Mercurial > repos > iuc > package_blast_plus_2_2_26

comparison tool_dependencies.xml @ 0:40c69b76b46e draft

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Uploaded using shell script solution to downloading appropriate binaries.
author iuc
date Fri, 30 Aug 2013 07:26:10 -0400
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children d3343fa55e9e
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-1:000000000000 0:40c69b76b46e
1 <?xml version="1.0"?>
2 <tool_dependency>
3 <package name="blast+" version="2.2.26+">
4 <install version="1.0">
5 <actions>
6 <action type="set_environment">
7 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
8 </action>
9 <!-- arch under Linux 32bit includes some variants like i386 and i686, so use as default -->
10 <action type="shell_command">
11 if [[ "$(uname)" == "Linux" ]]; then export FILENAME="ncbi-blast-2.2.26+-ia32-linux.tar.gz"; fi &amp;&amp;
12 if [[ "$(arch)" == "x86_64" ]]; then export FILENAME="ncbi-blast-2.2.26+-x64-linux.tar.gz"; fi &amp;&amp;
13 if [[ "$(uname)" == "Darwin" ]]; then export FILENAME="ncbi-blast-2.2.26+-universal-macosx.tar.gz"; fi &amp;&amp;
14 echo Fetching $FILENAME &amp;&amp;
15 if [[ "$(uname)" == "Linux" ]]; then wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.26/$FILENAME; fi &amp;&amp;
16 if [[ "$(uname)" == "Darwin" ]]; then curl -O ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.26/$FILENAME; fi &amp;&amp;
17 tar -zxvf $FILENAME &amp;&amp;
18 echo Downloaded and decompressed
19 </action>
20 <!-- move the binaries to the installation directory which is now on the $PATH -->
21 <action type="move_directory_files">
22 <source_directory>ncbi-blast-2.2.26+/bin</source_directory>
23 <destination_directory>$INSTALL_DIR</destination_directory>
24 </action>
25 </actions>
26 </install>
27 <readme>
28 Downloads the precompiled 32bit Linux, 64bit Linux, or Mac OS X BLAST+
29 binaries from the NCBI, which is faster than performing a local compliation,
30 avoids any issues with build dependencies, and is more reproducible between
31 installations as there is no variability from the compiler or library versions.
32
33 For more details, see:
34 http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&amp;PAGE_TYPE=BlastDocs&amp;DOC_TYPE=Download
35 </readme>
36 </package>
37 </tool_dependency>