Skip to content

Commit

Permalink
deploy: 4e4f7f3
Browse files Browse the repository at this point in the history
  • Loading branch information
@kelly-sovacool
kelly-sovacool committed Aug 26, 2024
1 parent b2d3092 commit b273a27
Show file tree
Hide file tree
Showing 3 changed files with 12 additions and 12 deletions.
4 changes: 2 additions & 2 deletions dev/index.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -187,11 +187,11 @@ <h2 id="toc-title">On this page</h2>



<!-- README.md is generated from README.qmd. Please edit that file -->
<section id="ccbr-tools" class="level1">
<h1>CCBR Tools</h1>
<!-- README.md is generated from README.qmd. Please edit that file -->
<p>Utilities for CCBR Bioinformatics Software</p>
<p><a href="https://github.com/CCBR/Tools/actions/workflows/build-python.yml"><img src="https://github.com/CCBR/Tools/actions/workflows/build-python.yml/badge.svg" class="img-fluid" alt="build"></a> <a href="https://github.com/CCBR/Tools/actions/workflows/docs-quartodoc.yml"><img src="https://github.com/CCBR/Tools/actions/workflows/docs-quartodoc.yml/badge.svg" class="img-fluid" alt="docs"></a> <a href="https://codecov.io/gh/CCBR/Tools"><img src="https://codecov.io/gh/CCBR/Tools/graph/badge.svg?token=O73NOR65B3" class="img-fluid" alt="codecov"></a></p>
<p><a href="https://github.com/CCBR/Tools/actions/workflows/build-python.yml"><img src="https://github.com/CCBR/Tools/actions/workflows/build-python.yml/badge.svg" class="img-fluid" alt="build"></a> <a href="https://github.com/CCBR/Tools/actions/workflows/docs-quartodoc.yml"><img src="https://github.com/CCBR/Tools/actions/workflows/docs-quartodoc.yml/badge.svg" class="img-fluid" alt="docs"></a> <a href="https://codecov.io/gh/CCBR/Tools"><img src="https://codecov.io/gh/CCBR/Tools/graph/badge.svg?token=O73NOR65B3" class="img-fluid" alt="codecov"></a> <a href="https://doi.org/10.5281/zenodo.13377166"><img src="https://zenodo.org/badge/DOI/10.5281/zenodo.13377166.svg" class="img-fluid" alt="DOI"></a></p>
<section id="installation" class="level2">
<h2 class="anchored" data-anchor-id="installation">Installation</h2>
<p>On biowulf you can access the latest release of <code>ccbr_tools</code> by loading the ccbrpipeliner module:</p>
Expand Down
2 changes: 1 addition & 1 deletion dev/search.json
View file
Original file line number Diff line number Diff line change
Expand Up @@ -186,7 +186,7 @@
"href": "index.html",
"title": "CCBR Tools",
"section": "",
"text": "Utilities for CCBR Bioinformatics Software\n \n\n\nOn biowulf you can access the latest release of ccbr_tools by loading the ccbrpipeliner module:\nmodule load ccbrpipeliner\nOutside of biowulf, you can install the package with pip:\npip install git+https://github.com/CCBR/Tools\nOr specify a specific tagged version or branch:\npip install git+https://github.com/CCBR/Tools@main\n\n\n\n\n\nccbr_tools --help\nUsage: ccbr_tools [OPTIONS] COMMAND [ARGS]...\n\n Utilities for CCBR Bioinformatics Software\n\n For more options, run: tool_name [command] --help\n\nOptions:\n -v, --version Show the version and exit.\n -h, --help Show this message and exit.\n\nCommands:\n cite Print the citation in the desired format\n version Print the version of ccbr_tools\n\nAll installed tools:\n ccbr_tools\n gb2gtf\n hf\n intersect\n jobby\n jobinfo\n peek\n\n\n\nimport ccbr_tools.pkg_util\nprint(ccbr_tools.pkg_util.get_version())\n0.1.0-dev\n\n\n\n\nCommand-line utilities in CCBR Tools.\n\nccbr_tools\ngb2gtf\nhf\nintersect\njobby\njobinfo\npeek\n\nRun a command with --help to learn how to use it.\n\n\n\nAdditional standalone scripts for various common tasks in scripts/ are added to the path when this package is installed. They are less robust than the CLI Utilities included in the package and do not have any unit tests.\n\nadd_gene_name_to_count_matrix.R\naggregate_data_tables.R\nargparse.bash\ncancel_snakemake_jobs.sh\ncreate_hpc_link.sh\nextract_value_from_json.py\nextract_value_from_yaml.py\nfilter_bam_by_readids.py\nfilter_fastq_by_readids_highmem.py\nfilter_fastq_by_readids_highmem_pe.py\ngather_cluster_stats.sh\ngather_cluster_stats_biowulf.sh\nget_buyin_partition_list.bash\nget_slurm_file_with_error.sh\ngsea_preranked.sh\nkaryoploter.R\nmake_labels_for_pipeliner.sh\nrawcounts2normalizedcounts_DESeq2.R\nrawcounts2normalizedcounts_limmavoom.R\nrun_jobby_on_nextflow_log\nrun_jobby_on_nextflow_log_full_format\nrun_jobby_on_snakemake_log\nrun_jobby_on_snakemake_log_full_format\nspooker\nwhich_vpn.sh\n\n\n\n\nPlease cite this software if you use it in a publication:\n\nSovacool K., Koparde V., Kuhn S., Tandon M., Huse S. CCBR Tools: Utilities for CCBR Bioinformatics Software URL: https://ccbr.github.io/Tools/\n\n\n\n@misc{YourReferenceHere,\nauthor = {Sovacool, Kelly and Koparde, Vishal and Kuhn, Skyler and Tandon, Mayank and Huse, Susan},\ntitle = {CCBR Tools: Utilities for CCBR Bioinformatics Software},\nurl = {https://ccbr.github.io/Tools/}\n}"
"text": "Utilities for CCBR Bioinformatics Software\n \n\n\nOn biowulf you can access the latest release of ccbr_tools by loading the ccbrpipeliner module:\nmodule load ccbrpipeliner\nOutside of biowulf, you can install the package with pip:\npip install git+https://github.com/CCBR/Tools\nOr specify a specific tagged version or branch:\npip install git+https://github.com/CCBR/Tools@main\n\n\n\n\n\nccbr_tools --help\nUsage: ccbr_tools [OPTIONS] COMMAND [ARGS]...\n\n Utilities for CCBR Bioinformatics Software\n\n For more options, run: tool_name [command] --help\n\nOptions:\n -v, --version Show the version and exit.\n -h, --help Show this message and exit.\n\nCommands:\n cite Print the citation in the desired format\n version Print the version of ccbr_tools\n\nAll installed tools:\n ccbr_tools\n gb2gtf\n hf\n intersect\n jobby\n jobinfo\n peek\n\n\n\nimport ccbr_tools.pkg_util\nprint(ccbr_tools.pkg_util.get_version())\n0.1.0-dev\n\n\n\n\nCommand-line utilities in CCBR Tools.\n\nccbr_tools\ngb2gtf\nhf\nintersect\njobby\njobinfo\npeek\n\nRun a command with --help to learn how to use it.\n\n\n\nAdditional standalone scripts for various common tasks in scripts/ are added to the path when this package is installed. They are less robust than the CLI Utilities included in the package and do not have any unit tests.\n\nadd_gene_name_to_count_matrix.R\naggregate_data_tables.R\nargparse.bash\ncancel_snakemake_jobs.sh\ncreate_hpc_link.sh\nextract_value_from_json.py\nextract_value_from_yaml.py\nfilter_bam_by_readids.py\nfilter_fastq_by_readids_highmem.py\nfilter_fastq_by_readids_highmem_pe.py\ngather_cluster_stats.sh\ngather_cluster_stats_biowulf.sh\nget_buyin_partition_list.bash\nget_slurm_file_with_error.sh\ngsea_preranked.sh\nkaryoploter.R\nmake_labels_for_pipeliner.sh\nrawcounts2normalizedcounts_DESeq2.R\nrawcounts2normalizedcounts_limmavoom.R\nrun_jobby_on_nextflow_log\nrun_jobby_on_nextflow_log_full_format\nrun_jobby_on_snakemake_log\nrun_jobby_on_snakemake_log_full_format\nspooker\nwhich_vpn.sh\n\n\n\n\nPlease cite this software if you use it in a publication:\n\nSovacool K., Koparde V., Kuhn S., Tandon M., Huse S. CCBR Tools: Utilities for CCBR Bioinformatics Software URL: https://ccbr.github.io/Tools/\n\n\n\n@misc{YourReferenceHere,\nauthor = {Sovacool, Kelly and Koparde, Vishal and Kuhn, Skyler and Tandon, Mayank and Huse, Susan},\ntitle = {CCBR Tools: Utilities for CCBR Bioinformatics Software},\nurl = {https://ccbr.github.io/Tools/}\n}"
},
{
"objectID": "index.html#installation",
Expand Down
18 changes: 9 additions & 9 deletions dev/sitemap.xml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -2,38 +2,38 @@
<urlset xmlns="http://www.sitemaps.org/schemas/sitemap/0.9">
<url>
<loc>https://ccbr.github.io/Tools/CONTRIBUTING.html</loc>
<lastmod>2024-08-26T22:26:40.377Z</lastmod>
<lastmod>2024-08-26T22:33:15.085Z</lastmod>
</url>
<url>
<loc>https://ccbr.github.io/Tools/reference/index.html</loc>
<lastmod>2024-08-26T22:27:10.182Z</lastmod>
<lastmod>2024-08-26T22:33:42.829Z</lastmod>
</url>
<url>
<loc>https://ccbr.github.io/Tools/reference/jobby.html</loc>
<lastmod>2024-08-26T22:27:10.226Z</lastmod>
<lastmod>2024-08-26T22:33:42.873Z</lastmod>
</url>
<url>
<loc>https://ccbr.github.io/Tools/reference/shell.html</loc>
<lastmod>2024-08-26T22:27:10.298Z</lastmod>
<lastmod>2024-08-26T22:33:42.945Z</lastmod>
</url>
<url>
<loc>https://ccbr.github.io/Tools/index.html</loc>
<lastmod>2024-08-26T22:26:40.377Z</lastmod>
<lastmod>2024-08-26T22:33:15.089Z</lastmod>
</url>
<url>
<loc>https://ccbr.github.io/Tools/reference/pipeline.html</loc>
<lastmod>2024-08-26T22:27:10.242Z</lastmod>
<lastmod>2024-08-26T22:33:42.889Z</lastmod>
</url>
<url>
<loc>https://ccbr.github.io/Tools/reference/peek.html</loc>
<lastmod>2024-08-26T22:27:10.242Z</lastmod>
<lastmod>2024-08-26T22:33:42.889Z</lastmod>
</url>
<url>
<loc>https://ccbr.github.io/Tools/reference/pkg_util.html</loc>
<lastmod>2024-08-26T22:27:10.286Z</lastmod>
<lastmod>2024-08-26T22:33:42.933Z</lastmod>
</url>
<url>
<loc>https://ccbr.github.io/Tools/CHANGELOG.html</loc>
<lastmod>2024-08-26T22:26:40.377Z</lastmod>
<lastmod>2024-08-26T22:33:15.085Z</lastmod>
</url>
</urlset>

0 comments on commit b273a27

Please sign in to comment.