# HG changeset patch
# User mvdbeek
# Date 1443187709 14400
# Node ID d05694dbe2d463402baaad126c4efc64e5aeb62d

planemo upload commit 92d32947393757598262fbaed175b2c6fd84c181

diff -r 000000000000 -r d05694dbe2d4 tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Fri Sep 25 09:28:29 2015 -0400
@@ -0,0 +1,57 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="ascp" version="3">
+        <repository changeset_revision="e053dbdb5302" name="package_ascp_3" owner="mvdbeek" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="ncbi_vdb" version="2.5.2">
+        <repository changeset_revision="a3f02a928f5e" name="package_ncbi_vdb_2_5_2" owner="mvdbeek" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="sra_toolkit" version="2.5.2">
+        <install version="1.0">
+            <actions>
+                <action type="set_environment_for_install">
+                    <repository changeset_revision="a3f02a928f5e" name="package_ncbi_vdb_2_5_2" owner="mvdbeek" toolshed="https://testtoolshed.g2.bx.psu.edu">
+                        <package name="ncbi_vdb" version="2.5.2" />
+                    </repository>
+                    <repository changeset_revision="f530f97e76ea" name="package_ngs_sdk_1_1_3" owner="mvdbeek" toolshed="https://testtoolshed.g2.bx.psu.edu">
+                        <package name="ngs_sdk" version="1.1.3" />
+                    </repository>
+                </action>
+                <action target_filename="sra-tools-2.5.2.tar.gz" type="download_file">https://github.com/ncbi/sra-tools/archive/2.5.2.tar.gz</action>
+                <action type="shell_command">tar -xf sra-tools-2.5.2.tar.gz</action>
+                <action type="change_directory">sra-tools-2.5.2</action>
+                <action type="shell_command">
+                    ./configure --prefix=$INSTALL_DIR -with-ngs-sdk-prefix=$NGS_SDK_DIR --with-ncbi-vdb-sources=$NCBI_VDB_DIR --with-ncbi-vdb-build=$NCBI_VDB_DIR --build=$INSTALL_DIR/build
+                    sed -i -e "109s/-static//" tools/copycat/Makefile
+                </action>
+                <action type="make_install" />
+                <action type="shell_command">
+                    $INSTALL_DIR/bin/vdb-config --restore-defaults
+                </action>
+                <action type="set_environment">
+                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>
+            Tools from NCBI SRA Toolkit for extracting FASTQ and SAM format reads from SRA format archives.
+            This software release was designed to run under Linux, MacOSX operating systems on Intel x86-compatible 64 bit architectures.
+            When running on Amazon EC2, be sure to keep in mind the size limitation of EBS storage devices when requesting a
+            download of a large SRA data set.
+
+            Build Requirements:
+            - make
+            - git
+            - gcc
+            - g++
+            - libxml2
+            - libcurl4
+            - zlib
+
+            On a debian based Linux OS use:
+
+            apt-get install build-essential libxml2-dev libcurl4-openssl-dev zlib-dev
+
+        </readme>
+    </package>
+</tool_dependency>