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changeset 31:7c0d935bd205

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Change tool_dependencies.xml to use package_defuse_0_6_1
author Jim Johnson <jj@umn.edu>
date Tue, 03 Sep 2013 10:59:43 -0500
parents d0f4f4918b78
children 8027fc53f3f9
files tool_dependencies.xml
diffstat 1 files changed, 4 insertions(+), 50 deletions(-) [+]
line wrap: on
line diff
--- a/tool_dependencies.xml	Tue Sep 03 07:02:54 2013 -0500
+++ b/tool_dependencies.xml	Tue Sep 03 10:59:43 2013 -0500
@@ -1,10 +1,10 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="boost" version="1.53.0">
-        <repository changeset_revision="a72f8efe9201" name="package_boost_1_53" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    <package name="defuse" version="0.6.1">
+        <repository changeset_revision="370c0672e531" name="package_defuse_0_6_1" owner="jjohnson" toolshed="http://testtoolshed.g2.bx.psu.edu" />
     </package>
-    <package name="samtools" version="0.1.18">
-        <repository changeset_revision="5f7ec5048224" name="package_samtools_0_1_18" owner="devteam" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    <package name="samtools" version="0.1.19">
+        <repository changeset_revision="06697b4877f9" name="package_samtools_0_1_19" owner="jjohnson" toolshed="http://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="bowtie" version="1.0.0">
         <repository changeset_revision="e682af6a72cd" name="package_bowtie_1_0_0" owner="jjohnson" toolshed="http://testtoolshed.g2.bx.psu.edu" />
@@ -15,50 +15,4 @@
     <package name="kent" version="latest">
         <repository changeset_revision="b05b788e3989" name="package_kent" owner="jjohnson" toolshed="http://testtoolshed.g2.bx.psu.edu" />
     </package>
-    <package name="defuse" version="0.6.1">
-        <install version="1.0">
-            <actions>
-                <action type="download_by_url">http://sourceforge.net/projects/defuse/files/defuse/0.6/defuse-0.6.1.tar.gz</action>
-                <!-- populate the environment variables from the dependent repos -->
-                <action type="set_environment_for_install">
-                    <repository changeset_revision="a72f8efe9201" name="package_boost_1_53" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" >
-                        <package name="boost" version="1.53.0" />
-                    </repository>
-                </action>
-                <action type="shell_command">export CPLUS_INCLUDE_PATH=$BOOST_ROOT_DIR:$CPLUS_INCLUDE_PATH &amp;&amp; cd tools &amp;&amp; make</action>
-                <!-- modify create_reference_dataset.pl to handle more than just human genomes -->
-                <action type="shell_command">
-                   cd scripts &amp;&amp; 
-                   cp create_reference_dataset.pl create_reference_dataset.pl.orig &amp;&amp; 
-                   cat create_reference_dataset.pl.orig |
-                   sed 's#wget_gunzip("ftp://hgdownload.cse.ucsc.edu/goldenPath/$ucsc_genome_version/database/rmsk.txt.gz", $repeats_filename);##' |
-                   sed 's#wget_gunzip("ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/intronEst.txt.gz", $est_alignments);##' |
-                   sed 's#^\(my .*ensembl_genome_version.*config.*get_value.*;\)#\1Qmy $ensembl_organism = $config->get_value("ensembl_organism");Qmy $ensembl_prefix = $config->get_value("ensembl_prefix");Qmy $ncbi_organism = $config->get_value("ncbi_organism");Qmy $ncbi_prefix = $config->get_value("ncbi_prefix");#' |
-                   sed 's/^\(sub wget_gunzip\)/sub try_wgetQ{Q my $url = shift;Q my $filename = shift;Q my $filename_gz = $filename.".gz";Q my $rslt = system "wget $url -O $filename_gz";Q if($rslt == 0)Q {Q  $rslt = system "gunzip $filename_gz";Q }Q return $rslt;Q}QQ\1/' |
-                   tr 'Q' '\n' |
-                   awk 'BEGIN{pfx="p1";fn="p2";}/if \(not -e \$repeats_filename\)/{pfx="rmsk";fn="repeats_filename";} /if \(not -e \$est_alignments\)/{pfx="intronEst";fn="est_alignments"} /ucsc_genome_version eq "hg18"/{printf("\tif (try_wget(\"ftp://hgdownload.cse.ucsc.edu/goldenPath/$ucsc_genome_version/database/%s.txt.gz\", \$%s) != 0)\n",pfx,fn);} $0 !~ /ucsc_genome_version eq "hg18/{print $0;}' |
-                   sed 's#UniGene/Homo_sapiens#UniGene/$ncbi_organism#' |
-                   sed 's/Hs.seq.uniq.gz/$ncbi_prefix.seq.uniq.gz/' |
-                   sed 's/homo_sapiens/$ensembl_organism/' |
-                   sed 's/Homo_sapiens/$ensembl_prefix/' |
-                   sed 's/hg19/$ucsc_genome_version/' > create_reference_dataset.pl
-                </action>
-                <action type="move_directory_files">
-                    <source_directory>.</source_directory>
-                    <destination_directory>$INSTALL_DIR</destination_directory>
-                </action>
-                <action type="set_environment">
-                    <environment_variable name="DEFUSE_PATH" action="set_to">$INSTALL_DIR</environment_variable>
-                </action>
-                <action type="set_environment">
-                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/tools</environment_variable>
-                </action>
-            </actions>
-        </install>
-        <readme>
-deFuse code
-To build the deFuse toolset you must have the boost c++ development libraries installed. If they are not installed on your system you can download them from the boost website. A full install of boost is not required. The easiest thing to do is to download the latest boost source tar.gz, extract it, then add the extracted path to the CPLUS_INCLUDE_PATH environment variable (in bash, `export CPLUS_INCLUDE_PATH=/boost/directory/:$CPLUS_INCLUDE_PATH`)
-        </readme>
-    </package>
-
 </tool_dependency>