===========================================================
.___ __ __
_________________ __ __ __| _/|__|/ |_
/ ___\_` __ \__ \ | | \/ __ | | \\_ __\
/ /_/ > | \// __ \| | / /_/ | | || |
\___ /|__| (____ /____/\____ | |__||__|
/_____/ \/ \/
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> Installation {#installpage}</div><div class="line"><a name="l00002"></a><span class="lineno"> 2</span> ============</div><div class="line"><a name="l00003"></a><span class="lineno"> 3</span> </div><div class="line"><a name="l00004"></a><span class="lineno"> 4</span> Dependencies</div><div class="line"><a name="l00005"></a><span class="lineno"> 5</span> ------------</div><div class="line"><a name="l00006"></a><span class="lineno"> 6</span> </div><div class="line"><a name="l00007"></a><span class="lineno"> 7</span> * [htslib](https://github.com/samtools/htslib)</div><div class="line"><a name="l00008"></a><span class="lineno"> 8</span> </div><div class="line"><a name="l00009"></a><span class="lineno"> 9</span> Note:</div><div class="line"><a name="l00010"></a><span class="lineno"> 10</span> </div><div class="line"><a name="l00011"></a><span class="lineno"> 11</span> 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> </div><div class="line"><a name="l00013"></a><span class="lineno"> 13</span> Installation</div><div class="line"><a name="l00014"></a><span class="lineno"> 14</span> ------------</div><div class="line"><a name="l00015"></a><span class="lineno"> 15</span> </div><div class="line"><a name="l00016"></a><span class="lineno"> 16</span> To install ivar, run the following commands.</div><div class="line"><a name="l00017"></a><span class="lineno"> 17</span> </div><div class="line"><a name="l00018"></a><span class="lineno"> 18</span> ```</div><div class="line"><a name="l00019"></a><span class="lineno"> 19</span> ./autogen.sh</div><div class="line"><a name="l00020"></a><span class="lineno"> 20</span> ./configure</div><div class="line"><a name="l00021"></a><span class="lineno"> 21</span> make</div><div class="line"><a name="l00022"></a><span class="lineno"> 22</span> make install</div><div class="line"><a name="l00023"></a><span class="lineno"> 23</span> ```</div><div class="line"><a name="l00024"></a><span class="lineno"> 24</span> </div><div class="line"><a name="l00025"></a><span class="lineno"> 25</span> 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> </div><div class="line"><a name="l00027"></a><span class="lineno"> 27</span> ```</div><div class="line"><a name="l00028"></a><span class="lineno"> 28</span> ./autogen.sh</div><div class="line"><a name="l00029"></a><span class="lineno"> 29</span> ./configure --with-hts=/prefix/to/bin/folder/with/htslib</div><div class="line"><a name="l00030"></a><span class="lineno"> 30</span> make</div><div class="line"><a name="l00031"></a><span class="lineno"> 31</span> make install</div><div class="line"><a name="l00032"></a><span class="lineno"> 32</span> ```</div><div class="line"><a name="l00033"></a><span class="lineno"> 33</span> </div><div class="line"><a name="l00034"></a><span class="lineno"> 34</span> 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> </div><div class="line"><a name="l00036"></a><span class="lineno"> 36</span> ```</div><div class="line"><a name="l00037"></a><span class="lineno"> 37</span> 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> ```</div><div class="line"><a name="l00039"></a><span class="lineno"> 39</span> </div><div class="line"><a name="l00040"></a><span class="lineno"> 40</span> 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> </div><div class="line"><a name="l00042"></a><span class="lineno"> 42</span> * OSX</div><div class="line"><a name="l00043"></a><span class="lineno"> 43</span> </div><div class="line"><a name="l00044"></a><span class="lineno"> 44</span> Using [homebrew](https://brew.sh/),</div><div class="line"><a name="l00045"></a><span class="lineno"> 45</span> </div><div class="line"><a name="l00046"></a><span class="lineno"> 46</span> ```</div><div class="line"><a name="l00047"></a><span class="lineno"> 47</span> brew install autoconf automake libtool</div><div class="line"><a name="l00048"></a><span class="lineno"> 48</span> ```</div><div class="line"><a name="l00049"></a><span class="lineno"> 49</span> </div><div class="line"><a name="l00050"></a><span class="lineno"> 50</span> * Ubuntu</div><div class="line"><a name="l00051"></a><span class="lineno"> 51</span> </div><div class="line"><a name="l00052"></a><span class="lineno"> 52</span> 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> </div><div class="line"><a name="l00054"></a><span class="lineno"> 54</span> ```</div><div class="line"><a name="l00055"></a><span class="lineno"> 55</span> apt-get install autotools-dev</div><div class="line"><a name="l00056"></a><span class="lineno"> 56</span> ```</div><div class="line"><a name="l00057"></a><span class="lineno"> 57</span> </div><div class="line"><a name="l00058"></a><span class="lineno"> 58</span> 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 -->
##############################################
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`