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miniconda3_packages-install
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miniconda3_packages-install
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#!/usr/bin/bash -i
###############################################
# Installing bioconda packages
#
# by LC, 2019
#
#
# NOTE: I copied the current conda env into
# bioconda/2020-11-06 and updated gatk
# to 4.1.9.0 and added the python gatktools
# module (this needed for CNNScoreVariants
# To install in the right env:
# $ conda info --envs
# # conda environments:
# #
# base * /shared/ucl/depts/cancer/apps/miniconda3
# /shared/ucl/depts/cancer/apps/miniconda3_gatk4.1.9.0
# $ conda config --append envs_dirs /shared/ucl/depts/cancer/apps/
# $ conda info --envs
# # conda environments:
# #
# base * /shared/ucl/depts/cancer/apps/miniconda3
# miniconda3_gatk4.1.9.0 /shared/ucl/depts/cancer/apps/miniconda3_gatk4.1.9.0
# $ conda install -n miniconda3_gatk4.1.9.0 gatktool
##########################################
#- gatk
conda install -c bioconda gatk4=4.1.8.1-0
#- deeptools
conda install -c bioconda deeptools
#- multiQC (install 1.6, 0.9 crashes on nextflow_chipseq)
#- config conda to download 1.6, normal installation would install 0.9 as described here (https://github.com/ewels/MultiQC/issues/729)
conda config --add channels defaults
conda config --add channels conda-forge
conda config --add channels bioconda
conda install -c bioconda multiqc multiqc=1.6
conda install -c bioconda control-freec
conda install -c bioconda -n miniconda3_gatk4.1.9.0 control-freec
#- UCSC bedGraphToBigWig, bigWigToWig, wigToBigWig
conda config --add channels defaults
conda config --add channels conda-forge
conda config --add channels bioconda
conda install -c bioconda ucsc-bedgraphtobigwig
conda install -c bioconda ucsc-bigwigtowig
conda install -c bioconda ucsc-wigtobigwig
#- nf-core
conda install -c bioconda nf-core
#- other
conda install -c bioconda phantompeakqualtools
conda install -c bioconda kallisto
conda install -c bioconda macs2
conda install -c bioconda trim-galore
conda install -c bioconda hisat2
conda install -c bioconda rseqc
conda install -c bioconda preseq
conda install -c bioconda qualimap
conda install -c bioconda subread
conda install -c bioconda stringtie
conda install -c bioconda bedtools
conda install -c bioconda snpEff
conda install -c bioconda intervene
conda install -c bioconda salmon openssl=1.0
conda install -c bioconda bioawk openssl=1.0
conda install -c bioconda bioconductor-dupradar
conda install -c conda-forge r-argparse
#- for ~/Scratch/victor dms_tools2 examples
conda install -c conda-forge imagemagick
conda install -c conda-forge r-ggseqlogo
#- issues
#---------
#- bedtools and other packages depend on (and therefore install) samtools, but the installed version gives me errors:
#- samtools: error while loading shared libraries: libcrypto.so.1.0.0: cannot open shared object file: No such file or directory
#- fix by downgrading openssl from 1.1 to 1.0 (https://github.com/bioconda/bioconda-recipes/issues/12100)
conda install -c bioconda openssl=1.0
#- biconda also installs R, and the bioconda R gets me this error:
#- /shared/ucl/depts/cancer/apps/miniconda3/lib/R/bin/exec/R: error while loading shared libraries: libiconv.so.2: cannot open shared object file: No such file or directory
#- so I have 2 options, either I make sure that bioconda is loaded first before r/recommended, or I just use the bioconda R and fix the above issue:
conda install -c bioconda libiconv openssl=1.0
#- biconda also installs perl, so if at some point I load bioconda and it changes to bioconda perl, i need a few modules that were not installed by default
conda install -c bioconda perl-dbi openssl=1.0
conda install -c bioconda perl-try-tiny openssl=1.0