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planemo upload commit 92d32947393757598262fbaed175b2c6fd84c181
author mvdbeek
date Fri, 25 Sep 2015 09:28:29 -0400
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children 531f4eea4196
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-1:000000000000 0:d05694dbe2d4
1 <?xml version="1.0"?>
2 <tool_dependency>
3 <package name="ascp" version="3">
4 <repository changeset_revision="e053dbdb5302" name="package_ascp_3" owner="mvdbeek" toolshed="https://testtoolshed.g2.bx.psu.edu" />
5 </package>
6 <package name="ncbi_vdb" version="2.5.2">
7 <repository changeset_revision="a3f02a928f5e" name="package_ncbi_vdb_2_5_2" owner="mvdbeek" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
8 </package>
9 <package name="sra_toolkit" version="2.5.2">
10 <install version="1.0">
11 <actions>
12 <action type="set_environment_for_install">
13 <repository changeset_revision="a3f02a928f5e" name="package_ncbi_vdb_2_5_2" owner="mvdbeek" toolshed="https://testtoolshed.g2.bx.psu.edu">
14 <package name="ncbi_vdb" version="2.5.2" />
15 </repository>
16 <repository changeset_revision="f530f97e76ea" name="package_ngs_sdk_1_1_3" owner="mvdbeek" toolshed="https://testtoolshed.g2.bx.psu.edu">
17 <package name="ngs_sdk" version="1.1.3" />
18 </repository>
19 </action>
20 <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>
21 <action type="shell_command">tar -xf sra-tools-2.5.2.tar.gz</action>
22 <action type="change_directory">sra-tools-2.5.2</action>
23 <action type="shell_command">
24 ./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
25 sed -i -e "109s/-static//" tools/copycat/Makefile
26 </action>
27 <action type="make_install" />
28 <action type="shell_command">
29 $INSTALL_DIR/bin/vdb-config --restore-defaults
30 </action>
31 <action type="set_environment">
32 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
33 </action>
34 </actions>
35 </install>
36 <readme>
37 Tools from NCBI SRA Toolkit for extracting FASTQ and SAM format reads from SRA format archives.
38 This software release was designed to run under Linux, MacOSX operating systems on Intel x86-compatible 64 bit architectures.
39 When running on Amazon EC2, be sure to keep in mind the size limitation of EBS storage devices when requesting a
40 download of a large SRA data set.
41
42 Build Requirements:
43 - make
44 - git
45 - gcc
46 - g++
47 - libxml2
48 - libcurl4
49 - zlib
50
51 On a debian based Linux OS use:
52
53 apt-get install build-essential libxml2-dev libcurl4-openssl-dev zlib-dev
54
55 </readme>
56 </package>
57 </tool_dependency>