archive:bioinformatic_tools:allpaths
Differences
This shows you the differences between two versions of the page.
| Both sides previous revision Previous revision Next revision | Previous revision | ||
|
archive:bioinformatic_tools:allpaths [2010/04/08 16:20] jstjohn Better version of the allpaths manual where the text is readable and the filesize is simaller. |
archive:bioinformatic_tools:allpaths [2015/07/28 06:22] (current) ceisenhart ↷ Page moved from bioinformatic_tools:allpaths to archive:bioinformatic_tools:allpaths |
||
|---|---|---|---|
| Line 19: | Line 19: | ||
| 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// | ||
| - | |||
| ===== Installation ===== | ===== Installation ===== | ||
| - | Installing into ~/programs/allpaths | + | Installed statically on isla.cse.ucsc.edu and transferred over. |
| + | |||
| + | Installed with boost_1.38 and gcc version 4.4. | ||
| + | |||
| + | The installed the binaries here: | ||
| + | /projects/lowelab/users/jstjohn/allpaths/bin | ||
| - | Configure error, requires boost with at least the Boost.System binaries installed. Now I am installing that... | + | and then I ziped them and transfered them via scp over to campusrocks. |
| - | + | ||
| - | Boost successfully installed. Now installing allpaths. Configure successful and currently building. --- //[[jstjohn@soe.ucsc.edu|John St. John]] 2010/04/07 00:53// | + | |
| + | To compile static I ran configure with "CXXFLAGS=-static". | ||
| - | Build unsuccessful: | + | 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. |
| - | ./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? | ||
| ===== References ===== | ===== References ===== | ||
| <refnotes>notes-separator: none</refnotes> | <refnotes>notes-separator: none</refnotes> | ||
| ~~REFNOTES cite~~ | ~~REFNOTES cite~~ | ||
archive/bioinformatic_tools/allpaths.1270743604.txt.gz · Last modified: 2010/04/08 16:20 by jstjohn
Except where otherwise noted, content on this wiki is licensed under the following license: CC Attribution-Noncommercial-Share Alike 3.0 Unported
