Jenkins update build 208.

usegalaxy-au · Sep 4, 2024 · 20f708b · 20f708b
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diff --git a/automated_tool_installation_log.tsv b/automated_tool_installation_log.tsv
@@ -7719,3 +7719,15 @@ Install	1583	28/08/24 15:41:12	pyprophet_export	True	Installed	galaxyp	3cf580bf2
 Install	1583	28/08/24 15:48:19	rnaquast	True	Installed	iuc	8e66f695d859	latest				Assembly	toolshed.g2.bx.psu.edu	/var/lib/jenkins/galaxy_tool_automation/install_build_1583/install_log.txt
 Install	1585	28/08/24 16:33:53	ragtag	True	Tests failed	iuc	b3c3217c0cbc	b3c3217c0cbc	Staging Testing	1/5		Assembly	toolshed.g2.bx.psu.edu	/var/lib/jenkins/galaxy_tool_automation/install_build_1585/install_log.txt
 Install	1589	29/08/24 11:01:54	ragtag	True	Installed	iuc	b3c3217c0cbc	b3c3217c0cbc		5/5		Assembly	toolshed.g2.bx.psu.edu	/var/lib/jenkins/galaxy_tool_automation/install_build_1589/install_log.txt
+Update	208	04/09/24 11:36:57	bakta	False	Tests failed	iuc	d77802fe76f7	d77802fe76f7	Staging Testing	0/6		Annotation	toolshed.g2.bx.psu.edu	/var/lib/jenkins/galaxy_tool_automation/update_build_208/install_log.txt
+Update	208	04/09/24 12:42:34	busco	False	Installed	iuc	2babe6d5c561	2babe6d5c561		8/8		Assembly	toolshed.g2.bx.psu.edu	/var/lib/jenkins/galaxy_tool_automation/update_build_208/install_log.txt
+Update	208	04/09/24 13:01:12	column_maker	False	Installed	devteam	aff5135563c6	aff5135563c6		18/18		Text Manipulation	toolshed.g2.bx.psu.edu	/var/lib/jenkins/galaxy_tool_automation/update_build_208/install_log.txt
+Update	208	04/09/24 13:04:46	funannotate_compare	False	Tests failed	iuc	0418d28136de	0418d28136de	Staging Testing	0/3		Annotation	toolshed.g2.bx.psu.edu	/var/lib/jenkins/galaxy_tool_automation/update_build_208/install_log.txt
+Update	208	04/09/24 13:44:06	multiqc	False	Installed	iuc	f7e2f1eb3a16	f7e2f1eb3a16		24/24		FASTQ Quality Control	toolshed.g2.bx.psu.edu	/var/lib/jenkins/galaxy_tool_automation/update_build_208/install_log.txt
+Update	208	04/09/24 13:46:50	openms_decoydatabase	False	Tests failed	galaxyp	06cca574e337	06cca574e337	Staging Testing	0/4		Proteomics	toolshed.g2.bx.psu.edu	/var/lib/jenkins/galaxy_tool_automation/update_build_208/install_log.txt
+Update	208	04/09/24 13:49:23	openms_xmlvalidator	False	Tests failed	galaxyp	ad2ba3a95a02	ad2ba3a95a02	Staging Testing	0/2		Proteomics	toolshed.g2.bx.psu.edu	/var/lib/jenkins/galaxy_tool_automation/update_build_208/install_log.txt
+Update	208	04/09/24 13:53:21	pear	False	Installed	iuc	f69501361cec	f69501361cec		2/2		FASTA/FASTQ	toolshed.g2.bx.psu.edu	/var/lib/jenkins/galaxy_tool_automation/update_build_208/install_log.txt
+Update	208	04/09/24 14:06:22	rgrnastar	False	Tests failed	iuc	4014de1b6daf	4014de1b6daf	Staging Testing	15/19		RNA-seq	toolshed.g2.bx.psu.edu	/var/lib/jenkins/galaxy_tool_automation/update_build_208/install_log.txt
+Update	208	04/09/24 14:32:42	rnaquast	False	Tests failed	iuc	f73ab5187eed	f73ab5187eed	Staging Testing	5/9		Assembly	toolshed.g2.bx.psu.edu	/var/lib/jenkins/galaxy_tool_automation/update_build_208/install_log.txt
+Update	208	04/09/24 14:50:06	rna_starsolo	False	Tests failed	iuc	45795f582ae9	45795f582ae9	Staging Testing	12/13		Mapping	toolshed.g2.bx.psu.edu	/var/lib/jenkins/galaxy_tool_automation/update_build_208/install_log.txt
+Update	208	04/09/24 15:10:13	samtools_view	False	Tests failed	iuc	2dce91e11ca7	2dce91e11ca7	Staging Testing	31/33		SAM/BAM	toolshed.g2.bx.psu.edu	/var/lib/jenkins/galaxy_tool_automation/update_build_208/install_log.txt
diff --git a/staging.gvl.org.au/annotation.yml b/staging.gvl.org.au/annotation.yml
@@ -2,18 +2,18 @@ tools:
 - name: abricate
   owner: iuc
   revisions:
-  - c2ef298da409
-  - 78c75f134c16
-  - 4efdca267d51
   - 6e9aea89e388
+  - 4efdca267d51
   - 3f3e247c053d
+  - 78c75f134c16
+  - c2ef298da409
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: aegean_canongff3
   owner: iuc
   revisions:
-  - c45c9dd066e2
   - 3f438bf5475d
+  - c45c9dd066e2
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: aegean_gaeval
@@ -33,62 +33,62 @@ tools:
 - name: aegean_parseval
   owner: iuc
   revisions:
-  - 1b52f0c8ad7f
   - d6c074a93c51
+  - 1b52f0c8ad7f
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: annotatemyids
   owner: iuc
   revisions:
+  - 44018dd6b447
+  - a79ee60b6926
+  - b5d8e5475247
   - 1aae04680c4b
+  - 3e1f6f6d557e
   - f29602ae449e
-  - 44018dd6b447
   - 133f36c29579
-  - cd2480f35935
   - fe3ca740a485
-  - 3e1f6f6d557e
+  - cd2480f35935
   - 4f2967b27e67
-  - b5d8e5475247
-  - a79ee60b6926
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: antismash
   owner: bgruening
   revisions:
-  - e78e25d3b4bd
   - bc88856eddab
+  - e78e25d3b4bd
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: augustus_training
   owner: bgruening
   revisions:
   - 7be22100e5e1
-  - 6519ebe25019
   - dc027fa56d55
+  - 6519ebe25019
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: augustus
   owner: bgruening
   revisions:
-  - 28433faa6e42
   - ca6d970d931c
+  - 28433faa6e42
   - 09855551d713
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: bakta
   owner: iuc
   revisions:
+  - da5f1924bb2e
   - 92eee5f31117
   - 728dacaf08a9
-  - da5f1924bb2e
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: barrnap
   owner: iuc
   revisions:
   - fe48aa4ccd5e
-  - 8fd427007e93
   - 7355bbf5e05f
+  - 8fd427007e93
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: braker3
@@ -100,24 +100,24 @@ tools:
 - name: chipseeker
   owner: rnateam
   revisions:
-  - 1b9a9409831d
   - 8bd92f2404dd
+  - 1b9a9409831d
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: cpat
   owner: bgruening
   revisions:
-  - 1ac12c0cc7a0
-  - 7ccc6234b54e
   - 8e9e228c54c4
+  - 7ccc6234b54e
+  - 1ac12c0cc7a0
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: eggnog_mapper
   owner: galaxyp
   revisions:
-  - 63662ae295d6
   - d9c3016f7283
   - 9d1fbff733cf
+  - 63662ae295d6
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: exonerate
@@ -142,59 +142,59 @@ tools:
   owner: iuc
   revisions:
   - 9c15ca7e764e
+  - 3bbe70fef6df
   - 9f2455341fac
+  - 756376aeb1ae
   - b6b5cd37f2a2
-  - 582fd74dc2a1
-  - 3bbe70fef6df
   - 14f588312c56
-  - 756376aeb1ae
+  - 582fd74dc2a1
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: funannotate_clean
   owner: iuc
   revisions:
+  - 0ffe5be70caf
   - 73428a792541
+  - 8e1ace8f77c6
   - a230ea445788
-  - 1691af4a0d17
-  - 0ffe5be70caf
   - 989f7c061f35
+  - 1691af4a0d17
   - 30fb23d4c31c
-  - 8e1ace8f77c6
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: funannotate_compare
   owner: iuc
   revisions:
-  - e94187d661df
   - 563a19373357
-  - 5a5ae61da69c
-  - 494f0bb4a993
   - 57c6718cbfcc
   - 30f08d74024f
+  - e94187d661df
+  - 494f0bb4a993
+  - 5a5ae61da69c
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: funannotate_predict
   owner: iuc
   revisions:
+  - 4b96ced19f75
   - 7abc5f6dd595
-  - f77d7b685bb3
+  - f31125bb85ea
   - 1bc5a03faf2e
-  - d6c7106b7b2e
-  - 4b96ced19f75
   - 2bba2ff070d9
-  - f31125bb85ea
+  - d6c7106b7b2e
+  - f77d7b685bb3
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: funannotate_sort
   owner: iuc
   revisions:
-  - b3cf4684e9c7
-  - d77fdcca400e
   - 54961e026fe4
+  - d3af38b9c7e1
   - 520e30695ec3
   - 52af33194019
-  - d3af38b9c7e1
   - fed64e676186
+  - d77fdcca400e
+  - b3cf4684e9c7
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: get_orfs_or_cdss
@@ -207,8 +207,8 @@ tools:
   owner: iuc
   revisions:
   - 07d7991bf205
-  - 79261884facd
   - 2aea122fbd25
+  - 79261884facd
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: goenrichment
@@ -220,8 +220,8 @@ tools:
 - name: goseq
   owner: iuc
   revisions:
-  - 8b3e3657034e
   - ef2ad746b589
+  - 8b3e3657034e
   - 602de62d995b
   - 43798b4caee0
   tool_panel_section_label: Annotation
@@ -254,9 +254,9 @@ tools:
 - name: interproscan
   owner: bgruening
   revisions:
-  - 98cafcbd2578
   - c55643c3d813
   - 74810db257cc
+  - 98cafcbd2578
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: jcvi_gff_stats
@@ -274,25 +274,25 @@ tools:
 - name: maker_map_ids
   owner: iuc
   revisions:
-  - 326f9c294b09
   - e906fa778440
+  - 326f9c294b09
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: maker
   owner: iuc
   revisions:
-  - d46d803ca6cc
   - 3c1a01127868
+  - d46d803ca6cc
   - 370c210d9541
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: mitos2
   owner: iuc
   revisions:
+  - b815ec682418
   - 033755194fe9
   - e95d52d295d7
   - c8ac28e8ac44
-  - b815ec682418
   - 624606f7c996
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
@@ -323,11 +323,11 @@ tools:
 - name: prokka
   owner: crs4
   revisions:
-  - eaee459f3d69
   - d643e3b03500
+  - bf68eb663bc3
   - a17498c603ec
+  - eaee459f3d69
   - 8a22554cdde2
-  - bf68eb663bc3
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: red
@@ -339,8 +339,8 @@ tools:
 - name: repeat_masker
   owner: bgruening
   revisions:
-  - 3f987772e283
   - ba6d2c32f797
+  - 3f987772e283
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: repeatmodeler
@@ -360,21 +360,21 @@ tools:
   owner: iuc
   revisions:
   - 268d162b9c49
-  - cfcf33df7fc0
   - 9473cd297a76
-  - 5b80f544c67f
   - 5a29ab10dba6
+  - cfcf33df7fc0
   - 8f92c2b26e6d
-  - 5c7b70713fb5
+  - 5b80f544c67f
   - 68693743661e
+  - 5c7b70713fb5
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: snpsift
   owner: iuc
   revisions:
+  - 09d6806c609e
   - 5fab4f81391d
   - 2b3e65a4252f
-  - 09d6806c609e
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: snptools
@@ -400,16 +400,16 @@ tools:
   owner: iuc
   revisions:
   - ba6f87115e13
-  - ac8250086ac3
-  - e1a9d6fd258d
-  - 37213cf56392
   - 200c378d85f3
-  - 809dfc93d593
   - 037a11682176
-  - 45083d070fb8
-  - 4839e590cb26
   - 51dd22484644
+  - 809dfc93d593
+  - e1a9d6fd258d
   - d03af1c7002c
+  - ac8250086ac3
+  - 37213cf56392
+  - 45083d070fb8
+  - 4839e590cb26
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: transit_gumbel