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mschubert / ebits

R bioinformatics toolkit incubator
Apache License 2.0
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Changing temporary directory #64

Closed zslastman closed 9 years ago

zslastman commented 9 years ago

So I'm using this over here on the cluster at EMBL (with my own ~/.batchjobs.R file) and it works perfectly except for one thing - I had to modify it to use an alternative tempdir() function, because our cluster needs to write things to a different directory ('scratch'), and will fail if given a '/tmp/' path.

mschubert commented 9 years ago

Hi Dermot (I assume?),

Happy to see this gets used over at the main site as well! :+1:

tempdir() respects the TMPDIR environment variable. If you set it to /scratch/... in your environment, a call to tempdir() will return a directory there instead of /tmp - so there is no need to change the call.

Note that we will phase out BatchJobs in favour of an rzmq solution because the former starts an R session per function call, which kills the file system for a lot of short-running calls (see this bug report and the hpc_2.0 branch). After this change, there will be no more temporary directories.

zslastman commented 9 years ago

Should have thought of that, thanks Michael - and yes, konrad gave me access. Can I invite other predocs here? I actually think we should vastly expand what you guys have done here. Even access to other people's buggy, uncommented code would have saved me a lot of time during my PhD - e.g. code for ggplot2 plots.

mschubert commented 9 years ago

Contributions always welcome! (for the main repositories please fork/branch and send a pull request)

Feel free to invite other predocs, I have (I think, please check) just given you the rights to add people to the "Predocs" group.