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comparison tool_dependencies.xml @ 0:ec8b334b5ebb draft

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planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
author mvdbeek
date Fri, 14 Aug 2015 12:23:28 -0400
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1 <?xml version="1.0"?>
2 <tool_dependency>
3 <package name="sra_toolkit" version="2.4.5">
4 <install version="1.0">
5 <actions>
6 <action type="make_directory">src</action>
7 <action type="make_directory">build</action>
8 <action type="change_directory">src</action>
9 <action type="shell_command">
10 git clone https://github.com/mdshw5/sra-tools.git
11 git clone https://github.com/mdshw5/ncbi-vdb.git
12 git clone https://github.com/mdshw5/ngs.git
13 LD_LIBRARY_PATH=LD_LIBRARY_PATH:$INSTALL_DIR/lib64:$INSTALL_DIR/lib
14 cd $INSTALL_DIR/src/ncbi-vdb
15 ./configure --prefix=$INSTALL_DIR --build-prefix=$INSTALL_DIR/build
16 make
17 make install
18 cd $INSTALL_DIR/src/ngs/ngs-sdk
19 ./configure --prefix=$INSTALL_DIR --build-prefix=$INSTALL_DIR/build
20 make
21 make install
22 cd $INSTALL_DIR/src/sra-tools
23 ./configure --prefix=$INSTALL_DIR --build-prefix=$INSTALL_DIR/build --with-ncbi-vdb-build=$INSTALL_DIR/build --with-ncbi-vdb-sources=$INSTALL_DIR/src/ncbi-vdb --with-ngs-sdk-prefix=$INSTALL_DIR
24 sed -i -e "109s///" tools/copycat/Makefile
25 make
26 make install
27 cd $INSTALL_DIR/bin
28 ./vdb-config -s "/repository/user/main/public/cache-enabled=false"
29 ./vdb-config -s "/repository/user/main/public/root=$INSTALL_DIR"
30 </action>
31 <action type="set_environment">
32 <environment_variable name="PATH" action="prepend_to">$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>