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archive:bioinformatic_tools:allpaths [2010/04/07 17:11]
jstjohn
archive:bioinformatic_tools:allpaths [2010/04/19 05:14]
jstjohn
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 ===== ALLPATHS ===== ===== ALLPATHS =====
-Attached is the Allpaths3 version 1.0 documentation converted from .docx format to .pdf. You can download this file by clicking the following link: {{:​bioinformatic_tools:​allpathsv3_manual_r1.0.pdf|allpathsv3_manual_r1.0.pdf}}.+Attached is the Allpaths3 version 1.0 documentation converted from .docx format to .pdf. You can download this file by clicking the following link: {{:​bioinformatic_tools:​allpathsv3_manual_r1.0_2.pdf|allpathsv3_manual}}. 
 ====Potential Pitfalls==== ====Potential Pitfalls====
 Designed to work with 100+ bp paired end reads from a *minimum of one short and one long set of libraries. Also the program expects 40X coverage from each of those libraries! Additionally they say it requires a minimum of 32Gb of ram which I assume means shared memory, so it may not work on our cluster. Maybe it would be useful to run on small portions of our data though? Designed to work with 100+ bp paired end reads from a *minimum of one short and one long set of libraries. Also the program expects 40X coverage from each of those libraries! Additionally they say it requires a minimum of 32Gb of ram which I assume means shared memory, so it may not work on our cluster. Maybe it would be useful to run on small portions of our data though?
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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?
 +
 +
 +Installed gcc-4.5! (had to do it myself, the sys admins wouldn'​t try)
 +
 +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:
 +----------------------------------------------------------------------
 +Libraries have been installed in:
 +   /​campusdata/​BME235/​lib/​../​lib64
 +
 +If you ever happen to want to link against installed libraries
 +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
 +more information,​ such as the ld(1) and ld.so(8) manual pages.
 +----------------------------------------------------------------------
 +
 +
 +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.txt · Last modified: 2015/07/28 06:22 by ceisenhart