Mercurial > repos > rnateam > blockclust

comparison tool_dependencies.xml @ 6:b77328c96ac9 draft

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Uploaded
author rnateam
date Tue, 22 Oct 2013 11:27:29 -0400
parents 49b72f1013b3
children a2aed24f5846
comparison
equal deleted inserted replaced
5:49b72f1013b3 6:b77328c96ac9
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool_dependency> 2 <tool_dependency>
3 <package name="blockclust" version="1.0"> 3 <package name="samtools" version="0.1.19">
4 <repository changeset_revision="54195f1d4b0f" name="package_samtools_0_1_19" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
5 </package>
6 <package name="blockclust" version="1.0">
4 <install version="1.0"> 7 <install version="1.0">
5 <actions> 8 <actions>
6 <action type="download_by_url">https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-1.0.tar.gz</action> 9 <action type="download_by_url">https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-1.0.tar.gz</action>
7 <action type="shell_command">make</action> 10 <action type="shell_command">make</action>
8 <action type="move_file"> 11 <action type="move_file">
19 </action> 22 </action>
20 <action type="move_file"> 23 <action type="move_file">
21 <source>blockclust.config</source> 24 <source>blockclust.config</source>
22 <destination>$INSTALL_DIR/data/</destination> 25 <destination>$INSTALL_DIR/data/</destination>
23 </action> 26 </action>
27 <action type="move_file">
28 <source>rfam_map.txt</source>
29 <destination>$INSTALL_DIR/data/</destination>
30 </action>
24 <action type="make_directory">$INSTALL_DIR/data/annotations</action> 31 <action type="make_directory">$INSTALL_DIR/data/annotations</action>
25 <action type="download_file">https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-data-1.0/annotations/dm3.tar.gz</action> 32 <action type="download_file">https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-data-1.0/annotations/dm3.tar.gz</action>
26 <action type="shell_command">tar xfvz dm3.tar.gz -C $INSTALL_DIR/data/annotations/</action> 33 <action type="shell_command">tar xfvz dm3.tar.gz -C $INSTALL_DIR/data/annotations/</action>
27 <action type="download_file">https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-data-1.0/annotations/hg19.tar.gz</action> 34 <action type="download_file">https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-data-1.0/annotations/hg19.tar.gz</action>
28 <action type="shell_command">tar xfvz hg19.tar.gz -C $INSTALL_DIR/data/annotations/</action> 35 <action type="shell_command">tar xfvz hg19.tar.gz -C $INSTALL_DIR/data/annotations/</action>
31 <action type="download_file">https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-data-1.0/annotations/panTro4.tar.gz</action> 38 <action type="download_file">https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-data-1.0/annotations/panTro4.tar.gz</action>
32 <action type="shell_command">tar xfvz panTro4.tar.gz -C $INSTALL_DIR/data/annotations/</action> 39 <action type="shell_command">tar xfvz panTro4.tar.gz -C $INSTALL_DIR/data/annotations/</action>
33 <action type="download_file">https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-data-1.0/annotations/rheMac3.tar.gz</action> 40 <action type="download_file">https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-data-1.0/annotations/rheMac3.tar.gz</action>
34 <action type="shell_command">tar xfvz rheMac3.tar.gz -C $INSTALL_DIR/data/annotations/</action> 41 <action type="shell_command">tar xfvz rheMac3.tar.gz -C $INSTALL_DIR/data/annotations/</action>
35 <action type="set_environment"> 42 <action type="set_environment">
36 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> 43 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
37 <environment_variable name="BLOCKCLUST_DATA_PATH" action="prepend_to">$INSTALL_DIR/data</environment_variable> 44 <environment_variable action="prepend_to" name="BLOCKCLUST_DATA_PATH">$INSTALL_DIR/data</environment_variable>
38 </action> 45 </action>
39 <action type="setup_r_environment"> 46 <action type="setup_r_environment">
40 <repository changeset_revision="e16e08f41ed7" name="package_r_3_0_1" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu"> 47 <repository changeset_revision="e16e08f41ed7" name="package_r_3_0_1" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
41 <package name="R_3_0_1" version="3.0.1" /> 48 <package name="R_3_0_1" version="3.0.1" />
42 </repository>
43 <repository changeset_revision="54195f1d4b0f" name="'package_samtools_0_1_19" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
44 <package name="samtools" version="0.1.19 " />
45 </repository> 49 </repository>
46 <r_package>http://cran.r-project.org/src/contrib/ggplot2_0.9.3.1.tar.gz</r_package> 50 <r_package>http://cran.r-project.org/src/contrib/ggplot2_0.9.3.1.tar.gz</r_package>
47 <r_package>http://cran.r-project.org/src/contrib/ape_3.0-11.tar.gz</r_package> 51 <r_package>http://cran.r-project.org/src/contrib/ape_3.0-11.tar.gz</r_package>
48 </action> 52 </action>
49 <action type="set_environment"> 53 <action type="set_environment">