edit log from update 167 to rename staging folder and preserve history

usegalaxy-au · Oct 18, 2023 · 59908ee · 59908ee
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diff --git a/.env b/.env
@@ -1,6 +1,6 @@
 STAGING_URL="https://staging.gvl.org.au"
 PRODUCTION_URL="https://usegalaxy.org.au"
-STAGING_TOOL_DIR="staging.usegalaxy.org.au"
+STAGING_TOOL_DIR="staging.gvl.org.au"
 PRODUCTION_TOOL_DIR="usegalaxy.org.au"
 
 BASE_LOG_DIR="/var/lib/jenkins/galaxy_tool_automation"

diff --git a/automated_tool_installation_log.tsv b/automated_tool_installation_log.tsv
@@ -5755,3 +5755,26 @@ Update	166	04/10/23 20:42:07	sklearn_numeric_clustering	False	Installed	bgruenin
 Update	166	04/10/23 20:42:58	sklearn_searchcv	False	Installed	bgruening	36e8d6d5d01b	36e8d6d5d01b				Machine Learning	toolshed.g2.bx.psu.edu	/var/lib/jenkins/galaxy_tool_automation/update_build_166/install_log.txt
 Update	166	04/10/23 20:43:44	sklearn_svm_classifier	False	Installed	bgruening	0630258dcf35	0630258dcf35				Machine Learning	toolshed.g2.bx.psu.edu	/var/lib/jenkins/galaxy_tool_automation/update_build_166/install_log.txt
 Update	166	04/10/23 20:44:28	sklearn_to_categorical	False	Installed	bgruening	61634a87efc7	61634a87efc7				Machine Learning	toolshed.g2.bx.psu.edu	/var/lib/jenkins/galaxy_tool_automation/update_build_166/install_log.txt
+Update	167	11/10/23 11:24:04	alphafold2	False	Shed-tools error	galaxy-australia		e4a053d67e24	Staging Installation			Proteomic AI	toolshed.g2.bx.psu.edu	/var/lib/jenkins/galaxy_tool_automation/update_build_167/install_log.txt
+Update	167	11/10/23 11:24:06	bwa_mem2	False	Shed-tools error	iuc		bfaa0d22c2e4	Staging Installation			Mapping	toolshed.g2.bx.psu.edu	/var/lib/jenkins/galaxy_tool_automation/update_build_167/install_log.txt
+Update	167	11/10/23 11:24:09	cat_bins	False	Shed-tools error	iuc		31853794ace2	Staging Installation			Metagenomic Analysis	toolshed.g2.bx.psu.edu	/var/lib/jenkins/galaxy_tool_automation/update_build_167/install_log.txt
+Update	167	11/10/23 11:24:11	chipseeker	False	Shed-tools error	rnateam		8bd92f2404dd	Staging Installation			Annotation	toolshed.g2.bx.psu.edu	/var/lib/jenkins/galaxy_tool_automation/update_build_167/install_log.txt
+Update	167	11/10/23 11:24:14	dada2_assigntaxonomyaddspecies	False	Shed-tools error	iuc		7c2100246a2f	Staging Installation			Metagenomic Analysis	toolshed.g2.bx.psu.edu	/var/lib/jenkins/galaxy_tool_automation/update_build_167/install_log.txt
+Update	167	11/10/23 11:24:16	deeptools_compute_gc_bias	False	Shed-tools error	bgruening		26983857c91a	Staging Installation			DeepTools	toolshed.g2.bx.psu.edu	/var/lib/jenkins/galaxy_tool_automation/update_build_167/install_log.txt
+Update	167	11/10/23 11:24:19	deeptools_compute_matrix_operations	False	Shed-tools error	bgruening		e6d0bff01239	Staging Installation			DeepTools	toolshed.g2.bx.psu.edu	/var/lib/jenkins/galaxy_tool_automation/update_build_167/install_log.txt
+Update	167	11/10/23 11:24:21	deeptools_plot_correlation	False	Shed-tools error	bgruening		bad3ca889618	Staging Installation			DeepTools	toolshed.g2.bx.psu.edu	/var/lib/jenkins/galaxy_tool_automation/update_build_167/install_log.txt
+Update	167	11/10/23 11:24:24	eggnog_mapper	False	Shed-tools error	galaxyp		d9c3016f7283	Staging Installation			Annotation	toolshed.g2.bx.psu.edu	/var/lib/jenkins/galaxy_tool_automation/update_build_167/install_log.txt
+Update	167	11/10/23 11:24:26	encyclopedia_encyclopedia	False	Shed-tools error	galaxyp		eac99effe86f	Staging Installation			Proteomics	toolshed.g2.bx.psu.edu	/var/lib/jenkins/galaxy_tool_automation/update_build_167/install_log.txt
+Update	167	11/10/23 11:24:29	encyclopedia_searchtolib	False	Shed-tools error	galaxyp		fb192dd6658a	Staging Installation			Proteomics	toolshed.g2.bx.psu.edu	/var/lib/jenkins/galaxy_tool_automation/update_build_167/install_log.txt
+Update	167	11/10/23 11:24:31	encyclopedia_walnut	False	Shed-tools error	galaxyp		0d2e93e01e68	Staging Installation			Proteomics	toolshed.g2.bx.psu.edu	/var/lib/jenkins/galaxy_tool_automation/update_build_167/install_log.txt
+Update	167	11/10/23 11:24:34	featurecounts	False	Shed-tools error	iuc		f9d49f5cb597	Staging Installation			RNA-seq	toolshed.g2.bx.psu.edu	/var/lib/jenkins/galaxy_tool_automation/update_build_167/install_log.txt
+Update	167	11/10/23 11:24:36	humann	False	Shed-tools error	iuc		fc6c328c292f	Staging Installation			Metagenomic Analysis	toolshed.g2.bx.psu.edu	/var/lib/jenkins/galaxy_tool_automation/update_build_167/install_log.txt
+Update	167	11/10/23 11:24:39	humann_regroup_table	False	Shed-tools error	iuc		e88b731dad59	Staging Installation			Metagenomic Analysis	toolshed.g2.bx.psu.edu	/var/lib/jenkins/galaxy_tool_automation/update_build_167/install_log.txt
+Update	167	11/10/23 11:24:42	humann_rename_table	False	Shed-tools error	iuc		094ad9c068af	Staging Installation			Metagenomic Analysis	toolshed.g2.bx.psu.edu	/var/lib/jenkins/galaxy_tool_automation/update_build_167/install_log.txt
+Update	167	11/10/23 11:24:44	kraken2tax	False	Shed-tools error	devteam		50bd98b3ae5a	Staging Installation			Metagenomic Analysis	toolshed.g2.bx.psu.edu	/var/lib/jenkins/galaxy_tool_automation/update_build_167/install_log.txt
+Update	167	11/10/23 11:24:47	merqury	False	Shed-tools error	iuc		09c589057ee8	Staging Installation			Assembly	toolshed.g2.bx.psu.edu	/var/lib/jenkins/galaxy_tool_automation/update_build_167/install_log.txt
+Update	167	11/10/23 11:24:49	openms_decoydatabase	False	Shed-tools error	galaxyp		25529df60a81	Staging Installation			Proteomics	toolshed.g2.bx.psu.edu	/var/lib/jenkins/galaxy_tool_automation/update_build_167/install_log.txt
+Update	167	11/10/23 11:24:52	openms_targetedfileconverter	False	Shed-tools error	galaxyp		9c70a651a53e	Staging Installation			Proteomics	toolshed.g2.bx.psu.edu	/var/lib/jenkins/galaxy_tool_automation/update_build_167/install_log.txt
+Update	167	11/10/23 11:24:55	openms_xmlvalidator	False	Shed-tools error	galaxyp		f036e8cf1a55	Staging Installation			Proteomics	toolshed.g2.bx.psu.edu	/var/lib/jenkins/galaxy_tool_automation/update_build_167/install_log.txt
+Update	167	11/10/23 11:24:57	rgrnastar	False	Shed-tools error	iuc		79de45b5069b	Staging Installation			RNA-seq	toolshed.g2.bx.psu.edu	/var/lib/jenkins/galaxy_tool_automation/update_build_167/install_log.txt
+Update	167	11/10/23 11:24:59	rna_starsolo	False	Shed-tools error	iuc		5ef7ec16b04f	Staging Installation			Mapping	toolshed.g2.bx.psu.edu	/var/lib/jenkins/galaxy_tool_automation/update_build_167/install_log.txt
diff --git a/staging.usegalaxy.org.au/annotation.yml → staging.gvl.org.au/annotation.yml b/staging.usegalaxy.org.au/annotation.yml → staging.gvl.org.au/annotation.yml
diff --git a/staging.usegalaxy.org.au/assembly.yml → staging.gvl.org.au/assembly.yml b/staging.usegalaxy.org.au/assembly.yml → staging.gvl.org.au/assembly.yml
diff --git a/...ing.usegalaxy.org.au/bacterial_typing.yml → staging.gvl.org.au/bacterial_typing.yml b/...ing.usegalaxy.org.au/bacterial_typing.yml → staging.gvl.org.au/bacterial_typing.yml
diff --git a/staging.usegalaxy.org.au/bb_tools.yml → staging.gvl.org.au/bb_tools.yml b/staging.usegalaxy.org.au/bb_tools.yml → staging.gvl.org.au/bb_tools.yml
diff --git a/staging.usegalaxy.org.au/bed.yml → staging.gvl.org.au/bed.yml b/staging.usegalaxy.org.au/bed.yml → staging.gvl.org.au/bed.yml
diff --git a/staging.usegalaxy.org.au/blast.yml → staging.gvl.org.au/blast.yml b/staging.usegalaxy.org.au/blast.yml → staging.gvl.org.au/blast.yml
diff --git a/staging.usegalaxy.org.au/chemicaltoolbox.yml → staging.gvl.org.au/chemicaltoolbox.yml b/staging.usegalaxy.org.au/chemicaltoolbox.yml → staging.gvl.org.au/chemicaltoolbox.yml
diff --git a/staging.usegalaxy.org.au/chip_seq.yml → staging.gvl.org.au/chip_seq.yml b/staging.usegalaxy.org.au/chip_seq.yml → staging.gvl.org.au/chip_seq.yml
diff --git a/...ing.usegalaxy.org.au/climate_analysis.yml → staging.gvl.org.au/climate_analysis.yml b/...ing.usegalaxy.org.au/climate_analysis.yml → staging.gvl.org.au/climate_analysis.yml
diff --git a/...segalaxy.org.au/collection_operations.yml → staging.gvl.org.au/collection_operations.yml b/...segalaxy.org.au/collection_operations.yml → staging.gvl.org.au/collection_operations.yml
diff --git a/staging.usegalaxy.org.au/convert_formats.yml → staging.gvl.org.au/convert_formats.yml b/staging.usegalaxy.org.au/convert_formats.yml → staging.gvl.org.au/convert_formats.yml
diff --git a/staging.usegalaxy.org.au/deeptools.yml → staging.gvl.org.au/deeptools.yml b/staging.usegalaxy.org.au/deeptools.yml → staging.gvl.org.au/deeptools.yml
diff --git a/...ng.usegalaxy.org.au/dna_metabarcoding.yml → staging.gvl.org.au/dna_metabarcoding.yml b/...ng.usegalaxy.org.au/dna_metabarcoding.yml → staging.gvl.org.au/dna_metabarcoding.yml
diff --git a/staging.usegalaxy.org.au/emboss.yml → staging.gvl.org.au/emboss.yml b/staging.usegalaxy.org.au/emboss.yml → staging.gvl.org.au/emboss.yml
diff --git a/staging.usegalaxy.org.au/epigenetics.yml → staging.gvl.org.au/epigenetics.yml b/staging.usegalaxy.org.au/epigenetics.yml → staging.gvl.org.au/epigenetics.yml
diff --git a/staging.usegalaxy.org.au/fastafastq.yml → staging.gvl.org.au/fastafastq.yml b/staging.usegalaxy.org.au/fastafastq.yml → staging.gvl.org.au/fastafastq.yml
diff --git a/...segalaxy.org.au/fastq_quality_control.yml → staging.gvl.org.au/fastq_quality_control.yml b/...segalaxy.org.au/fastq_quality_control.yml → staging.gvl.org.au/fastq_quality_control.yml
diff --git a/...laxy.org.au/fetch_alignmentssequences.yml → ....gvl.org.au/fetch_alignmentssequences.yml b/...laxy.org.au/fetch_alignmentssequences.yml → ....gvl.org.au/fetch_alignmentssequences.yml
diff --git a/...laxy.org.au/fetch_sequencesalignments.yml → ....gvl.org.au/fetch_sequencesalignments.yml b/...laxy.org.au/fetch_sequencesalignments.yml → ....gvl.org.au/fetch_sequencesalignments.yml
diff --git a/staging.usegalaxy.org.au/filter_and_sort.yml → staging.gvl.org.au/filter_and_sort.yml b/staging.usegalaxy.org.au/filter_and_sort.yml → staging.gvl.org.au/filter_and_sort.yml
diff --git a/staging.usegalaxy.org.au/gemini_tools.yml → staging.gvl.org.au/gemini_tools.yml b/staging.usegalaxy.org.au/gemini_tools.yml → staging.gvl.org.au/gemini_tools.yml
diff --git a/staging.usegalaxy.org.au/genome_editing.yml → staging.gvl.org.au/genome_editing.yml b/staging.usegalaxy.org.au/genome_editing.yml → staging.gvl.org.au/genome_editing.yml
diff --git a/staging.usegalaxy.org.au/get_data.yml → staging.gvl.org.au/get_data.yml b/staging.usegalaxy.org.au/get_data.yml → staging.gvl.org.au/get_data.yml
diff --git a/...ng.usegalaxy.org.au/graphdisplay_data.yml → staging.gvl.org.au/graphdisplay_data.yml b/...ng.usegalaxy.org.au/graphdisplay_data.yml → staging.gvl.org.au/graphdisplay_data.yml
diff --git a/staging.usegalaxy.org.au/hca_single_cell.yml → staging.gvl.org.au/hca_single_cell.yml b/staging.usegalaxy.org.au/hca_single_cell.yml → staging.gvl.org.au/hca_single_cell.yml
diff --git a/staging.usegalaxy.org.au/hicexplorer.yml → staging.gvl.org.au/hicexplorer.yml b/staging.usegalaxy.org.au/hicexplorer.yml → staging.gvl.org.au/hicexplorer.yml
diff --git a/staging.usegalaxy.org.au/imaging.yml → staging.gvl.org.au/imaging.yml b/staging.usegalaxy.org.au/imaging.yml → staging.gvl.org.au/imaging.yml
diff --git a/staging.usegalaxy.org.au/ivar.yml → staging.gvl.org.au/ivar.yml b/staging.usegalaxy.org.au/ivar.yml → staging.gvl.org.au/ivar.yml
diff --git a/...galaxy.org.au/join_subtract_and_group.yml → ...ng.gvl.org.au/join_subtract_and_group.yml b/...galaxy.org.au/join_subtract_and_group.yml → ...ng.gvl.org.au/join_subtract_and_group.yml
diff --git a/...ing.usegalaxy.org.au/machine_learning.yml → staging.gvl.org.au/machine_learning.yml b/...ing.usegalaxy.org.au/machine_learning.yml → staging.gvl.org.au/machine_learning.yml
diff --git a/staging.usegalaxy.org.au/mapping.yml → staging.gvl.org.au/mapping.yml b/staging.usegalaxy.org.au/mapping.yml → staging.gvl.org.au/mapping.yml
diff --git a/staging.usegalaxy.org.au/metabolomics.yml → staging.gvl.org.au/metabolomics.yml b/staging.usegalaxy.org.au/metabolomics.yml → staging.gvl.org.au/metabolomics.yml
diff --git a/...usegalaxy.org.au/metagenomic_analysis.yml → staging.gvl.org.au/metagenomic_analysis.yml b/...usegalaxy.org.au/metagenomic_analysis.yml → staging.gvl.org.au/metagenomic_analysis.yml
diff --git a/staging.usegalaxy.org.au/mimodd.yml → staging.gvl.org.au/mimodd.yml b/staging.usegalaxy.org.au/mimodd.yml → staging.gvl.org.au/mimodd.yml
diff --git a/staging.usegalaxy.org.au/mothur.yml → staging.gvl.org.au/mothur.yml b/staging.usegalaxy.org.au/mothur.yml → staging.gvl.org.au/mothur.yml
diff --git a/....usegalaxy.org.au/multiple_alignments.yml → staging.gvl.org.au/multiple_alignments.yml b/....usegalaxy.org.au/multiple_alignments.yml → staging.gvl.org.au/multiple_alignments.yml
diff --git a/staging.usegalaxy.org.au/nanopore.yml → staging.gvl.org.au/nanopore.yml b/staging.usegalaxy.org.au/nanopore.yml → staging.gvl.org.au/nanopore.yml
diff --git a/staging.usegalaxy.org.au/none.yml → staging.gvl.org.au/none.yml b/staging.usegalaxy.org.au/none.yml → staging.gvl.org.au/none.yml
diff --git a/...y.org.au/operate_on_genomic_intervals.yml → ...l.org.au/operate_on_genomic_intervals.yml b/...y.org.au/operate_on_genomic_intervals.yml → ...l.org.au/operate_on_genomic_intervals.yml
diff --git a/staging.usegalaxy.org.au/other_tools.yml → staging.gvl.org.au/other_tools.yml b/staging.usegalaxy.org.au/other_tools.yml → staging.gvl.org.au/other_tools.yml
diff --git a/staging.usegalaxy.org.au/phylogenetics.yml → staging.gvl.org.au/phylogenetics.yml b/staging.usegalaxy.org.au/phylogenetics.yml → staging.gvl.org.au/phylogenetics.yml
diff --git a/staging.usegalaxy.org.au/picard.yml → staging.gvl.org.au/picard.yml b/staging.usegalaxy.org.au/picard.yml → staging.gvl.org.au/picard.yml
diff --git a/staging.usegalaxy.org.au/proteomic_ai.yml → staging.gvl.org.au/proteomic_ai.yml b/staging.usegalaxy.org.au/proteomic_ai.yml → staging.gvl.org.au/proteomic_ai.yml
diff --git a/staging.usegalaxy.org.au/proteomics.yml → staging.gvl.org.au/proteomics.yml b/staging.usegalaxy.org.au/proteomics.yml → staging.gvl.org.au/proteomics.yml
diff --git a/staging.usegalaxy.org.au/qiime_2.yml → staging.gvl.org.au/qiime_2.yml b/staging.usegalaxy.org.au/qiime_2.yml → staging.gvl.org.au/qiime_2.yml
diff --git a/staging.usegalaxy.org.au/rad_seq.yml → staging.gvl.org.au/rad_seq.yml b/staging.usegalaxy.org.au/rad_seq.yml → staging.gvl.org.au/rad_seq.yml
diff --git a/staging.usegalaxy.org.au/rna_seq.yml → staging.gvl.org.au/rna_seq.yml b/staging.usegalaxy.org.au/rna_seq.yml → staging.gvl.org.au/rna_seq.yml
diff --git a/staging.usegalaxy.org.au/rseqc.yml → staging.gvl.org.au/rseqc.yml b/staging.usegalaxy.org.au/rseqc.yml → staging.gvl.org.au/rseqc.yml
diff --git a/staging.usegalaxy.org.au/sambam.yml → staging.gvl.org.au/sambam.yml b/staging.usegalaxy.org.au/sambam.yml → staging.gvl.org.au/sambam.yml
diff --git a/staging.usegalaxy.org.au/send_data.yml → staging.gvl.org.au/send_data.yml b/staging.usegalaxy.org.au/send_data.yml → staging.gvl.org.au/send_data.yml
diff --git a/staging.usegalaxy.org.au/single_cell.yml → staging.gvl.org.au/single_cell.yml b/staging.usegalaxy.org.au/single_cell.yml → staging.gvl.org.au/single_cell.yml
diff --git a/...ng.usegalaxy.org.au/species_abundance.yml → staging.gvl.org.au/species_abundance.yml b/...ng.usegalaxy.org.au/species_abundance.yml → staging.gvl.org.au/species_abundance.yml
diff --git a/staging.usegalaxy.org.au/statistics.yml → staging.gvl.org.au/statistics.yml b/staging.usegalaxy.org.au/statistics.yml → staging.gvl.org.au/statistics.yml
diff --git a/...ng.usegalaxy.org.au/text_manipulation.yml → staging.gvl.org.au/text_manipulation.yml b/...ng.usegalaxy.org.au/text_manipulation.yml → staging.gvl.org.au/text_manipulation.yml
diff --git a/staging.usegalaxy.org.au/variant_calling.yml → staging.gvl.org.au/variant_calling.yml b/staging.usegalaxy.org.au/variant_calling.yml → staging.gvl.org.au/variant_calling.yml
diff --git a/staging.usegalaxy.org.au/vcfbcf.yml → staging.gvl.org.au/vcfbcf.yml b/staging.usegalaxy.org.au/vcfbcf.yml → staging.gvl.org.au/vcfbcf.yml
diff --git a/staging.usegalaxy.org.au/viral_tools.yml → staging.gvl.org.au/viral_tools.yml b/staging.usegalaxy.org.au/viral_tools.yml → staging.gvl.org.au/viral_tools.yml