Mercurial > repos > vmarcon > repet_tedenovo
comparison README.txt @ 0:baea09e6722b draft default tip
1st Uploaded
| author | vmarcon |
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| date | Mon, 06 Feb 2017 13:31:53 -0500 |
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| -1:000000000000 | 0:baea09e6722b |
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| 1 REPET dependency | |
| 2 | |
| 3 For REPET version 2.5.1 (REPET with some patchs, please contact urgi-contact@versailles.inra.fr to get it) | |
| 4 | |
| 5 REPET dependency handle the creation of essential environment variables. | |
| 6 | |
| 7 !!!!WARNING : REPET has to be installed!!!! | |
| 8 | |
| 9 | |
| 10 After you have install your tool with this dependency, please go to check if defined environment variables suit with your configuration. | |
| 11 Check this file : | |
| 12 ***tool_dependency_dir***/repet/2.5/vmarcon/package_repet_2_5/***revision***/env.sh | |
| 13 Please replace with correct values : | |
| 14 * tool_dependency_dir (value in galaxy.ini file) | |
| 15 * revision | |
| 16 | |
| 17 Then in this file (env.sh) modify variable value in order to adjust it to your | |
| 18 system : | |
| 19 - Database connexion (REPET_HOST, REPET_USER, REPET_PW, REPET_DB, REPET_PORT) | |
| 20 - Job manager (REPET_JOB_MANAGER, REPET_QUEUE) | |
| 21 - Working environment (REPET_PATH, REPET_NUCL_BANK, REPET_PROT_BANK, REPET_HMM_PROFILES, REPET_RDNA_BANK) | |
| 22 | |
| 23 If you want REPET working in a specific temporary directory, fill the variable REPET_TMP_DIR. | |
| 24 | |
| 25 If you don't want to use one or several databanks, remove the corresponding variable. | |
| 26 | |
| 27 If you notice a problem running Grouper on step 3, please complete LIB_GCC4_8_2 and LD_LIBRARY_PATH variable. | |
| 28 | |
| 29 | |
| 30 ------------- | |
| 31 Galaxy Page | |
| 32 ------------- | |
| 33 | |
| 34 !!!! To get the content of the page and example datasets, please ask it sendig an e-mail at urgi-contact@versailles.inra.fr . !!!! | |
| 35 | |
| 36 To explain in detail to your users how TEdenovo_lite works, please make a galaxy Page: | |
| 37 - Connect in your Galaxy. | |
| 38 - Go to the "Saved Pages" (User > Saved Pages). | |
| 39 - Create a new page ("Add new Page" button in the top right corner) named 'tedenovo'. | |
| 40 - Click on "tedenovo" and "Edit content". | |
| 41 - Paste the content of the URGI TEdenovo page. | |
| 42 - Save. | |
| 43 | |
| 44 Now you have to create the two Embed Galaxy Object (example on the blue and green area). | |
| 45 - On the URGI TEdenovo page, download "DmelChr4.fa" by clicking on "Save dataset" (green area). | |
| 46 - Upload this file on your Galaxy instance where REPET Lite is installed IN A NEW HISTORY. | |
| 47 - Rename this dataset "DmelChr4.fa". | |
| 48 - Launch "Repet Lite - TEdenovo" with "DmelChr4.fa" as Fasta alignment input, "Yes" to get classification informations. | |
| 49 - Go back to the page in edition mode. | |
| 50 - Add the green area - Embed Datasets - DmelChr4.fa | |
| 51 - Add the blue area - Embed Histories - your history with TEdenovo result. | |
| 52 - Save again. | |
| 53 | |
| 54 To publish your page: | |
| 55 - Go to the list of "Saved Pages" | |
| 56 - Click on "tedenovo" and "Share or Publish" | |
| 57 - And "Make Page Accessible and Publish" | |
| 58 | |
| 59 Now this page is accessible with the URL shown and in Shared Data > Published Pages | |
| 60 | |
| 61 | |
| 62 -------------------- | |
| 63 Vizualisation plugin | |
| 64 -------------------- | |
| 65 | |
| 66 We developped a plugin to vizualise the statistical output (".classif_stats.txt"). | |
| 67 Please send an e-mail at urgi-contact@versailles.inra.fr to get it. | |
| 68 | |
| 69 |