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robmaz / distmap

Sequence alignment on Hadoop
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Rm move perlmodules to libperl #42

Closed robmaz closed 6 years ago

robmaz commented 6 years ago

New idea: move only the actual perl modules, leave the other scripts in bin (at least for now). While this should be a standard location anyway, I use also the RealBin mechanism to add it to the search path, so hopefully the modules will be found one way or another.

robmaz commented 6 years ago

I think the imported modules should all inherit the modified search path from distmap.

R.

2017-12-04 14:20 GMT+01:00 Daniel Gómez-Sánchez notifications@github.com:

Assigned #42 https://github.com/robmaz/distmap/pull/42 to @robmaz https://github.com/robmaz.

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magicDGS commented 6 years ago

I rebased this branch too (please, use git checkout rm_move_jars && git reset --hard origin/rm_move_jars to update your local copy).

Regarding the imported modules, my guess is that they are called as perl scripts in the MapReduce jobs, so I doubt that the imports are applied from the distmap. But I am not sure if it is like that, or it just generate scripts for the MapReduce (that's it, another script without dependencies).

Up to you if you wanna check before merging or if it is ok to introduce a temporary regression to be fixed in the future. If you aren't sure, you can open an issue to trace back to this commit if the behaviour is broken, for easy debugging).

robmaz commented 6 years ago

The actual mapper is a shell script written by HadoopMapping::write_hadoop_mapping_job I don't think anything tries to load modules non-locally. But we'll see.