Mercurial > repos > iuc > package_sra_toolkit_2_6_2
comparison tool_dependencies.xml @ 0:98414d1f9480 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sra_toolkit_2_6_2 commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
author | iuc |
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date | Tue, 17 May 2016 14:14:22 -0400 |
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1 <?xml version="1.0"?> | |
2 <tool_dependency> | |
3 <package name="perl" version="5.18.1"> | |
4 <repository changeset_revision="35f117d7396b" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> | |
5 </package> | |
6 <package name="libmagic" version="5.25"> | |
7 <repository changeset_revision="21b08f55a6ac" name="package_libmagic_5_25" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> | |
8 </package> | |
9 <package name="ncbi_vdb" version="2.6.2"> | |
10 <repository changeset_revision="be38d36c735d" name="package_ncbi_vdb_2_6_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> | |
11 </package> | |
12 <package name="ngs_sdk" version="1.2.3"> | |
13 <repository changeset_revision="3da0f4d34e92" name="package_ngs_sdk_1_2_3" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> | |
14 </package> | |
15 <package name="sra_toolkit" version="2.6.2"> | |
16 <install version="1.0"> | |
17 <actions> | |
18 <action sha256sum="7aa1ec118486cd877bf2976818a3f319674584f3d04931a6ce2a92f6a9defbc1" 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="35f117d7396b" name="package_perl_5_18" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> | |
21 <package name="perl" version="5.18.1" /> | |
22 </repository> | |
23 <repository changeset_revision="21b08f55a6ac" name="package_libmagic_5_25" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> | |
24 <package name="libmagic" version="5.25" /> | |
25 </repository> | |
26 <repository changeset_revision="be38d36c735d" name="package_ncbi_vdb_2_6_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> | |
27 <package name="ncbi_vdb" version="2.6.2" /> | |
28 </repository> | |
29 <repository changeset_revision="3da0f4d34e92" name="package_ngs_sdk_1_2_3" owner="iuc" toolshed="https://toolshed.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> |