archive:bioinformatic_tools:arachne
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archive:bioinformatic_tools:arachne [2010/04/06 00:41] jstjohn |
archive:bioinformatic_tools:arachne [2015/07/28 06:22] ceisenhart ↷ Page moved from bioinformatic_tools:arachne to archive:bioinformatic_tools:arachne |
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| ====High Level Overview==== | ====High Level Overview==== | ||
| Arachne was the first program developed by the Broad institute to assemble "long reads from sanger-method sequencing"[(cite:broad>http://www.broadinstitute.org/science/programs/genome-biology/computational-rd/computational-research-and-development)]. They have a more current program named [[bioinformatic_tools:allpaths|AllPaths]] that they claim is better suited to shorter sequence reads (100+ bp)[(cite:broad)]. Arachne may be download from [[ftp://ftp.broadinstitute.org/pub/crd/ARACHNE/|here]], and there is a [[http://www.broadinstitute.org/crd/wiki/index.php/Arachne_Main_Page|documentation wiki]] set up for it as well. | Arachne was the first program developed by the Broad institute to assemble "long reads from sanger-method sequencing"[(cite:broad>http://www.broadinstitute.org/science/programs/genome-biology/computational-rd/computational-research-and-development)]. They have a more current program named [[bioinformatic_tools:allpaths|AllPaths]] that they claim is better suited to shorter sequence reads (100+ bp)[(cite:broad)]. Arachne may be download from [[ftp://ftp.broadinstitute.org/pub/crd/ARACHNE/|here]], and there is a [[http://www.broadinstitute.org/crd/wiki/index.php/Arachne_Main_Page|documentation wiki]] set up for it as well. | ||
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| + | Arachne also requires GCC-4.3+. | ||
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| + | ====Installation==== | ||
| + | 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: | ||
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| + | /projects/lowelab/users/jstjohn/Arachne | ||
| + | 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”. | ||
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| + | 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. | ||
| ===== References ===== | ===== References ===== | ||
| <refnotes>notes-separator: none</refnotes> | <refnotes>notes-separator: none</refnotes> | ||
| ~~REFNOTES cite~~ | ~~REFNOTES cite~~ | ||
archive/bioinformatic_tools/arachne.txt · Last modified: 2015/07/28 06:22 by ceisenhart
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