From 39bbdaf2391a1f3c06516477421ff3088aeff997 Mon Sep 17 00:00:00 2001 From: rfeng2023 Date: Mon, 2 Oct 2023 18:18:53 +0000 Subject: [PATCH] Update YAML files and Markdown table --- container/README.md | 3 ++- container/readme/containers.md | 3 ++- container/rna_quantification/rna_quantification.yml | 3 ++- 3 files changed, 6 insertions(+), 3 deletions(-) diff --git a/container/README.md b/container/README.md index 009583040..23003f9d5 100644 --- a/container/README.md +++ b/container/README.md @@ -87,7 +87,7 @@ On occasion, you may see errors that a download or upload has failed while build | r-watershedr | [Link](https://github.com/nicolerg/WatershedR) | [Link](https://anaconda.org/dnachun/r-watershedr) | rare_variation | 1.0.0 | dnachun | MIT | | bamtools | [Link](https://github.com/pezmaster31/bamtools) | [Link](https://anaconda.org/bioconda/bamtools) | rna_quantification | 2.5.2 | bioconda | MIT | | bedtools | [Link](https://github.com/arq5x/bedtools2) | [Link](https://anaconda.org/bioconda/bedtools) | rna_quantification | 2.31.0 | bioconda | MIT | -| deepTools | [Link](https://github.com/deeptools/deepTools) | [Link](https://anaconda.org/bioconda/deeptools) | rna_quantification | | Bioconda | GPL‑3.0‑or‑later | +| deeptools | [Link](https://github.com/deeptools/deepTools) | [Link](https://anaconda.org/bioconda/deeptools) | rna_quantification | 3.5.2 | Bioconda | GPL‑3.0‑or‑later | | fastp | [Link](https://github.com/OpenGene/fastp) | [Link](https://anaconda.org/bioconda/fastp) | rna_quantification | 0.23.4 | bioconda | MIT | | fastqc | [Link](https://github.com/s-andrews/FastQC) | [Link](https://anaconda.org/bioconda/fastqc) | rna_quantification | 0.12.1 | bioconda | GPL‑3.0‑or‑later | | gffread | [Link](https://github.com/gpertea/gffread) | [Link](https://anaconda.org/bioconda/gffread) | rna_quantification | 0.12.7 | bioconda | MIT | @@ -99,6 +99,7 @@ On occasion, you may see errors that a download or upload has failed while build | picard | [Link](https://github.com/broadinstitute/picard) | [Link](https://anaconda.org/bioconda/picard) | rna_quantification | 3.1.0 | bioconda | MIT | | pyarrow | [Link](https://pypi.org/project/pyarrow/) | [Link](https://anaconda.org/conda-forge/pyarrow) | rna_quantification | 13.0.0 | conda‑forge | Apache‑2.0 | | pybigwig | [Link](https://pypi.org/project/pyBigWig/) | [Link](https://anaconda.org/bioconda/pybigwig) | rna_quantification | 0.3.22 | bioconda | MIT | +| r-ape | [Link](https://github.com/emmanuelparadis/ape) | [Link](https://anaconda.org/conda-forge/r-ape) | rna_quantification | 5.7 | conda‑forge | GPL‑3.0‑or‑later | | rnaseqc | [Link](https://github.com/getzlab/rnaseqc) | [Link](https://anaconda.org/dnachun/rnaseqc) | rna_quantification | 2.4.2 | dnachun | BSD‑3‑Clause | | rsem | [Link](https://github.com/deweylab/RSEM) | [Link](https://anaconda.org/bioconda/rsem) | rna_quantification | 1.3.3 | bioconda | GPL‑3.0‑or‑later | | star | [Link](https://github.com/alexdobin/STAR) | [Link](https://anaconda.org/bioconda/star) | rna_quantification | 2.7.11a | bioconda | GPL‑3.0‑or‑later | diff --git a/container/readme/containers.md b/container/readme/containers.md index fd0b9348e..8e749f45b 100644 --- a/container/readme/containers.md +++ b/container/readme/containers.md @@ -44,7 +44,7 @@ | r-watershedr | [Link](https://github.com/nicolerg/WatershedR) | [Link](https://anaconda.org/dnachun/r-watershedr) | rare_variation | 1.0.0 | dnachun | MIT | | bamtools | [Link](https://github.com/pezmaster31/bamtools) | [Link](https://anaconda.org/bioconda/bamtools) | rna_quantification | 2.5.2 | bioconda | MIT | | bedtools | [Link](https://github.com/arq5x/bedtools2) | [Link](https://anaconda.org/bioconda/bedtools) | rna_quantification | 2.31.0 | bioconda | MIT | -| deepTools | [Link](https://github.com/deeptools/deepTools) | [Link](https://anaconda.org/bioconda/deeptools) | rna_quantification | | Bioconda | GPL‑3.0‑or‑later | +| deeptools | [Link](https://github.com/deeptools/deepTools) | [Link](https://anaconda.org/bioconda/deeptools) | rna_quantification | 3.5.2 | Bioconda | GPL‑3.0‑or‑later | | fastp | [Link](https://github.com/OpenGene/fastp) | [Link](https://anaconda.org/bioconda/fastp) | rna_quantification | 0.23.4 | bioconda | MIT | | fastqc | [Link](https://github.com/s-andrews/FastQC) | [Link](https://anaconda.org/bioconda/fastqc) | rna_quantification | 0.12.1 | bioconda | GPL‑3.0‑or‑later | | gffread | [Link](https://github.com/gpertea/gffread) | [Link](https://anaconda.org/bioconda/gffread) | rna_quantification | 0.12.7 | bioconda | MIT | @@ -56,6 +56,7 @@ | picard | [Link](https://github.com/broadinstitute/picard) | [Link](https://anaconda.org/bioconda/picard) | rna_quantification | 3.1.0 | bioconda | MIT | | pyarrow | [Link](https://pypi.org/project/pyarrow/) | [Link](https://anaconda.org/conda-forge/pyarrow) | rna_quantification | 13.0.0 | conda‑forge | Apache‑2.0 | | pybigwig | [Link](https://pypi.org/project/pyBigWig/) | [Link](https://anaconda.org/bioconda/pybigwig) | rna_quantification | 0.3.22 | bioconda | MIT | +| r-ape | [Link](https://github.com/emmanuelparadis/ape) | [Link](https://anaconda.org/conda-forge/r-ape) | rna_quantification | 5.7 | conda‑forge | GPL‑3.0‑or‑later | | rnaseqc | [Link](https://github.com/getzlab/rnaseqc) | [Link](https://anaconda.org/dnachun/rnaseqc) | rna_quantification | 2.4.2 | dnachun | BSD‑3‑Clause | | rsem | [Link](https://github.com/deweylab/RSEM) | [Link](https://anaconda.org/bioconda/rsem) | rna_quantification | 1.3.3 | bioconda | GPL‑3.0‑or‑later | | star | [Link](https://github.com/alexdobin/STAR) | [Link](https://anaconda.org/bioconda/star) | rna_quantification | 2.7.11a | bioconda | GPL‑3.0‑or‑later | diff --git a/container/rna_quantification/rna_quantification.yml b/container/rna_quantification/rna_quantification.yml index 860450a34..9c227d496 100644 --- a/container/rna_quantification/rna_quantification.yml +++ b/container/rna_quantification/rna_quantification.yml @@ -7,7 +7,7 @@ channels: dependencies: - bamtools=2.5.2 - bedtools=2.31.0 - - deepTools + - deeptools=3.5.2 - fastp=0.23.4 - fastqc=0.12.1 - gffread=0.12.7 @@ -20,6 +20,7 @@ dependencies: - picard=3.1.0 - pyarrow=13.0.0 - pybigwig=0.3.22 + - r-ape=5.7 - rnaseqc=2.4.2 - rsem=1.3.3 - samtools=1.17