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1 RTG Galaxy tools
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2 ----------------
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3
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4 Install:
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5
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6 Copy lib/galaxy/datatypes/rtg.py and the tools/rtg directory to the same locations in your galaxy distribution.
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7
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8 Then edit the following files:
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9
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10 galaxy_dist/tools/rtg/rtg-galaxy.cfg
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11
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12 change the rtg variable to point at the rtg file in your RTG installation directory
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13
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14 galaxy_dist/lib/galaxy/datatypes/registry.py
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15 add
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16 , rtg
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17 to the list of imports beginning with data, tabular, interval...
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18
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19
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20 galaxy_dist/tool_conf.xml
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21 Within the <toolbox> node, add
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22
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23 <section name="Realtime Genomics" id="rtg">
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24 <label text="Data formatting" id="formatting" />
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25 <tool file="rtg/format_fasta.xml" />
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26 <tool file="rtg/format_fastq.xml" />
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27 <tool file="rtg/cg2sdf.xml" />
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28 <tool file="rtg/sdf2fasta.xml" />
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29 <label text="Read mapping" id="mapping" />
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30 <tool file="rtg/map.xml" />
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31 <tool file="rtg/cgmap.xml" />
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32 <tool file="rtg/mapf.xml" />
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33 <tool file="rtg/mapx.xml" />
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34 <label text="Variant detection" id="variant" />
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35 <tool file="rtg/snp.xml" />
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36 <tool file="rtg/coverage.xml" />
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37 <tool file="rtg/snpintersection.xml" />
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38 <label text="Simulation" id="sim" />
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39 <tool file="rtg/genomesim.xml" />
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40 <tool file="rtg/cgsim.xml" />
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41 <tool file="rtg/readsim.xml" />
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42 <tool file="rtg/snpsim.xml" />
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43 </section>
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44
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45 galaxy_dist/datatypes_config.xml
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46 Within the <datatypes><registration> node, add
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47
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48 <!-- Start RTG Datatypes -->
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49 <datatype extension="rtg_sdf" type="galaxy.datatypes.rtg:Sdf"/>
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50 <datatype extension="tsvcg" type="galaxy.datatypes.rtg:Cgtsv" display_in_upload="true"/>
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51 <datatype extension="samix" type="galaxy.datatypes.rtg:Samix" display_in_upload="true"/>
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52 <!-- End RTG Datatypes -->
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53
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54 Within the <datatypes><sniffers> node, add
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55 <sniffer type="galaxy.datatypes.rtg:Samix"/>
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56 <sniffer type="galaxy.datatypes.rtg:Cgtsv"/>
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