workshops.md
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@@ -18,10 +18,13 @@ Complete workshop data files and scripts: [biogrids_workshop.tar.gz](downloads/b
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Download and install biogrids CLI client then run:
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+
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```
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biogrids activate <site name> <user name> <activation key>
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```
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+
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#### Linux
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+
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```
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curl -kLO https://biogrids.org/wiki/downloads/biogrids-1.0.694-Linux.tgz
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tar zxf biogrids-1.0.694-Linux.tgz
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@@ -29,35 +32,47 @@ cd biogrids-1.0.694-Linux
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```
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#### OSX
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+
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```
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curl -kLO https://biogrids.org/wiki/downloads/biogrids-1.0.694-Darwin.tgz
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tar zxf biogrids-1.0.694-Darwin.tgz
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cd biogrids-1.0.694-Darwin
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```
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-#### Run biogrids
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+#### Activate biogrids
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```
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./biogrids activate biogrid-production jvinent1 70rYFTDnmCr93VUklfbf1s3M4jdyC9bFVYHew==
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+```
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+
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+### Install software with BioGrids
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+
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+```
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./biogrids install fastqc trimmomatic samtools star subread igv
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```
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-Change back to home directory
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+When finished, verify applications are installed:
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```
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-cd
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+./biogrids installed
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```
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-### Install software with BioGrids
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### Download and uncompress tutorial files
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-### Run RNA-Seq workflow
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-
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-Download then uncompress:
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```
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+cd # make sure we are in home dir
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curl -kLO https://biogrids.org/wiki/downloads/biogrids_workshop.tar.gz
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tar zxf biogrids_workshop.tar.gz
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cd biogrids_workshop
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+```
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+
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+### Run RNA-Seq workflow
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+
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+```
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+cd biogrids_workshop
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./runMOV10.sh ./raw_fastq/ENCODE_MOV10.fq
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```
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+Successful completion of the workflow will create a new directory name 'results'.
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+
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+Output from the RNA-Seq workflow is stored there.
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View results with IGV:
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```
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@@ -72,6 +87,31 @@ Within IGV:
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3: File / Load from file... ( .bam file)
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+## RNA-Seq Workflow on AWS
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+
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+### Start an EC2 Instance
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+
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+Log in to the AWS console: aws.amazon.com
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+Start a t2.micro instance (free tier)
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+The last prompt when lanuching will ask you to select a key pair. Create a new key pair if this is the first time you have used EC2 or select an existing key pair.
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+
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+If creating a new keypair you must download the .pem file. You will need this to access the EC2 instance launched with that key pair.
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+
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+We reccomend keeping your .pem key files in .ssh directory in your home.
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+
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+Copy the .pem file to .ssh and set the mode to user read only:
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+```
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+cp my_key_file.pem ~/.ssh
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+cd ~/.ssh
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+chmod 400 my_key_file.pem
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+ls -l my_key_file.pem
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+```
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+
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+
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+
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+
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+---
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+
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### Genome Resources
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ENCODE data files can be found here for CalTech RNA-Seq :