Mercurial > repos > nilesh > sickle
comparison tool_dependencies.xml @ 4:98e35d7ce5c9
sickle now refers to zlib in its own directory
| author | nilesh |
|---|---|
| date | Fri, 12 Jul 2013 13:49:15 -0500 |
| parents | 21af95369da7 |
| children | 4f6349319c0a |
comparison
equal
deleted
inserted
replaced
| 3:8d697edc2f55 | 4:98e35d7ce5c9 |
|---|---|
| 1 <?xml version="1.0"?> | 1 <?xml version="1.0"?> |
| 2 <tool_dependency> | 2 <tool_dependency> |
| 3 <package name="zlib" version="1.2.8"> | 3 <package name="zlib" version="1.2.8"> |
| 4 <install version="1.0"> | 4 <install version="1.0"> |
| 5 <actions> | 5 <actions> |
| 6 <action type="download_by_url">http://zlib.net/zlib-1.2.8.tar.gz</action> | 6 <action type="download_by_url">http://zlib.net/zlib-1.2.8.tar.gz</action> |
| 7 <action type="shell_command">./configure</action> | 7 <action type="shell_command">./configure --prefix=$INSTALL_DIR/zlib</action> |
| 8 <action type="shell_command">./configure --prefix=$INSTALL_DIR/zlib</action> | |
| 9 <action type="shell_command">make</action> | 8 <action type="shell_command">make</action> |
| 10 <action type="shell_command">make install prefix=$INSTALL_DIR/zlib</action> | 9 <action type="shell_command">make install prefix=$INSTALL_DIR/zlib</action> |
| 11 <action type="set_environment"> | 10 <action type="set_environment"> |
| 12 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> | 11 <environment_variable name="ZLIB_PATH" action="set_to">$INSTALL_DIR/zlib/lib</environment_variable> |
| 12 </action> | |
| 13 </actions> | |
| 14 <action type="set_environment"> | |
| 15 <environment_variable name="LD_LIBRARY_PATH" action="prepend_to">$INSTALL_DIR/zlib/lib</environment_variable> | |
| 13 </action> | 16 </action> |
| 14 </actions> | 17 </actions> |
| 15 </install> | 18 </install> |
| 16 <readme> | 19 <readme> |
| 17 Tabix version 0.2.6. Tabix was written by Heng Li. The BGZF library was originally implemented by Bob Handsaker and modified by Heng Li for remote file access and in-memory caching. | 20 zlib is designed to be a free, general-purpose, legally unencumbered -- that is, not covered by any patents -- lossless data-compression library for use on virtually any computer hardware and operating system. The zlib data format is itself portable across platforms. |
| 18 </readme> | 21 </readme> |
| 19 </package> | 22 </package> |
| 20 <package name="sickle" version="1.2.8"> | 23 <package name="sickle" version="1.21.0"> |
| 21 <install version="1.0"> | 24 <install version="1.0"> |
| 22 <actions> | 25 <actions> |
| 23 <action type="shell_command">git clone https://github.com/najoshi/sickle.git</action> | 26 <action type="shell_command">git clone https://github.com/najoshi/sickle.git</action> |
| 24 <action type="shell_command">make</action> | 27 <action type="shell_command">make LIBS="-L$ENV[ZLIB_PATH] -lz"</action> |
| 25 <action type="move_file"> | 28 <action type="move_file"> |
| 26 <source>sickle</source> | 29 <source>sickle</source> |
| 27 <destination>$INSTALL_DIR/bin</destination> | 30 <destination>$INSTALL_DIR/bin</destination> |
| 28 </action> | 31 </action> |
| 29 <action type="set_environment"> | 32 <action type="set_environment"> |
| 30 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> | 33 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> |
| 31 </action> | 34 </action> |
| 32 </actions> | 35 </actions> |
| 33 </install> | 36 </install> |
| 34 <readme> | 37 <readme> |
| 35 Tabix version 0.2.6. Tabix was written by Heng Li. The BGZF library was originally implemented by Bob Handsaker and modified by Heng Li for remote file access and in-memory caching. | 38 Sickle requires a C compiler; GCC or clang are recommended. Sickle relies on Heng Li's kseq.h, which is bundled with the source. It also requires zlib, which is included in this repo. |
| 36 </readme> | 39 </readme> |
| 37 </package> | 40 </package> |
| 38 </tool_dependency> | 41 </tool_dependency> |