Skip to content

Commit

Permalink
Update YAML files and Markdown table
Browse files Browse the repository at this point in the history
  • Loading branch information
@rfeng2023
rfeng2023 committed Oct 2, 2023
1 parent 236161f commit 39bbdaf
Show file tree
Hide file tree
Showing 3 changed files with 6 additions and 3 deletions.
3 changes: 2 additions & 1 deletion container/README.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -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 |
Expand All @@ -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 |
Expand Down
3 changes: 2 additions & 1 deletion container/readme/containers.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -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 |
Expand All @@ -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 |
Expand Down
3 changes: 2 additions & 1 deletion container/rna_quantification/rna_quantification.yml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand All @@ -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
Expand Down

0 comments on commit 39bbdaf

Please sign in to comment.