Mercurial > repos > iuc > package_sra_toolkit_2_5_2

comparison tool_dependencies.xml @ 0:91924fa830bb draft

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author iuc
date Sun, 06 Dec 2015 08:59:25 -0500
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1 <?xml version="1.0"?>
2 <tool_dependency>
3 <package name="perl" version="5.18.1">
4 <repository changeset_revision="2590d4683481" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
5 </package>
6 <package name="ncbi_vdb" version="2.5.2">
7 <repository changeset_revision="b0638a3ba7e6" name="package_ncbi_vdb_2_5_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
8 </package>
9 <package name="ngs_sdk" version="1.1.3">
10 <repository changeset_revision="1381744a8a09" name="package_ngs_sdk_1_1_3" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
11 </package>
12 <package name="sra_toolkit" version="2.5.2">
13 <install version="1.0">
14 <actions>
15 <action type="download_by_url">https://github.com/ncbi/sra-tools/archive/2.5.2.tar.gz</action>
16 <action type="set_environment_for_install">
17 <repository changeset_revision="2590d4683481" name="package_perl_5_18" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
18 <package name="perl" version="5.18.1" />
19 </repository>
20 <repository changeset_revision="b0638a3ba7e6" name="package_ncbi_vdb_2_5_2" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
21 <package name="ncbi_vdb" version="2.5.2" />
22 </repository>
23 <repository changeset_revision="1381744a8a09" name="package_ngs_sdk_1_1_3" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
24 <package name="ngs_sdk" version="1.1.3" />
25 </repository>
26 </action>
27 <action type="shell_command">
28 ./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=$INSTALL_DIR/build
29 </action>
30 <action type="shell_command">
31 sed -i -e "109s/-static//" tools/copycat/Makefile
32 </action>
33 <action type="make_install" />
34 <action type="set_environment">
35 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
36 </action>
37 </actions>
38 </install>
39 <readme>
40 Tools from NCBI SRA Toolkit for extracting FASTQ and SAM format reads from SRA format archives.
41 This software release was designed to run under Linux, MacOSX operating systems on Intel x86-compatible 64 bit architectures.
42 When running on Amazon EC2, be sure to keep in mind the size limitation of EBS storage devices when requesting a
43 download of a large SRA data set.
44
45 Build Requirements:
46 - make
47 - git
48 - gcc
49 - g++
50 - libxml2
51 - libcurl4
52 - zlib
53
54 On a debian based Linux OS use:
55
56 apt-get install build-essential libxml2-dev libcurl4-openssl-dev zlib-dev
57
58 </readme>
59 </package>
60 </tool_dependency>