Mercurial > repos > iuc > package_samtools_0_1_19

diff tool_dependencies.xml @ 1:00e17a794a2e

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Also install bcftools and misc utility commands when installing samtools.
author Jim Johnson <jj@umn.edu>
date Tue, 17 Sep 2013 11:36:59 -0500
parents cb87eae7fc3e
children b471600c8a3b
line wrap: on
line diff
--- a/tool_dependencies.xml	Mon Aug 19 17:19:38 2013 -0400
+++ b/tool_dependencies.xml	Tue Sep 17 11:36:59 2013 -0500
@@ -6,10 +6,25 @@
                 <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="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>
                 </action>
@@ -38,6 +53,29 @@
          cat         concatenate BAMs
          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
         </readme>
     </package>
 </tool_dependency>