Mercurial > repos > stef > qdnaseq

annotate tool_dependencies.xml @ 20:ecc807c0f4f5 draft

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author stef
date Tue, 17 Jun 2014 05:14:40 -0400
parents eefb834376ba
children 45c44ee8ab1a
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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3
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4 <set_environment version="1.0">
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5 <environment_variable name="QDNASEQ_SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
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6 </set_environment>
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8 <package name="R" version="3.0.3">
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9 <repository changeset_revision="232ebc8b1c0d" name="package_r_3_0_3" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu/" />
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10 </package>
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11
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12 <package name="bioc_qdnaseq" version="1.0.5">
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13 <install version="1.0">
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14 <actions>
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15 <action type="shell_command">echo "[DEBUG] INSTALL DIR: $INSTALL_DIR"</action>
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16 <action type="shell_command">echo "[DEBUG] REPOS INSTALL DIR: $REPOSITORY_INSTALL_DIR"</action>
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18 <action type="shell_command">echo "[DEBUG] BEFORE:" &amp;&amp; pwd</action>
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19 <action type="shell_command">echo "[DEBUG] DIR LISTING:" &amp;&amp; ls -l</action>
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20 <action type="shell_command">echo "[DEBUG] DIR LISTING ONE UP:" &amp;&amp; ls -l ../</action>
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21 <action type="move_file">
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22 <source>"../QDNAseq.R"</source>
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23 <destination>./</destination>
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24 </action>
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26 <action type="shell_command">echo "[DEBUG] AFTER:" &amp;&amp; pwd</action>
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27 <action type="shell_command">echo "[DEBUG] DIR LISTING:" &amp;&amp; ls -l</action>
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29 <action type="set_environment_for_install">
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30 <repository changeset_revision="232ebc8b1c0d" name="package_r_3_0_3" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu/">
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31 <package name="R" version="3.0.3" />
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32 </repository>
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33 </action>
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34 <action type="set_environment">
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35 <environment_variable action="prepend_to" name="R_LIBS">$INSTALL_DIR/bin</environment_variable>
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36 </action>
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37 <action type="shell_command">echo "[DEBUG] NOW ABOUT TO DOWNLOAD"</action>
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39 <action type="download_file">http://bioconductor.org/packages/release/bioc/src/contrib/QDNAseq_1.0.5.tar.gz</action>
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41 <action type="shell_command">echo "[DEBUG] WORKING DIR:" &amp;&amp; pwd</action>
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42 <action type="shell_command">echo "[DEBUG] DIR LISTING:" &amp;&amp; ls -l</action>
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43
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44 <action type="shell_command">echo "[DEBUG] NOW ABOUT TO INSTALL"</action>
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45 <action type="shell_command">export R_LIBS=$INSTALL_DIR &amp;&amp; R CMD INSTALL --build QDNAseq_1.0.5.tar.gz</action>
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46 <!--<action type="shell_command">R CMD INSTALL QDNAseq_1.0.5.tar.gz</action>-->
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47 </actions>
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48 </install>
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49
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50 <readme>
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51 Should install QDNAseq package from bioconductor.
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52 </readme>
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53 </package>
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54
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55 </tool_dependency>