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Patch minimus2 during install (bug reported in 2011 not yet fixed in amos source)
author Jim Johnson <jj@umn.edu>
date Fri, 19 Jul 2013 08:01:23 -0500
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1 <?xml version='1.0' encoding='utf-8'?>
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2 <tool_dependency>
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3 <package name="boost" version="1.53.0">
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4 <repository changeset_revision="a72f8efe9201" name="package_boost_1_53" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
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5 </package>
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6 <package name="mummer" version="3.23">
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7 <repository changeset_revision="8268327cce24" name="package_mummer_3_23" owner="jjohnson" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
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8 </package>
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9 <package name="amos" version="3.1.0">
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10 <install version="1.0">
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11 <actions>
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12 <action type="download_by_url">http://sourceforge.net/projects/amos/files/amos/3.1.0/amos-3.1.0.tar.gz</action>
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b5e98e4efb18 Patch minimus2 during install (bug reported in 2011 not yet fixed in amos source)
Jim Johnson <jj@umn.edu>
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13 <!-- patch this, since it has been a bug since 2011 -->
b5e98e4efb18 Patch minimus2 during install (bug reported in 2011 not yet fixed in amos source)
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parents: 0
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14 <action type="shell_command">sed -i.bak 's/dumpreads \(\$[(]BANK[)]\) \(-[mM]\) \(\$[(]REFCOUNT[)]\)/dumpreads \2 \3 \1/' src/Pipeline/minimus2.acf</action>
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15 <action type="shell_command">./configure --prefix=$INSTALL_DIR</action>
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16 <action type="shell_command">make</action>
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17 <action type="shell_command">make install</action>
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18 <action type="set_environment">
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19 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
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20 </action>
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21 </actions>
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22 </install>
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23 <readme>
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24 http://sourceforge.net/projects/amos/
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25 AMOS is a collection of tools and class interfaces for the assembly of DNA reads. The package includes a robust infrastructure, modular assembly pipelines, and tools for overlapping, consensus generation, contigging, and assembly manipulation.
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26 </readme>
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27 </package>
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28 </tool_dependency>