You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
The amount of effort you put in juicer looks really incredible. Being a total newbie, I try to run juicer on Google Colab in CPU mode. And yeah, Google Colab is really a gold standard now, so I've supposed there would be no entanglements - just as there were no problems with the HiCCUPS colab referenced in the wiki (thanks!).
As you can infer, I was wrong.
Here is my Colab code:
# Install dependencies (we have Linux Ubuntu here)
!apt install samtools bwa
# Clone the repository
!git clone https://github.com/aidenlab/juicer.git
# Arrange generic folder structure
!mkdir references fastq restriction_sites aligned hic_results
# Get the examples
# Note the -P trick:
# it's not that easy to perform a long-playing `cd` in colab!
!wget -P references https://s3.amazonaws.com/juicerawsmirror/opt/juicer/references/Homo_sapiens_assembly19.fasta
!wget -P references https://s3.amazonaws.com/juicerawsmirror/opt/juicer/references/Homo_sapiens_assembly19.fasta.amb
!wget -P references https://s3.amazonaws.com/juicerawsmirror/opt/juicer/references/Homo_sapiens_assembly19.fasta.ann
!wget -P references https://s3.amazonaws.com/juicerawsmirror/opt/juicer/references/Homo_sapiens_assembly19.fasta.bwt
!wget -P references https://s3.amazonaws.com/juicerawsmirror/opt/juicer/references/Homo_sapiens_assembly19.fasta.pac
!wget -P references https://s3.amazonaws.com/juicerawsmirror/opt/juicer/references/Homo_sapiens_assembly19.fasta.sa
!wget -P restriction_sites https://s3.amazonaws.com/juicerawsmirror/opt/juicer/restriction_sites/hg19_MboI.txt
# In Colab, we run in CPU mode
!ln -s juicer/CPU scripts
# Do I need to add `/common/` ?..
!cd scripts; wget https://hicfiles.tc4ga.com/public/juicer/juicer_tools.1.9.9_jcuda.0.8.jar
!cd scripts; ln -s juicer_tools.1.9.9_jcuda.0.8.jar juicer_tools.jar
# It insists...
!rm -rf aligned
!./scripts/juicer.sh -D `pwd` -g "hg19"
Dear AidenLab,
The amount of effort you put in
juicerlooks really incredible. Being a total newbie, I try to runjuiceron Google Colab in CPU mode. And yeah, Google Colab is really a gold standard now, so I've supposed there would be no entanglements - just as there were no problems with the HiCCUPS colab referenced in the wiki (thanks!).As you can infer, I was wrong.
Here is my Colab code:
It is based on https://github.com/aidenlab/juicer/wiki/Installation
I get the following output:
Details
What am I doing wrong?
The text was updated successfully, but these errors were encountered: