Mercurial > repos > iuc > package_blast_plus_2_2_26

comparison tool_dependencies.xml @ 2:0e536576294c draft

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Experimental shell script solution to downloading appropriate binaries.
author peterjc
date Wed, 14 Aug 2013 09:07:45 -0400
parents 9ff9bfdcd04f
children c85236cd100d
comparison
equal deleted inserted replaced
1:9ff9bfdcd04f 2:0e536576294c
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool_dependency> 2 <tool_dependency>
3 <package name="boost" version="1.53.0">
4 <repository changeset_revision="a72f8efe9201" name="package_boost_1_53" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
5 </package>
6 <package name="blast+" version="2.2.26+"> 3 <package name="blast+" version="2.2.26+">
7 <install version="1.0"> 4 <install version="1.0">
8 <actions> 5 <actions>
9 <action type="download_by_url">ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.26/ncbi-blast-2.2.26+-src.tar.gz</action> 6 <action type="set_environment">
10 <!-- populate the environment variables from the dependent repos --> 7 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
11 <action type="set_environment_for_install">
12 <repository changeset_revision="f5b13e56a321" name="package_boost_1_53" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu">
13 <package name="boost" version="1.53.0" />
14 </repository>
15 </action> 8 </action>
16 <action type="shell_command">cd c++ &amp;&amp; ./configure --with-boost=$BOOST_ROOT_DIR --prefix=$INSTALL_DIR &amp;&amp; make &amp;&amp; make install</action> 9 <!-- arch under Linux 32bit includes some variants like i386 and i686, so use as default -->
17 <action type="set_environment"> 10 <action type="shell_command">
18 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> 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 </action>
19 <!-- move the binaries to the installation directory which is now on the $PATH -->
20 <action type="move_directory_files">
21 <source_directory>ncbi-blast-2.2.26+/bin</source_directory>
22 <destination_directory>$INSTALL_DIR</destination_directory>
19 </action> 23 </action>
20 </actions> 24 </actions>
21 </install> 25 </install>
22 <readme> 26 <readme>
23 Downloads and compiles BLAST+ from the NCBI, which assumes you have 27 Downloads the precompiled 32bit Linux, 64bit Linux, or Mac OS X BLAST+
24 all the required build dependencies installed. See: 28 binaries from the NCBI, which is faster than performing a local compliation,
29 avoids any issues with build dependencies, and is more reproducible between
30 installations as there is no variability from the compiler or library versions.
31
32 For more details, see:
25 http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&amp;PAGE_TYPE=BlastDocs&amp;DOC_TYPE=Download 33 http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&amp;PAGE_TYPE=BlastDocs&amp;DOC_TYPE=Download
26 </readme> 34 </readme>
27 </package> 35 </package>
28 </tool_dependency> 36 </tool_dependency>