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annotate tool_dependencies.xml @ 9:480491c2ce1c

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author biomonika <biomonika@psu.edu>
date Mon, 25 Aug 2014 13:29:42 -0400
parents 5573c2fa9824
children 66d7b41f74b1
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1 <tool_dependency>
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2 <set_environment version="1.0">
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3 <environment_variable name="LINKYX_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
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4 </set_environment>
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5
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6 <package name="samtools" version="0.1.18">
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7 <install version="1.0">
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8 <actions>
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9 <action type="download_by_url">http://sourceforge.net/projects/samtools/files/samtools/0.1.18/samtools-0.1.18.tar.bz2</action>
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10 <action type="shell_command">sed -i 's/O2/O2 -fPIC/‘ Makefile</action>
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11 <action type="shell_command">make</action>
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12 <action type="move_file">
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13 <source>samtools</source>
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14 <destination>$INSTALL_DIR/bin</destination>
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15 </action>
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16 <action type="move_file">
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17 <source>libbam.a</source>
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18 <destination>$INSTALL_DIR/bin</destination>
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19 </action>
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20 <action type="move_file">
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21 <source>bam.h</source>
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22 <destination>$INSTALL_DIR/bin</destination>
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23 </action>
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24 <action type="set_environment">
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25 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
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26 </action>
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27 <action type="set_environment">
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28 <environment_variable name="SAMTOOLS" action="set_to">$INSTALL_DIR/bin</environment_variable>
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29 </action>
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30 </actions>
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31 </install>
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32 <readme>Compiling samtools with fPIC in order to create bam.h and compiled libbam.a files</readme>
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33 </package>
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34
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35 <package name="perl" version="5.18.1">
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36 <repository name="package_perl_5_18" owner="iuc" prior_installation_required="True" />
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37 </package>
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38
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39 <package name="bioperl" version="1.6.922">
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40 <install version="1.0">
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41 <actions>
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42 <action type="setup_perl_environment">
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43 <repository changeset_revision="28865aa39fbb" name="package_perl_5_18" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
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44 <package name="perl" version="5.18.1" />
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45 </repository>
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46 <!-- allow downloading and installing an Perl package from cpan.org-->
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47 <package>Bio::DB::Sam</package>
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48 <package>http://search.cpan.org/CPAN/authors/id/L/LD/LDS/Bio-SamTools-1.39.tar.gz</package>
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49 <package>Bio::DB::Fasta</package>
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50 <package>http://search.cpan.org/CPAN/authors/id/C/CJ/CJFIELDS/BioPerl-1.6.901.tar.gz</package>
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51 <package>File::Slurp</package>
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52 <package>http://search.cpan.org/CPAN/authors/id/D/DR/DROLSKY/File-Slurp-9999.13.tar.gz</package>
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53 </action>
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54 </actions>
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55 </install>
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56 <readme>
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57 Installing dependencies. Bio::DB::Sam needs to know location of bam.h and compiled libbam.a files, therefore environmental variable SAMTOOLS needs to be correctly set.
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58 </readme>
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59 </package>
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60 </tool_dependency>