# HG changeset patch
# User mvdbeek
# Date 1446637919 18000
# Node ID 88273fd00182c1b83aad6f8e6aa1a41a7bf6983c

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/packages/package_sra_toolkit_2_5_2 commit 70fadb7e8972b1db550d0e067584930ce1ec8673-dirty

diff -r 000000000000 -r 88273fd00182 tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Wed Nov 04 06:51:59 2015 -0500
@@ -0,0 +1,61 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="ascp" version="3">
+        <repository changeset_revision="e109f0ec22c3" name="package_ascp_3" owner="mvdbeek" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="perl" version="5.18.1">
+        <repository changeset_revision="8b3509930a44" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="ncbi_vdb" version="2.5.2">
+        <repository changeset_revision="1d307129f4f2" name="package_ncbi_vdb_2_5_2" owner="mvdbeek" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="ngs_sdk" version="1.1.3">
+        <repository changeset_revision="2cc3f1941cb5" name="package_ngs_sdk_1_1_3" owner="mvdbeek" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="sra_toolkit" version="2.5.2">
+        <install version="1.0">
+            <actions>
+                <action type="download_by_url">https://github.com/ncbi/sra-tools/archive/2.5.2.tar.gz</action>
+                <action type="set_environment_for_install">
+                    <repository changeset_revision="8b3509930a44" name="package_perl_5_18" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
+                        <package name="perl" version="5.18.1" />
+                    </repository>
+                    <repository changeset_revision="1d307129f4f2" name="package_ncbi_vdb_2_5_2" owner="mvdbeek" toolshed="https://toolshed.g2.bx.psu.edu">
+                        <package name="ncbi_vdb" version="2.5.2" />
+                    </repository>
+                    <repository changeset_revision="2cc3f1941cb5" name="package_ngs_sdk_1_1_3" owner="mvdbeek" toolshed="https://toolshed.g2.bx.psu.edu">
+                        <package name="ngs_sdk" version="1.1.3" />
+                    </repository>
+                </action>
+                <action type="shell">
+                    ./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=$INSTALL_DIR/build
+                </action>
+                <action type="shell_command">sed -i -e "109s/-static//" tools/copycat/Makefile</action>
+                <action type="make_install" />
+                <action type="set_environment">
+                    <environment_variable action="prepend_to" name="PATH">$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>