Add tools

envs/global_packages.txt

@@ -1,30 +1,47 @@
 ark
+bamtools
 bcftools
 bedtools
 curl
+deeptools
 diffutils
+ensembl-vep
 fastqc
+fastp
 findutils
 gatk4
 gawk
+gffread
 git
 go-ghq
 grep
+gtex-pipeline-gene_model
+gtex-pipeline-qtl
+gtex-pipeline-rnaseq
 htslib
 kent-tools
+king
 less
+metal
+multiqc
 pandoc
 parallel
 picard
 plink
 plink2
 python=3.12
+quantas
 r-base=4.4
+regtools
 ripgrep
+rnaseqc
+rsem
 ruby
+samtools
 sed
 snpeff
 snpsift
+star
 tree
 trimmomatic
 unzip

envs/python_packages.txt

@@ -22,6 +22,8 @@ jupyterhub
 markdown
 markdown-kernel
 matplotlib-base
+mofapy2
+multipy
 nb_conda_kernels
 nbconvert-core
 nbdime
@@ -35,7 +37,10 @@ pandas
 pillow
 ptpython
 pyarrow
+pybigwig
+python-ldstore
 python-lsp-server
+qvalue
 scikit-learn
 scipy
 seaborn

envs/r_packages.txt

@@ -14,6 +14,7 @@ bioconductor-sesamedata
 bioconductor-variantannotation
 r-abind
 r-ape
+r-bedtoolsr
 r-bigsnpr
 r-biocmanager
 r-bitops
@@ -43,7 +44,6 @@ r-mvsusier
 r-pacman
 r-pecotmr
 r-pgenlibr
-r-plink2r
 r-plinkqc
 r-profvis
 r-qgg