archive:bioinformatic_tools:allpaths
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archive:bioinformatic_tools:allpaths [2010/04/07 09:22] jstjohn |
archive:bioinformatic_tools:allpaths [2015/07/28 06:22] (current) ceisenhart ↷ Page moved from bioinformatic_tools:allpaths to archive:bioinformatic_tools:allpaths |
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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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| 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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| + | Installed with boost_1.38 and gcc version 4.4. | ||
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| + | The installed the binaries here: | ||
| + | /projects/lowelab/users/jstjohn/allpaths/bin | ||
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| + | and then I ziped them and transfered them via scp over to campusrocks. | ||
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| + | To compile static I ran configure with "CXXFLAGS=-static". | ||
| - | Configure error, requires boost with at least the Boost.System binaries installed. Now I am installing that... | + | 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. |
| - | + | ||
| - | Boost successfully installed. Now installing allpaths. Configure successful and currently building. --- //[[jstjohn@soe.ucsc.edu|John St. John]] 2010/04/07 00:53// | + | |
| - | Build unsuccessfull: | ||
| - | ./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~~ | ||
archive/bioinformatic_tools/allpaths.1270632179.txt.gz · Last modified: 2010/04/07 09:22 by jstjohn
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