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annotate tool_dependencies.xml @ 2:bc4451edb703 draft

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Update Orione citation. Update dependency to SSPACE Basic v2.1 . Add <citations>.
author crs4
date Mon, 27 Oct 2014 14:11:57 -0400
parents 93fa7ecb5292
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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="bowtie" version="1.0.0">
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4 <repository changeset_revision="9fcaaedbbfd6" name="package_bowtie_1_0_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
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5 </package>
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6 <package name="sspace" version="2.1">
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7 <install version="1.0">
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8 <actions>
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9 <action target_filename="sspace_basic-2.1.tar.gz" type="download_by_url">https://github.com/nsoranzo/sspace_basic/archive/v2.1.tar.gz</action>
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10 <action type="move_directory_files">
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11 <source_directory>.</source_directory>
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12 <destination_directory>$INSTALL_DIR</destination_directory>
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13 </action>
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14 <action type="set_environment">
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15 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable>
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16 </action>
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17 </actions>
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18 </install>
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19 <readme>
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93fa7ecb5292 Directly call SSPACE, remove sspace.py and hidden library file output. Use $GALAXY_SLOTS instead of $SSPACE_SITE_OPTIONS. Add readme.rst .
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20 Configuration: Previously (until Release 0), the SSPACE_SITE_OPTIONS variable in the installed env.sh file was used to adjust the number of threads to use in Bowtie alignment (-T). This is not used anymore and may be removed.
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21 </readme>
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22 </package>
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23 </tool_dependency>