Jenkins update build 225.

usegalaxy-au · Dec 25, 2024 · e9f631a · e9f631a
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diff --git a/automated_tool_installation_log.tsv b/automated_tool_installation_log.tsv
@@ -8247,3 +8247,9 @@ Update	224	18/12/24 03:39:45	uniprotxml_downloader	False	Installed	galaxyp	4ddc8
 Update	224	18/12/24 03:40:28	volcanoplot	False	Installed	iuc	99ace6c1ff57	99ace6c1ff57				Graph/Display Data	toolshed.g2.bx.psu.edu	/var/lib/jenkins/galaxy_tool_automation/update_build_224/install_log.txt
 Install	1714	20/12/24 00:07:24	ncbi_fcs_gx	True	Tests failed	iuc	32d058f3462a	32d058f3462a	Staging Testing	1/2		FASTA/FASTQ	toolshed.g2.bx.psu.edu	/var/lib/jenkins/galaxy_tool_automation/install_build_1714/install_log.txt
 Install	1716	20/12/24 03:02:03	ncbi_fcs_gx	True	Installed	iuc	32d058f3462a	32d058f3462a				FASTA/FASTQ	toolshed.g2.bx.psu.edu	/var/lib/jenkins/galaxy_tool_automation/install_build_1716/install_log.txt
+Update	225	25/12/24 01:34:51	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_225/install_log.txt
+Update	225	25/12/24 01:43:30	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_225/install_log.txt
+Update	225	25/12/24 01:49:10	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_225/install_log.txt
+Update	225	25/12/24 02:03:32	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_225/install_log.txt
+Update	225	25/12/24 02:22:18	sistr_cmd	False	Installed	nml	cf767360ede1	cf767360ede1		2/2		Bacterial Typing	toolshed.g2.bx.psu.edu	/var/lib/jenkins/galaxy_tool_automation/update_build_225/install_log.txt
+Update	225	25/12/24 02:38:52	staramr	False	Installed	nml	3548a93b39c1	3548a93b39c1		10/10		Metagenomic Analysis	toolshed.g2.bx.psu.edu	/var/lib/jenkins/galaxy_tool_automation/update_build_225/install_log.txt
diff --git a/staging.gvl.org.au/annotation.yml b/staging.gvl.org.au/annotation.yml
@@ -2,25 +2,25 @@ tools:
 - name: abricate
   owner: iuc
   revisions:
+  - 3f3e247c053d
   - 6e9aea89e388
+  - 78c75f134c16
   - 4efdca267d51
   - c2ef298da409
-  - 78c75f134c16
-  - 3f3e247c053d
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: aegean_canongff3
   owner: iuc
   revisions:
-  - 3f438bf5475d
   - c45c9dd066e2
+  - 3f438bf5475d
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: aegean_gaeval
   owner: iuc
   revisions:
-  - 8dc7512c9dc9
   - 1dd7adc21b6d
+  - 8dc7512c9dc9
   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:
-  - d6c074a93c51
   - 1b52f0c8ad7f
+  - d6c074a93c51
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: annotatemyids
   owner: iuc
   revisions:
-  - a79ee60b6926
-  - 133f36c29579
+  - 44018dd6b447
+  - b5d8e5475247
   - 3e1f6f6d557e
+  - cd2480f35935
   - 1aae04680c4b
+  - fe3ca740a485
   - 4f2967b27e67
+  - a79ee60b6926
+  - 133f36c29579
   - f29602ae449e
-  - 44018dd6b447
-  - fe3ca740a485
-  - b5d8e5475247
-  - cd2480f35935
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: antismash
@@ -63,36 +63,36 @@ tools:
   owner: bgruening
   revisions:
   - 6519ebe25019
-  - f1e653756174
   - aada0deea587
   - dc027fa56d55
   - 7be22100e5e1
+  - f1e653756174
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: augustus
   owner: bgruening
   revisions:
-  - 0fc0f9cf035a
-  - ca6d970d931c
   - 09855551d713
+  - ca6d970d931c
   - bd0e53f3a891
+  - 0fc0f9cf035a
   - 28433faa6e42
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: bakta
   owner: iuc
   revisions:
-  - d77802fe76f7
-  - 728dacaf08a9
   - 92eee5f31117
   - da5f1924bb2e
+  - d77802fe76f7
+  - 728dacaf08a9
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: barrnap
   owner: iuc
   revisions:
-  - 8fd427007e93
   - 7355bbf5e05f
+  - 8fd427007e93
   - fe48aa4ccd5e
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
@@ -118,17 +118,17 @@ tools:
 - name: cpat
   owner: bgruening
   revisions:
-  - 7ccc6234b54e
-  - 8e9e228c54c4
   - 1ac12c0cc7a0
+  - 8e9e228c54c4
+  - 7ccc6234b54e
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: eggnog_mapper
   owner: galaxyp
   revisions:
   - 63662ae295d6
-  - d9c3016f7283
   - 9d1fbff733cf
+  - d9c3016f7283
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: exonerate
@@ -158,61 +158,61 @@ tools:
 - name: funannotate_annotate
   owner: iuc
   revisions:
-  - 3bbe70fef6df
-  - 9f2455341fac
   - 9c15ca7e764e
-  - b6b5cd37f2a2
-  - 582fd74dc2a1
-  - 756376aeb1ae
   - 14f588312c56
+  - 756376aeb1ae
+  - 582fd74dc2a1
+  - 9f2455341fac
+  - b6b5cd37f2a2
+  - 3bbe70fef6df
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: funannotate_clean
   owner: iuc
   revisions:
-  - 73428a792541
-  - 989f7c061f35
-  - a230ea445788
-  - 0ffe5be70caf
   - 8e1ace8f77c6
+  - 0ffe5be70caf
+  - 73428a792541
   - 30fb23d4c31c
   - 1691af4a0d17
+  - a230ea445788
+  - 989f7c061f35
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: funannotate_compare
   owner: iuc
   revisions:
-  - 5a5ae61da69c
   - e94187d661df
   - 57c6718cbfcc
+  - 0418d28136de
   - 494f0bb4a993
-  - 563a19373357
   - 30f08d74024f
-  - 0418d28136de
+  - 5a5ae61da69c
+  - 563a19373357
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: funannotate_predict
   owner: iuc
   revisions:
-  - d6c7106b7b2e
-  - 2bba2ff070d9
-  - 1bc5a03faf2e
-  - 4b96ced19f75
   - f31125bb85ea
+  - 2bba2ff070d9
   - f77d7b685bb3
+  - 4b96ced19f75
+  - 1bc5a03faf2e
+  - d6c7106b7b2e
   - 7abc5f6dd595
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: funannotate_sort
   owner: iuc
   revisions:
-  - b3cf4684e9c7
-  - fed64e676186
   - 54961e026fe4
-  - 52af33194019
   - d77fdcca400e
-  - d3af38b9c7e1
+  - b3cf4684e9c7
+  - 52af33194019
   - 520e30695ec3
+  - fed64e676186
+  - d3af38b9c7e1
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: get_orfs_or_cdss
@@ -238,10 +238,10 @@ tools:
 - name: goseq
   owner: iuc
   revisions:
-  - 602de62d995b
   - ef2ad746b589
   - 8b3e3657034e
   - 43798b4caee0
+  - 602de62d995b
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: goslimmer
@@ -265,8 +265,8 @@ tools:
 - name: infernal
   owner: bgruening
   revisions:
-  - c9e29ac5d099
   - 477d829d3250
+  - c9e29ac5d099
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: interproscan
@@ -299,19 +299,19 @@ tools:
 - name: maker
   owner: iuc
   revisions:
-  - d46d803ca6cc
-  - 3c1a01127868
   - 370c210d9541
+  - 3c1a01127868
+  - d46d803ca6cc
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: mitos2
   owner: iuc
   revisions:
-  - e95d52d295d7
+  - 033755194fe9
   - 624606f7c996
   - c8ac28e8ac44
-  - 033755194fe9
   - b815ec682418
+  - e95d52d295d7
   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:
+  - 8a22554cdde2
   - d643e3b03500
+  - bf68eb663bc3
   - a17498c603ec
-  - 8a22554cdde2
   - eaee459f3d69
-  - bf68eb663bc3
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: red
@@ -376,8 +376,8 @@ tools:
 - name: repeatmodeler
   owner: csbl
   revisions:
-  - 41bfbaf3c959
   - 8661b2607b7e
+  - 41bfbaf3c959
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: sanntis_marine
@@ -401,23 +401,23 @@ tools:
 - name: snpeff
   owner: iuc
   revisions:
-  - 5c7b70713fb5
   - 5a29ab10dba6
-  - 68693743661e
-  - 8f92c2b26e6d
-  - c7275bd8b4d6
+  - 5c7b70713fb5
   - 6322be79bd8e
-  - 268d162b9c49
+  - c7275bd8b4d6
+  - 8f92c2b26e6d
   - 5b80f544c67f
   - cfcf33df7fc0
+  - 68693743661e
+  - 268d162b9c49
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: snpsift
   owner: iuc
   revisions:
-  - 09d6806c609e
-  - 2b3e65a4252f
   - 5fab4f81391d
+  - 2b3e65a4252f
+  - 09d6806c609e
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: snptools
@@ -442,18 +442,18 @@ tools:
 - name: tbprofiler
   owner: iuc
   revisions:
-  - d03af1c7002c
+  - 4839e590cb26
+  - 037a11682176
+  - 8cb134b8c1a5
   - 51dd22484644
+  - 200c378d85f3
+  - 37213cf56392
   - 809dfc93d593
   - e1a9d6fd258d
-  - 45083d070fb8
-  - 4839e590cb26
   - ac8250086ac3
-  - 37213cf56392
-  - 200c378d85f3
-  - 037a11682176
+  - d03af1c7002c
   - ba6f87115e13
-  - 8cb134b8c1a5
+  - 45083d070fb8
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: transit_gumbel