knitr::opts_chunk$set(eval=FALSE)
The API assumes the following: - SciDB EE (enterprise edition) is installed. (Install instructions are here. Contact support@paradigm4.com for login credentials)
Follow the steps below to set up the security settings for the API to work:
At this point, you should be able to run the following:
iquery --auth-file ~/.scidb_root_auth -aq "show_user();" iquery --auth-file ~/.scidb_root_auth -aq "list()" iquery --auth-file ~/.scidb_root_auth -aq "list('libraries')"
Consult this gist
Install via extra-scidb-libs
NOTE
/var/lib/shim/conf
. sudo service shimsvc restart
secure_scan
First the dependencies
roxygen2
-- only if you are building this package on the target machine# Ubuntu sudo apt-get install libxml2-dev # Centos 6 sudo yum install libxml2-dev # need the Centos equivalent here (auto-prompted by R roxgen2 install below) # Centos 7 sudo yum install libxml2-devel # need the Centos equivalent here (auto-prompted by R roxgen2 install below)
yum install postgresql93-devel.x86_64
yum install libcurl-devel
Next, install the following R packages from CRAN
sudo R # install bioconductor using # https://bioconductor.org/install/ # install Biobase BiocManager::install('Biobase') # Then install a few dependencies install.packages(c('roxygen2', 'tidyr', 'RPostgreSQL', 'devtools', 'yaml', 'knitr', 'reshape', 'reshape2'));
Next we install the SciDB related R package via devtools
sudo R --slave -e "devtools::install_github('Paradigm4/scidbr')"
This API's R package can be installed in two ways:
sudo R --slave -e "devtools::install_github('Paradigm4/revealgenomics')"
(assuming the directory choice described above):
# Scenario 1 # When user `scidb` has sudo privileges USER=ksen pushd /home/$USER/coding/downloads/revealgenomics/; R --slave -e "library(roxygen2); roxygenize()" && cd .. && sudo R CMD build revealgenomics && sudo R CMD INSTALL revealgenomics_0.1.tar.gz ; popd # Scenario 2 # When you are logged in as root, but user `ksenshar` has copy of package USER=ksenshar pushd /home/$USER/coding/downloads/revealgenomics/; R --slave -e "library(roxygen2); roxygenize()" && cd /home/$USER/coding/downloads/ && R CMD build revealgenomics && R CMD INSTALL revealgenomics_0.1.tar.gz; popd # Scenario 3 # As root, get package from github into `/tmp`, and install for all users pushd /tmp/; git clone https://github.com/paradigm4/revealgenomics.git; cd revealgenomics; R --slave -e "library(roxygen2); roxygenize()" && cd /tmp/ && R CMD build revealgenomics && R CMD INSTALL revealgenomics_0.1.tar.gz && rm -rf revealgenomics; popd
Now let us get to using the package:
library(revealgenomics) rg_connect('root', ROOTPASSWORD)
init_db(arrays_to_init = 'PROJECT') # CAUTION: To be used with care by DB admin only init_db(arrays_to_init = get_entity_names()) # EXTREME CAUTION: To be used with extreme care by DB admin only; initializes all arrays
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