Mercurial > repos > rnateam > blockclust

comparison tool_dependencies.xml @ 7:e6f49ee3509c draft

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Uploaded
author rnateam
date Mon, 21 Jul 2014 09:19:13 -0400
parents a50bd507edfe
children c1cc480c53da
comparison
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6:6721468f2f9f 7:e6f49ee3509c
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool_dependency> 2 <tool_dependency>
3 <package name="samtools" version="0.1.19"> 3 <package name="samtools" version="0.1.19">
4 <repository changeset_revision="6b6b5498d9a2" name="package_samtools_0_1_19" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> 4 <repository changeset_revision="279806044d60" name="package_samtools_0_1_19" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
5 </package> 5 </package>
6 <package name="R_3_0_1" version="3.0.1"> 6 <package name="R_3_0_1" version="3.0.1">
7 <repository changeset_revision="c5ff6dd33c79" name="package_r_3_0_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> 7 <repository changeset_revision="c5ff6dd33c79" name="package_r_3_0_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
8 </package> 8 </package>
9 <package name="eden" version="1.1"> 9 <package name="eden" version="1.1">
10 <repository changeset_revision="532625813f2e" name="package_eden_1_1" owner="rnateam" toolshed="https://toolshed.g2.bx.psu.edu" /> 10 <repository changeset_revision="8087eef83c35" name="package_eden_1_1" owner="rnateam" toolshed="https://toolshed.g2.bx.psu.edu" />
11 </package> 11 </package>
12 <package name="mcl" version="12.135"> 12 <package name="mcl" version="12.135">
13 <repository changeset_revision="9f59d1a59999" name="package_mcl_12_135" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> 13 <repository changeset_revision="9f59d1a59999" name="package_mcl_12_135" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
14 </package> 14 </package>
15 <package name="blockclust_rlibs" version="1.0"> 15 <package name="blockclust_rlibs" version="1.0">
70 <source>rfam_map.txt</source> 70 <source>rfam_map.txt</source>
71 <destination>$INSTALL_DIR/data/</destination> 71 <destination>$INSTALL_DIR/data/</destination>
72 </action> 72 </action>
73 <action type="make_directory">$INSTALL_DIR/data/annotations</action> 73 <action type="make_directory">$INSTALL_DIR/data/annotations</action>
74 <action type="download_file">https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-data-1.0/annotations/dm3.tar.gz</action> 74 <action type="download_file">https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-data-1.0/annotations/dm3.tar.gz</action>
75 <action type="shell_command">cd ..; tar xfvz dm3.tar.gz -C $INSTALL_DIR/data/annotations/</action> 75 <action type="shell_command">tar xfvz dm3.tar.gz -C $INSTALL_DIR/data/annotations/</action>
76 <action type="download_file">https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-data-1.0/annotations/hg19.tar.gz</action> 76 <action type="download_file">https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-data-1.0/annotations/hg19.tar.gz</action>
77 <action type="shell_command">cd ..; tar xfvz hg19.tar.gz -C $INSTALL_DIR/data/annotations/</action> 77 <action type="shell_command">tar xfvz hg19.tar.gz -C $INSTALL_DIR/data/annotations/</action>
78 <action type="download_file">https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-data-1.0/annotations/mm10.tar.gz</action> 78 <action type="download_file">https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-data-1.0/annotations/mm10.tar.gz</action>
79 <action type="shell_command">cd ..; tar xfvz mm10.tar.gz -C $INSTALL_DIR/data/annotations/</action> 79 <action type="shell_command">tar xfvz mm10.tar.gz -C $INSTALL_DIR/data/annotations/</action>
80 <action type="download_file">https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-data-1.0/annotations/panTro4.tar.gz</action> 80 <action type="download_file">https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-data-1.0/annotations/panTro4.tar.gz</action>
81 <action type="shell_command">cd ..; tar xfvz panTro4.tar.gz -C $INSTALL_DIR/data/annotations/</action> 81 <action type="shell_command">tar xfvz panTro4.tar.gz -C $INSTALL_DIR/data/annotations/</action>
82 <action type="download_file">https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-data-1.0/annotations/rheMac3.tar.gz</action> 82 <action type="download_file">https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-data-1.0/annotations/rheMac3.tar.gz</action>
83 <action type="shell_command">cd ..; tar xfvz rheMac3.tar.gz -C $INSTALL_DIR/data/annotations/</action> 83 <action type="shell_command">tar xfvz rheMac3.tar.gz -C $INSTALL_DIR/data/annotations/</action>
84 <action type="download_file">https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-data-1.0/annotations/celWS235.tar.gz</action> 84 <action type="download_file">https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-data-1.0/annotations/celWS235.tar.gz</action>
85 <action type="shell_command">cd ..; tar xfvz celWS235.tar.gz -C $INSTALL_DIR/data/annotations/</action> 85 <action type="shell_command">tar xfvz celWS235.tar.gz -C $INSTALL_DIR/data/annotations/</action>
86 <action type="download_file">https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-data-1.0/annotations/tair10.tar.gz</action> 86 <action type="download_file">https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-data-1.0/annotations/tair10.tar.gz</action>
87 <action type="shell_command">cd ..; tar xfvz tair10.tar.gz -C $INSTALL_DIR/data/annotations/</action> 87 <action type="shell_command">tar xfvz tair10.tar.gz -C $INSTALL_DIR/data/annotations/</action>
88 <action type="download_file">https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-data-1.0/models.tar.gz</action> 88 <action type="download_file">https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-data-1.0/models.tar.gz</action>
89 <action type="shell_command">cd ..; tar xfvz models.tar.gz -C $INSTALL_DIR/data/</action> 89 <action type="shell_command">tar xfvz models.tar.gz -C $INSTALL_DIR/data/</action>
90 <action type="set_environment"> 90 <action type="set_environment">
91 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> 91 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
92 <environment_variable action="set_to" name="BLOCKCLUST_DATA_PATH">$INSTALL_DIR/data</environment_variable> 92 <environment_variable action="set_to" name="BLOCKCLUST_DATA_PATH">$INSTALL_DIR/data</environment_variable>
93 </action> 93 </action>
94 </actions> 94 </actions>