Mercurial > repos > matt-shirley > ncbi_sra_toolkit
annotate tool_dependencies.xml @ 20:281f34ece271
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author | Matt Shirley <mdshw5@gmail.com> |
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date | Mon, 30 Mar 2015 20:59:06 -0400 |
parents | 6d25dfb4dbb4 |
children | 847db227d9ce |
rev | line source |
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2 | 1 <?xml version="1.0"?> |
2 <tool_dependency> | |
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3 <package name="sra_toolkit" version="2.4.5"> |
2 | 4 <install version="1.0"> |
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Should have linked the damn thing.
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5 <actions> |
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Matt Shirley <mdshw5@gmail.com>
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6 <action type="make_directory">src</action> |
c71031b17e08
Avoid relative paths, and rename "ncbi" dir
Matt Shirley <mdshw5@gmail.com>
parents:
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7 <action type="make_directory">build</action> |
c71031b17e08
Avoid relative paths, and rename "ncbi" dir
Matt Shirley <mdshw5@gmail.com>
parents:
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8 <action type="change_directory">src</action> |
19 | 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 </action> | |
15 <action type="change_directory">./ncbi-vdb</action> | |
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c71031b17e08
Avoid relative paths, and rename "ncbi" dir
Matt Shirley <mdshw5@gmail.com>
parents:
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diff
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16 <action type="autoconf">--prefix=$INSTALL_DIR --build-prefix=$INSTALL_DIR/build</action> |
19 | 17 <action type="change_directory">../ngs/ngs-sdk</action> |
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c71031b17e08
Avoid relative paths, and rename "ncbi" dir
Matt Shirley <mdshw5@gmail.com>
parents:
14
diff
changeset
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18 <action type="autoconf">--prefix=$INSTALL_DIR --build-prefix=$INSTALL_DIR/build</action> |
19 | 19 <action type="change_directory">../../sra-tools</action> |
20 | 20 <action type="shell_command">echo $PWD</action> |
15
c71031b17e08
Avoid relative paths, and rename "ncbi" dir
Matt Shirley <mdshw5@gmail.com>
parents:
14
diff
changeset
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21 <action type="autoconf">--prefix=$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 --with-magic-prefix=/dev/null</action> |
11
91558de676f4
Update to latest toolkit version - fix installation issues.
Matt Shirley <mdshw5@gmail.com>
parents:
10
diff
changeset
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22 <action type="shell_command">sed -i -e "s|\$(HOME)|$INSTALL_DIR|g" -e "s|cache-enabled = \"true\"|cache-enabled = \"false\"|" $INSTALL_DIR/ncbi/default.kfg</action> |
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a8261e9cbe13
Add install directory to PATH.
Matt Shirley <mdshw5@gmail.com>
parents:
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23 <action type="set_environment"><environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable></action> |
2 | 24 </actions> |
25 </install> | |
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91558de676f4
Update to latest toolkit version - fix installation issues.
Matt Shirley <mdshw5@gmail.com>
parents:
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26 <readme> |
91558de676f4
Update to latest toolkit version - fix installation issues.
Matt Shirley <mdshw5@gmail.com>
parents:
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27 Tools from NCBI SRA Toolkit for extracting FASTQ and SAM format reads from SRA format archives. |
7 | 28 This software release was designed to run under Linux, MacOSX operating systems on Intel x86-compatible 64 bit architectures. |
29 When running on Amazon EC2, be sure to keep in mind the size limitation of EBS storage devices when requesting a | |
2 | 30 download of a large SRA data set. |
31 | |
32 Build Requirements: | |
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parents:
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33 - make |
91558de676f4
Update to latest toolkit version - fix installation issues.
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parents:
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34 - git |
91558de676f4
Update to latest toolkit version - fix installation issues.
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parents:
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35 - gcc |
91558de676f4
Update to latest toolkit version - fix installation issues.
Matt Shirley <mdshw5@gmail.com>
parents:
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36 - g++ |
91558de676f4
Update to latest toolkit version - fix installation issues.
Matt Shirley <mdshw5@gmail.com>
parents:
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37 - libxml2 |
91558de676f4
Update to latest toolkit version - fix installation issues.
Matt Shirley <mdshw5@gmail.com>
parents:
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38 - libcurl4 |
91558de676f4
Update to latest toolkit version - fix installation issues.
Matt Shirley <mdshw5@gmail.com>
parents:
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39 - zlib |
7 | 40 |
2 | 41 On a debian based Linux OS use: |
42 | |
43 apt-get install build-essential libxml2-dev libcurl4-openssl-dev zlib-dev | |
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91558de676f4
Update to latest toolkit version - fix installation issues.
Matt Shirley <mdshw5@gmail.com>
parents:
10
diff
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44 |
2 | 45 </readme> |
46 </package> | |
47 </tool_dependency> |