e-clouds Solution MAIN GOAL WORKSHOP FIRST PART - RUNNING A SINGLE JOB ON e-clouds

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1 MAIN GOAL Know in practical way the main services offered by e-clouds, a marketplace to run scientific applications in the Cloud in an easy and scalable way. WORKSHOP FIRST PART - RUNNING A SINGLE JOB ON e-clouds Follow the next steps to complete the Workshop on e-clouds 1. Go to the e-clouds main page: You will see the list of applications offered through e-clouds.

2 2. Log in with your specific account: and password: bios2015x (X must be replaced in both fields by the number delivered during the course). 3. Once you have been logged in, you will be in the e-clouds dashboard. You can navigate through the page, view the Executions list, Apps deployed on e-clouds, My Data (here you will find your private and public directories and you could upload files to the platform, see the result files and download them).

3 4. Select New Execution Button to launch your first execution in e-clouds. In the next interface you have to complete some parameters. You should use the values shown in the next figure. In the application field, you must select Blastp ( ), this is the version of Blastp deployed on e-clouds. Then press Create Execution Button 5. In the next the interface, enter and select the execution parameters.

4 6. Press the Select File button, to choose the Query for search (Fasta sequences), then select ProteinasParaBlast.txt. 7. Choose the options selected in the next figure. Database: ACLAME, Output Format: Tabular and the Expected Value: 10. Output Directory (select Outputs). Then press Next Step.

5 8. The next step is to choose the instance type to execute the job. How is illustrated in the following figure, you will select m1.large, next press Calculate and then Finish and Show Summary.

6 9. Finally you will review the execution and launch it on e-clouds pressing the Launch Execution button. You will be redirected to the Dashboard. 10. In this case, you have launched an execution with a file of 48 sequences to compare them against the database ACLAME. In the next session you will divide this file into two parts each one with 24 sequences. This is done to show how to run a parallel job in e-clouds.

7 WORKSHOP SECOND PART - RUNNING SEVERAL JOBS ON e-clouds 1. Divide the file of 48 sequences in two files of 24 sequences each one. Download the file of e-clouds: Go to My Data and then select the BiosWorkshop2015 folder and download the file ProteinasParaBlastp.txt 2. Open a text editor like notepad, sublime text, emacs, vi, etc. Find the 25th sequence and create a new file containing the sequences 1 to 24, and another one containing the sequences 25 to 48. You can easily find the sequence 25th searching for the following term: >orf00006_1 NODE_1_length_4148_cov_ , this is the beginning of the 25th sequence. You can call both files secuences1to24.txt and sequences25to48.txt.

8 3. Go to MyData and in the root folder of your workspace and create a folder called ParallelJob. You need to press the New Folder button and then in the New Directory interface write the folder name. 4. Go to the ParallelJob folder and then upload the two files created in Step 2 (secuences1to24.txt and sequences25to48.txt). Press the Upload button and then select the file secuences1to24.txt and press the button Create Cloud File.

9 Repeat the process to upload the file sequences25to48.txt 5. Get into the folder ParallelJob and you will find the 2 files uploaded previously.

10 6. Go to executions and create a New Execution. This time you will choose BlastpParallel ( ). 7. Press the Create Execution button. In the next interface you will have to select the folder that contains several files with multiple sequences in the Query for search parameter. In this case you will have to choose the folder ParallelJob as shown in the new figure.

11

12 8. The next step is to choose the instance type to execute the job. How is illustrated in the following figure, you will select m1.large, next press Calculate and then Finish and Show Summary.

13 9. Finally you will review the execution and launch it on e-clouds pressing the Launch Execution button. You will be redirected to the Dashboard. 10. In this case, you have launched an execution with two Blastp jobs, each one analyzing 24 sequences against the database ACLAME.

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