archive:bioinformatic_tools:allpaths
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archive:bioinformatic_tools:allpaths [2010/04/07 07:54] 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_2.pdf|allpathsv3_manual}}. | ||
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| + | ====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? | ||
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| ====High Level Overview==== | ====High Level Overview==== | ||
| ALLPATHS is the most recent (as of this writing) tool developed by the broad institute to assemble shotgun sequences[(cite:broad>http://www.broadinstitute.org/science/programs/genome-biology/computational-rd/computational-research-and-development)]. The broad institute claims that version 3 of the program can assemble up to mammalian sized genomes if the reads are at least 100+ base pairs[(cite:broad)]. Version 3 (currently 3.2) of the program may be downloaded from [[ftp://ftp.broad.mit.edu/pub/crd/ALLPATHS/Release-3-0/|here]] and that folder also contains some documentation on how to use the program. Also the program ships with test data that you can assemble. | ALLPATHS is the most recent (as of this writing) tool developed by the broad institute to assemble shotgun sequences[(cite:broad>http://www.broadinstitute.org/science/programs/genome-biology/computational-rd/computational-research-and-development)]. The broad institute claims that version 3 of the program can assemble up to mammalian sized genomes if the reads are at least 100+ base pairs[(cite:broad)]. Version 3 (currently 3.2) of the program may be downloaded from [[ftp://ftp.broad.mit.edu/pub/crd/ALLPATHS/Release-3-0/|here]] and that folder also contains some documentation on how to use the program. Also the program ships with test data that you can assemble. | ||
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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 | ||
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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? | ||
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| + | Installed gcc-4.5! (had to do it myself, the sys admins wouldn't try) | ||
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| + | 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. | ||
| + | ---------------------------------------------------------------------- | ||
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| + | |||
| + | While attempting to install Allpaths I get an error right away for all methods other than setting | ||
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| + | 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
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