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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/qiime">Debian Med / qiime</a>
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<h4>
Commits:
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<strong><a href="https://salsa.debian.org/med-team/qiime/commit/ab34735db47e5102f44ff8b0809710b77dd67022">ab34735d</a></strong>
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<span>by Andreas Tille</span>
<i>at 2018-10-28T17:07:53Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Remove more remainings of qiime1
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<h4>2 changed files:</h4>
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debian/qiime.1.ronn
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debian/qiime.dirs
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<h4>Changes:</h4>
<li id="681f70686630aa79dadb3801860ddb2d691d21b3">
<a href="https://salsa.debian.org/med-team/qiime/commit/ab34735db47e5102f44ff8b0809710b77dd67022#681f70686630aa79dadb3801860ddb2d691d21b3"><strong>debian/qiime.1.ronn</strong>
deleted
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">qiime(1) -- Quantitative Insights Into Microbial Ecology</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">This is a short manpage for QIIME on Debian/Bio-Linux.</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">You should refer to the main QIIME documentation at</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">/usr/share/doc/qiime/html/index.html and also the QIIME section of the</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">Bio-Linux tutorial at http://environmentalomics.org/bio-linux-training/.</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext">## INVOCATION:</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">To run any QIIME command such as "validate_mapping_file.py":</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext"> _$_ `qiime` validate_mapping_file [...]</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext">or just type 'qiime' to get a customised shell environment where all QIIME commands</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext">are available exactly as documented, ie:</span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext"> _$_ `qiime`</span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext"> _$ qiime >_ `validate_mapping_file.py` [...]</span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext">## PARAMETERS FILE:</span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext">For certain QIIME commands, you are asked to indicate where your QIIME</span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext">parameters file is. You can find an example file in the location</span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext">/usr/share/doc/qiime/qiime_parameters_example.txt but the recommendation</span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="plaintext">as of QIIME 1.7.0 is to only set values that you want to override and to</span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="plaintext">let QIIME pick defaults for the others.</span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="plaintext">## QIIME CONFIGURATION:</span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="plaintext">QIIME reads configuration information from the file specified by</span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="plaintext">**$QIIME_CONFIG_FP** or by default from **/etc/qiime/qiime_config**.</span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="plaintext">It is unlikely you will need to change the settings in this file,</span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="plaintext">but if you do you should copy it as **.qiime_config** in your home directory.</span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="plaintext">## GREENGENES DATA:</span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="plaintext">The qiime-data package now provides copies of the Greengenes core alignment</span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="plaintext">template plus the lanemask file in **/usr/share/qiime/data** but you still need</span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="plaintext">to download some extra data to use QIIME properly. Taxonomic databases are</span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="plaintext">being updated all the time and you need to be sure which version you are</span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="plaintext">using. See the QIIME main docs for more info on what you need.</span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="plaintext">## PROGRAMS INVOKED BY QIIME:</span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="plaintext">QIIME calls many applications and libraries in the course of performing an</span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="plaintext">analysis. For consistency, it is important to know what versions were installed</span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="plaintext">at the time of the analysis. To obtain a complete report type</span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="plaintext"> `print_qiime_config_all`</span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="plaintext">**NB:** The official release of QIIME stipulates very particular versions of all these</span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="plaintext">programs in order to guarantee consistent results. This version of QIIME uses updated</span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="plaintext">versions that are packages in the Debian software repository. If you want to obtain ressults</span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="plaintext">consistent with the official QIIME pipeline then you need to install QIIME as set out on</span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="plaintext">the main website.</span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="plaintext">## UCLUST and USEARCH:</span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="plaintext">You may install these manually if you want to use them, but as of QIIME 1.9</span>
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61
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="plaintext">all features should be available via the free SumaClust and vSearch programs.</span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="plaintext">uClust and uSearch are not free software and come with usage restrictions</span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="plaintext">for non-paying users.</span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="plaintext">For more info, try running 'uclust' or 'usearch' at the QIIME prompt.</span>
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="plaintext">## For more information about QIIME, please visit the home page at:</span>
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68
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="plaintext"> http://qiime.org</span>
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="plaintext">## QIIME was packaged as part of the Bio-Linux project.</span>
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72
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="plaintext"> http://environmentalomics.org/bio-linux</span></pre>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">usr/lib/qiime/bin</span></pre>
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