# HG changeset patch
# User bgruening
# Date 1399062661 14400
# Node ID b64dcea4531a6d7354dc66000cdff8fbe01ee602
# Parent  f63ccb331626a1d3eef7d30fdb3f41fbea1dcd54
Uploaded

diff -r f63ccb331626 -r b64dcea4531a macs2_macros.xml
--- a/macs2_macros.xml	Thu May 01 17:07:46 2014 -0400
+++ b/macs2_macros.xml	Fri May 02 16:31:01 2014 -0400
@@ -10,7 +10,10 @@
 
     <xml name="conditional_effective_genome_size">
         <conditional name="effective_genome_size_options">
-            <param name="effective_genome_size_options_selector" type="select" label="Effective genome size" help="--gsize">
+            <param name="effective_genome_size_options_selector" type="select" label="Effective genome size"
+                help="The effective genome size is the portion of the genome that is mappable. Large fractions of the genome are stretches of NNNN that should be discarded.
+                    Also, if repetitive regions were not included in the mapping of reads, the effective genome size needs to be adjusted accordingly.
+                    See Table 2 of http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0030377 or http://www.nature.com/nbt/journal/v27/n1/fig_tab/nbt.1518_T1.html for several effective genome sizes. (--gsize)">
                 <option value="2451960000">Human (2.451.960.000)</option>
                 <option value="2150570000">Mouse (2.150.570.000)</option>
                 <option value="121400000">Fly (121.400.000)</option>
diff -r f63ccb331626 -r b64dcea4531a tool_dependencies.xml
--- a/tool_dependencies.xml	Thu May 01 17:07:46 2014 -0400
+++ b/tool_dependencies.xml	Fri May 02 16:31:01 2014 -0400
@@ -38,8 +38,6 @@
                 <!-- exporting the CFLAGS and CPPFLAGS are due to http://stackoverflow.com/questions/22313407/clang-error-unknown-argument-mno-fused-madd-python-package-installation-fa -->
                 <action type="shell_command">
                     export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp;
-                    export CFLAGS=-Qunused-arguments &amp;&amp;
-                    export CPPFLAGS=-Qunused-arguments &amp;&amp;
                     python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin
                 </action>
                 <action type="set_environment">