Mercurial > repos > jjohnson > package_blat_server
comparison tool_dependencies.xml @ 0:455a4bd49c52 draft default tip
Uploaded
| author | jjohnson |
|---|---|
| date | Fri, 08 Nov 2013 10:10:54 -0500 |
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| -1:000000000000 | 0:455a4bd49c52 |
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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> |