Team:Vanderbilt Software/User Guide
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- | <p>It's important to understand the difference between the software <em>darwin</em> and the utility <em>dwndiff</em>. Over the summer, the team produced <em>dwndiff</em>, which is a command-line utility for producing what are called "diff" files suitable for use with genomic data. <em>darwin</em>, on the other hand, is the overall vision of the software team: to produce a solution for tracking changes to all sorts of genomic data. Given input files, the dwndiff utility can speedily produce output files which can be used with an external version control system much more easily. Examples of such version control systems include <a href="http://git-scm.com/">git</a>, <a href="http://subversion.apache.org">svn</a>, <a href="mercurial.selenic.com/">hg</a>.</p> | + | <p>It's important to understand the difference between the software <em>darwin</em> and the utility <em>dwndiff</em>. Over the summer, the team produced <em>dwndiff</em>, which is a command-line utility for producing what are called "diff" files suitable for use with genomic data. <em>darwin</em>, on the other hand, is the overall vision of the software team: to produce a solution for tracking changes to all sorts of genomic data. Given input files, the dwndiff utility can speedily produce output files which can be used with an external version control system much more easily. Examples of such version control systems include <a href="http://git-scm.com/">git</a>, <a href="http://subversion.apache.org">svn</a>, and <a href="mercurial.selenic.com/">hg</a>.</p> |
<p>Using dwndiff is somewhat complex at first, but let's start with the most obvious solution: the "help" command:</p> | <p>Using dwndiff is somewhat complex at first, but let's start with the most obvious solution: the "help" command:</p> | ||
<pre>$ ./dwndiff --help | <pre>$ ./dwndiff --help | ||
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for any corresponding short options. | for any corresponding short options. | ||
</pre> | </pre> | ||
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+ | <p>Let's break this down into multiple cases:</p> | ||
+ | <ol> | ||
+ | <li>Given a genomic file, convert it to a version-controllable format, which we call vcsfmt.</li> | ||
+ | <li>Given two vcsfmt files, find the difference between them and produce a file to be put under version control, which we call vcscmp.</li> | ||
+ | </ol> | ||
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Revision as of 02:10, 18 October 2014
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User Guide |
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It's important to understand the difference between the software darwin and the utility dwndiff. Over the summer, the team produced dwndiff, which is a command-line utility for producing what are called "diff" files suitable for use with genomic data. darwin, on the other hand, is the overall vision of the software team: to produce a solution for tracking changes to all sorts of genomic data. Given input files, the dwndiff utility can speedily produce output files which can be used with an external version control system much more easily. Examples of such version control systems include git, svn, and hg. Using dwndiff is somewhat complex at first, but let's start with the most obvious solution: the "help" command: $ ./dwndiff --help Usage: dwndiff [OPTION...] FILE... dwndiff is a command-line tool to format DNA sequences for use in version control systems. It is intended to be used as a backend for version control tools which act upon biological data. It defaults to 'format' mode, where it formats a given DNA sequence (through stdin, or the given files) to a special format, appending the '.vcsfmt' suffix. If given the '-c' option, however, it will take two files, convert them to .vcsfmt format if necessary, and produce a .vcscmp file which can be used in version control software. -p, --preformat_loc=DIR Location of pre-existing .vcsfmt files for given input DNA -w, --write Write output to file(s) instead of stdout -c, --compare If two files given, produce unix diff-compatible comparison .vcscmp file -v, --verbose Produce verbose output -?, --help Give this help list --usage Give a short usage message -V, --version Print program version Mandatory or optional arguments to long options are also mandatory or optional for any corresponding short options. Let's break this down into multiple cases:
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