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archive:bioinformatic_tools:allpaths [2010/04/07 09:23] 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, but for a full sized mammalian genome they recommend 512Gb of ram!! I assume they mean shared memory here so this program may be a no go. I am building the program but stopping short of installing it due to these limitations. | + | 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? |
====High Level Overview==== | ====High Level Overview==== | ||
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- | Build unsuccessfull: | + | Build unsuccessful: |
./ParallelVecUtilities.h: In function 'void ParallelSort(vec<T>&)':\\ | ./ParallelVecUtilities.h: In function 'void ParallelSort(vec<T>&)':\\ | ||
./ParallelVecUtilities.h:27: error: '__gnu_parallel' has not been declared\\ | ./ParallelVecUtilities.h:27: error: '__gnu_parallel' has not been declared\\ | ||
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./ParallelVecUtilities.h: In function 'void ParallelWhatPermutation(const V&, vec<T3>&, C, bool)':\\ | ./ParallelVecUtilities.h: In function 'void ParallelWhatPermutation(const V&, vec<T3>&, C, bool)':\\ | ||
./ParallelVecUtilities.h:316: error: '__gnu_parallel' has not been declared | ./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) | ||
+ | |||
+ | 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~~ |