Jenkins update build 217.

usegalaxy-au · Oct 31, 2024 · 144a418 · 144a418
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diff --git a/automated_tool_installation_log.tsv b/automated_tool_installation_log.tsv
@@ -7999,3 +7999,20 @@ Update	216	30/10/24 06:44:39	pretext_snapshot	False	Errored	iuc	326098bc19cc	326
 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
 Install	1692	30/10/24 22:24:23	alphafold2	False	Installed	galaxy-australia	3f188450ca4f	latest				Proteomic AI	toolshed.g2.bx.psu.edu	/var/lib/jenkins/galaxy_tool_automation/install_build_1692/install_log.txt
+Update	217	31/10/24 04:52:05	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_217/install_log.txt
+Update	217	31/10/24 05:07:46	busco	False	Installed	iuc	e5c372c91e46	e5c372c91e46				Assembly	toolshed.g2.bx.psu.edu	/var/lib/jenkins/galaxy_tool_automation/update_build_217/install_log.txt
+Update	217	31/10/24 05:11:34	cuffmerge	False	Installed	devteam	04adc9db1581	04adc9db1581		1/1		RNA-seq	toolshed.g2.bx.psu.edu	/var/lib/jenkins/galaxy_tool_automation/update_build_217/install_log.txt
+Update	217	31/10/24 05:15:42	cutesv	False	Tests failed	iuc	cb441f258c37	cb441f258c37	Staging Testing	1/2		Variant Calling	toolshed.g2.bx.psu.edu	/var/lib/jenkins/galaxy_tool_automation/update_build_217/install_log.txt
+Update	217	31/10/24 05:19:35	dorado	False	Tests failed	galaxy-australia	c2a23340f233	c2a23340f233	Staging Testing	0/3		Nanopore	toolshed.g2.bx.psu.edu	/var/lib/jenkins/galaxy_tool_automation/update_build_217/install_log.txt
+Update	217	31/10/24 05:44:34	featurecounts	False	Tests failed	iuc	1b851f87fbe0	1b851f87fbe0	Staging Testing	6/7		RNA-seq	toolshed.g2.bx.psu.edu	/var/lib/jenkins/galaxy_tool_automation/update_build_217/install_log.txt
+Update	217	31/10/24 05:56:02	freebayes	False	Installed	devteam	3e954e7125bf	3e954e7125bf		9/9		Variant Calling	toolshed.g2.bx.psu.edu	/var/lib/jenkins/galaxy_tool_automation/update_build_217/install_log.txt
+Update	217	31/10/24 06:18:38	hifiasm	False	Installed	bgruening	5161f204ba63	5161f204ba63		15/15		Assembly	toolshed.g2.bx.psu.edu	/var/lib/jenkins/galaxy_tool_automation/update_build_217/install_log.txt
+Update	217	31/10/24 06:19:15	music_compare	False	Installed	bgruening	7009462b958f	7009462b958f				Single-cell	toolshed.g2.bx.psu.edu	/var/lib/jenkins/galaxy_tool_automation/update_build_217/install_log.txt
+Update	217	31/10/24 06:19:54	music_construct_eset	False	Installed	bgruening	7022ce682d2f	7022ce682d2f				Single-cell	toolshed.g2.bx.psu.edu	/var/lib/jenkins/galaxy_tool_automation/update_build_217/install_log.txt
+Update	217	31/10/24 06:20:32	music_deconvolution	False	Installed	bgruening	e7b79fd6b595	e7b79fd6b595				Single-cell	toolshed.g2.bx.psu.edu	/var/lib/jenkins/galaxy_tool_automation/update_build_217/install_log.txt
+Update	217	31/10/24 06:21:07	music_inspect_eset	False	Installed	bgruening	94c0b3baf8fd	94c0b3baf8fd				Single-cell	toolshed.g2.bx.psu.edu	/var/lib/jenkins/galaxy_tool_automation/update_build_217/install_log.txt
+Update	217	31/10/24 06:21:44	music_manipulate_eset	False	Installed	bgruening	192355cd1641	192355cd1641				Single-cell	toolshed.g2.bx.psu.edu	/var/lib/jenkins/galaxy_tool_automation/update_build_217/install_log.txt
+Update	217	31/10/24 06:26:48	pretext_snapshot	False	Installed	iuc	326098bc19cc	326098bc19cc		2/2		Graph/Display Data	toolshed.g2.bx.psu.edu	/var/lib/jenkins/galaxy_tool_automation/update_build_217/install_log.txt
+Update	217	31/10/24 06:29:35	recetox_aplcms_correct_time	False	Installed	recetox	30bf4e35da3e	30bf4e35da3e		1/1		Metabolomics	toolshed.g2.bx.psu.edu	/var/lib/jenkins/galaxy_tool_automation/update_build_217/install_log.txt
+Update	217	31/10/24 06:30:18	scanpy_remove_confounders	False	Installed	iuc	c5541bfb8feb	c5541bfb8feb				Single-cell	toolshed.g2.bx.psu.edu	/var/lib/jenkins/galaxy_tool_automation/update_build_217/install_log.txt
+Update	217	31/10/24 06:35:11	ucsc_twobittofa	False	Installed	iuc	e9bbe2f71784	e9bbe2f71784		1/1		Convert Formats	toolshed.g2.bx.psu.edu	/var/lib/jenkins/galaxy_tool_automation/update_build_217/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:
-  - 6e9aea89e388
   - 78c75f134c16
-  - 4efdca267d51
   - c2ef298da409
+  - 4efdca267d51
   - 3f3e247c053d
+  - 6e9aea89e388
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: aegean_canongff3
@@ -26,8 +26,8 @@ tools:
 - name: aegean_locuspocus
   owner: iuc
   revisions:
-  - 1fdc517743e6
   - c4ac24510b55
+  - 1fdc517743e6
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: aegean_parseval
@@ -40,58 +40,58 @@ tools:
 - name: annotatemyids
   owner: iuc
   revisions:
+  - 133f36c29579
   - fe3ca740a485
-  - b5d8e5475247
   - 3e1f6f6d557e
-  - f29602ae449e
-  - 133f36c29579
-  - 44018dd6b447
   - 1aae04680c4b
-  - 4f2967b27e67
   - cd2480f35935
   - a79ee60b6926
+  - b5d8e5475247
+  - 4f2967b27e67
+  - 44018dd6b447
+  - f29602ae449e
   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:
   - dc027fa56d55
-  - f1e653756174
   - 6519ebe25019
+  - f1e653756174
   - 7be22100e5e1
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: augustus
   owner: bgruening
   revisions:
   - 09855551d713
-  - 28433faa6e42
   - bd0e53f3a891
   - ca6d970d931c
+  - 28433faa6e42
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: bakta
   owner: iuc
   revisions:
-  - d77802fe76f7
-  - 92eee5f31117
   - da5f1924bb2e
+  - 92eee5f31117
+  - d77802fe76f7
   - 728dacaf08a9
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: barrnap
   owner: iuc
   revisions:
-  - 8fd427007e93
   - 7355bbf5e05f
   - fe48aa4ccd5e
+  - 8fd427007e93
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: braker3
@@ -117,16 +117,16 @@ tools:
   owner: bgruening
   revisions:
   - 7ccc6234b54e
-  - 8e9e228c54c4
   - 1ac12c0cc7a0
+  - 8e9e228c54c4
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: eggnog_mapper
   owner: galaxyp
   revisions:
+  - 63662ae295d6
   - 9d1fbff733cf
   - d9c3016f7283
-  - 63662ae295d6
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: exonerate
@@ -150,60 +150,60 @@ tools:
 - name: funannotate_annotate
   owner: iuc
   revisions:
-  - 14f588312c56
+  - 582fd74dc2a1
   - b6b5cd37f2a2
+  - 9c15ca7e764e
   - 9f2455341fac
-  - 582fd74dc2a1
   - 3bbe70fef6df
+  - 14f588312c56
   - 756376aeb1ae
-  - 9c15ca7e764e
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: funannotate_clean
   owner: iuc
   revisions:
-  - 0ffe5be70caf
   - 989f7c061f35
   - 73428a792541
-  - a230ea445788
   - 8e1ace8f77c6
-  - 30fb23d4c31c
+  - 0ffe5be70caf
+  - a230ea445788
   - 1691af4a0d17
+  - 30fb23d4c31c
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: funannotate_compare
   owner: iuc
   revisions:
   - 30f08d74024f
-  - 494f0bb4a993
-  - 57c6718cbfcc
+  - e94187d661df
   - 563a19373357
+  - 494f0bb4a993
   - 5a5ae61da69c
   - 0418d28136de
-  - e94187d661df
+  - 57c6718cbfcc
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: funannotate_predict
   owner: iuc
   revisions:
+  - 1bc5a03faf2e
   - f77d7b685bb3
+  - f31125bb85ea
   - 2bba2ff070d9
-  - d6c7106b7b2e
-  - 1bc5a03faf2e
   - 4b96ced19f75
   - 7abc5f6dd595
-  - f31125bb85ea
+  - d6c7106b7b2e
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: funannotate_sort
   owner: iuc
   revisions:
   - 54961e026fe4
+  - d77fdcca400e
   - 520e30695ec3
   - d3af38b9c7e1
-  - b3cf4684e9c7
-  - d77fdcca400e
   - fed64e676186
+  - b3cf4684e9c7
   - 52af33194019
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
@@ -216,9 +216,9 @@ tools:
 - name: gff_to_prot
   owner: iuc
   revisions:
+  - 79261884facd
   - 2aea122fbd25
   - 07d7991bf205
-  - 79261884facd
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: goenrichment
@@ -257,16 +257,16 @@ tools:
 - name: infernal
   owner: bgruening
   revisions:
-  - 477d829d3250
   - c9e29ac5d099
+  - 477d829d3250
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: interproscan
   owner: bgruening
   revisions:
   - 98cafcbd2578
-  - 74810db257cc
   - c55643c3d813
+  - 74810db257cc
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: jcvi_gff_stats
@@ -291,19 +291,19 @@ tools:
 - name: maker
   owner: iuc
   revisions:
-  - 370c210d9541
   - 3c1a01127868
+  - 370c210d9541
   - d46d803ca6cc
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: mitos2
   owner: iuc
   revisions:
-  - b815ec682418
-  - 624606f7c996
   - e95d52d295d7
+  - 624606f7c996
   - 033755194fe9
   - c8ac28e8ac44
+  - b815ec682418
   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:
-  - d643e3b03500
+  - eaee459f3d69
   - 8a22554cdde2
   - bf68eb663bc3
+  - d643e3b03500
   - a17498c603ec
-  - eaee459f3d69
   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
@@ -393,22 +393,22 @@ tools:
 - name: snpeff
   owner: iuc
   revisions:
-  - 8f92c2b26e6d
   - 5a29ab10dba6
-  - ca2b512e8d7c
-  - 5b80f544c67f
-  - cfcf33df7fc0
+  - 6322be79bd8e
+  - 5c7b70713fb5
+  - 8f92c2b26e6d
   - 68693743661e
+  - 5b80f544c67f
   - 268d162b9c49
-  - 5c7b70713fb5
-  - 6322be79bd8e
+  - ca2b512e8d7c
+  - cfcf33df7fc0
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: snpsift
   owner: iuc
   revisions:
-  - 2b3e65a4252f
   - 5fab4f81391d
+  - 2b3e65a4252f
   - 09d6806c609e
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
@@ -421,8 +421,8 @@ tools:
 - name: sortmerna
   owner: rnateam
   revisions:
-  - eb35257d2e29
   - 10b84b577117
+  - eb35257d2e29
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: tbl2gff3
@@ -435,16 +435,16 @@ tools:
   owner: iuc
   revisions:
   - 51dd22484644
-  - 4839e590cb26
+  - e1a9d6fd258d
   - 37213cf56392
-  - 809dfc93d593
-  - ac8250086ac3
-  - ba6f87115e13
   - d03af1c7002c
   - 45083d070fb8
-  - 200c378d85f3
-  - e1a9d6fd258d
+  - ba6f87115e13
+  - 809dfc93d593
   - 037a11682176
+  - 4839e590cb26
+  - ac8250086ac3
+  - 200c378d85f3
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: transit_gumbel