diff --git a/README.md b/README.md index ee9d10c..2ab7ce1 100755 --- a/README.md +++ b/README.md @@ -18,7 +18,7 @@ NGSeasy (beta): A [Dockerized](https://www.docker.com/) NGS pipeline and tool-bo [**NGSeasy is completely open source and we encourage interested folks to jump in and get involved in the dev with us.**](https://github.com/KHP-Informatics/ngseasy.git) -## NGSeasy: Genome Comparison & Analytic Testing ([GCAT](http://www.bioplanet.com/gcat)) Reports +## NGSeasy: Genome Comparison & Analytic Testing ([GCAT](http://www.bioplanet.com/gcat)) Reports Here we provide a quick look at basic NGSeasy performance (more results coming soon). |GCAT Report|Test Data |Pipeline| @@ -48,7 +48,7 @@ Please contact us for help/guidance on using the beta release. **Please Direct all queries to [https://github.com/KHP-Informatics/ngseasy/issues]** -When sending bug reports etc please provide:- +When sending bug reports etc please provide:- - Date of Download - OS and version @@ -148,7 +148,7 @@ git clone https://github.com/KHP-Informatics/ngseasy.git - Default install directory is `/home/${USER}` - in this example user home is `/home/ec2-user` -- `make INTSALLDIR="/home/ec2-user" all` +- `make INTSALLDIR="/home/ec2-user" all` - sets up top level directory structure - gets all docker images - gets indexed hg19 and b37 genomes @@ -167,7 +167,7 @@ cd ngseasy ## 1. make INTSALLDIR="/home/ec2-user" all -## 2. +## 2. sudo make install ``` @@ -204,7 +204,7 @@ Upload: 5.18 Mbit/s ## Install time on Amazon EC2 -Connection Speed: ~ 800 Mbit/s +Connection Speed: ~ 800 Mbit/s ``` real 94m54.237s @@ -212,7 +212,7 @@ user 12m26.960s sys 28m46.648s ``` -Note: We have only tested NGSeasy installation on Amazon EC2, Openstack and UK University Networks. These are all fairly fast networks with speeds exceeding 800 Mbit/s on average. +Note: We have only tested NGSeasy installation on Amazon EC2, Openstack and UK University Networks. These are all fairly fast networks with speeds exceeding 800 Mbit/s on average. ## Running NGSeasy for the first time on the test data @@ -275,6 +275,14 @@ We have adapted the current best practices from the Genome Analysis Toolkit (GAT As the containers themselves can be run as executables with pre-specified cpu and RAM resources, the orchestration of the pipeline can be placed under the control of conventional load balancers if this mode is required. +## Genomes + +| Genome | +|--------| +|hs37d5| +|b37| +|hg19| +|hs38DH| **************** @@ -577,7 +585,7 @@ ngs_projects |__raw_fastq |__config_files |__run_logs -|__ngseasy_resources +|__ngseasy_resources | |__ project_id | @@ -777,4 +785,4 @@ sudo docker build -t compbio/ngseasy-snpeff:${VERSION} . - http://plagnol-lab.blogspot.co.uk/2013/11/faq-and-clarifications-for-exomedepth-r.html ************************* -(C) 2015 Stephen J Newhouse & Amos Folarin +(C) 2015 Stephen J Newhouse & Amos Folarin