Comments (2)
This is how I did it:
- Install Conda environment with all the dependencies (there might be some extra dependencies but I don't remeber which ones I added) and activate
mamba create --name squire --override-channels -c iuc -c bioconda -c conda-forge -c defaults -c r python=2.7.13 bioconductor-deseq2=1.16.1 r-base=3.4.1 r-pheatmap bioconductor-vsn bioconductor-biocparallel=1.12.0 star=2.5.3a bedtools=2.25.0 samtools=1.1 stringtie=1.3.3 igvtools=2.3.93 ucsc-genepredtobed ucsc-gtftogenepred ucsc-genepredtogtf ucsc-bedgraphtobigwig r-hexbin r-stringr r-ggrepel`
source activate squire
- Get SQuIRE from GitHub (I used my commit 868dd88 but I don't see why it shouldn't work with the latest original one)
git clone [email protected]:opplatek/SQuIRE.git
- Install SQuIRE with pip
cd SQuIRE/
pip install -e .
from squire.
Related Issues (20)
- consensus regions/length issue
- the meaning of clean outputs and how to make a custom bed file
- count function start from external BAM file HOT 1
- Issue installing SQuIRE
- Description of the count step output missing HOT 1
- Normalization HOT 1
- Generation of final BAM with re-distribute reads according to EM
- Error while running call
- issue with squire count:local variable 'prev_TE_ID' referenced before assignment
- Error with squire Call
- I can´t to install SQuiRE in conda HOT 2
- squire requires two conflicting python versions? HOT 1
- Count does not consider strangeness HOT 1
- Call Output
- T2T Reference Genome HOT 1
- FPKM counts are more than Tot_counts in Squire Count output.
- support Nanopore direct RNA sequencing data ?
- Antisense transcription quantification
- Unable to Install SQuIRE HOT 3
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from squire.