# HG changeset patch
# User mvdbeek
# Date 1439645588 14400
# Node ID ce7da2f8d213b3396efc8a48774bb1ec6f5ab3cf

planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty

diff -r 000000000000 -r ce7da2f8d213 tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Sat Aug 15 09:33:08 2015 -0400
@@ -0,0 +1,48 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <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="ncbi_ngs" version="1.1.3">
+        <repository changeset_revision="f090c319428b" name="package_ngs_1_1_3" 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 target_filename="sra-tools-2.5.2.tar.gz" type="download_by_url">https://github.com/ncbi/sra-tools/archive/2.5.2.tar.gz</action>
+            <action type="shell_command">
+            ./configure --prefix=$INSTALL_DIR --build-prefix=$INSTALL_DIR/build
+            sed -i -e "109s/-static//" tools/copycat/Makefile
+            make
+            make install
+            cd $INSTALL_DIR/bin
+            ./vdb-config -s "/repository/user/main/public/cache-enabled=false"
+            ./vdb-config -s "/repository/user/main/public/root=$INSTALL_DIR"
+            </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>