Mercurial > repos > iuc > package_blast_plus_2_2_28

annotate tool_dependencies.xml @ 0:d794cb2b0f45 draft

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Uploaded definition based on that for BLAST+ 2.2.26
author peterjc
date Mon, 23 Sep 2013 07:21:23 -0400
parents
children 5a449da71d08
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d794cb2b0f45 Uploaded definition based on that for BLAST+ 2.2.26
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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="blast+" version="2.2.28">
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4 <install version="1.0">
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5 <actions>
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6 <action type="set_environment">
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7 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
d794cb2b0f45 Uploaded definition based on that for BLAST+ 2.2.26
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8 </action>
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9 <!-- arch under Linux 32bit includes some variants like i386 and i686, so use as default -->
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10 <action type="shell_command">
d794cb2b0f45 Uploaded definition based on that for BLAST+ 2.2.26
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11 if [[ "$(uname)" == "Linux" ]]; then export FILENAME="ncbi-blast-2.2.28+-ia32-linux.tar.gz"; fi &amp;&amp;
d794cb2b0f45 Uploaded definition based on that for BLAST+ 2.2.26
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12 if [[ "$(arch)" == "x86_64" ]]; then export FILENAME="ncbi-blast-2.2.28+-x64-linux.tar.gz"; fi &amp;&amp;
d794cb2b0f45 Uploaded definition based on that for BLAST+ 2.2.26
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13 if [[ "$(uname)" == "Darwin" ]]; then export FILENAME="ncbi-blast-2.2.28+-universal-macosx.tar.gz"; fi &amp;&amp;
d794cb2b0f45 Uploaded definition based on that for BLAST+ 2.2.26
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14 echo Fetching $FILENAME &amp;&amp;
d794cb2b0f45 Uploaded definition based on that for BLAST+ 2.2.26
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15 if [[ "$(uname)" == "Linux" ]]; then wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.28/$FILENAME; fi &amp;&amp;
d794cb2b0f45 Uploaded definition based on that for BLAST+ 2.2.26
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16 if [[ "$(uname)" == "Darwin" ]]; then curl -O ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.28/$FILENAME; fi &amp;&amp;
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17 tar -zxvf $FILENAME &amp;&amp;
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18 echo Downloaded and decompressed
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19 </action>
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20 <!-- move the binaries to the installation directory which is now on the $PATH -->
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21 <action type="move_directory_files">
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22 <source_directory>ncbi-blast-2.2.28+/bin</source_directory>
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23 <destination_directory>$INSTALL_DIR</destination_directory>
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24 </action>
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25 </actions>
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26 </install>
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27 <readme>
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28 Downloads the precompiled 32bit Linux, 64bit Linux, or Mac OS X BLAST+
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29 binaries from the NCBI, which is faster than performing a local compliation,
d794cb2b0f45 Uploaded definition based on that for BLAST+ 2.2.26
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30 avoids any issues with build dependencies, and is more reproducible between
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31 installations as there is no variability from the compiler or library versions.
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32
d794cb2b0f45 Uploaded definition based on that for BLAST+ 2.2.26
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33 For more details, see:
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34 http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&amp;PAGE_TYPE=BlastDocs&amp;DOC_TYPE=Download
d794cb2b0f45 Uploaded definition based on that for BLAST+ 2.2.26
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35 </readme>
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36 </package>
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37 </tool_dependency>