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Update setup_python_envs.sh
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amizeranschi authored Oct 18, 2024
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2 changes: 1 addition & 1 deletion bcbio_wrapper_scripts/environment/setup_python_envs.sh
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Expand Up @@ -27,7 +27,7 @@ if [[ ! -d ${bcbio_install_path:?}/extra ]]; then
${bcbio_install_path:?}/extra/bin/extra_mamba install --name py3 --yes -c conda-forge -c bioconda kraken2 krakenuniq blast spades masurca quast \
flye shasta repeatmodeler repeatmasker gxx_linux-64 wget git bedops vcftools pyyaml perl-yaml tectonic gnuplot "openjdk>=12" gatk4 r-rjava \
perl-encode-locale "sra-tools>=2.11" perl-net-ssleay entrez-direct tassel beagle gcta "gdal>=2.0.1" plink "bcftools>=1.15" "samtools>=1.15" haploview \
"ensembl-vep>=109" "perl-bioperl>=1.7.2" "r-base>=4.2" r-essentials r-xml r-knitr r-markdown r-rmarkdown r-shiny r-shinyngs r-rcpp r-devtools r-reticulate \
"ensembl-vep>=109" "perl-bioperl>=1.7.2" "r-base>=4.2" r-essentials r-xml r-knitr r-markdown r-rmarkdown r-shiny r-shinyngs r-rcpp r-remotes r-reticulate \
perl-bio-tools-run-alignment-tcoffee r-terra r-rgdal r-ragg r-ade4 r-aghmatrix bioconductor-ahmeshdbs bioconductor-annotationdbi bioconductor-annotationhub r-bedr \
r-bglr r-candisc r-car bioconductor-chipseeker bioconductor-clusterprofiler r-cmplot r-corrgram r-corrplot r-data.table bioconductor-deseq2 bioconductor-do.db \
r-doparallel bioconductor-dose "r-dbplyr=2.3.0" r-dplyr r-dt r-emmeans bioconductor-enrichplot bioconductor-ensembldb bioconductor-gdsfmt bioconductor-geneoverlap \
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