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1 REPET dependency
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2
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3 For REPET version 2.5.1 (REPET with some patchs, please contact urgi-contact@versailles.inra.fr to get it)
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4
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5 REPET dependency handle the creation of essential environment variables.
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6
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7 !!!!WARNING : REPET has to be installed!!!!
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8
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9
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10 After you have install your tool with this dependency, please go to check if defined environment variables suit with your configuration.
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11 Check this file :
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12 ***tool_dependency_dir***/repet/2.5/vmarcon/package_repet_2_5/***revision***/env.sh
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13 Please replace with correct values :
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14 * tool_dependency_dir (value in galaxy.ini file)
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15 * revision
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16
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17 Then in this file (env.sh) modify variable value in order to adjust it to your
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18 system :
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19 - Database connexion (REPET_HOST, REPET_USER, REPET_PW, REPET_DB, REPET_PORT)
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20 - Job manager (REPET_JOB_MANAGER, REPET_QUEUE)
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21 - Working environment (REPET_PATH, REPET_NUCL_BANK, REPET_PROT_BANK, REPET_HMM_PROFILES, REPET_RDNA_BANK)
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22
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23 If you want REPET working in a specific temporary directory, fill the variable REPET_TMP_DIR.
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24
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25 If you don't want to use one or several databanks, remove the corresponding variable.
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26
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27 If you notice a problem running Grouper on step 3, please complete LIB_GCC4_8_2 and LD_LIBRARY_PATH variable.
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28
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29
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30 -------------
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31 Galaxy Page
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32 -------------
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33
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34 !!!! To get the content of the page and example datasets, please ask it sendig an e-mail at urgi-contact@versailles.inra.fr . !!!!
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35
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36 To explain in detail to your users how TEdenovo_lite works, please make a galaxy Page:
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37 - Connect in your Galaxy.
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38 - Go to the "Saved Pages" (User > Saved Pages).
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39 - Create a new page ("Add new Page" button in the top right corner) named 'tedenovo'.
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40 - Click on "tedenovo" and "Edit content".
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41 - Paste the content of the URGI TEdenovo page.
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42 - Save.
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43
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44 Now you have to create the two Embed Galaxy Object (example on the blue and green area).
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45 - On the URGI TEdenovo page, download "DmelChr4.fa" by clicking on "Save dataset" (green area).
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46 - Upload this file on your Galaxy instance where REPET Lite is installed IN A NEW HISTORY.
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47 - Rename this dataset "DmelChr4.fa".
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48 - Launch "Repet Lite - TEdenovo" with "DmelChr4.fa" as Fasta alignment input, "Yes" to get classification informations.
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49 - Go back to the page in edition mode.
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50 - Add the green area - Embed Datasets - DmelChr4.fa
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51 - Add the blue area - Embed Histories - your history with TEdenovo result.
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52 - Save again.
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53
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54 To publish your page:
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55 - Go to the list of "Saved Pages"
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56 - Click on "tedenovo" and "Share or Publish"
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57 - And "Make Page Accessible and Publish"
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58
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59 Now this page is accessible with the URL shown and in Shared Data > Published Pages
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60
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61
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62 --------------------
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63 Vizualisation plugin
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64 --------------------
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65
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66 We developped a plugin to vizualise the statistical output (".classif_stats.txt").
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67 Please send an e-mail at urgi-contact@versailles.inra.fr to get it.
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68
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69
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