Jenkins update build 228.

usegalaxy-au · Jan 15, 2025 · 49b4b8f · 49b4b8f
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diff --git a/automated_tool_installation_log.tsv b/automated_tool_installation_log.tsv
@@ -8263,3 +8263,14 @@ Update	227	08/01/25 01:35:14	infernal	False	Tests failed	bgruening	3711f654044e
 Update	227	08/01/25 01:41:07	krakentools_alpha_diversity	False	Tests failed	iuc	78b69342c280	78b69342c280	Staging Testing	3/5		Metagenomic Analysis	toolshed.g2.bx.psu.edu	/var/lib/jenkins/galaxy_tool_automation/update_build_227/install_log.txt
 Update	227	08/01/25 01:41:59	phyloseq_from_dada2	False	Installed	iuc	56155859de27	56155859de27				Metagenomic Analysis	toolshed.g2.bx.psu.edu	/var/lib/jenkins/galaxy_tool_automation/update_build_227/install_log.txt
 Update	227	08/01/25 01:55:13	quast	False	Tests failed	iuc	a3b35edea53a	a3b35edea53a	Staging Testing	11/13		Assembly	toolshed.g2.bx.psu.edu	/var/lib/jenkins/galaxy_tool_automation/update_build_227/install_log.txt
+Update	228	15/01/25 01:26:38	anndata_export	False	Installed	iuc	83609ef746e9	83609ef746e9		1/1		Single-cell	toolshed.g2.bx.psu.edu	/var/lib/jenkins/galaxy_tool_automation/update_build_228/install_log.txt
+Update	228	15/01/25 01:35:52	anndata_import	False	Installed	iuc	13cf83ced60c	13cf83ced60c		8/8		Single-cell	toolshed.g2.bx.psu.edu	/var/lib/jenkins/galaxy_tool_automation/update_build_228/install_log.txt
+Update	228	15/01/25 01:50:20	anndata_inspect	False	Installed	iuc	33c0081e16c6	33c0081e16c6		16/16		Single-cell	toolshed.g2.bx.psu.edu	/var/lib/jenkins/galaxy_tool_automation/update_build_228/install_log.txt
+Update	228	15/01/25 02:11:37	anndata_manipulate	False	Installed	iuc	d1e49c3c0aa2	d1e49c3c0aa2		22/22		Single-cell	toolshed.g2.bx.psu.edu	/var/lib/jenkins/galaxy_tool_automation/update_build_228/install_log.txt
+Update	228	15/01/25 02:18:26	featurecounts	False	Tests failed	iuc	5dbff3a5845a	5dbff3a5845a	Staging Testing	6/7		RNA-seq	toolshed.g2.bx.psu.edu	/var/lib/jenkins/galaxy_tool_automation/update_build_228/install_log.txt
+Update	228	15/01/25 02:27:04	infernal	False	Tests failed	bgruening	3711f654044e	3711f654044e	Staging Testing	7/12		Annotation	toolshed.g2.bx.psu.edu	/var/lib/jenkins/galaxy_tool_automation/update_build_228/install_log.txt
+Update	228	15/01/25 02:32:48	krakentools_alpha_diversity	False	Tests failed	iuc	78b69342c280	78b69342c280	Staging Testing	3/5		Metagenomic Analysis	toolshed.g2.bx.psu.edu	/var/lib/jenkins/galaxy_tool_automation/update_build_228/install_log.txt
+Update	228	15/01/25 02:40:44	modify_loom	False	Installed	iuc	a7b951572609	a7b951572609		6/6		Single-cell	toolshed.g2.bx.psu.edu	/var/lib/jenkins/galaxy_tool_automation/update_build_228/install_log.txt
+Update	228	15/01/25 02:41:21	phyloseq_from_dada2	False	Installed	iuc	bda00cb136ee	bda00cb136ee				Metagenomic Analysis	toolshed.g2.bx.psu.edu	/var/lib/jenkins/galaxy_tool_automation/update_build_228/install_log.txt
+Update	228	15/01/25 02:54:43	quast	False	Tests failed	iuc	a3b35edea53a	a3b35edea53a	Staging Testing	11/13		Assembly	toolshed.g2.bx.psu.edu	/var/lib/jenkins/galaxy_tool_automation/update_build_228/install_log.txt
+Update	228	15/01/25 03:08:54	scanpy_filter	False	Installed	iuc	5b3c1679d29b	5b3c1679d29b		14/14		Single-cell	toolshed.g2.bx.psu.edu	/var/lib/jenkins/galaxy_tool_automation/update_build_228/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:
-  - 3f3e247c053d
   - 78c75f134c16
-  - 4efdca267d51
   - c2ef298da409
+  - 4efdca267d51
+  - 3f3e247c053d
   - 6e9aea89e388
   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
@@ -26,66 +26,66 @@ 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
   owner: iuc
   revisions:
-  - 1b52f0c8ad7f
   - d6c074a93c51
+  - 1b52f0c8ad7f
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: annotatemyids
   owner: iuc
   revisions:
-  - cd2480f35935
-  - 1aae04680c4b
-  - 44018dd6b447
   - fe3ca740a485
-  - 3e1f6f6d557e
-  - 133f36c29579
   - a79ee60b6926
-  - 4f2967b27e67
-  - b5d8e5475247
+  - 44018dd6b447
   - f29602ae449e
+  - 133f36c29579
+  - b5d8e5475247
+  - 1aae04680c4b
+  - 3e1f6f6d557e
+  - 4f2967b27e67
+  - cd2480f35935
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: antismash
   owner: bgruening
   revisions:
-  - bc88856eddab
   - e78e25d3b4bd
+  - bc88856eddab
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: augustus_training
   owner: bgruening
   revisions:
-  - dc027fa56d55
-  - f1e653756174
-  - 6519ebe25019
   - 7be22100e5e1
   - aada0deea587
+  - f1e653756174
+  - dc027fa56d55
+  - 6519ebe25019
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: augustus
   owner: bgruening
   revisions:
+  - 28433faa6e42
   - 09855551d713
-  - 0fc0f9cf035a
   - bd0e53f3a891
+  - 0fc0f9cf035a
   - ca6d970d931c
-  - 28433faa6e42
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: bakta
   owner: iuc
   revisions:
+  - 728dacaf08a9
   - 92eee5f31117
-  - d77802fe76f7
   - da5f1924bb2e
-  - 728dacaf08a9
+  - d77802fe76f7
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: barrnap
@@ -105,8 +105,8 @@ tools:
 - name: chipseeker
   owner: rnateam
   revisions:
-  - 1b9a9409831d
   - 8bd92f2404dd
+  - 1b9a9409831d
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: compleasm
@@ -119,16 +119,16 @@ tools:
   owner: bgruening
   revisions:
   - 8e9e228c54c4
-  - 1ac12c0cc7a0
   - 7ccc6234b54e
+  - 1ac12c0cc7a0
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: eggnog_mapper
   owner: galaxyp
   revisions:
   - 63662ae295d6
-  - 9d1fbff733cf
   - d9c3016f7283
+  - 9d1fbff733cf
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: exonerate
@@ -158,60 +158,60 @@ tools:
 - name: funannotate_annotate
   owner: iuc
   revisions:
-  - 14f588312c56
+  - 9c15ca7e764e
   - 3bbe70fef6df
   - 756376aeb1ae
-  - b6b5cd37f2a2
+  - 14f588312c56
   - 582fd74dc2a1
-  - 9c15ca7e764e
   - 9f2455341fac
+  - b6b5cd37f2a2
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: funannotate_clean
   owner: iuc
   revisions:
-  - 0ffe5be70caf
-  - 989f7c061f35
-  - 1691af4a0d17
   - 8e1ace8f77c6
   - 73428a792541
   - 30fb23d4c31c
+  - 1691af4a0d17
+  - 989f7c061f35
+  - 0ffe5be70caf
   - a230ea445788
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: funannotate_compare
   owner: iuc
   revisions:
-  - 563a19373357
-  - 30f08d74024f
   - 0418d28136de
+  - 57c6718cbfcc
   - 5a5ae61da69c
   - 494f0bb4a993
-  - 57c6718cbfcc
+  - 30f08d74024f
+  - 563a19373357
   - e94187d661df
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: funannotate_predict
   owner: iuc
   revisions:
-  - 2bba2ff070d9
   - 4b96ced19f75
+  - f31125bb85ea
+  - 2bba2ff070d9
   - f77d7b685bb3
-  - 1bc5a03faf2e
   - d6c7106b7b2e
-  - f31125bb85ea
   - 7abc5f6dd595
+  - 1bc5a03faf2e
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: funannotate_sort
   owner: iuc
   revisions:
-  - fed64e676186
   - d3af38b9c7e1
-  - d77fdcca400e
   - b3cf4684e9c7
-  - 52af33194019
+  - fed64e676186
+  - d77fdcca400e
   - 54961e026fe4
+  - 52af33194019
   - 520e30695ec3
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
@@ -224,9 +224,9 @@ tools:
 - name: gff_to_prot
   owner: iuc
   revisions:
+  - 07d7991bf205
   - 2aea122fbd25
   - 79261884facd
-  - 07d7991bf205
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: goenrichment
@@ -239,9 +239,9 @@ tools:
   owner: iuc
   revisions:
   - ef2ad746b589
-  - 8b3e3657034e
-  - 602de62d995b
   - 43798b4caee0
+  - 602de62d995b
+  - 8b3e3657034e
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: goslimmer
@@ -272,9 +272,9 @@ tools:
 - name: interproscan
   owner: bgruening
   revisions:
-  - 98cafcbd2578
   - 74810db257cc
   - c55643c3d813
+  - 98cafcbd2578
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: jcvi_gff_stats
@@ -292,26 +292,26 @@ 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:
-  - 370c210d9541
   - d46d803ca6cc
   - 3c1a01127868
+  - 370c210d9541
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: mitos2
   owner: iuc
   revisions:
-  - 033755194fe9
   - b815ec682418
-  - c8ac28e8ac44
   - 624606f7c996
+  - c8ac28e8ac44
   - e95d52d295d7
+  - 033755194fe9
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: mob_suite
@@ -353,11 +353,11 @@ tools:
 - name: prokka
   owner: crs4
   revisions:
-  - eaee459f3d69
-  - a17498c603ec
   - bf68eb663bc3
-  - 8a22554cdde2
+  - a17498c603ec
+  - eaee459f3d69
   - d643e3b03500
+  - 8a22554cdde2
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: red
@@ -401,22 +401,22 @@ tools:
 - name: snpeff
   owner: iuc
   revisions:
-  - cfcf33df7fc0
+  - 8f92c2b26e6d
   - 5b80f544c67f
-  - 68693743661e
-  - 5a29ab10dba6
+  - c7275bd8b4d6
   - 5c7b70713fb5
-  - 6322be79bd8e
   - 268d162b9c49
-  - 8f92c2b26e6d
-  - c7275bd8b4d6
+  - 68693743661e
+  - cfcf33df7fc0
+  - 6322be79bd8e
+  - 5a29ab10dba6
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: snpsift
   owner: iuc
   revisions:
-  - 5fab4f81391d
   - 09d6806c609e
+  - 5fab4f81391d
   - 2b3e65a4252f
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
@@ -442,18 +442,18 @@ tools:
 - name: tbprofiler
   owner: iuc
   revisions:
-  - d03af1c7002c
-  - 4839e590cb26
-  - 200c378d85f3
-  - 51dd22484644
+  - e1a9d6fd258d
   - 37213cf56392
+  - 4839e590cb26
+  - 037a11682176
   - 8cb134b8c1a5
-  - ba6f87115e13
   - 809dfc93d593
-  - ac8250086ac3
-  - e1a9d6fd258d
-  - 037a11682176
   - 45083d070fb8
+  - ba6f87115e13
+  - 51dd22484644
+  - 200c378d85f3
+  - d03af1c7002c
+  - ac8250086ac3
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: transit_gumbel