README
¶
About
Shock is a platform to support computation, storage, and distribution. Designed from the ground up to be fast, scalable, fault tolerant, federated.
Shock is RESTful. Accessible from desktops, HPC systems, exotic hardware, the cloud and your smartphone.
Shock is for scientific data. One of the challenges of large volume scientific data is that without often complex metadata it is of little to no value. Shock allows storage and querying of complex metadata.
Shock is a data management system. The long term goals of Shock include the ability to annotate, anonymize, convert, filter, perform quality control, and statically subsample at line speed bioinformatics sequence data. Extensible plug-in architecture is in development.
Most importantly Shock is still very much in development. Be patient and contribute.
Shock is actively being developed at github.com/MG-RAST/Shock.
Building
Shock (requires mongodb=>2.0.3, go=>1.1.0 golang.org, git, mercurial and bazaar). You must also set the $GOPATH and $GOROOT environment variables before installing Shock. There are two options for installing Shock.
OPTION 1: The recommended method for installing Shock is to download the Makefile located here to your $GOPATH directory and then run:
make install
OPTION 2: You could alternatively install Shock by running:
go get github.com/MG-RAST/Shock/...
The upside to using OPTION 1 is that this will insert the Shock version number into your Shock server to be displayed when the server is started and this will also generate the Shock documentation locally to be hosted by the server. The built binaries will be located in the env configured $GOPATH/bin/ directory.
Dockerfile
Alternativly your can use Docker to compile Shock. The Dockerfile in directory "docker" in this repository compiles Shock statically.
docker build -t shock:latest docker/Dockerfile
If you only want the binary you can create an container from the image an copy the binary to your host. This will copy the shock-server binary to your current working directory
docker run --name shock shock:latest ls
docker cp shock:/gopath/bin/shock-server .
docker rm shock
MongoDB
In ubuntu you can simply install mongo with:
sudo apt-get install -y mongodb-server
If you do not want to use a package manager to install mongodb, use:
curl -s http://downloads.mongodb.org/linux/mongodb-linux-x86_64-2.4.14.tgz | tar -v -C /mongodb/ -xz
If you do not use a service manager such as systemd, you can start mongodb like this, in foreground:
/mongodb/bin/mongod --dbpath /data/
or in background:
nohup /mongodb/bin/mongod --dbpath /mnt/db/ &
Configuration
The Shock configuration file is in INI file format. There is a template of the config file located at the root level of the repository.
Running
To run:
shock-server -conf <path_to_config_file>
Documentation
For further information about Shock's functionality, please refer to our github wiki.
Directories
¶
| Path | Synopsis |
|---|---|
|
auth
Package auth implements http request authentication
|
Package auth implements http request authentication |
|
auth/basic
Package basic implements basic auth decoding and self contained user authentication
|
Package basic implements basic auth decoding and self contained user authentication |
|
auth/globus
Package globus implements Globus Online Nexus authentication
|
Package globus implements Globus Online Nexus authentication |
|
auth/mgrast
Package globus implements MG-RAST OAuth authentication
|
Package globus implements MG-RAST OAuth authentication |
|
conf
Package conf parses start up args and config file
|
Package conf parses start up args and config file |
|
controller/node
Package node implements /node resource
|
Package node implements /node resource |
|
controller/node/acl
Package acl implements /node/:id/acl resource
|
Package acl implements /node/:id/acl resource |
|
controller/preauth
Package preauth implements /preauth resource
|
Package preauth implements /preauth resource |
|
db
Package db to connect to mongodb
|
Package db to connect to mongodb |
|
errors
Package contains error strings and patterns for common errors
|
Package contains error strings and patterns for common errors |
|
logger
Package logger implements async log web api messages
|
Package logger implements async log web api messages |
|
node/file
Package contains Node File struct and MultiReaderAt implementation
|
Package contains Node File struct and MultiReaderAt implementation |
|
node/file/format/fasta
Package to read and write FASTA format files
|
Package to read and write FASTA format files |
|
node/file/format/fastq
Package to read and write FASTQ format files
|
Package to read and write FASTQ format files |
|
node/file/format/line
Package to read and index lines of a file
|
Package to read and index lines of a file |
|
node/file/format/multi
Package to read and auto-detect format of fasta & fastq files
|
Package to read and auto-detect format of fasta & fastq files |
|
node/file/format/sam
Package to read and write SAM format files
|
Package to read and write SAM format files |
|
node/file/format/seq
Package contains interfaces for fasta & fastq & and multi packages
|
Package contains interfaces for fasta & fastq & and multi packages |
|
preauth
Package preauth implements persistent storage and retrieval of preauth requests
|
Package preauth implements persistent storage and retrieval of preauth requests |