|
0
|
1 <?xml version="1.0"?>
|
|
|
2 <tool_dependency>
|
|
|
3 <package name="tabix" version="0.2.6">
|
|
|
4 <install version="1.0">
|
|
|
5 <actions>
|
|
|
6 <action type="download_by_url">http://sourceforge.net/projects/samtools/files/tabix/tabix-0.2.6.tar.bz2</action>
|
|
|
7 <action type="shell_command">make</action>
|
|
|
8 <action type="move_file">
|
|
|
9 <source>tabix</source>
|
|
|
10 <destination>$INSTALL_DIR/bin</destination>
|
|
|
11 </action>
|
|
|
12 <action type="move_file">
|
|
|
13 <source>bgzip</source>
|
|
|
14 <destination>$INSTALL_DIR/bin</destination>
|
|
|
15 </action>
|
|
|
16 <action type="set_environment">
|
|
|
17 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
|
|
|
18 <environment_variable name="TABIX_BIN_PATH" action="set_to">$INSTALL_DIR/bin</environment_variable>
|
|
|
19 </action>
|
|
|
20 </actions>
|
|
|
21 </install>
|
|
|
22 <readme>
|
|
|
23 Installs tabix version 0.2.6. Available binaries: tabix, bgzip
|
|
|
24 http://samtools.sourceforge.net/tabix.shtml
|
|
|
25
|
|
|
26 Tabix indexes a TAB-delimited genome position file in.tab.bgz and creates an index file in.tab.bgz.tbi when region is absent from the command-line.
|
|
|
27 The input data file must be position sorted and compressed by bgzip which has a gzip(1) like interface. After indexing,
|
|
|
28 tabix is able to quickly retrieve data lines overlapping regions specified in the format "chr:beginPos-endPos".
|
|
|
29 Fast data retrieval also works over network if URI is given as a file name and in this case the index file will be downloaded if it is not present locally.
|
|
|
30 </readme>
|
|
|
31 </package>
|
|
|
32 </tool_dependency>
|
