Mercurial > repos > lionelguy > spades

annotate tools/spades_2_5/tool_dependencies.xml @ 5:2f7860a0017b draft

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author lionelguy
date Thu, 12 Sep 2013 07:48:50 -0400
parents d82f18c76309
children 1b1af74a54ae
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0f8b2da62d7d Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
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1 <?xml version="1.0"?>
0f8b2da62d7d Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
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2 <tool_dependency>
0f8b2da62d7d Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
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3 <package name="spades" version="2.5.0">
0f8b2da62d7d Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
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4 <install version="1.0">
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5 <actions>
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d82f18c76309 Uploaded spades wrapper 0.6. Supports spades 2.5.1. Also removes the need for the hack at installation time, by fixing the problem with input files. Shows the license for the tool as well.
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6 <action type="download_by_url">http://spades.bioinf.spbau.ru/release2.5.1/SPAdes-2.5.1-Linux.tar.gz</action>
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0f8b2da62d7d Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
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7 <!-- Copying the whole bin folder -->
0f8b2da62d7d Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
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8 <action type="make_directory">$INSTALL_DIR/bin</action>
0f8b2da62d7d Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
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9 <action type="make_directory">$INSTALL_DIR/share</action>
0f8b2da62d7d Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
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10 <action type="move_directory_files">
0f8b2da62d7d Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
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11 <source_directory>bin</source_directory>
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12 <destination_directory>$INSTALL_DIR/bin</destination_directory>
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13 </action>
0f8b2da62d7d Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
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14 <action type="move_directory_files">
0f8b2da62d7d Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
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15 <source_directory>share</source_directory>
0f8b2da62d7d Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
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16 <destination_directory>$INSTALL_DIR/share</destination_directory>
0f8b2da62d7d Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
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17 </action>
0f8b2da62d7d Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
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18 <!-- This is required to have spades accept .dat files -->
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d82f18c76309 Uploaded spades wrapper 0.6. Supports spades 2.5.1. Also removes the need for the hack at installation time, by fixing the problem with input files. Shows the license for the tool as well.
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19 <!-- <action type="shell_command">sed -i -e "s/\('\.fa', '\.fasta', '\.fq', '\.fastq', '\.gz'\)/\\1, '.dat'/" $INSTALL_DIR/share/spades/spades_pipeline/support.py</action> -->
d82f18c76309 Uploaded spades wrapper 0.6. Supports spades 2.5.1. Also removes the need for the hack at installation time, by fixing the problem with input files. Shows the license for the tool as well.
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20 <!-- <action type="set_environment"> -->
d82f18c76309 Uploaded spades wrapper 0.6. Supports spades 2.5.1. Also removes the need for the hack at installation time, by fixing the problem with input files. Shows the license for the tool as well.
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parents: 1
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21 <!-- <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> -->
d82f18c76309 Uploaded spades wrapper 0.6. Supports spades 2.5.1. Also removes the need for the hack at installation time, by fixing the problem with input files. Shows the license for the tool as well.
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22 <!-- </action> -->
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0f8b2da62d7d Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
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23 </actions>
0f8b2da62d7d Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
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24 </install>
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25 <readme>
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d82f18c76309 Uploaded spades wrapper 0.6. Supports spades 2.5.1. Also removes the need for the hack at installation time, by fixing the problem with input files. Shows the license for the tool as well.
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26 This installs SPAdes 2.5.1.
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0f8b2da62d7d Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
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27
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d82f18c76309 Uploaded spades wrapper 0.6. Supports spades 2.5.1. Also removes the need for the hack at installation time, by fixing the problem with input files. Shows the license for the tool as well.
lionelguy
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28 See manual here http://spades.bioinf.spbau.ru/release2.5.1/manual.html
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0f8b2da62d7d Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
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29 See also here http://bioinf.spbau.ru/en/spades
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30 </readme>
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31 </package>
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32 </tool_dependency>
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