Mercurial > repos > iuc > package_blast_plus_2_2_26

annotate tool_dependencies.xml @ 5:ebde5fa60194 draft

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Fixed bash syntax error in fall back messages
author peterjc
date Thu, 20 Feb 2014 05:38:56 -0500
parents c83440a9bdfb
children 1c54472887ca
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1 <?xml version='1.0' encoding='utf-8'?>
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2 <tool_dependency>
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3 <package name="blast+" version="2.2.26+">
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4 <install version="1.0">
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5 <actions_group>
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6 <!-- Download the binaries for BLAST+ compatible with 64-bit OSX. -->
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7 <actions os="darwin" architecture="x86_64">
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8 <action type="download_by_url">ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.26/ncbi-blast-2.2.26+-universal-macosx.tar.gz</action>
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9 <action type="move_directory_files">
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10 <source_directory>bin</source_directory>
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11 <destination_directory>$INSTALL_DIR</destination_directory>
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12 </action>
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13 </actions>
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14 <!-- Download the binaries for BLAST+ compatible with 32-bit OSX. -->
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15 <actions os="darwin" architecture="i386">
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16 <action type="download_by_url">ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.26/ncbi-blast-2.2.26+-universal-macosx.tar.gz</action>
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17 <action type="move_directory_files">
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18 <source_directory>bin</source_directory>
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19 <destination_directory>$INSTALL_DIR</destination_directory>
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20 </action>
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21 </actions>
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22 <!-- Download the binaries for BLAST+ compatible with 64-bit Linux. -->
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23 <actions os="linux" architecture="x86_64">
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24 <action type="download_by_url">ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.26/ncbi-blast-2.2.26+-x64-linux.tar.gz</action>
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25 <action type="move_directory_files">
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26 <source_directory>bin</source_directory>
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27 <destination_directory>$INSTALL_DIR</destination_directory>
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28 </action>
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29 </actions>
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30 <!-- Download the binaries for BLAST+ compatible with 32-bit Linux (i386). -->
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31 <actions os="linux" architecture="i386">
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32 <action type="download_by_url">ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.26/ncbi-blast-2.2.26+-ia32-linux.tar.gz</action>
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33 <action type="move_directory_files">
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34 <source_directory>bin</source_directory>
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35 <destination_directory>$INSTALL_DIR</destination_directory>
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36 </action>
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37 </actions>
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38 <!-- Download the binaries for BLAST+ compatible with 32-bit Linux (i686). -->
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39 <actions os="linux" architecture="i686">
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40 <action type="download_by_url">ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.26/ncbi-blast-2.2.26+-ia32-linux.tar.gz</action>
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41 <action type="move_directory_files">
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42 <source_directory>bin</source_directory>
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43 <destination_directory>$INSTALL_DIR</destination_directory>
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44 </action>
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45 </actions>
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46 <!-- This actions tag is only processed if none of the above tags resulted in a successful installation. -->
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47 <actions>
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48 <action type="shell_command">echo "ERROR: Automated installation on your operating system and CPU architecture combination is not yet supported."</action>
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49 <action type="shell_command">echo "Your machine details (the output from 'uname' and 'arch'):"</action>
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50 <action type="shell_command">uname</action>
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51 <action type="shell_command">arch</action>
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52 <action type="shell_command">echo "Please report this via https://github.com/peterjc/galaxy_blast/issues - thank you!"</action>
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53 <action type="shell_command">false</action>
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54 <!-- The 'false' command will return an error, so Galaxy should treat this as a failed install -->
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55 </actions>
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56 <!-- The $PATH environment variable is only set if one of the above <actions> tags resulted in a successful installation. -->
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57 <action type="set_environment">
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58 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
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59 </action>
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60 </actions_group>
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61 </install>
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62 <readme>
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63 Downloads the precompiled 32bit Linux, 64bit Linux, or Mac OS X BLAST+
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64 binaries from the NCBI, which is faster than performing a local compliation,
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65 avoids any issues with build dependencies, and is more reproducible between
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66 installations as there is no variability from the compiler or library versions.
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67
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68 For more details, see:
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69 http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&amp;PAGE_TYPE=BlastDocs&amp;DOC_TYPE=Download
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70 </readme>
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71 </package>
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72 </tool_dependency>