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archive:bioinformatic_tools:allpaths [2010/04/07 08:37] jstjohn |
archive:bioinformatic_tools:allpaths [2010/04/07 09:35] jstjohn |
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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.pdf|allpathsv3_manual_r1.0.pdf}}. | ||
====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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Boost successfully installed. Now installing allpaths. Configure successful and currently building. --- //[[jstjohn@soe.ucsc.edu|John St. John]] 2010/04/07 00:53// | 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 | ||
===== References ===== | ===== References ===== | ||
<refnotes>notes-separator: none</refnotes> | <refnotes>notes-separator: none</refnotes> | ||
~~REFNOTES cite~~ | ~~REFNOTES cite~~ |