From 6cb1decdc95084c60724bffd15944fb40d0a8fd8 Mon Sep 17 00:00:00 2001 From: Daniel Nachun Date: Thu, 20 Mar 2025 10:51:10 -0700 Subject: [PATCH 1/2] add tools --- envs/global_packages.txt | 18 ++++++++++++++++++ envs/python_packages.txt | 5 +++++ envs/r_packages.txt | 2 +- 3 files changed, 24 insertions(+), 1 deletion(-) diff --git a/envs/global_packages.txt b/envs/global_packages.txt index 8d9521c..8c15fb6 100644 --- a/envs/global_packages.txt +++ b/envs/global_packages.txt @@ -1,30 +1,48 @@ 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 +kallisto 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 diff --git a/envs/python_packages.txt b/envs/python_packages.txt index cdd887e..32c3273 100644 --- a/envs/python_packages.txt +++ b/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 diff --git a/envs/r_packages.txt b/envs/r_packages.txt index a7d76bf..1e7744c 100644 --- a/envs/r_packages.txt +++ b/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 From 5f72e512de3c336feba89feb8f96b5ec78ec3397 Mon Sep 17 00:00:00 2001 From: Daniel Nachun Date: Thu, 20 Mar 2025 14:10:42 -0700 Subject: [PATCH 2/2] add tools --- envs/global_packages.txt | 1 - 1 file changed, 1 deletion(-) diff --git a/envs/global_packages.txt b/envs/global_packages.txt index 8c15fb6..36b914a 100644 --- a/envs/global_packages.txt +++ b/envs/global_packages.txt @@ -19,7 +19,6 @@ gtex-pipeline-gene_model gtex-pipeline-qtl gtex-pipeline-rnaseq htslib -kallisto kent-tools king less