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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
#
#- deeptools
conda install -c bioconda deeptools
conda config --add channels defaults
conda config --add channels conda-forge
conda config --add channels bioconda
conda install -c bioconda multiqc
#- 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 fastqc
conda install -c bioconda trim-galore
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
conda install -c bioconda bioconductor-dupradar
conda install -c bioconda umi_tools
conda install -c bioconda cnvkit
conda install -c bioconda control-freec
conda install -c bioconda perl-http-cookies
conda install -c bioconda perl-www-mechanize
conda install -c bioconda perl-lwp-protocol-https
conda install -c bioconda perl-dbi
conda install -c bioconda perl-dbd-mysql
#- issues
#---------
#- 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
##############################################################
############ THE BELOW WAS DONE IN MYRIAD ####################
#### LEAVING IT IN HERE IN CASE I FIND THE SAME ISSUES #######
##############################################################
#- 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 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