Mercurial > repos > iuc > package_blat_35x1

comparison tool_dependencies.xml @ 3:883c4e993d46 draft

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author bgruening
date Thu, 30 Jan 2014 08:40:09 -0500
parents 501650db563f
children 2fb6c037b814
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2:501650db563f 3:883c4e993d46
6 Thanks to Nicola Soranzo. 6 Thanks to Nicola Soranzo.
7 The problem is that the binaries are not versioned and we can't guarantee reproducibility. 7 The problem is that the binaries are not versioned and we can't guarantee reproducibility.
8 The source packages are versioned and are stored for a long time. 8 The source packages are versioned and are stored for a long time.
9 --> 9 -->
10 <action type="download_by_url" target_filename="blatSrc.zip">http://hgwdev.cse.ucsc.edu/~kent/src/blatSrc35.zip</action> 10 <action type="download_by_url" target_filename="blatSrc.zip">http://hgwdev.cse.ucsc.edu/~kent/src/blatSrc35.zip</action>
11 <action type="shell_command">export HOME=$INSTALL_DIR &amp;&amp; mkdir -p $HOME/bin/$MACHTYPE &amp;&amp; make MACHTYPE=`uname -m` &amp;&amp; mv $HOME/bin/$MACHTYPE/* $HOME/bin/</action> 11 <action type="shell_command">export HOME=$INSTALL_DIR &amp;&amp; mkdir -p $HOME/bin/`uname -m` &amp;&amp; make MACHTYPE=`uname -m` &amp;&amp; mv $HOME/bin/$MACHTYPE/* $HOME/bin/</action>
12 <action type="set_environment"> 12 <action type="set_environment">
13 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin/</environment_variable> 13 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin/</environment_variable>
14 <environment_variable name="BLAT_PATH" action="set_to">$INSTALL_DIR</environment_variable> 14 <environment_variable name="BLAT_PATH" action="set_to">$INSTALL_DIR</environment_variable>
15 </action> 15 </action>
16 16
19 </install> 19 </install>
20 <readme> 20 <readme>
21 BLAT sequence aligner from the UCSC: http://genome.ucsc.edu/FAQ/FAQblat.html 21 BLAT sequence aligner from the UCSC: http://genome.ucsc.edu/FAQ/FAQblat.html
22 Git development repository: http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git 22 Git development repository: http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git
23 23
24 This reporsitory contains the following binaries:
25 - blat
26 - faToNib
27 - faToTwoBit
28 - gfClient
29 - gfServer
30 - nibFrag
31 - pslPretty
32 - pslReps
33 - pslSort
34 - twoBitInfo
35 - twoBitToFa
36
24 Please note that the BLAT source and executables are freely available for 37 Please note that the BLAT source and executables are freely available for
25 academic, nonprofit and personal use. Commercial licensing information is 38 academic, nonprofit and personal use. Commercial licensing information is
26 available on the Kent Informatics website (http://www.kentinformatics.com/). 39 available on the Kent Informatics website (http://www.kentinformatics.com/).
27 </readme> 40 </readme>
28 </package> 41 </package>