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mbbu / HPC_ToDo

Things that Need to be done on the HPC.
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Installing some R Packages in the Qiime environment #10

Closed kipkurui closed 4 years ago

kipkurui commented 5 years ago

The packages are DECIPHER and phangorn, which are the packages required for the last step of this pipeline. @espirado, are you around to assist?

espirado commented 5 years ago

Am not around yet but il be there before thursday most probably.

On Tue, 24 Sep 2019, 08:59 Caleb Kipkurui, notifications@github.com wrote:

Assigned #10 https://github.com/mbbu/HPC_ToDo/issues/10 to @espirado https://github.com/espirado.

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wanjauk commented 5 years ago

In addition to the above packages, these packeges are also required in downstream analysis: metagenomeSeq, vegan, ggplot2, dplyr, gridExtra and renozao/NMF@devel.

espirado commented 5 years ago

The packages have been installed on the R module in the hpc. Any person using R installed on the hpc can use them. I have managed to installed all the packages except phangorn which there is some errors compiling the package due to the gcc environment but am hoping i will resolve it by tomorrow.

kipkurui commented 5 years ago

Thanks Andrew. You can also try and set them up in the conda environment, which could be easier to set up.

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From: andrew espira notifications@github.com Sent: Thursday, September 26, 2019 1:37:34 PM To: mbbu/HPC_ToDo HPC_ToDo@noreply.github.com Cc: Caleb Kipkurui calebkibet88@gmail.com; Assign assign@noreply.github.com Subject: Re: [mbbu/HPC_ToDo] Installing some R Packages in the Qiime environment (#10)

The packages have been installed on the R module in the hpc. Any person using R installed on the hpc can use them. I have managed to installed all the packages except phangorn which there is some errors compiling the package due to the gcc environment but am hoping i will resolve it by tomorrow.

— You are receiving this because you were assigned. Reply to this email directly, view it on GitHubhttps://github.com/mbbu/HPC_ToDo/issues/10?email_source=notifications&email_token=AA4WPT75W2UEDRGAZ3SE65TQLS3J5A5CNFSM4IZ3CWT2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD7VSVFQ#issuecomment-535505558, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AA4WPTZUVI7LYWNYRGCA7DLQLS3J5ANCNFSM4IZ3CWTQ.