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kelly-sovacool committed Aug 26, 2024
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6 changes: 5 additions & 1 deletion dev/CHANGELOG.html
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<h2 id="toc-title">On this page</h2>

<ul>
<li><a href="#tools-0.1.0" id="toc-tools-0.1.0" class="nav-link active" data-scroll-target="#tools-0.1.0">Tools 0.1.0</a>
<li><a href="#tools-development-version" id="toc-tools-development-version" class="nav-link active" data-scroll-target="#tools-development-version">Tools development version</a></li>
<li><a href="#tools-0.1.0" id="toc-tools-0.1.0" class="nav-link" data-scroll-target="#tools-0.1.0">Tools 0.1.0</a>
<ul class="collapse">
<li><a href="#cli-utilities" id="toc-cli-utilities" class="nav-link" data-scroll-target="#cli-utilities">CLI Utilities</a></li>
<li><a href="#external-scripts" id="toc-external-scripts" class="nav-link" data-scroll-target="#external-scripts">External Scripts</a></li>
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<section id="tools-development-version" class="level2">
<h2 class="anchored" data-anchor-id="tools-development-version">Tools development version</h2>
</section>
<section id="tools-0.1.0" class="level2">
<h2 class="anchored" data-anchor-id="tools-0.1.0">Tools 0.1.0</h2>
<p>The Tools repository is now restructured as a Python package. All previous python scripts which included command line utilities have been moved to <code>src/</code>, and all other scripts have been moved to <code>scripts/</code>. In both cases, they are available in the path when the package is installed.</p>
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11 changes: 2 additions & 9 deletions dev/search.json
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"section": "Tools 0.1.0",
"text": "Tools 0.1.0\nThe Tools repository is now restructured as a Python package. All previous python scripts which included command line utilities have been moved to src/, and all other scripts have been moved to scripts/. In both cases, they are available in the path when the package is installed.\nFunctions which were part of both XAVIER and RENEE are available for re-use in other bioinformatics pipelines for tasks such as determining the HPC environment, retrieving available genome annotations, and printing citation and version information. Explore the ccbr_tools reference documentation for more information: https://ccbr.github.io/Tools/latest/reference/\n\nCLI Utilities\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\nExternal Scripts\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"
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18 changes: 9 additions & 9 deletions dev/sitemap.xml
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