Bug #7170

[Documentation] Various small bugs in the CLI SDK install guide

Added by Pjotr Prins over 3 years ago. Updated over 3 years ago.

Status:
New
Priority:
Normal
Assigned To:
-
Category:
Documentation
Target version:
Start date:
08/31/2015
Due date:
% Done:

0%

Estimated time:
Story points:
-

Description

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 '
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

Related issues

Related to Arvados - Bug #7356: [Documentation] Various small bugs in the install guideNew09/18/2015

Associated revisions

Revision 102d9383 (diff)
Added by Brett Smith over 3 years ago

7170: Fix Ruby configure switch typo.

--no-install-rdoc should be spelled --disable-install-rdoc.
Refs #7170.

History

#1 Updated by Joshua Randall over 3 years ago

I was just about to file a '--disable-install-rdoc' bug as well, but found this one already existing:

Several install doc pages mention how to install Ruby from source (e.g. http://doc.arvados.org/install/install-api-server.html, http://doc.arvados.org/install/install-workbench-app.html). The installation instructions include a configure command line with the option '--no-install-rdoc' but with the referenced Ruby version (2.1.6) this option is not recognised and gives an error (I've replaced it with '--disable-install-rdoc').

#2 Updated by Brett Smith over 3 years ago

  • Subject changed from Update/fixes for arv client installation to [Documentation] Various small bugs in the CLI SDK install guide
  • Assigned To deleted (Ward Vandewege)

#3 Updated by Brett Smith over 3 years ago

  • Target version set to Arvados Future Sprints

Also available in: Atom PDF