Setting up a portable RNA-Seq pipeline for CBIO

04/16/2018

05:05 PM Support #25: Configure NGI-RNAseq pipeline to run on hex

For now I do not think we will make changes on the main code. So yes, all that we would need to do is merge the main ... Gerrit Botha

04:50 PM Support #25: Configure NGI-RNAseq pipeline to run on hex

Aha, yes you're right - if we specify -r dev with the run (using our repo fork) it does pick up the uct_hex profile. ... Katie Lennard

04:44 PM Support #25: Configure NGI-RNAseq pipeline to run on hex

Hi Katie,
Everything is on the ```dev``` branch: https://github.com/uct-cbio/RNAseq/tree/dev . So should things no... Gerrit Botha

04:31 PM Support #25: Configure NGI-RNAseq pipeline to run on hex

Gerrit I see even though you noticed that the uct_hex.conf was only on the dev branch it looks like the master branch... Katie Lennard

03:55 PM Support #25: Configure NGI-RNAseq pipeline to run on hex

I've tested the custom build singularity image described above. This specific repository (https://github.com/nf-core/... Katie Lennard

04/12/2018

05:28 PM Support #25: Configure NGI-RNAseq pipeline to run on hex

Thanks Gerrit, much appreciated - I'll go through this and do some testing on the new image. Katie Lennard

05:04 PM Support #25: Configure NGI-RNAseq pipeline to run on hex

Hi Katie,
I did the following.
1. Made a fork of the stable RNASeq pipeline to here: https://github.com/uct-cbi... Gerrit Botha

04/11/2018

11:41 AM Support #25: Configure NGI-RNAseq pipeline to run on hex

Katie if this is the Docker file you are using https://github.com/ewels/nf-core-RNAseq/blob/master/Dockerfile you wou... Gerrit Botha

11:28 AM Support #25: Configure NGI-RNAseq pipeline to run on hex

Katie Lennard wrote:
> Oh dear..Ok we'll have to get rebuild the image then I guess..See latest response from Phil o... Katie Lennard

11:23 AM Support #25: Configure NGI-RNAseq pipeline to run on hex

Oh dear..Ok we'll have to get rebuild the image then I guess..See latest response from Phil on this https://github.co... Katie Lennard

11:18 AM Support #25: Configure NGI-RNAseq pipeline to run on hex

OK that is fine Katie.
Just on the overlay issue. Overlayfs is only available for kernel 3.18 or higher: https://w... Gerrit Botha

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

Hi Gerrit,
At the moment the main problem is that I can't download the development version of the Singularity imag... Katie Lennard

10:55 AM Support #25: Configure NGI-RNAseq pipeline to run on hex

Hi Katie,
1. Can you please point me to the Docker / Singularity file on GitHub which you have an issue with?
2... Gerrit Botha

04/10/2018

05:33 PM Support #25: Configure NGI-RNAseq pipeline to run on hex

Gerrit Botha wrote:
> So what happens if you do use the ```--size``` flag with a rough estimate of the container siz... Katie Lennard

02:22 PM Support #25: Configure NGI-RNAseq pipeline to run on hex

So what happens if you do use the ```--size``` flag with a rough estimate of the container size?
Ok, try running t... Gerrit Botha

01:41 PM Support #25: Configure NGI-RNAseq pipeline to run on hex

Development branch with custom 'uct_hex' profile up and running but having issues with the singularity image specifie... Katie Lennard

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