# HG changeset patch
# User morinlab
# Date 1480892975 18000
# Node ID fa8f8d81b13e2114b1594508254e47ef31c92e7f

Uploaded

diff -r 000000000000 -r fa8f8d81b13e tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Sun Dec 04 18:09:35 2016 -0500
@@ -0,0 +1,51 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="gnu_coreutils" version="8.25">
+        <repository changeset_revision="7241ed879fb4" name="package_gnu_coreutils_8_25" owner="morinlab" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="perl" version="5.18.1">
+        <install version="1.0">
+            <actions>
+                <!-- install perl -->
+                <action sha256sum="655e11a8ffba8853efcdce568a142c232600ed120ac24aaebb4e6efe74e85b2b" type="download_by_url">
+                https://depot.galaxyproject.org/software/perl/perl_5.18_src_all.tar.gz
+                </action>
+                <action type="shell_command">./Configure -des -Dprefix=$INSTALL_DIR -Dstartperl='#!/usr/bin/env perl'</action>
+                <action type="make_install" />
+                <action type="change_directory">..</action>
+                <action sha256sum="5c69adb47ab828aa3e8b5be89b88cd49c6a0d0dae2e8b3bca17a9ce699190e7b" type="download_file">
+                http://www.cpan.org/authors/id/A/AP/APEIRON/local-lib-1.008009.tar.gz
+                </action>
+                <action type="shell_command">tar xfvz local-lib-1.008009.tar.gz</action>
+                <action type="change_directory">local-lib-1.008009</action>
+                <!-- TODO: Here we need to use the new installed perl binary -->
+                <!-- Test whether $TMP_WORK_DIR exists (introduced in galaxy release 15.07).
+                If not, fall back to using mktemp. Should be set to HOME=$TEMP_WORK_DIR in the future. -->
+                <action type="shell_command">if [ -d "$TMP_WORK_DIR" ] ; then export HOME=$TMP_WORK_DIR ; else export HOME=`mktemp -d` ; fi ; export PATH=$INSTALL_DIR/bin/:$PATH; perl Makefile.PL --bootstrap=$INSTALL_DIR/local-lib/ --no-manpages</action>
+                <action type="shell_command">make install</action>
+                <action type="shell_command">export PATH=$INSTALL_DIR/bin/:$PATH; eval $(perl -I$INSTALL_DIR/local-lib/lib/perl5 -Mlocal::lib=$INSTALL_DIR/local-lib)</action>
+                <action type="change_directory">..</action>
+                <!-- install cpanminus into our new perl environment -->
+                <action sha256sum="0b67f5c721259d4185bacdcbc87b835821246fe8ac7ad980d3b1a18ecdd10ff6" type="download_file">
+                https://raw.github.com/miyagawa/cpanminus/c0c88f71118ecec334d62ba280e883933e7a6d39/cpanm
+                </action>
+                <!-- prepending means that the new install perl binary will be used after the pipe -->
+                <action type="shell_command">if [ -d "$TMP_WORK_DIR" ] ; then export HOME=$TMP_WORK_DIR ; else export HOME=`mktemp -d` ; fi ; unset PERL_MB_OPT PERL_MM_OPT ; export PERL5LIB=$INSTALL_DIR/lib/perl5/:$PERL5LIB ; export PATH=$INSTALL_DIR/bin/:$PATH ; cat cpanm | perl - App::cpanminus</action>
+                <action type="shell_command">LC_ALL=C sed -i.bak -e 's|#!$INSTALL_DIR/bin/|#!/usr/bin/env |' $INSTALL_DIR/bin/*</action>
+                <action type="set_environment">
+                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
+                    <environment_variable action="prepend_to" name="PERL5LIB">$INSTALL_DIR/lib/perl5</environment_variable>
+                    <environment_variable action="set_to" name="PERL_ROOT_DIR">$INSTALL_DIR</environment_variable>
+                    <environment_variable action="set_to" name="PERL_LOCALLIB_DIR">$INSTALL_DIR/local-lib</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>
+            Perl 5 is a highly capable, feature-rich programming language with over 25 years of development.
+            https://www.perl.org/
+
+            This repository contains local-lib and cpanm in addition.
+            It is recommended to use something like "cpanm --local-lib=$PERL_ROOT_DIR XML::Parser" to install additional perl modules.
+        </readme>
+    </package>
+</tool_dependency>