This shows you the differences between two versions of the page.
Both sides previous revision Previous revision Next revision | Previous revision Next revision Both sides next revision | ||
archive:bioinformatic_tools:allpaths [2010/04/07 09:24] jstjohn |
archive:bioinformatic_tools:allpaths [2010/04/08 16:20] jstjohn Better version of the allpaths manual where the text is readable and the filesize is simaller. |
||
---|---|---|---|
Line 1: | Line 1: | ||
===== 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==== | ||
Line 39: | Line 40: | ||
./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? | ||
===== References ===== | ===== References ===== | ||
<refnotes>notes-separator: none</refnotes> | <refnotes>notes-separator: none</refnotes> | ||
~~REFNOTES cite~~ | ~~REFNOTES cite~~ |