Mercurial > repos > devteam > package_fastx_toolkit_0_0_13

annotate tool_dependencies.xml @ 3:7d6cc3605cee draft

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Uploaded updated tool dependency definition.
author devteam
date Tue, 10 Sep 2013 16:41:48 -0400
parents b2814057f286
children e76e81b3eccf
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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="fastx_toolkit" version="0.0.13">
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4 <install version="1.0">
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5 <actions_group>
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6 <actions architecture="x86_64" os="linux">
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7 <action type="download_by_url">http://hannonlab.cshl.edu/fastx_toolkit/fastx_toolkit_0.0.13_binaries_Linux_2.6_amd64.tar.bz2</action>
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8 <action type="move_directory_files">
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9 <source_directory>./bin</source_directory>
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10 <destination_directory>$INSTALL_DIR/bin</destination_directory>
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11 </action>
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12 </actions>
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13 <actions architecture="i386" os="linux">
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14 <action type="download_by_url">http://hannonlab.cshl.edu/fastx_toolkit/fastx_toolkit_0.0.13_binaries_Linux_2.6_i686.tar.bz2</action>
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15 <action type="move_directory_files">
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16 <source_directory>./bin</source_directory>
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17 <destination_directory>$INSTALL_DIR/bin</destination_directory>
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18 </action>
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19 </actions>
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20 <actions architecture="i686" os="linux">
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21 <action type="download_by_url">http://hannonlab.cshl.edu/fastx_toolkit/fastx_toolkit_0.0.13_binaries_Linux_2.6_i686.tar.bz2</action>
b2814057f286 Uploaded tool dependency definition with architecture-dependent installation recipes.
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22 <action type="move_directory_files">
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23 <source_directory>./bin</source_directory>
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24 <destination_directory>$INSTALL_DIR/bin</destination_directory>
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25 </action>
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26 </actions>
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27 <actions architecture="i386" os="darwin">
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28 <action type="download_by_url">http://hannonlab.cshl.edu/fastx_toolkit/fastx_toolkit_0.0.13_binaries_MacOSX.10.5.8_i386.tar.bz2</action>
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29 <action type="move_directory_files">
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30 <source_directory>./bin</source_directory>
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31 <destination_directory>$INSTALL_DIR/bin</destination_directory>
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32 </action>
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33 </actions>
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34 <actions architecture="x86_64" os="darwin">
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35 <action type="download_by_url">http://hannonlab.cshl.edu/fastx_toolkit/fastx_toolkit_0.0.13_binaries_MacOSX.10.5.8_i386.tar.bz2</action>
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36 <action type="move_directory_files">
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37 <source_directory>./bin</source_directory>
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38 <destination_directory>$INSTALL_DIR/bin</destination_directory>
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39 </action>
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40 </actions>
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41 <actions>
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42 <package name="libgtextutils" version="0.6">
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43 <repository changeset_revision="e28dc3aa1665" name="package_libgtextutils_0_6" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
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44 </package>
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45 <action type="download_by_url">http://hannonlab.cshl.edu/fastx_toolkit/fastx_toolkit-0.0.13.tar.bz2</action>
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46 <action type="set_environment_for_install">
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47 <repository changeset_revision="e28dc3aa1665" name="package_libgtextutils_0_6" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu">
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48 <package name="libgtextutils" version="0.6" />
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49 </repository>
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50 </action>
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51 <action type="shell_command">./configure --prefix=$INSTALL_DIR --disable-wall</action>
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52 <action type="shell_command">make &amp;&amp; make install</action>
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53 </actions>
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54 <action type="set_environment">
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55 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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56 </action>
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57 </actions_group>
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58 </install>
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59 <readme>
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60 The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.
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62 Next-Generation sequencing machines usually produce FASTA or FASTQ files, containing multiple short-reads sequences (possibly with quality information).
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64 The main processing of such FASTA/FASTQ files is mapping (aka aligning) the sequences to reference genomes or other databases using specialized programs. Example of such mapping programs are: Blat, SHRiMP, LastZ, MAQ and many many others.
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66 However, it is sometimes more productive to preprocess the FASTA/FASTQ files before mapping the sequences to the genome - manipulating the sequences to produce better mapping results.
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68 The FASTX-Toolkit tools perform some of these preprocessing tasks.
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69 </readme>
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70 </package>
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71 </tool_dependency>