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              grep rough audit - static analysis tool
                  v2.8 written by @Wireghoul
=================================[justanotherhacker.com]===
ivar-1.2.3+dfsg/docs/html/_i_n_s_t_a_l_l_a_t_i_o_n_8md_source.html-67-<div class="contents">
ivar-1.2.3+dfsg/docs/html/_i_n_s_t_a_l_l_a_t_i_o_n_8md_source.html:68:<div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno">    1</span>&#160;Installation {#installpage}</div><div class="line"><a name="l00002"></a><span class="lineno">    2</span>&#160;============</div><div class="line"><a name="l00003"></a><span class="lineno">    3</span>&#160;</div><div class="line"><a name="l00004"></a><span class="lineno">    4</span>&#160;Dependencies</div><div class="line"><a name="l00005"></a><span class="lineno">    5</span>&#160;------------</div><div class="line"><a name="l00006"></a><span class="lineno">    6</span>&#160;</div><div class="line"><a name="l00007"></a><span class="lineno">    7</span>&#160;* [htslib](https://github.com/samtools/htslib)</div><div class="line"><a name="l00008"></a><span class="lineno">    8</span>&#160;</div><div class="line"><a name="l00009"></a><span class="lineno">    9</span>&#160;Note:</div><div class="line"><a name="l00010"></a><span class="lineno">   10</span>&#160;</div><div class="line"><a name="l00011"></a><span class="lineno">   11</span>&#160;It is highly recommended that [samtools](https://github.com/samtools/samtools) also be installed alongside iVar. iVar uses the output of samtools mpileup to call variants and generate consensus sequences. In addition, samtools `sort` and `index` commands are very useful to setup a pipeline using iVar.</div><div class="line"><a name="l00012"></a><span class="lineno">   12</span>&#160;</div><div class="line"><a name="l00013"></a><span class="lineno">   13</span>&#160;Installation</div><div class="line"><a name="l00014"></a><span class="lineno">   14</span>&#160;------------</div><div class="line"><a name="l00015"></a><span class="lineno">   15</span>&#160;</div><div class="line"><a name="l00016"></a><span class="lineno">   16</span>&#160;To install ivar, run the following commands.</div><div class="line"><a name="l00017"></a><span class="lineno">   17</span>&#160;</div><div class="line"><a name="l00018"></a><span class="lineno">   18</span>&#160;```</div><div class="line"><a name="l00019"></a><span class="lineno">   19</span>&#160;./autogen.sh</div><div class="line"><a name="l00020"></a><span class="lineno">   20</span>&#160;./configure</div><div class="line"><a name="l00021"></a><span class="lineno">   21</span>&#160;make</div><div class="line"><a name="l00022"></a><span class="lineno">   22</span>&#160;make install</div><div class="line"><a name="l00023"></a><span class="lineno">   23</span>&#160;```</div><div class="line"><a name="l00024"></a><span class="lineno">   24</span>&#160;</div><div class="line"><a name="l00025"></a><span class="lineno">   25</span>&#160;If htslib has been installed in a non standard location, please run,</div><div class="line"><a name="l00026"></a><span class="lineno">   26</span>&#160;</div><div class="line"><a name="l00027"></a><span class="lineno">   27</span>&#160;```</div><div class="line"><a name="l00028"></a><span class="lineno">   28</span>&#160;./autogen.sh</div><div class="line"><a name="l00029"></a><span class="lineno">   29</span>&#160;./configure --with-hts=/prefix/to/bin/folder/with/htslib</div><div class="line"><a name="l00030"></a><span class="lineno">   30</span>&#160;make</div><div class="line"><a name="l00031"></a><span class="lineno">   31</span>&#160;make install</div><div class="line"><a name="l00032"></a><span class="lineno">   32</span>&#160;```</div><div class="line"><a name="l00033"></a><span class="lineno">   33</span>&#160;</div><div class="line"><a name="l00034"></a><span class="lineno">   34</span>&#160;Also, please add the following to your .bashrc so that iVar can find htslib dynamic libraries during runtime.</div><div class="line"><a name="l00035"></a><span class="lineno">   35</span>&#160;</div><div class="line"><a name="l00036"></a><span class="lineno">   36</span>&#160;```</div><div class="line"><a name="l00037"></a><span class="lineno">   37</span>&#160;export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/path/to/hts/lib/folder</div><div class="line"><a name="l00038"></a><span class="lineno">   38</span>&#160;```</div><div class="line"><a name="l00039"></a><span class="lineno">   39</span>&#160;</div><div class="line"><a name="l00040"></a><span class="lineno">   40</span>&#160;Installing [GNU Autotools](https://www.gnu.org/software/automake/manual/html_node/Autotools-Introduction.html#Autotools-Introduction),</div><div class="line"><a name="l00041"></a><span class="lineno">   41</span>&#160;</div><div class="line"><a name="l00042"></a><span class="lineno">   42</span>&#160;* OSX</div><div class="line"><a name="l00043"></a><span class="lineno">   43</span>&#160;</div><div class="line"><a name="l00044"></a><span class="lineno">   44</span>&#160;Using [homebrew](https://brew.sh/),</div><div class="line"><a name="l00045"></a><span class="lineno">   45</span>&#160;</div><div class="line"><a name="l00046"></a><span class="lineno">   46</span>&#160;```</div><div class="line"><a name="l00047"></a><span class="lineno">   47</span>&#160;brew install autoconf automake libtool</div><div class="line"><a name="l00048"></a><span class="lineno">   48</span>&#160;```</div><div class="line"><a name="l00049"></a><span class="lineno">   49</span>&#160;</div><div class="line"><a name="l00050"></a><span class="lineno">   50</span>&#160;* Ubuntu</div><div class="line"><a name="l00051"></a><span class="lineno">   51</span>&#160;</div><div class="line"><a name="l00052"></a><span class="lineno">   52</span>&#160;Using [APT](https://help.ubuntu.com/lts/serverguide/apt.html) on Ubuntu,</div><div class="line"><a name="l00053"></a><span class="lineno">   53</span>&#160;</div><div class="line"><a name="l00054"></a><span class="lineno">   54</span>&#160;```</div><div class="line"><a name="l00055"></a><span class="lineno">   55</span>&#160;apt-get install autotools-dev</div><div class="line"><a name="l00056"></a><span class="lineno">   56</span>&#160;```</div><div class="line"><a name="l00057"></a><span class="lineno">   57</span>&#160;</div><div class="line"><a name="l00058"></a><span class="lineno">   58</span>&#160;For bug reports please email gkarthik[at]scripps.edu or raise an issue on Github.</div></div><!-- fragment --></div><!-- contents -->
ivar-1.2.3+dfsg/docs/html/_i_n_s_t_a_l_l_a_t_i_o_n_8md_source.html-69-<!-- start footer part -->
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ivar-1.2.3+dfsg/debian/createmanpages-4-
ivar-1.2.3+dfsg/debian/createmanpages:5:VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//' -e 's/[+~]dfsg$//'`
ivar-1.2.3+dfsg/debian/createmanpages-6-NAME=`grep "^Description:" debian/control | sed 's/^Description: *//' | head -n1`