Mercurial > repos > iuc > package_sra_toolkit_2_6_2

comparison tool_dependencies.xml @ 0:4503178d0713 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sra_toolkit_2_6_2 commit b3cb19dca2651e57fccc84cc09c8ad2202502528
author iuc
date Tue, 17 May 2016 04:33:59 -0400
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children 635c214d2e01
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-1:000000000000 0:4503178d0713
1 <?xml version="1.0"?>
2 <tool_dependency>
3 <package name="perl" version="5.18.1">
4 <repository changeset_revision="95dad0955d7e" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
5 </package>
6 <package name="libmagic" version="5.25">
7 <repository changeset_revision="c7b9857a1522" name="package_libmagic_5_25" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
8 </package>
9 <package name="ncbi_vdb" version="2.6.2">
10 <repository changeset_revision="62f37b0b1373" name="package_ncbi_vdb_2_6_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
11 </package>
12 <package name="ngs_sdk" version="1.2.3">
13 <repository changeset_revision="af8bc70ca765" name="package_ngs_sdk_1_2_3" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
14 </package>
15 <package name="sra_toolkit" version="2.6.2">
16 <install version="1.0">
17 <actions>
18 <action type="download_by_url">https://github.com/ncbi/sra-tools/archive/2.6.2.tar.gz</action>
19 <action type="set_environment_for_install">
20 <repository changeset_revision="95dad0955d7e" name="package_perl_5_18" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
21 <package name="perl" version="5.18.1" />
22 </repository>
23 <repository changeset_revision="c7b9857a1522" name="package_libmagic_5_25" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
24 <package name="libmagic" version="5.25" />
25 </repository>
26 <repository changeset_revision="62f37b0b1373" name="package_ncbi_vdb_2_6_2" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
27 <package name="ncbi_vdb" version="2.6.2" />
28 </repository>
29 <repository changeset_revision="af8bc70ca765" name="package_ngs_sdk_1_2_3" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
30 <package name="ngs_sdk" version="1.2.3" />
31 </repository>
32 </action>
33 <action type="shell_command">
34 ./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=$INSTALL_DIR
35 </action>
36 <action type="make_install" />
37 <action type="set_environment">
38 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
39 </action>
40 </actions>
41 </install>
42 <readme>
43 Tools from NCBI SRA Toolkit for extracting FASTQ and SAM format reads from SRA format archives.
44 This software release was designed to run under Linux, MacOSX operating systems on Intel x86-compatible 64 bit architectures.
45 When running on Amazon EC2, be sure to keep in mind the size limitation of EBS storage devices when requesting a
46 download of a large SRA data set.
47
48 Build Requirements:
49 - make
50 - git
51 - gcc
52 - g++
53 - libxml2
54 - libcurl4
55 - zlib
56
57 On a debian based Linux OS use:
58
59 apt-get install build-essential libxml2-dev libcurl4-openssl-dev zlib-dev
60
61 </readme>
62 </package>
63 </tool_dependency>