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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="tandem_repeats_finder" version="4.0">
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4 <repository changeset_revision="a2e1d1f25e35" name="tandem_repeats_finder" owner="urgi-team" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
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5 </package>
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6 <package name="mgescan" version="3">
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7 <install version="1.0">
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8 <actions_group>
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9 <actions architecture="x86_64" os="linux">
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10 <action type="download_by_url">
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11 https://github.com/MGEScan/mgescan/archive/1.0.tar.gz
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12 </action>
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13 <action type="move_directory_files">
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14 <source_directory>.</source_directory>
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15 <destination_directory>$INSTALL_DIR</destination_directory>
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16 </action>
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17 </actions>
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18 <actions>
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19 <action type="download_by_url">
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20 https://github.com/MGEScan/mgescan/archive/1.0.tar.gz
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21 </action>
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22 <action type="set_environment_for_install">
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23 <repository changeset_revision="a2e1d1f25e35" name="tandem_repeats_finder" owner="urgi-team" toolshed="https://toolshed.g2.bx.psu.edu">
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24 <package name="trf" version="4.0" />
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25 </repository>
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26 </action>
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27 <action type="shell_command">cd mgescan-1.0</action>
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28 <action type="shell_command">python setup.py install</action>
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29 <action type="move_file">
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30 <source>mgescan</source>
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31 <destination>$INSTALL_DIR/bin</destination>
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32 </action>
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33 </actions>
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34 <action type="set_environment">
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35 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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36 <environment_variable action="set_to" name="SAMTOOLS_ROOT_PATH">$INSTALL_DIR</environment_variable>
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37 </action>
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38 </actions_group>
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39 </install>
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40 <readme>
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41 Program: mgescan (Tools for identifying LTR & nonLTR)
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42 Version: 3.0
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43
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44 Usage:
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45 mgescan both <genome_dir> [--output=<data_dir>] [--mpi=<num>]
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46 mgescan ltr <genome_dir> [--output=<data_dir>] [--mpi=<num>]
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47 mgescan nonltr <genome_dir> [--output=<data_dir>] [--mpi=<num>]
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48 mgescan (-h | --help)
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49 mgescan --version
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50
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51 </readme>
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52 </package>
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53 </tool_dependency>
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