Arvados

For installation of Arvados on the UMCU HPC cluster I wrote an updated version of the online info.

Notably: The Ruby installation configure is wrong on the main page, it should be

./configure --disable-install-rdoc

instead of --no-install-rdoc. Also

env PYCURL_SSL_LIBRARY=nss pip install arvados-python-client

should be set before installation, these days.

Below my writeup

• INSTALL ARVADOS client

To run the Arvados client one needs both the Ruby and Python tools
with specific versions of the interpreters.

We use a destination dir named

ARV_CLI_DIR=/hpc/local/CentOS6/cog_bioinf/arvados
  ARV_RUBY_DIR=$ARV_CLI_DIR/ruby
  ARV_PYTHON_DIR=$ARV_CLI_DIR/python27

Get current token from the Curoverse Cloud, i.e. menu->current token:

HISTIGNORE=$HISTIGNORE:'export ARVADOS_API_TOKEN=*'
  export ARVADOS_API_TOKEN=5vbht7zy20xxxx6brq035yk56av
  export ARVADOS_API_HOST=qr1hi.arvadosapi.com
  unset ARVADOS_API_HOST_INSECURE

According to http://doc.arvados.org/sdk/cli/install.html check the
Ruby version, mine reads

ruby -v
  ruby 1.7.8

So an update is required

mkdir -p ~/src
  cd ~/src
  curl http://cache.ruby-lang.org/pub/ruby/2.1/ruby-2.1.6.tar.gz | tar xz
  cd ruby-2.1.6
  ./configure --disable-install-rdoc --prefix=$ARV_RUBY_DIR
  make install

Update the path to

export PATH=$ARV_RUBY_DIR/bin:$PATH

Check the environment

ruby -v
  gem env

and you should be good to go using gem etc.

gem install arvados-cli

Now you should be able to

arv user current

and upload a file

arv keep put math.c

Now this gives an error because arv-put is actually part of the Python SDK. So install
that according to http://doc.arvados.org/sdk/python/sdk-python.html

virtualenv --python=python2.7 $ARV_PYTHON_DIR

Change into the virtualenv

source $ARV_PYTHON_DIR/bin/activate
  which pip
    /hpc/local/CentOS6/cog_bioinf/arvados/python27/bin/pip

Good. Install the tools, note we need to set pycurl to point at a suitable
library (the alternative is openssl)

export PYCURL_SSL_LIBRARY=nss
  pip install arvados-python-client

And now we should be able to upload a file

arv keep put math.c
    Collection saved as 'Saved at 2015-08-31 09:02:30 UTC by pprins@hpcs01.op.umcutrecht.nl'
    qr1hi-4zz18-w0zfbypgi9bynag

Now the beast is installed. Just set the ARV environment vars at the top and
enter the virtualenv using activate.

arv --version
    /hpc/local/CentOS6/cog_bioinf/arvados/ruby/lib/ruby/gems/2.1.0/gems/arvados-cli-0.1.20150821195137/bin/arv