annotate tool_dependencies.xml @ 5:923adc89c666 draft

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author bgruening
date Tue, 22 Jul 2014 12:04:37 -0400
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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="ncurses" version="5.9">
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4 <repository changeset_revision="71e3f4bfd1a9" name="package_ncurses_5_9" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
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5 </package>
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6 <package name="zlib" version="1.2.8">
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7 <repository changeset_revision="63a4a902cda2" name="package_zlib_1_2_8" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
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8 </package>
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9 <package name="samtools" version="0.1.19">
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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://downloads.sourceforge.net/project/samtools/samtools/0.1.19/samtools-0.1.19.tar.bz2</action>
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13 <action type="set_environment_for_install">
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14 <repository changeset_revision="71e3f4bfd1a9" name="package_ncurses_5_9" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu">
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15 <package name="ncurses" version="5.9" />
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16 </repository>
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17 <repository changeset_revision="63a4a902cda2" name="package_zlib_1_2_8" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu">
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18 <package name="zlib" version="1.2.8" />
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19 </repository>
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20 </action>
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21 <action type="shell_command">sed -i 's/-lcurses/-lncurses/' Makefile</action>
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22 <action type="shell_command">sed -i -e "s|CFLAGS=\s*-g\s*-Wall\s*-O2\s*|CFLAGS= -g -Wall -O2 -I$NCURSES_INCLUDE_PATH/ncurses/ -I$NCURSES_INCLUDE_PATH -L$NCURSES_LIB_PATH|g" Makefile</action>
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23 <action type="shell_command">make</action>
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24 <action type="move_file">
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25 <source>samtools</source>
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26 <destination>$INSTALL_DIR/bin</destination>
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27 </action>
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28 <action type="set_environment">
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29 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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30 </action>
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31 </actions>
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32 </install>
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33 <readme>
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34 Program: samtools (Tools for alignments in the SAM format)
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35 Version: 0.1.19
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36
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37 Usage: samtools &lt;command&gt; [options]
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39 Command: view SAM&lt;-&gt;BAM conversion
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40 sort sort alignment file
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41 mpileup multi-way pileup
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42 depth compute the depth
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43 faidx index/extract FASTA
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44 tview text alignment viewer
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45 index index alignment
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46 idxstats BAM index stats (r595 or later)
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47 fixmate fix mate information
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48 flagstat simple stats
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49 calmd recalculate MD/NM tags and '=' bases
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50 merge merge sorted alignments
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51 rmdup remove PCR duplicates
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52 reheader replace BAM header
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53 cat concatenate BAMs
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54 targetcut cut fosmid regions (for fosmid pool only)
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55 phase phase heterozygotes
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00e17a794a2e Also install bcftools and misc utility commands when installing samtools.
Jim Johnson <jj@umn.edu>
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57 Requirements: libncurses header files
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58 </readme>
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59 </package>
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60 </tool_dependency>