Mercurial > repos > jeremie > package_pindel_0_2_5

annotate tool_dependencies.xml @ 27:ae37c0fd6590 draft default tip

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author jeremie
date Fri, 20 Jun 2014 10:40:33 -0400
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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="samtools" version="0.1.18">
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4 <repository changeset_revision="171cd8bc208d" name="package_samtools_0_1_18" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" prior_installation_required="True" />
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5 </package>
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6 <package name="pindel" version="0.2.5">
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7 <install version="1.0">
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8 <actions>
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9 <!-- <action type="shell_command">git clone https://github.com/genome/pindel.git pindel</action> -->
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10 <action type="download_by_url" target_filename="pindel-master.zip">https://github.com/genome/pindel/archive/master.zip</action>
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11 <action type="shell_command">ls ..</action>
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12 <action type="shell_command">
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13 echo "$samtools
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14 samtools
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15 $PATH
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16 $INSTALL_DIR"
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17 </action>
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18 <!-- <action type="shell_command">ls</action> -->
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19 <!-- <action type="move_directory_files">
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20 <source_directory>.</source_directory>
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21 <destination_directory>$INSTALL_DIR</destination_directory>
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22 </action>
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23 <action type="shell_command">unzip pindel-master.zip -d pindel</action>
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24 <action type="shell_command">cd master</action> -->
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25 <!-- <action type="shell_command">sed '50d' Makefile</action> -->
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26 <!-- <action type="shell_command">make Makefile.local</action> -->
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27 <action type="shell_command">
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28 echo "SAMTOOLS=
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29 THREADS=
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30 COLOUSINGBD15_TIME=60
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31 COLOWOBD15_TIME=80
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32 SIM1CHRVS20305_TIME=60" > Makefile.local
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33 </action>
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34 <action type="shell_command">make SAMTOOLS=samtools THREADS=2</action>
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35 <action type="move_file">
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36 <source>pindel</source>
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37 <destination>$INSTALL_DIR/</destination>
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38 </action>
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39 <action type="set_environment">
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40 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
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41 </action>
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42 </actions>
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43 </install>
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44 <readme>
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45 </readme>
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46 </package>
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47 </tool_dependency>