changeset 2:b471600c8a3b draft

Uploaded

--- a/tool_dependencies.xml	Tue Sep 17 11:36:59 2013 -0500
+++ b/tool_dependencies.xml	Sun Apr 27 14:28:10 2014 -0400
@@ -1,32 +1,26 @@
 <?xml version="1.0"?>
 <tool_dependency>
+    <package name="ncurses" version="5.9">
+        <repository changeset_revision="9ed7af129bd3" name="package_ncurses_5_9" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
+    </package>
     <package name="samtools" version="0.1.19">
         <install version="1.0">
             <actions>
                 <action type="download_by_url">http://downloads.sourceforge.net/project/samtools/samtools/0.1.19/samtools-0.1.19.tar.bz2</action>
-                <action type="shell_command">sed -i.bak 's/-lcurses/-lncurses/' Makefile</action>
+                <action type="set_environment_for_install">
+                    <repository changeset_revision="9ed7af129bd3" name="package_ncurses_5_9" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu">
+                        <package name="ncurses" version="5.9" />
+                    </repository>
+                </action>
+                <action type="shell_command">sed -i 's/-lcurses/-lncurses/' Makefile</action>
+                <action type="shell_command">sed -i -e "s|CFLAGS=\s*-g\s*-Wall\s*-O2\s*|CFLAGS= -g -Wall -O2 -I$NCURSES_INCLUDE_PATH/ncurses/ -L$NCURSES_LIB_PATH|g" Makefile</action>
                 <action type="shell_command">make</action>
-                <action type="shell_command">chmod ugo+rx misc/*.p?</action>
-                <action type="shell_command">mkdir misc/bin</action>
-                <action type="shell_command">cp -p `find misc -type f -perm -555` misc/bin/</action>
                 <action type="move_file">
                     <source>samtools</source>
                     <destination>$INSTALL_DIR/bin</destination>
                 </action>
-                <action type="move_file">
-                    <source>bcftools/bcftools</source>
-                    <destination>$INSTALL_DIR/bin</destination>
-                </action>
-                <action type="move_file">
-                    <source>bcftools/vcfutils.pl</source>
-                    <destination>$INSTALL_DIR/bin</destination>
-                </action>
-                <action type="move_directory_files">
-                    <source_directory>misc/bin</source_directory>
-                    <destination_directory>$INSTALL_DIR/bin</destination_directory>
-                </action>
                 <action type="set_environment">
-                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
                 </action>
             </actions>
         </install>
@@ -54,28 +48,7 @@
          targetcut   cut fosmid regions (for fosmid pool only)
          phase       phase heterozygotes
 
-This also installs bcftools and misc utility commands:
-        bcftools
-        vcfutils.pl
-        ace2sam
-        bamcheck
-        blast2sam.pl
-        bowtie2sam.pl
-        export2sam.pl
-        interpolate_sam.pl
-        maq2sam-long
-        maq2sam-short
-        md5fa
-        md5sum-lite
-        novo2sam.pl
-        psl2sam.pl
-        sam2vcf.pl
-        samtools.pl
-        soap2sam.pl
-        varfilter.py
-        wgsim
-        wgsim_eval.pl
-        zoom2sam.pl
+Requirements: libncurses header files
         </readme>
     </package>
 </tool_dependency>