diff README.txt @ 0:baea09e6722b draft default tip

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