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REPET dependency

For REPET version 2.5.1 (REPET with some patchs, please contact [e-mail] to get it)

REPET dependency handle the creation of essential environment variables. 

!!!!WARNING : REPET has to be installed!!!!


After you have install your tool with this dependency, please go to check if defined environment variables suit with your configuration.
Check this file : 
***tool_dependency_dir***/repet/2.5/vmarcon/package_repet_2_5/***revision***/env.sh
Please replace with correct values : 
  * tool_dependency_dir (value in galaxy.ini file)
  * revision

Then in this file (env.sh) modify variable value in order to adjust it to your
system : 
 - Database connexion (REPET_HOST, REPET_USER, REPET_PW, REPET_DB, REPET_PORT)
 - Job manager (REPET_JOB_MANAGER, REPET_QUEUE)
 - Working environment (REPET_PATH, REPET_NUCL_BANK, REPET_PROT_BANK, REPET_HMM_PROFILES, REPET_RDNA_BANK)

If you want REPET working in a specific temporary directory, fill the variable REPET_TMP_DIR.

If you don't want to use one or several databanks, remove the corresponding variable.

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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 Galaxy Page
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!!!! To get the content of the page and example datasets, please ask it sendig an e-mail at [e-mail] . !!!!

To explain in detail to your users how TEdenovo_lite works, please make a galaxy Page: 
- Connect in your Galaxy.
- Go to the "Saved Pages" (User > Saved Pages).
- Create a new page ("Add new Page" button in the top right corner) named 'tedenovo'.
- Click on "tedenovo" and "Edit content".
- Paste the content of the URGI TEdenovo page.
- Save.

Now you have to create the two Embed Galaxy Object (example on the blue and green area).
- On the URGI TEdenovo page, download "DmelChr4.fa" by clicking on "Save dataset" (green area).
- Upload this file on your Galaxy instance where REPET Lite is installed IN A NEW HISTORY.
- Rename this dataset "DmelChr4.fa".
- Launch "Repet Lite - TEdenovo" with "DmelChr4.fa" as Fasta alignment input, "Yes" to get classification informations.
- Go back to the page in edition mode.
- Add the green area - Embed Datasets - DmelChr4.fa
- Add the blue area - Embed Histories - your history with TEdenovo result.
- Save again.

To publish your page:
- Go to the list of "Saved Pages" 
- Click on "tedenovo" and "Share or Publish"
- And "Make Page Accessible and Publish"

Now this page is accessible with the URL shown and in Shared Data > Published Pages


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Vizualisation plugin
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We developped a plugin to vizualise the statistical output (".classif_stats.txt"). 
Please send an e-mail at [e-mail] to get it.