Jenkins update build 216.

usegalaxy-au · Oct 30, 2024 · dfce093 · dfce093
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diff --git a/automated_tool_installation_log.tsv b/automated_tool_installation_log.tsv
@@ -7981,3 +7981,20 @@ Update	215	23/10/24 07:35:35	snpeff	False	Installed	iuc	ca2b512e8d7c	ca2b512e8d7
 Install	1685	24/10/24 05:15:33	aarnet_filesender	True	Installed	galaxy-australia	8a4b0f14aa4e	latest		2/2		Send Data	toolshed.g2.bx.psu.edu	/var/lib/jenkins/galaxy_tool_automation/install_build_1685/install_log.txt
 Install	1687	29/10/24 00:49:41	cemitool	True	Installed	iuc	9d93999d9028	9d93999d9028		3/3		RNA-seq	toolshed.g2.bx.psu.edu	/var/lib/jenkins/galaxy_tool_automation/install_build_1687/install_log.txt
 Install	1689	29/10/24 02:51:46	alphafold2	False	Installed	galaxy-australia	e7f1b552a695	latest				Proteomic AI	toolshed.g2.bx.psu.edu	/var/lib/jenkins/galaxy_tool_automation/install_build_1689/install_log.txt
+Update	216	30/10/24 01:36:47	agat	False	Tests failed	bgruening	d6ede73082da	d6ede73082da	Staging Testing	15/16		Convert Formats	toolshed.g2.bx.psu.edu	/var/lib/jenkins/galaxy_tool_automation/update_build_216/install_log.txt
+Update	216	30/10/24 01:37:32	alevin	False	Installed	bgruening	b0fe3e482cb7	b0fe3e482cb7				Single-cell	toolshed.g2.bx.psu.edu	/var/lib/jenkins/galaxy_tool_automation/update_build_216/install_log.txt
+Update	216	30/10/24 06:41:38	busco	False	Tests failed	iuc	e5c372c91e46	e5c372c91e46	Staging Testing	0/8		Assembly	toolshed.g2.bx.psu.edu	/var/lib/jenkins/galaxy_tool_automation/update_build_216/install_log.txt
+Update	216	30/10/24 06:42:04	cuffmerge	False	Errored	devteam	04adc9db1581	04adc9db1581	Staging Installation			RNA-seq	toolshed.g2.bx.psu.edu	/var/lib/jenkins/galaxy_tool_automation/update_build_216/install_log.txt
+Update	216	30/10/24 06:42:20	cutesv	False	Errored	iuc	cb441f258c37	cb441f258c37	Staging Installation			Variant Calling	toolshed.g2.bx.psu.edu	/var/lib/jenkins/galaxy_tool_automation/update_build_216/install_log.txt
+Update	216	30/10/24 06:42:35	dorado	False	Errored	galaxy-australia	c2a23340f233	c2a23340f233	Staging Installation			Nanopore	toolshed.g2.bx.psu.edu	/var/lib/jenkins/galaxy_tool_automation/update_build_216/install_log.txt
+Update	216	30/10/24 06:42:52	featurecounts	False	Errored	iuc	1b851f87fbe0	1b851f87fbe0	Staging Installation			RNA-seq	toolshed.g2.bx.psu.edu	/var/lib/jenkins/galaxy_tool_automation/update_build_216/install_log.txt
+Update	216	30/10/24 06:43:07	freebayes	False	Errored	devteam	3e954e7125bf	3e954e7125bf	Staging Installation			Variant Calling	toolshed.g2.bx.psu.edu	/var/lib/jenkins/galaxy_tool_automation/update_build_216/install_log.txt
+Update	216	30/10/24 06:43:24	hifiasm	False	Errored	bgruening	5161f204ba63	5161f204ba63	Staging Installation			Assembly	toolshed.g2.bx.psu.edu	/var/lib/jenkins/galaxy_tool_automation/update_build_216/install_log.txt
+Update	216	30/10/24 06:43:35	music_compare	False	Errored	bgruening	7009462b958f	7009462b958f	Staging Installation			Single-cell	toolshed.g2.bx.psu.edu	/var/lib/jenkins/galaxy_tool_automation/update_build_216/install_log.txt
+Update	216	30/10/24 06:43:48	music_construct_eset	False	Errored	bgruening	7022ce682d2f	7022ce682d2f	Staging Installation			Single-cell	toolshed.g2.bx.psu.edu	/var/lib/jenkins/galaxy_tool_automation/update_build_216/install_log.txt
+Update	216	30/10/24 06:44:00	music_deconvolution	False	Errored	bgruening	e7b79fd6b595	e7b79fd6b595	Staging Installation			Single-cell	toolshed.g2.bx.psu.edu	/var/lib/jenkins/galaxy_tool_automation/update_build_216/install_log.txt
+Update	216	30/10/24 06:44:12	music_inspect_eset	False	Errored	bgruening	94c0b3baf8fd	94c0b3baf8fd	Staging Installation			Single-cell	toolshed.g2.bx.psu.edu	/var/lib/jenkins/galaxy_tool_automation/update_build_216/install_log.txt
+Update	216	30/10/24 06:44:24	music_manipulate_eset	False	Errored	bgruening	192355cd1641	192355cd1641	Staging Installation			Single-cell	toolshed.g2.bx.psu.edu	/var/lib/jenkins/galaxy_tool_automation/update_build_216/install_log.txt
+Update	216	30/10/24 06:44:39	pretext_snapshot	False	Errored	iuc	326098bc19cc	326098bc19cc	Staging Installation			Graph/Display Data	toolshed.g2.bx.psu.edu	/var/lib/jenkins/galaxy_tool_automation/update_build_216/install_log.txt
+Update	216	30/10/24 06:44:51	scanpy_remove_confounders	False	Errored	iuc	c5541bfb8feb	c5541bfb8feb	Staging Installation			Single-cell	toolshed.g2.bx.psu.edu	/var/lib/jenkins/galaxy_tool_automation/update_build_216/install_log.txt
+Update	216	30/10/24 06:45:07	ucsc_twobittofa	False	Errored	iuc	e9bbe2f71784	e9bbe2f71784	Staging Installation			Convert Formats	toolshed.g2.bx.psu.edu	/var/lib/jenkins/galaxy_tool_automation/update_build_216/install_log.txt
diff --git a/staging.gvl.org.au/annotation.yml b/staging.gvl.org.au/annotation.yml
@@ -2,11 +2,11 @@ tools:
 - name: abricate
   owner: iuc
   revisions:
-  - 4efdca267d51
-  - 6e9aea89e388
-  - 3f3e247c053d
-  - 78c75f134c16
   - c2ef298da409
+  - 78c75f134c16
+  - 3f3e247c053d
+  - 6e9aea89e388
+  - 4efdca267d51
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: aegean_canongff3
@@ -19,8 +19,8 @@ tools:
 - name: aegean_gaeval
   owner: iuc
   revisions:
-  - 1dd7adc21b6d
   - 8dc7512c9dc9
+  - 1dd7adc21b6d
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: aegean_locuspocus
@@ -33,23 +33,23 @@ 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:
+  - 1aae04680c4b
+  - 44018dd6b447
   - fe3ca740a485
-  - cd2480f35935
-  - 3e1f6f6d557e
-  - f29602ae449e
-  - b5d8e5475247
   - 133f36c29579
-  - 44018dd6b447
-  - 4f2967b27e67
-  - 1aae04680c4b
+  - f29602ae449e
   - a79ee60b6926
+  - 4f2967b27e67
+  - b5d8e5475247
+  - cd2480f35935
+  - 3e1f6f6d557e
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: antismash
@@ -62,36 +62,36 @@ tools:
 - name: augustus_training
   owner: bgruening
   revisions:
-  - 6519ebe25019
-  - dc027fa56d55
-  - 7be22100e5e1
   - f1e653756174
+  - 7be22100e5e1
+  - dc027fa56d55
+  - 6519ebe25019
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: augustus
   owner: bgruening
   revisions:
+  - 09855551d713
   - 28433faa6e42
   - ca6d970d931c
-  - 09855551d713
   - bd0e53f3a891
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: bakta
   owner: iuc
   revisions:
-  - d77802fe76f7
   - da5f1924bb2e
-  - 728dacaf08a9
   - 92eee5f31117
+  - d77802fe76f7
+  - 728dacaf08a9
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: barrnap
   owner: iuc
   revisions:
   - 7355bbf5e05f
-  - fe48aa4ccd5e
   - 8fd427007e93
+  - fe48aa4ccd5e
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: braker3
@@ -103,8 +103,8 @@ tools:
 - name: chipseeker
   owner: rnateam
   revisions:
-  - 8bd92f2404dd
   - 1b9a9409831d
+  - 8bd92f2404dd
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: compleasm
@@ -116,17 +116,17 @@ tools:
 - name: cpat
   owner: bgruening
   revisions:
-  - 7ccc6234b54e
   - 8e9e228c54c4
   - 1ac12c0cc7a0
+  - 7ccc6234b54e
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: eggnog_mapper
   owner: galaxyp
   revisions:
-  - 9d1fbff733cf
   - d9c3016f7283
   - 63662ae295d6
+  - 9d1fbff733cf
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: exonerate
@@ -150,61 +150,61 @@ tools:
 - name: funannotate_annotate
   owner: iuc
   revisions:
+  - b6b5cd37f2a2
   - 9c15ca7e764e
-  - 582fd74dc2a1
   - 756376aeb1ae
-  - b6b5cd37f2a2
-  - 3bbe70fef6df
-  - 14f588312c56
   - 9f2455341fac
+  - 582fd74dc2a1
+  - 14f588312c56
+  - 3bbe70fef6df
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: funannotate_clean
   owner: iuc
   revisions:
-  - 8e1ace8f77c6
-  - 0ffe5be70caf
-  - a230ea445788
-  - 30fb23d4c31c
   - 73428a792541
   - 989f7c061f35
+  - 30fb23d4c31c
   - 1691af4a0d17
+  - 0ffe5be70caf
+  - 8e1ace8f77c6
+  - a230ea445788
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: funannotate_compare
   owner: iuc
   revisions:
-  - 494f0bb4a993
-  - 563a19373357
-  - 5a5ae61da69c
-  - e94187d661df
   - 30f08d74024f
+  - e94187d661df
+  - 563a19373357
   - 0418d28136de
+  - 494f0bb4a993
+  - 5a5ae61da69c
   - 57c6718cbfcc
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: funannotate_predict
   owner: iuc
   revisions:
-  - 7abc5f6dd595
-  - 4b96ced19f75
-  - 2bba2ff070d9
-  - d6c7106b7b2e
   - 1bc5a03faf2e
+  - d6c7106b7b2e
+  - 2bba2ff070d9
   - f77d7b685bb3
+  - 7abc5f6dd595
+  - 4b96ced19f75
   - f31125bb85ea
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: funannotate_sort
   owner: iuc
   revisions:
+  - 520e30695ec3
+  - 52af33194019
+  - d3af38b9c7e1
   - 54961e026fe4
+  - d77fdcca400e
   - fed64e676186
-  - d3af38b9c7e1
-  - 52af33194019
   - b3cf4684e9c7
-  - 520e30695ec3
-  - d77fdcca400e
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: get_orfs_or_cdss
@@ -217,8 +217,8 @@ tools:
   owner: iuc
   revisions:
   - 79261884facd
-  - 2aea122fbd25
   - 07d7991bf205
+  - 2aea122fbd25
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: goenrichment
@@ -230,10 +230,10 @@ tools:
 - name: goseq
   owner: iuc
   revisions:
-  - ef2ad746b589
-  - 8b3e3657034e
   - 43798b4caee0
+  - 8b3e3657034e
   - 602de62d995b
+  - ef2ad746b589
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: goslimmer
@@ -257,8 +257,8 @@ tools:
 - name: infernal
   owner: bgruening
   revisions:
-  - 477d829d3250
   - c9e29ac5d099
+  - 477d829d3250
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: interproscan
@@ -284,26 +284,26 @@ 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
   - 370c210d9541
-  - d46d803ca6cc
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: mitos2
   owner: iuc
   revisions:
+  - e95d52d295d7
+  - 033755194fe9
   - 624606f7c996
   - b815ec682418
-  - 033755194fe9
   - c8ac28e8ac44
-  - e95d52d295d7
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: mob_suite
@@ -345,11 +345,11 @@ tools:
 - name: prokka
   owner: crs4
   revisions:
-  - 8a22554cdde2
-  - bf68eb663bc3
   - d643e3b03500
-  - a17498c603ec
+  - bf68eb663bc3
   - eaee459f3d69
+  - 8a22554cdde2
+  - a17498c603ec
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: red
@@ -361,15 +361,15 @@ 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
   owner: csbl
   revisions:
-  - 41bfbaf3c959
   - 8661b2607b7e
+  - 41bfbaf3c959
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: sanntis_marine
@@ -394,22 +394,22 @@ tools:
   owner: iuc
   revisions:
   - 5c7b70713fb5
-  - 68693743661e
   - 5a29ab10dba6
-  - 268d162b9c49
-  - 8f92c2b26e6d
-  - 6322be79bd8e
   - 5b80f544c67f
-  - cfcf33df7fc0
+  - 268d162b9c49
   - ca2b512e8d7c
+  - cfcf33df7fc0
+  - 68693743661e
+  - 6322be79bd8e
+  - 8f92c2b26e6d
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: snpsift
   owner: iuc
   revisions:
+  - 09d6806c609e
   - 2b3e65a4252f
   - 5fab4f81391d
-  - 09d6806c609e
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: snptools
@@ -421,8 +421,8 @@ tools:
 - name: sortmerna
   owner: rnateam
   revisions:
-  - 10b84b577117
   - eb35257d2e29
+  - 10b84b577117
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: tbl2gff3
@@ -434,17 +434,17 @@ tools:
 - name: tbprofiler
   owner: iuc
   revisions:
-  - 809dfc93d593
+  - 037a11682176
+  - 51dd22484644
+  - 45083d070fb8
+  - 200c378d85f3
+  - d03af1c7002c
+  - e1a9d6fd258d
   - 4839e590cb26
   - 37213cf56392
-  - 45083d070fb8
   - ba6f87115e13
-  - e1a9d6fd258d
-  - d03af1c7002c
-  - 200c378d85f3
-  - 037a11682176
+  - 809dfc93d593
   - ac8250086ac3
-  - 51dd22484644
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: transit_gumbel