Setting up a portable RNA-Seq pipeline for CBIO

04/09/2018

12:56 PM Support #30: Update Nextflow to version 0.27.6

Katie Lennard wrote:
> Gerrit Botha wrote:
> > Try again. I opened up read permissions to the binary.
>
> Hmmm, ... Katie Lennard

12:54 PM Support #30: Update Nextflow to version 0.27.6

Gerrit Botha wrote:
> Try again. I opened up read permissions to the binary.
Hmmm, kry nou:
Downloading nextflow... Katie Lennard

11:43 AM Support #30: Update Nextflow to version 0.27.6

Try again. I opened up read permissions to the binary. Gerrit Botha

11:38 AM Support #30: Update Nextflow to version 0.27.6

Have added lines to .bashrc but can't test nextflow (version -v):
/bin/bash: /opt/exp_soft/cbio/nextflow/nextflow:... Katie Lennard

11:13 AM Support #30: Update Nextflow to version 0.27.6

Gerrit Botha wrote:
> Ok it is setup in ```/opt/exp_soft/cbio/nextflow```
>
> Add the following lines in your ```... Katie Lennard

10:59 AM Support #30: Update Nextflow to version 0.27.6

Ok it is setup in ```/opt/exp_soft/cbio/nextflow```
Add the following lines in your ```.bashrc```
~~~
JAVA_C... Gerrit Botha

10:09 AM Support #30 (In Progress): Update Nextflow to version 0.27.6

Ok Katie, will do it in the next hour or so. Will get back to you. Gerrit Botha

09:51 AM Support #30 (In Progress): Update Nextflow to version 0.27.6

The RNAseq pipeline requires an updated version of Nextflow (currently 0.26.3, need 0.27.6) Katie Lennard

11:14 AM Support #25: Configure NGI-RNAseq pipeline to run on hex

Gerrit Botha wrote:
> Hi Katie,
>
> Initially asked me if the info you are planning to share in this ticket shoul... Katie Lennard

11:08 AM Support #25: Configure NGI-RNAseq pipeline to run on hex

Hi Katie,
Initially asked me if the info you are planning to share in this ticket should go in the ticket or on th... Gerrit Botha

04/06/2018

03:38 PM Support #25 (In Progress): Configure NGI-RNAseq pipeline to run on hex

Katie Lennard

12:54 PM Gmail - NGI-RNAseq igenomes setup.pdf

Email communication with NGI-RNAseq autor Phil Ewels regarding correct setup of pipeline on UCT hex Katie Lennard

03/15/2018

04:39 PM Support #24: Setting up the NGI-RNAseq pipeline on UCT Hex

Katie I've talked to Chris Fields he is working with Jenny. He will check if he can make their pipeline available. He... Gerrit Botha

03:07 PM Support #25: Configure NGI-RNAseq pipeline to run on hex

Katie just a note. The section `singularity.cacheDir = "/scratch/DB/bio/singularity-containers` in our `config.txt` i... Gerrit Botha

02:55 PM Support #25 (In Progress): Configure NGI-RNAseq pipeline to run on hex

Pertinent points for setup of NGI-RNAseq pipeline on UCT hex
*Main pipeline source code is at https://github.com/Sci... Katie Lennard

03/14/2018

10:13 PM Support #24 (New): Setting up the NGI-RNAseq pipeline on UCT Hex

Katie received a support request to analyse human RNA-Seq data. We do not have a pipeline ready for just pushing RNA-... Gerrit Botha