macs2 
 
-This version has been substantially modified both to adapt it to MACS 2.1.0, and
+This version has been substantially modified both to adapt it to MACS 2.1, and
 to re-implement the internal workings of the tool to conform with current
 practices in invoking commands from Galaxy, and to add new functionality.
 
 ========== ======================================================================
 Version    Changes
 ---------- ----------------------------------------------------------------------
+2.1.1.0    - Update to use MACS 2.1.1 and use conda to resolve dependencies
 2.1.0-6    - Add bedSort step into bigWig file generation; terminate with error
              when MACS finishes with non-zero exit code.
 2.1.0-5    - User must explicitly specify the format for the inputs (to allow
--- a/macs21_wrapper.xml	Wed Mar 22 11:24:52 2017 -0400
+++ b/macs21_wrapper.xml	Fri Mar 09 09:21:56 2018 -0500
@@ -1,15 +1,17 @@
-<tool id="macs2_1_peakcalling" name="MACS2.1.0" version="2.1.0-6">
+<tool id="macs2_1_peakcalling" name="MACS2.1.1" version="2.1.1.0">
   <description>Model-based Analysis of ChIP-Seq: peak calling</description>
   <requirements>
     <requirement type="package" version="2.7">python</requirement>
-    <requirement type="package" version="1.9">numpy</requirement>
-    <requirement type="package" version="2.1.0.20140616">macs2</requirement>
-    <requirement type="package" version="3.1.2">R</requirement>
-    <requirement type="package" version="2.0">ucsc_tools_for_macs21</requirement>
+    <requirement type="package" version="2.1.1">macs2</requirement>
+    <requirement type="package" version="3.4">R</requirement>
+    <requirement type="package" version="357">ucsc-fetchchromsizes</requirement>
+    <requirement type="package" version="357">ucsc-bedclip</requirement>
+    <requirement type="package" version="357">ucsc-bedsort</requirement>
+    <requirement type="package" version="357">ucsc-bedgraphtobigwig</requirement>
   </requirements>
   <version_command>macs2 --version</version_command>
-  <command interpreter="python">
-    macs21_wrapper.py callpeak
+  <command><![CDATA[
+    python $__tool_directory__/macs21_wrapper.py callpeak
     ##
     ## ChIP-seq input
     $input_chipseq_file1
@@ -96,7 +98,7 @@
     #else
        --output-peaks=$output_peaks_file
     #end if
-  </command>
+  ]]></command>
   <inputs>
     <!--experiment name used as base for output file names -->
     <param name="experiment_name" type="text" value="MACS2.1.0 in Galaxy" size="50"
--- a/tool_dependencies.xml	Wed Mar 22 11:24:52 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,72 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-  <!-- Dependencies from main/test toolsheds -->
-  <package name="numpy" version="1.9">
-    <repository changeset_revision="1e2b7e63dec2" name="package_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-  </package>
-  <package name="R" version="3.1.2">
-    <repository changeset_revision="1ca39eb16186" name="package_r_3_1_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-  </package>
-  <!-- Subset of UCSC tools -->
-  <package name="ucsc_tools_for_macs21" version="2.0">
-      <install version="1.0">
-            <actions>
-	      <!-- fetchChromSizes -->
-              <action type="download_binary">
-                <url_template architecture="x86_64" os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/fetchChromSizes</url_template>
-              </action>
-              <action type="chmod">
-                <file mode="755">$INSTALL_DIR/fetchChromSizes</file>
-              </action>
-	      <!-- bedClip -->
-              <action type="download_binary">
-                <url_template architecture="x86_64" os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedClip</url_template>
-              </action>
-              <action type="chmod">
-                <file mode="755">$INSTALL_DIR/bedClip</file>
-              </action>
-	      <!-- bedSort -->
-              <action type="download_binary">
-                <url_template architecture="x86_64" os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedSort</url_template>
-              </action>
-              <action type="chmod">
-                <file mode="755">$INSTALL_DIR/bedSort</file>
-              </action>
-	      <!-- bedGraphToBigWig -->
-              <action type="download_binary">
-                <url_template architecture="x86_64" os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedGraphToBigWig</url_template>
-              </action>
-              <action type="chmod">
-                <file mode="755">$INSTALL_DIR/bedGraphToBigWig</file>
-              </action>
-              <action type="set_environment">
-                <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable>
-              </action>
-	    </actions>
-      </install>
-  </package>
-  <!-- MACS 2.1.0 -->
-  <package name="macs2" version="2.1.0.20140616">
-      <install version="1.0">
-            <actions>
-              <action type="download_by_url">https://pypi.python.org/packages/source/M/MACS2/MACS2-2.1.0.20140616.tar.gz</action>
-	      <!-- Install environment for main & test toolsheds -->
-              <action type="set_environment_for_install">
-		<repository changeset_revision="1e2b7e63dec2" name="package_numpy_1_9" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
-		  <package name="numpy" version="1.9" />
-		</repository>
-	      </action>
-              <action type="make_directory">$INSTALL_DIR/lib/python</action>
-              <action type="shell_command">
-                export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp; 
-                python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin
-              </action>
-              <action type="set_environment">
-                <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
-                <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
-              </action>
-            </actions>
-      </install>
-      <readme>Macs2.1 depends on having python2.7 and numpy 1.8 installed on all nodes of the work cluster</readme>
-    </package>
-</tool_dependency>