# HG changeset patch
# User bgruening
# Date 1386167628 18000
# Node ID 2a846521018aef710b849506bf10bd18dd9687b7
# Parent  886b67f8694d7c5c150d00c84a2b742bde03a88e
Uploaded

diff -r 886b67f8694d -r 2a846521018a tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Nov 19 18:50:28 2013 -0500
+++ b/tool_dependencies.xml	Wed Dec 04 09:33:48 2013 -0500
@@ -1,95 +1,69 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="libgd" version="2.1.0">
-        <repository changeset_revision="55e3d764c6c2" name="package_libgd_2_1" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="perl" version="5.18.1">
-        <repository changeset_revision="ab58b9f990c5" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="expat" version="2.1.0">
-        <repository changeset_revision="8fc96166cddd" name="package_expat_2_1" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="bzlib" version="1.0.6">
-        <repository changeset_revision="04e1967b1722" name="package_bzlib_1_0" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="libpng" version="1.2.5">
-        <repository changeset_revision="a80a3062f066" name="package_libpng_1_2" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="trans_proteomic_pipeline" version="4.6.3">
-        <install version="1.0">
-            <actions>
-                <action type="setup_perl_environment">
-                    <repository changeset_revision="ab58b9f990c5" name="package_perl_5_18" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
-                        <package name="perl" version="5.18.1" />
-                    </repository>
-                    <repository changeset_revision="8fc96166cddd" name="package_expat_2_1" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu">
-                        <package name="expat" version="2.1.0" />
-                    </repository>
-                    <!-- allow downloading and installing an Perl package from cpan.org-->
-                   
-                    <package>http://search.cpan.org/CPAN/authors/id/T/TO/TODDR/XML-Parser-2.41.tar.gz</package>
-                    <!-- Also possible but not reproducible, due to the fact that always the latest version is installed.
-                        <package>XML::Parser</package>
-                    -->
-                   <package>http://search.cpan.org/CPAN/authors/id/L/LD/LDS/CGI.pm-3.43.tar.gz</package>
-                </action>
-                <action type="change_directory">..</action>
-                <action type="download_file">https://downloads.sourceforge.net/project/sashimi/Trans-Proteomic%20Pipeline%20%28TPP%29/TPP%20v4.6%20%28occupy%29%20rev%203/TPP-4.6.3.tgz</action>
-                <!-- populate the environment variables from the dependend repos -->
-                <action type="set_environment_for_install">
-                    <repository changeset_revision="55e3d764c6c2" name="package_libgd_2_1" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
-                        <package name="libgd" version="2.1.0" />
-                    </repository>
-                    <repository changeset_revision="a80a3062f066" name="package_libpng_1_2" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
-                        <package name="libpng" version="1.2.5" />
-                    </repository>
-                    <repository changeset_revision="04e1967b1722" name="package_bzlib_1_0" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
-                        <package name="bzlib" version="1.0.6" />
-                    </repository>
-                </action>
-                <action type="shell_command">tar xfz TPP-4.6.3.tgz</action>
-                <!-- doanload patched version of htmldoc to prevent a TPP crashed during compilation -->
-                <action type="download_file">https://github.com/bgruening/download_store/raw/master/htmldoc/htmldoc_1.8.27-8ubuntu1.debian.tar.gz</action>
-                <action type="shell_command">rm ./TPP-4.6.3/trans_proteomic_pipeline/extern/htmldoc.tgz</action>
-                <action type="shell_command">mv htmldoc_1.8.27-8ubuntu1.debian.tar.gz ./TPP-4.6.3/trans_proteomic_pipeline/extern/htmldoc.tgz</action>
-                <!--
-                <action type="move_file" rename_to="htmldoc.tgz">
-                    <source>htmldoc-1.8.27-8.debian.patched.tar.gz</source>
-                    <destination>./TPP-4.6.3/trans_proteomic_pipeline/extern/</destination>
-                </action>
-                -->
-                <action type="change_directory">./TPP-4.6.3/trans_proteomic_pipeline/src/</action>
-                <action type="shell_command">echo 'TPP_ROOT=$INSTALL_DIR/tpp/' &gt; Makefile.config.incl</action>
-                <action type="shell_command">echo 'TPP_WEB=/tpp/' &gt;&gt; Makefile.config.incl</action>
-                <action type="shell_command">echo 'CGI_USER_DIR=$INSTALL_DIR/cgi-bin/' &gt;&gt; Makefile.config.incl</action>
+  <package name="blast+" version="2.2.28">
+    <repository changeset_revision="5a449da71d08" name="package_blast_plus_2_2_28" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+  </package>
+<!--  <package name="hmmer" version="3.1b1">
+    <repository name="package_hmmer_3_1" owner="lionelguy" />
+  </package>-->
+  <package name="aragorn" version="1.2.36">
+    <repository changeset_revision="d561a0a9f601" name="package_aragorn_1_2_36" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+  </package>
+  <package name="prodigal" version="2.60">
+    <repository changeset_revision="10f5ca5854c1" name="package_prodigal_2_60" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+  </package>
+  <package name="barrnap" version="0.2">
+    <repository changeset_revision="cea428082a70" name="package_barrnap_0_2" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+  </package>
+  <package name="infernal" version="1.1rc4">
+    <repository changeset_revision="bdf8789c423c" name="package_infernal_1_1rc4" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+  </package>
+  <package name="bioperl" version="1.6.922">
+    <repository changeset_revision="bd1fcedd9aad" name="package_bioperl_1_6" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+  </package>
+  <package name="perl" version="5.18.1">
+      <repository changeset_revision="ab58b9f990c5" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+  </package>
+  <package name="prokka_perl" version="1.7">
+    <install version="1.0">
+      <actions>
+         <action type="setup_perl_environment">
+            <repository changeset_revision="ab58b9f990c5" name="package_perl_5_18" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
+               <package name="perl" version="5.18.1" />
+            </repository>
+            <!-- allow downloading and installing an Perl package from cpan.org-->
+            <package>http://search.cpan.org/CPAN/authors/id/P/PE/PEVANS/Scalar-List-Utils-1.35.tar.gz</package> <!-- File::Cpoy -->
+            <package>File::Copy</package>
+            <package>http://search.cpan.org/CPAN/authors/id/J/JV/JV/Getopt-Long-2.42.tar.gz</package>
+            <package>FindBin </package>
+            <package>http://search.cpan.org/CPAN/authors/id/R/RJ/RJBS/Time-Piece-1.24.tar.gz</package>
+         </action>
+      </actions>
+    </install>
+    <readme>
+        Prokka Perl dependencies. File::Copy, FindBin, Getopt::Long, List::Util, Scalar::Util, Time::Piece, Time::Seconds;
+    </readme>
+  </package>
+  <package name="prokka" version="1.7">
+    <install version="1.0">
+      <actions>
+        <action type="download_by_url">http://www.vicbioinformatics.com/prokka-1.7.tar.gz</action>
+        <action type="move_directory_files">
+          <source_directory>.</source_directory>
+          <destination_directory>$INSTALL_DIR</destination_directory>
+        </action>
+        <action type="set_environment">
+          <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
+        </action>
+      </actions>
+    </install>
+    <readme>
+Warning: Prokka includes custom databases and is thus about a 2.0 GB download!
 
-                <!--
-                    TPP is fails with a error due to an deprecated use of qw()
-                    See the rant @ http://blogs.perl.org/users/rurban/2010/09/qw-in-list-context-deprecated.html
-                -->
-                <action type="shell_command">sed -i -e 's/qw(.*) /(&amp;) /' ../perl/tpp_models.pl</action>
-                <action type="shell_command">sed -i -e 's/qw(.*) /(&amp;) /' ../CGI/show_nspbin.pl</action>
-                <action type="shell_command">sed -i -e 's/qw(.*) /(&amp;) /' ../perl/exporTPP.pl</action>
+Dependencies of Prokka which needs to be installed separately:
+- tbl2asn ( http://www.ncbi.nlm.nih.gov/genbank/tbl2asn2/ ) &gt;= 21.0 ;
+- GNU Parallel ( http://www.gnu.org/software/parallel/ ) &gt;= 20130422 ;
 
-                <action type="shell_command">export PERL5LIB=$INSTALL_DIR/lib/perl5/:$PERL5LIB &amp;&amp; export PATH=$PERL_ROOT_DIR/bin/:$PATH &amp;&amp; export PERL5LIB=$PERL_ROOT_DIR/lib/perl5:$PERL5LIB &amp;&amp; make</action>
-                <action type="shell_command">make install</action>
-                <action type="set_environment">
-                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/tpp/bin</environment_variable>
-                    <environment_variable action="prepend_to" name="PERL5LIB">$INSTALL_DIR/lib/perl5</environment_variable>
-                    <environment_variable action="set_to" name="TPP_ROOT_PATH">$INSTALL_DIR</environment_variable>
-                </action>
-            </actions>
-        </install>
-        <readme>
-            Installs and complils the trans proteomic pipeline in version 4.6.3.
-            The Trans-Proteomic Pipeline (TPP) is a collection of integrated tools for MS/MS proteomics, developed at the SPC.
-
-            http://tools.proteomecenter.org/
-
-            Dependencies: e2fslibs-dev (e2fsprogs-devel)
-
-            PATH will be set.
-            TPP_ROOT_PATH will point to the root path of the installation.
-        </readme>
-    </package>
+    </readme>
+  </package>
 </tool_dependency>