# HG changeset patch
# User Matt Shirley <mdshw5@gmail.com>
# Date 1372535384 14400
# Node ID 2295c666e6ce97eeeb46db5a119432ea20c4f90d
# Parent  5f57967aac3e5492fb5aeae147efec551b795e1f
debug prefetch caching and accession input for fastq_dump

diff -r 5f57967aac3e -r 2295c666e6ce fastq_dump.xml
--- a/fastq_dump.xml	Sat Jun 29 11:14:03 2013 -0400
+++ b/fastq_dump.xml	Sat Jun 29 15:49:44 2013 -0400
@@ -11,8 +11,8 @@
   <inputs>
     <conditional name="input">
       <param name="input_select" type="select" label="Select input type">
-        <option value="accession">SRR accession</option>
-        <option value="sra">SRA archive in current history</option>
+        <option value="accession_number">SRR accession</option>
+        <option value="file">SRA archive in current history</option>
       </param>
       <when value="file">
 	<param format="sra" name="input" type="data" label="sra archive"/>
diff -r 5f57967aac3e -r 2295c666e6ce tool_dependencies.xml
--- a/tool_dependencies.xml	Sat Jun 29 11:14:03 2013 -0400
+++ b/tool_dependencies.xml	Sat Jun 29 15:49:44 2013 -0400
@@ -8,7 +8,7 @@
 	<action type="shell_command">make static</action>
 	<action type="shell_command">make</action>
 	<action type="make_directory">$INSTALL_DIR/bin</action>	
-	<action type="shell_command">sed -i -e 's/HOME/INSTALL_DIR/g' bin64/ncbi/default.kfg</action>
+	<action type="shell_command">sed -i -e "s/\$(HOME)/$INSTALL_DIR/g' bin64/ncbi/default.kfg</action>
 	<action type="shell_command">cp --recursive --dereference bin64/* $INSTALL_DIR/bin</action>
 	<action type="set_environment"><environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable></action>
       </actions>