archive:bioinformatic_tools:allpaths
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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 [2010/04/19 06:21] jstjohn |
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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? | 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 | ||
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| + | 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 | ||
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| + | LD_LIBRARY_PATH=/campusdata/BME235/lib:/campusdata/BME235/lib64:$LD_LIBRARY_PATH | ||
| + | export LD_LIBRARY_PATH | ||
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| + | Note if you want to run the install via a script, an example script that sets up environmental variables is here: | ||
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| + | /campusdata/BME235/programs/allpaths/allpaths3-3.2/installallpaths.sh | ||
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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: | ||
| + | /campus/BME235/programs/allpaths/allpaths3-3.2/installallpaths.sh.o2730 | ||
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| + | /campusdata/BME235/programs/allpaths/allpaths3-3.2/src/paths/MuxWalkGraph.cc:740: undefined reference to `digraphE<KmerPath>::TransferEdges(int, int, unsigned char)' | ||
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| ===== References ===== | ===== References ===== | ||
| <refnotes>notes-separator: none</refnotes> | <refnotes>notes-separator: none</refnotes> | ||
| ~~REFNOTES cite~~ | ~~REFNOTES cite~~ | ||
archive/bioinformatic_tools/allpaths.txt · Last modified: 2015/07/28 06:22 by ceisenhart
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