search

ChangLab / ATACPrimerTool

Primer design for ATAC-qPCR
12 stars 7 forks source link

FindNormPeaks.sh dependencies #10

Open Just08 opened 1 year ago

Just08 commented 1 year ago

Hi,

I'm trying to make a conda environment to be able to run your script FindNormPeaks.sh but there is a lot of conflict between the packages I'm asking for and so my environment is not created . I ask r-base=3.4.2 samtools=1.3 bedtools=2.27.0.0 bioconductor-deseq2 macs2 homer from bioconda channel . Do you have more precise information about the dependencies to make this script work.

Thanks in advance

katieyost commented 1 year ago

Hi,

The following conda environment works for me. This should also address the conflict between pypiper and newer versions of attmap. Also I found it easier to install DESeq2 in R directly than through conda. 

conda create -n apt python=2.7 r-base=3.6.3 samtools=1.6 bedtools=2.30.0 homer=4.11 macs2=2.1.4
conda activate apt
pip install attmap==0.12.11
pip install --user https://github.com/databio/pypiper/archive/refs/tags/v0.10.0.tar.gz
#install DESeq2 in R using BiocManager::install("DESeq2", force = TRUE)