Mercurial > repos > iuc > package_trnascan_1_3_1

annotate tool_dependencies.xml @ 2:a3c3535a61a5 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_trnascan_1_3_1 commit 025696892784ba9fd07404ce4d21f3dca4ac1a1e-dirty
author iuc
date Fri, 17 Jul 2015 14:18:37 -0400
parents a3fb2752c340
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1 <tool_dependency>
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2 <package name="tRNAscan-SE" version="1.3.1">
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3 <install version="1.0">
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4 <actions>
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5 <action type="download_by_url">http://lowelab.ucsc.edu/software/tRNAscan-SE.tar.gz</action>
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6 <action type="make_directory">$INSTALL_DIR/bin/</action>
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7 <action type="make_directory">$INSTALL_DIR/lib/tRNAscan-SE/</action>
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8 <action type="make_directory">$INSTALL_DIR/man/</action>
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9 <!-- replacing the hardcoded pathvariables with the real ones -->
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a3c3535a61a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_trnascan_1_3_1 commit 025696892784ba9fd07404ce4d21f3dca4ac1a1e-dirty
iuc
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10 <action type="shell_command">sed -i.bak -e "s|^BINDIR = .*|BINDIR = $INSTALL_DIR/bin/|" Makefile</action>
a3c3535a61a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_trnascan_1_3_1 commit 025696892784ba9fd07404ce4d21f3dca4ac1a1e-dirty
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11 <action type="shell_command">sed -i.bak -e "s|^LIBDIR = .*|LIBDIR = $INSTALL_DIR/lib/tRNAscan-SE/|" Makefile</action>
a3c3535a61a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_trnascan_1_3_1 commit 025696892784ba9fd07404ce4d21f3dca4ac1a1e-dirty
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12 <action type="shell_command">sed -i.bak -e "s|^MANDIR = .*|MANDIR = $INSTALL_DIR/man|" Makefile</action>
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13 <action type="make_install"/>
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15 <!-- for some reason infernal needs to be directly under the bin/ from tRNAScan -->
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a3c3535a61a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_trnascan_1_3_1 commit 025696892784ba9fd07404ce4d21f3dca4ac1a1e-dirty
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16 <action type="download_file">ftp://selab.janelia.org/pub/software/infernal/infernal-1.0.2.tar.gz</action>
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17 <action type="shell_command">tar xfvz infernal-1.0.2.tar.gz</action>
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18 <action type="shell_command">cd infernal-1.0.2 &amp;&amp; ./configure --prefix=$INSTALL_DIR &amp;&amp; make &amp;&amp; make install</action>
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19 <action type="set_environment">
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20 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
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21 <environment_variable name="PERL5LIB" action="prepend_to">$INSTALL_DIR/bin/</environment_variable>
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22 </action>
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23 </actions>
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24 </install>
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25 <readme>Compiling and running tRNAScan-SE requires gcc a PERL environment.</readme>
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26 </package>
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27 </tool_dependency>