Mercurial > repos > jjohnson > package_blat_server

comparison tool_dependencies.xml @ 0:5920144e9e9b draft default tip

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author jjohnson
date Fri, 08 Nov 2013 16:16:31 -0500
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1 <?xml version="1.0"?>
2 <tool_dependency>
3 <package name="blat_server" version="latest">
4 <install version="1.0">
5 <actions_group>
6
7 <actions os="linux" architecture="x86_64">
8 <action type="download_file">ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/blat/blat</action>
9 <action type="download_file">ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/blat/gfServer</action>
10 <action type="download_file">ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/blat/gfClient</action>
11 <action type="download_file">ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/faToTwoBit</action>
12 <action type="shell_command">chmod ugo+x *</action>
13 <action type="move_directory_files">
14 <source_directory>.</source_directory>
15 <destination_directory>$INSTALL_DIR/bin</destination_directory>
16 </action>
17 </actions>
18
19 <actions os="darwin" architecture="x86_64">
20 <action type="download_file">ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/blat</action>
21 <action type="download_file">ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/gfClient</action>
22 <action type="download_file">ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/gfServer</action>
23 <action type="download_file">ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/faToTwoBit</action>
24 <action type="shell_command">chmod ugo+x *</action>
25 <action type="move_directory_files">
26 <source_directory>.</source_directory>
27 <destination_directory>$INSTALL_DIR/bin</destination_directory>
28 </action>
29 </actions>
30
31 <actions>
32 <action type="download_by_url" target_filename="kent.zip">http://hgdownload.cse.ucsc.edu/admin/jksrc.zip</action>
33 <action type="shell_command">
34 export MACHTYPE=`uname -m`;
35 export BINDIR=$INSTALL_DIR/bin; mkdir $INSTALL_DIR/bin;
36 cd src/lib; make;
37 cd ../jkOwnLib; make;
38 cd ../blat; make;
39 cd ../gfClient; make;
40 cd ../gfServer; make;
41 cd ../utils; mv makefile makefile.orig; grep -v -E 'pslLiftSubrangeBlat|raSqlQuery|scaffoldFaToAgp' makefile.orig > makefile; make
42 </action>
43 </actions>
44 <action type="set_environment">
45 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
46 </action>
47 </actions_group>
48 </install>
49 <readme>
50 Downloads and installs the latest kent blat server tools (blat, gfServer, gfClient, faToTwoBit).
51 It will try to install executable files from: UCSC ftp://hgdownload.cse.ucsc.edu/admin/exe/
52 otherwise it will try to compile from source from: UCSC at: http://hgdownload.cse.ucsc.edu/admin/jksrc.zip
53 ( The website doesn't offer previously released versions. )
54
55 NOTE: A license is required for use in a COMMERCIAL system.
56
57 Blat source and executables are freely available for academic, nonprofit and personal use.
58 Commercial licensing information is available on the Kent Informatics website (http://www.kentinformatics.com/).
59
60 </readme>
61 </package>
62
63 </tool_dependency>