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kelly-sovacool committed Aug 26, 2024
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11 changes: 7 additions & 4 deletions dev/index.html
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Expand Up @@ -199,7 +199,7 @@ <h2 class="anchored" data-anchor-id="installation">Installation</h2>
<p>Outside of biowulf, you can install the package with pip:</p>
<div class="sourceCode" id="cb2"><pre class="sourceCode sh code-with-copy"><code class="sourceCode bash"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true" tabindex="-1"></a><span class="ex">pip</span> install git+https://github.com/CCBR/Tools</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<p>Or specify a specific tagged version or branch:</p>
<div class="sourceCode" id="cb3"><pre class="sourceCode sh code-with-copy"><code class="sourceCode bash"><span id="cb3-1"><a href="#cb3-1" aria-hidden="true" tabindex="-1"></a><span class="ex">pip</span> install git+https://github.com/CCBR/Tools@main</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="sourceCode" id="cb3"><pre class="sourceCode sh code-with-copy"><code class="sourceCode bash"><span id="cb3-1"><a href="#cb3-1" aria-hidden="true" tabindex="-1"></a><span class="ex">pip</span> install git+https://github.com/CCBR/Tools@v0.1.0</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</section>
<section id="usage" class="level2">
<h2 class="anchored" data-anchor-id="usage">Usage</h2>
Expand Down Expand Up @@ -233,7 +233,7 @@ <h3 class="anchored" data-anchor-id="cli">CLI</h3>
<h3 class="anchored" data-anchor-id="python">Python</h3>
<div class="sourceCode" id="cb6"><pre class="sourceCode python code-with-copy"><code class="sourceCode python"><span id="cb6-1"><a href="#cb6-1" aria-hidden="true" tabindex="-1"></a><span class="im">import</span> ccbr_tools.pkg_util</span>
<span id="cb6-2"><a href="#cb6-2" aria-hidden="true" tabindex="-1"></a><span class="bu">print</span>(ccbr_tools.pkg_util.get_version())</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<pre><code>0.1.0-dev</code></pre>
<pre><code>0.1.1-dev</code></pre>
</section>
</section>
<section id="cli-utilities" class="level2">
Expand Down Expand Up @@ -285,14 +285,17 @@ <h2 class="anchored" data-anchor-id="external-scripts">External Scripts</h2>
<h2 class="anchored" data-anchor-id="citation">Citation</h2>
<p>Please cite this software if you use it in a publication:</p>
<blockquote class="blockquote">
<p>Sovacool K., Koparde V., Kuhn S., Tandon M., Huse S. CCBR Tools: Utilities for CCBR Bioinformatics Software URL: https://ccbr.github.io/Tools/</p>
<p>Sovacool K., Koparde V., Kuhn S., Tandon M., Huse S. (2024). CCBR Tools: Utilities for CCBR Bioinformatics Software (version v0.1.0). DOI: 10.5281/zenodo.13377166 URL: https://ccbr.github.io/Tools/</p>
</blockquote>
<section id="bibtex-entry" class="level3">
<h3 class="anchored" data-anchor-id="bibtex-entry">Bibtex entry</h3>
<pre><code>@misc{YourReferenceHere,
author = {Sovacool, Kelly and Koparde, Vishal and Kuhn, Skyler and Tandon, Mayank and Huse, Susan},
doi = {10.5281/zenodo.13377166},
month = {8},
title = {CCBR Tools: Utilities for CCBR Bioinformatics Software},
url = {https://ccbr.github.io/Tools/}
url = {https://ccbr.github.io/Tools/},
year = {2024}
}</code></pre>


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8 changes: 4 additions & 4 deletions dev/search.json
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Expand Up @@ -186,21 +186,21 @@
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"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@v0.1.0\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())\n0.1.1-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. (2024). CCBR Tools: Utilities for CCBR Bioinformatics Software (version v0.1.0). DOI: 10.5281/zenodo.13377166 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},\ndoi = {10.5281/zenodo.13377166},\nmonth = {8},\ntitle = {CCBR Tools: Utilities for CCBR Bioinformatics Software},\nurl = {https://ccbr.github.io/Tools/},\nyear = {2024}\n}"
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"text": "On 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"
"text": "On 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@v0.1.0"
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"text": "ccbr_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"
"text": "ccbr_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())\n0.1.1-dev"
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Expand All @@ -221,7 +221,7 @@
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