From 13effa6a931e28531e829346968676e39c12ac68 Mon Sep 17 00:00:00 2001 From: rfeng2023 <126488688+rfeng2023@users.noreply.github.com> Date: Mon, 2 Oct 2023 10:26:26 -0400 Subject: [PATCH 1/6] update container --- container/containers.csv | 1 + 1 file changed, 1 insertion(+) diff --git a/container/containers.csv b/container/containers.csv index fce1547ff..3d694ed6d 100644 --- a/container/containers.csv +++ b/container/containers.csv @@ -101,3 +101,4 @@ openpyxl,https://pypi.org/project/openpyxl/,Python,,N/A,conda-forge,universal,MI pytables,https://pypi.org/project/tables/,Python,,N/A,conda-forge,universal,BSD-3-Clause,https://anaconda.org/conda-forge/pytables, scikit-learn,https://pypi.org/project/scikit-learn/,Python,,N/A,conda-forge,universal,BSD-3-Clause,https://anaconda.org/conda-forge/scikit-learn, hello,https://www.gnu.org/software/hello/,C/C++,2.12.1,N/A,dnachun,hello,GPL-3.0-or-later,https://anaconda.org/dnachun/hello, +deepTools,https://github.com/deeptools/deepTools,Python,,N/A,Bioconda,rna_quantification,GPL-3.0-or-later,https://anaconda.org/bioconda/deeptools, \ No newline at end of file From b148f34897782770723a568dfadf30f6ebb2fc9e Mon Sep 17 00:00:00 2001 From: rfeng2023 Date: Mon, 2 Oct 2023 14:30:24 +0000 Subject: [PATCH 2/6] Update YAML files and Markdown table --- container/README.md | 1 + container/readme/containers.md | 1 + container/rna_quantification/rna_quantification.yml | 1 + 3 files changed, 3 insertions(+) diff --git a/container/README.md b/container/README.md index 685d404d4..009583040 100644 --- a/container/README.md +++ b/container/README.md @@ -87,6 +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 | | 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 | diff --git a/container/readme/containers.md b/container/readme/containers.md index 423b580ce..fd0b9348e 100644 --- a/container/readme/containers.md +++ b/container/readme/containers.md @@ -44,6 +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 | | 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 | diff --git a/container/rna_quantification/rna_quantification.yml b/container/rna_quantification/rna_quantification.yml index d16b79542..860450a34 100644 --- a/container/rna_quantification/rna_quantification.yml +++ b/container/rna_quantification/rna_quantification.yml @@ -7,6 +7,7 @@ channels: dependencies: - bamtools=2.5.2 - bedtools=2.31.0 + - deepTools - fastp=0.23.4 - fastqc=0.12.1 - gffread=0.12.7 From 106702679775a40032c4d828b03cd3c530d6b96c Mon Sep 17 00:00:00 2001 From: rfeng2023 <126488688+rfeng2023@users.noreply.github.com> Date: Mon, 2 Oct 2023 14:14:25 -0400 Subject: [PATCH 3/6] update container --- container/containers.csv | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/container/containers.csv b/container/containers.csv index 3d694ed6d..6e4bb8dd9 100644 --- a/container/containers.csv +++ b/container/containers.csv @@ -101,4 +101,5 @@ openpyxl,https://pypi.org/project/openpyxl/,Python,,N/A,conda-forge,universal,MI pytables,https://pypi.org/project/tables/,Python,,N/A,conda-forge,universal,BSD-3-Clause,https://anaconda.org/conda-forge/pytables, scikit-learn,https://pypi.org/project/scikit-learn/,Python,,N/A,conda-forge,universal,BSD-3-Clause,https://anaconda.org/conda-forge/scikit-learn, hello,https://www.gnu.org/software/hello/,C/C++,2.12.1,N/A,dnachun,hello,GPL-3.0-or-later,https://anaconda.org/dnachun/hello, -deepTools,https://github.com/deeptools/deepTools,Python,,N/A,Bioconda,rna_quantification,GPL-3.0-or-later,https://anaconda.org/bioconda/deeptools, \ No newline at end of file +deeptools,https://github.com/deeptools/deepTools,Python,3.5.2,N/A,Bioconda,rna_quantification,GPL-3.0-or-later,https://anaconda.org/bioconda/deeptools, +r-ape,https://github.com/emmanuelparadis/ape,R,5.7,N/A,conda-forge,rna_quantification,GPL-3.0-or-later,https://anaconda.org/conda-forge/r-ape, \ No newline at end of file From 39bbdaf2391a1f3c06516477421ff3088aeff997 Mon Sep 17 00:00:00 2001 From: rfeng2023 Date: Mon, 2 Oct 2023 18:18:53 +0000 Subject: [PATCH 4/6] 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 From 5e95bea79c851f5c9b24dcfafa456ca97a8bc31c Mon Sep 17 00:00:00 2001 From: rfeng2023 <126488688+rfeng2023@users.noreply.github.com> Date: Mon, 2 Oct 2023 14:30:31 -0400 Subject: [PATCH 5/6] update version --- container/containers.csv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/container/containers.csv b/container/containers.csv index 6e4bb8dd9..43a2d4130 100644 --- a/container/containers.csv +++ b/container/containers.csv @@ -101,5 +101,5 @@ openpyxl,https://pypi.org/project/openpyxl/,Python,,N/A,conda-forge,universal,MI pytables,https://pypi.org/project/tables/,Python,,N/A,conda-forge,universal,BSD-3-Clause,https://anaconda.org/conda-forge/pytables, scikit-learn,https://pypi.org/project/scikit-learn/,Python,,N/A,conda-forge,universal,BSD-3-Clause,https://anaconda.org/conda-forge/scikit-learn, hello,https://www.gnu.org/software/hello/,C/C++,2.12.1,N/A,dnachun,hello,GPL-3.0-or-later,https://anaconda.org/dnachun/hello, -deeptools,https://github.com/deeptools/deepTools,Python,3.5.2,N/A,Bioconda,rna_quantification,GPL-3.0-or-later,https://anaconda.org/bioconda/deeptools, +deeptools,https://github.com/deeptools/deepTools,Python,3.5.4,N/A,Bioconda,rna_quantification,GPL-3.0-or-later,https://anaconda.org/bioconda/deeptools, r-ape,https://github.com/emmanuelparadis/ape,R,5.7,N/A,conda-forge,rna_quantification,GPL-3.0-or-later,https://anaconda.org/conda-forge/r-ape, \ No newline at end of file From bdb4f7599f1c5edd4274fc32b30abf8851d73e1f Mon Sep 17 00:00:00 2001 From: rfeng2023 Date: Mon, 2 Oct 2023 18:31:31 +0000 Subject: [PATCH 6/6] Update YAML files and Markdown table --- container/README.md | 2 +- container/readme/containers.md | 2 +- container/rna_quantification/rna_quantification.yml | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/container/README.md b/container/README.md index 23003f9d5..92da30888 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 | 3.5.2 | Bioconda | GPL‑3.0‑or‑later | +| deeptools | [Link](https://github.com/deeptools/deepTools) | [Link](https://anaconda.org/bioconda/deeptools) | rna_quantification | 3.5.4 | 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 | diff --git a/container/readme/containers.md b/container/readme/containers.md index 8e749f45b..5f784e48d 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 | 3.5.2 | Bioconda | GPL‑3.0‑or‑later | +| deeptools | [Link](https://github.com/deeptools/deepTools) | [Link](https://anaconda.org/bioconda/deeptools) | rna_quantification | 3.5.4 | 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 | diff --git a/container/rna_quantification/rna_quantification.yml b/container/rna_quantification/rna_quantification.yml index 9c227d496..ed82a40e1 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=3.5.2 + - deeptools=3.5.4 - fastp=0.23.4 - fastqc=0.12.1 - gffread=0.12.7