archive:bioinformatic_tools:allpaths
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archive:bioinformatic_tools:allpaths [2010/04/19 05:14] jstjohn |
archive:bioinformatic_tools:allpaths [2015/07/28 06:22] (current) ceisenhart ↷ Page moved from bioinformatic_tools:allpaths to archive:bioinformatic_tools:allpaths |
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| Perhaps our data will not behave nicely with this algorithm? Also they didn't say whether or not they combine the reads from those three sources, or somehow analyze them separately and merge them at some point. Perhaps reading more into their documentation or publications will answer some of these questions. --- //[[jstjohn@soe.ucsc.edu|John St. John]] 2010/04/05 17:50// | Perhaps our data will not behave nicely with this algorithm? Also they didn't say whether or not they combine the reads from those three sources, or somehow analyze them separately and merge them at some point. Perhaps reading more into their documentation or publications will answer some of these questions. --- //[[jstjohn@soe.ucsc.edu|John St. John]] 2010/04/05 17:50// | ||
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| ===== Installation ===== | ===== Installation ===== | ||
| - | Installing into ~/programs/allpaths | + | Installed statically on isla.cse.ucsc.edu and transferred over. |
| - | + | ||
| - | Configure error, requires boost with at least the Boost.System binaries installed. Now I am installing that... | + | |
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| - | Boost successfully installed. Now installing allpaths. Configure successful and currently building. --- //[[jstjohn@soe.ucsc.edu|John St. John]] 2010/04/07 00:53// | + | |
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| - | + | ||
| - | Build unsuccessful: | + | |
| - | + | ||
| - | ./ParallelVecUtilities.h: In function 'void ParallelSort(vec<T>&)':\\ | + | |
| - | ./ParallelVecUtilities.h:27: error: '__gnu_parallel' has not been declared\\ | + | |
| - | ./ParallelVecUtilities.h: In function 'void ParallelSort(vec<T>&, StrictWeakOrdering)':\\ | + | |
| - | ./ParallelVecUtilities.h:35: error: '__gnu_parallel' has not been declared\\ | + | |
| - | ./ParallelVecUtilities.h: In function 'void ParallelReverseSort(vec<T>&)':\\ | + | |
| - | ./ParallelVecUtilities.h:42: error: '__gnu_parallel' has not been declared\\ | + | |
| - | ./ParallelVecUtilities.h: In function 'void ParallelReverseSort(vec<T>&, StrictWeakOrdering)':\\ | + | |
| - | ./ParallelVecUtilities.h:50: error: '__gnu_parallel' has not been declared\\ | + | |
| - | ./ParallelVecUtilities.h: In function 'void ParallelWhatPermutation(const V&, vec<T3>&, C, bool)':\\ | + | |
| - | ./ParallelVecUtilities.h:316: error: '__gnu_parallel' has not been declared | + | |
| - | + | ||
| - | Reading deeper into the documentation (the PDF attached to this page), I see that it requires gcc-4.3+. Campusrocks currently has gcc-4.1 installed. Perhaps if we compile the latest gcc we can install this program? | + | |
| - | Installed gcc-4.5! (had to do it myself, the sys admins wouldn't try) | + | Installed with boost_1.38 and gcc version 4.4. |
| - | Note, if you compile with gcc-4.5 (or any of the other cc/c++-4.5) you will need to do one of the following: | + | The installed the binaries here: |
| - | ---------------------------------------------------------------------- | + | /projects/lowelab/users/jstjohn/allpaths/bin |
| - | Libraries have been installed in: | + | |
| - | /campusdata/BME235/lib/../lib64 | + | |
| - | If you ever happen to want to link against installed libraries | + | and then I ziped them and transfered them via scp over to campusrocks. |
| - | in a given directory, LIBDIR, you must either use libtool, and | + | |
| - | specify the full pathname of the library, or use the `-LLIBDIR' | + | |
| - | flag during linking and do at least one of the following: | + | |
| - | - add LIBDIR to the `LD_LIBRARY_PATH' environment variable | + | |
| - | during execution | + | |
| - | - add LIBDIR to the `LD_RUN_PATH' environment variable | + | |
| - | during linking | + | |
| - | - use the `-Wl,-rpath -Wl,LIBDIR' linker flag | + | |
| - | - have your system administrator add LIBDIR to `/etc/ld.so.conf' | + | |
| - | See any operating system documentation about shared libraries for | + | To compile static I ran configure with "CXXFLAGS=-static". |
| - | more information, such as the ld(1) and ld.so(8) manual pages. | + | |
| - | ---------------------------------------------------------------------- | + | |
| + | They also installed graphviz on the computer which is necessary to view some of the output, although I am pretty sure this isn't a pre-requisite to compile the program as the configure script never bugged me about specifying the graphviz source and/or binary. | ||
| - | While attempting to install Allpaths I get an error right away for all methods other than setting | ||
| - | LD_LIBRARY_PATH=/campusdata/BME235/lib:/campusdata/BME235/lib64 | ||
| ===== References ===== | ===== References ===== | ||
| <refnotes>notes-separator: none</refnotes> | <refnotes>notes-separator: none</refnotes> | ||
| ~~REFNOTES cite~~ | ~~REFNOTES cite~~ | ||
archive/bioinformatic_tools/allpaths.1271654076.txt.gz · Last modified: 2010/04/19 05:14 by jstjohn
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