Install in a Mac using miniconda 4.9.2

ramongallego commented 3 years ago

I am also trying to run decona on a Mac BigSur - I had the same issue but I don't have an Ubuntu machine - Any ideas on how to install in a Mac with conda4.9.2?

Originally posted by @ramongallego in https://github.com/Saskia-Oosterbroek/decona/issues/5#issuecomment-812325726

Saskia-Oosterbroek commented 3 years ago

Hello Ramon,

Unfortunately use with Mac is currently not supported. It was developed for use with Linux. The Ubuntu terminal app on Windows also works but is only recommended for smaller datasets.

Saskia

ramongallego commented 3 years ago

Hello Saskia,

Thanks for the update - not what I hoped but thanks anyway!

Ramón

ramongallego commented 2 years ago

Hello Saskia,

Pinging you again on this. Another option that I thought I can use to test decona on our dataset is by implementing it in Google Colab. I have found a few tutorials on how to get Miniconda installed in Colab - would it be possible to run decona using miniconda? And if so, which version do you recommend I shouls install? Many thanks once more

Saskia-Oosterbroek commented 2 years ago

Hi Ramón! You may have already tried by now (I was on a holiday). I use Miniconda 3 myself. I didn't know about Google Colab, but that looks pretty useful! I wonder how much space and computing power they allow you to use though.. Let me know if it works :) Best, Saskia

ramongallego commented 2 years ago

Hi Saskia,

I end up ditching the google colab option - because each time you want to use it, you get an empty environment, it required installing conda and decona each time you want to run it, so it is not very practical. What I end up doing is setting up a virtual machine in Google Cloud and it works great- You have to pay for it, but I hope my institution can foot the bill.

I have a couple of questions / suggestions regarding the output - is this a good forum for them? Happy to repost wherever it is better.

I get a folder for each fastq file initially on my folder. I think this was designed with one fastq per barcode/sample in mind. In my case, it was only one sample but with the original output structure from Nanopore with one fastq per 4k reads. On each folder I get the initial, filtered and fasta-ed sequence files, the representatives from each cluster and the sequences that ended on each cluster. I could use the info from cluster_representatives.fast.clstr to parse how many sequences entered on each cluster - do you have a script to do that? I guess something that later returns a table on the shape of

cluster	barcode	#seqs
106-24	barcode01	345
713-2	barcode01	1650

and another fasta with

>106-24
ATGCGAGAA
>713-2
ACGTG

If not, no worries - I'll try to make one and push it your way

In each folder there is a subfolder named multi-seq with Racon Medaka and recluster - are they in order ? Is Racon the first round and medaka the second round of polishing?.

~I couldn't find a txt file with the original command the user ran - that would be useful for reproducibility and whatnot~ [Yes I found it under the report, duh! ]

Again, many thanks and congratulations for this great tool!

Saskia-Oosterbroek / decona

Install in a Mac using miniconda 4.9.2 #8