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chapmanb / bcbb

Incubator for useful bioinformatics code, primarily in Python and R
http://bcbio.wordpress.com
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Problem installing install_biolinux #69

Closed inti closed 11 years ago

inti commented 11 years ago

Hi, I have the following issue. On my cluster configuration I jump into a public server and from there to the actual head node of the cluster. The set up does not need me to have a password for the cluster since it is done using ssh keys. When I try to install the bcbio_nextgen it aks me for my password. How can I get around this password if I do not have one or what should I enter?

Thanks in advance, inti pedroso

$ python bcbio_nextgen_install.py install_directory data_directory Installing tools... [localhost] Executing task 'install_biolinux' INFO: Config start time: 2013-02-05 14:51:19.267698 INFO: This is a Base Flavor - no overrides DBG [init.py]: Minimal Edition 1.5.3 INFO: This is a minimal INFO: Distribution ubuntu INFO: Get local environment INFO: Ubuntu setup DBG [distribution.py]: Debian-shared setup DBG [distribution.py]: Source=quantal DBG [distribution.py]: Checking target distribution ubuntu [localhost] run: cat /proc/version [localhost] Login password for 'pedrosoi':

chapmanb commented 11 years ago

Inti; Thanks for trying out the new install procedure. What it requires is to be able to do ssh localhost. If you don't have login passwords you can set this up to be passwordless with keys by doing:

$ cat .ssh/id_rsa.pub >> .ssh/authorized_keys

Then double check that ssh localhost no longer requires a password. If you're running in a cluster environment where you don't have root, you should also pass the --nosudo argument to bcbio_nextgen_install.py.

Hope this gets it working for you. Let us know if you run into more issues.

inti commented 11 years ago

Hi, that worked. I had to also do chmod 600 ~/.ssh/authorized_keys

Cheers, Inti