From f0f1e476e1a248a8bf950f2356094cedf150a3d0 Mon Sep 17 00:00:00 2001
From: kelly-sovacool <kelly-sovacool@users.noreply.github.com>
Date: Mon, 26 Aug 2024 22:20:24 +0000
Subject: [PATCH] deploy: 1d783fedef98614025f421b7213114562c1f86b3

---
 dev/CHANGELOG.html |  6 +++++-
 dev/search.json    | 11 ++---------
 dev/sitemap.xml    | 18 +++++++++---------
 3 files changed, 16 insertions(+), 19 deletions(-)

diff --git a/dev/CHANGELOG.html b/dev/CHANGELOG.html
index b23aa4f..39a7d27 100644
--- a/dev/CHANGELOG.html
+++ b/dev/CHANGELOG.html
@@ -129,7 +129,8 @@
     <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>
@@ -144,6 +145,9 @@ <h2 id="toc-title">On this page</h2>
 
 
 
+<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>
diff --git a/dev/search.json b/dev/search.json
index a44dca1..a66444c 100644
--- a/dev/search.json
+++ b/dev/search.json
@@ -295,19 +295,12 @@
       "pkg_util"
     ]
   },
-  {
-    "objectID": "CHANGELOG.html",
-    "href": "CHANGELOG.html",
-    "title": "CCBR Tools",
-    "section": "",
-    "text": "The 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\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"
-  },
   {
     "objectID": "CHANGELOG.html#tools-0.1.0",
     "href": "CHANGELOG.html#tools-0.1.0",
     "title": "CCBR Tools",
-    "section": "",
-    "text": "The 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\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"
+    "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"
   },
   {
     "objectID": "CHANGELOG.html#tools-0.0.1",
diff --git a/dev/sitemap.xml b/dev/sitemap.xml
index 33f550c..ad03713 100644
--- a/dev/sitemap.xml
+++ b/dev/sitemap.xml
@@ -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>2024-08-26T22:14:11.527Z</lastmod>
+    <lastmod>2024-08-26T22:19:39.479Z</lastmod>
   </url>
   <url>
     <loc>https://ccbr.github.io/Tools/reference/index.html</loc>
-    <lastmod>2024-08-26T22:14:39.511Z</lastmod>
+    <lastmod>2024-08-26T22:20:15.523Z</lastmod>
   </url>
   <url>
     <loc>https://ccbr.github.io/Tools/reference/jobby.html</loc>
-    <lastmod>2024-08-26T22:14:39.559Z</lastmod>
+    <lastmod>2024-08-26T22:20:15.571Z</lastmod>
   </url>
   <url>
     <loc>https://ccbr.github.io/Tools/reference/shell.html</loc>
-    <lastmod>2024-08-26T22:14:39.635Z</lastmod>
+    <lastmod>2024-08-26T22:20:15.643Z</lastmod>
   </url>
   <url>
     <loc>https://ccbr.github.io/Tools/index.html</loc>
-    <lastmod>2024-08-26T22:14:11.527Z</lastmod>
+    <lastmod>2024-08-26T22:19:39.479Z</lastmod>
   </url>
   <url>
     <loc>https://ccbr.github.io/Tools/reference/pipeline.html</loc>
-    <lastmod>2024-08-26T22:14:39.579Z</lastmod>
+    <lastmod>2024-08-26T22:20:15.587Z</lastmod>
   </url>
   <url>
     <loc>https://ccbr.github.io/Tools/reference/peek.html</loc>
-    <lastmod>2024-08-26T22:14:39.575Z</lastmod>
+    <lastmod>2024-08-26T22:20:15.587Z</lastmod>
   </url>
   <url>
     <loc>https://ccbr.github.io/Tools/reference/pkg_util.html</loc>
-    <lastmod>2024-08-26T22:14:39.623Z</lastmod>
+    <lastmod>2024-08-26T22:20:15.631Z</lastmod>
   </url>
   <url>
     <loc>https://ccbr.github.io/Tools/CHANGELOG.html</loc>
-    <lastmod>2024-08-26T22:14:11.527Z</lastmod>
+    <lastmod>2024-08-26T22:19:39.479Z</lastmod>
   </url>
 </urlset>