archive:bioinformatic_tools:allpaths
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archive:bioinformatic_tools:allpaths [2010/04/19 06:21] jstjohn |
archive:bioinformatic_tools:allpaths [2010/05/06 17:43] jstjohn |
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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. |
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| - | 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: | + | |
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| - | ./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 | + | |
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| - | 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? | + | |
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| - | Installed gcc-4.5! (had to do it myself, the sys admins wouldn't try) | + | |
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| - | The gcc/g++-4.5 libraries are installed in: | + | |
| - | /campusdata/BME235/lib | + | |
| - | /campusdata/BME235/lib64 | + | |
| - | To compile with the gcc 4.5 compilers you need to have your environment properly set up so that everything knows where to look for the linked libraries. I did this by setting my LD_LIBRARY_PATH variable as follows in my .profile | + | Installed with boost_1.38 and gcc version 4.4. |
| - | LD_LIBRARY_PATH=/campusdata/BME235/lib:/campusdata/BME235/lib64:$LD_LIBRARY_PATH | + | The installed the binaries here: |
| - | export LD_LIBRARY_PATH | + | /projects/lowelab/users/jstjohn/allpaths/bin |
| - | Note if you want to run the install via a script, an example script that sets up environmental variables is here: | + | and then I ziped them and transfered them via scp over to campusrocks. |
| - | /campusdata/BME235/programs/allpaths/allpaths3-3.2/installallpaths.sh | + | To compile static I ran configure with "CXXFLAGS=-static". |
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| - | I have encountered a new error much further along in the compilation. To view the error see the last 40 lines of file: | + | 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. |
| - | /campus/BME235/programs/allpaths/allpaths3-3.2/installallpaths.sh.o2730 | + | |
| - | /campusdata/BME235/programs/allpaths/allpaths3-3.2/src/paths/MuxWalkGraph.cc:740: undefined reference to `digraphE<KmerPath>::TransferEdges(int, int, unsigned char)' | ||
archive/bioinformatic_tools/allpaths.txt · Last modified: 2015/07/28 06:22 by ceisenhart
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