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MSKCC cBio cluster documentation
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Please install dependencies needed for avro #267

Closed ratsch closed 9 years ago

ratsch commented 9 years ago

I'm trying to install avro 1.7.7 (http://mirrors.gigenet.com/apache/avro/avro-1.7.7/avro-src-1.7.7.tar.gz), but there are several missing dependencies including maven. Can you please try to compile avro and install dependencies that will be revealed one-by-one? (all of those should be standard centos packages). Thanks!

tatarsky commented 9 years ago

I will look after I clear the GPFS array matter. This sounds like a great time for the HPC director to learn the software deployment methods of the cluster.

jchodera commented 9 years ago

Please coordinate with Juan on that directly.

tatarsky commented 9 years ago

I will do so.

tatarsky commented 9 years ago

While I prepare that training, please note that Maven was added as a module after reviewing other options for its deployment. I am seeing what else is needed (first item needed was mvn aka maven)

module add maven

As its a Java application you will likely need to proceed in a interactive qsub to avoid the stack limits on the head node.

tatarsky commented 9 years ago

So its passed the java and apache tests but when it hits python3 its complaining of setuptools missing. Before I continue on this, what pyhton3 are you intending to use with this? The module? 

which python3
/opt/python/3.2.1/bin/python3

Or a personally compiled python3.

tatarsky commented 9 years ago

c/c++ passes test with "module add cmake" csharp passes test with "module add mono" perl passes with a few added depends

Items still failing due to missing items and please advise if you care:

js (I assume javascript). Wants some compiler I don't know. ruby. Wants some ruby thing php. Wants a whole bunch of php unit test items

Holding before I consume more cycles if the above passing languages meet your needs. Sort of a kitchen sink of a package here.

tatarsky commented 9 years ago

This BTW is a terrible training example due to its complexity. Dropping that suggestion.

tatarsky commented 9 years ago

Also it appears it can be downloaded for individual languages if that better meets your needs than "all these languages". Example from a mirror:

http://mirrors.advancedhosters.com/apache/avro/avro-1.7.7/

tatarsky commented 9 years ago

Question on this has gone unanswered for > a month. Closing. Requestor can reopen if still desired and items above that didn't build are needed.