I installed the OMA.2.1.1 on a HPC cluster with slurm. AS the HPC cluster has no connection to the internet for the safety.
So when I run the software, the error is Resolving www.geneontology.org... failed: Name or service not known. wget: unable to resolve host address `www.geneontology.org' Error, (in wget) wget failed
What should I do to solve this problem?
Hi @Young,
OMA needs the ontology definition from geneontology and converts it into an internal datastructure. The simplest solution is to run the conversion step of oma (run bin/oma -c) on a machine with internet access and copy the resulting files GOdata.drw* in the newly created folder data to the cluster.
Cheers Adrian
if you have installed OMA standalone on the cluster, the files from the data folder need to be stored in ${HOME}/.oma/. So you should end up with something like ${HOME}/.oma/GOdata.drw.gz
I coped the GOdata.drw-20180108.gz and GOdata.drw.gz to the home/.oma folder, http://ibb.co/mFOKP6,
But it doesn't work.
As I use HPC cluster with slurm, my home folder is HOME/sdau_ssli_1 and I have no root permissions. Is this the point that causes the problem?
I don't understand where you checked. in home/.oma, HOME/sdau_ssli_1/.oma or somewhere else. It should be in a subfolder called ".oma" in your home directory. you should be able to see the files if you run ls $HOME/.oma in the slurm cluster. If this is the place where you stored them, please check with
find /HOME/sdau_ssli_1/Software-W/OMA -name "darwinit" | xargs grep datadirname
the full path where oma is checking for the GOdata.drw.gz file.
Log in to answer this question.
If the cluster has no internet connection you could figure out what OMA needs from geneontology.org and see if you can provide it locally as a downloaded file.
I am tagging one of the developers adrian.altenhoff to see if he can provide any additional clues.
Thanks for your advice.
Hi @adrian.altenhoff Thanks for your kindly reply.
I copied the GOdata.drw-20180108.gz and GOdata.drw.gz to the data folder. Please see the screenshot http://ibb.co/bwgZMm
And then I use the ToyExample to do the test. But it seems do not work. See the screenshot. http://ibb.co/mSsPMm
Please use
ADD REPLY/ADD COMMENTwhen responding to existing posts to keep threads logically organized. This comment belongs under @Adrian's answer.Hi @Young, if you have installed OMA standalone on the cluster, the files from the data folder need to be stored in ${HOME}/.oma/. So you should end up with something like ${HOME}/.oma/GOdata.drw.gz
Hi @adrian.altenhoff
Thanks for your kindly reply.
I copied the GOdata.drw-20180108.gz and GOdata.drw.gz to the data folder. Please see the screenshot. http://ibb.co/bwgZMm
And then I use the ToyExample to do the test. But it seems do not work. See the screenshot. http://ibb.co/mSsPMm
This time I sorted the GOdata.drw.gz and GOdata.drw-20180108.gz files in the /HOME/sdau_ssli_1/Software-W/OMA folder where I installed the OMA standalone. http://ibb.co/dhZyE6
But this doesn't help.
no, it should be in your home/.oma folder.
ls ~/.oma/should list those filesI checked the /HOME/sdau_ssli_1/.oma/, and I can see the two files and data file. http://ibb.co/kbgiMm
Is it right this time? But it doesn't work, the error is wget failed.
Please use
ADD REPLY/ADD COMMENTwhen responding to existing posts to keep threads logically organized.ALL of these comment belongs under @Adrian's answers/comments.
Hi @genomax, I am sorry to disturb you. But everytime I press the 'ADD REPLY/ADD COMMENT'button, nothing has happened. Then I press the link button, the browser shows me the 'Add your answer'box. I do not know why my response belongs to your answer.
You need to have javascript turned on (white list biostars.org for scripting). Once you click
ADD COMMENT/ADD REPLYa new window should open where you can type your response in.You are not disturbing me but entering responses as new answers makes it very hard to figure out what a real answer is for someone who will find this thread by searching in future.