Jenkins install build 1367.

usegalaxy-au · Dec 12, 2023 · 8d28417 · 8d28417
1 parent ccc248e
commit 8d28417
Show file tree

Hide file tree

Showing 96 changed files with 2,206 additions and 2,210 deletions.
diff --git a/automated_tool_installation_log.tsv b/automated_tool_installation_log.tsv
@@ -6080,3 +6080,4 @@ Update	175	06/12/23 17:11:16	scanpy_cluster_reduce_dimension	False	Installed	iuc
 Update	175	06/12/23 17:21:30	scanpy_filter	False	Tests failed	iuc	a03ff8633507	a03ff8633507	Staging Testing	7/8		Single-cell	toolshed.g2.bx.psu.edu	/var/lib/jenkins/galaxy_tool_automation/update_build_175/install_log.txt
 Update	175	06/12/23 17:26:45	scanpy_normalize	False	Tests failed	iuc	94c19fb1281c	94c19fb1281c	Staging Testing	2/4		Single-cell	toolshed.g2.bx.psu.edu	/var/lib/jenkins/galaxy_tool_automation/update_build_175/install_log.txt
 Install	1364	07/12/23 11:03:21	autodock_vina_prepare_ligand	True	Installed	bgruening	50871000e977	50871000e977		1/1	1/1	ChemicalToolBox	toolshed.g2.bx.psu.edu	/var/lib/jenkins/galaxy_tool_automation/install_build_1364/install_log.txt
+Install	1367	12/12/23 14:41:38	braker3	True	Installed	genouest	5460380cc057	latest				Annotation	toolshed.g2.bx.psu.edu	/var/lib/jenkins/galaxy_tool_automation/install_build_1367/install_log.txt
diff --git a/requests/new_braker.yml b/requests/new_braker.yml
diff --git a/staging.gvl.org.au/annotation.yml b/staging.gvl.org.au/annotation.yml
@@ -2,10 +2,10 @@ tools:
 - name: abricate
   owner: iuc
   revisions:
-  - 6e9aea89e388
-  - c2ef298da409
-  - 78c75f134c16
   - 3f3e247c053d
+  - 78c75f134c16
+  - c2ef298da409
+  - 6e9aea89e388
   - 4efdca267d51
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
@@ -36,38 +36,38 @@ tools:
 - name: annotatemyids
   owner: iuc
   revisions:
-  - 4f2967b27e67
-  - b5d8e5475247
-  - cd2480f35935
-  - fe3ca740a485
   - f29602ae449e
-  - 1aae04680c4b
   - 44018dd6b447
+  - fe3ca740a485
+  - cd2480f35935
+  - b5d8e5475247
   - 133f36c29579
   - 3e1f6f6d557e
+  - 4f2967b27e67
+  - 1aae04680c4b
   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
   - 6519ebe25019
   - 7be22100e5e1
-  - dc027fa56d55
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: augustus
   owner: bgruening
   revisions:
+  - 09855551d713
   - ca6d970d931c
   - 28433faa6e42
-  - 09855551d713
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: bakta
@@ -79,9 +79,15 @@ tools:
 - name: barrnap
   owner: iuc
   revisions:
-  - 8fd427007e93
   - fe48aa4ccd5e
   - 7355bbf5e05f
+  - 8fd427007e93
+  tool_panel_section_label: Annotation
+  tool_shed_url: toolshed.g2.bx.psu.edu
+- name: braker3
+  owner: genouest
+  revisions:
+  - 5460380cc057
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: chipseeker
@@ -100,8 +106,8 @@ tools:
   owner: galaxyp
   revisions:
   - d9c3016f7283
-  - 63662ae295d6
   - 9d1fbff733cf
+  - 63662ae295d6
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: exonerate
@@ -119,36 +125,36 @@ tools:
 - name: funannotate_annotate
   owner: iuc
   revisions:
-  - 9f2455341fac
   - b6b5cd37f2a2
-  - 14f588312c56
   - 582fd74dc2a1
+  - 14f588312c56
+  - 9f2455341fac
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: funannotate_clean
   owner: iuc
   revisions:
-  - 30fb23d4c31c
-  - 0ffe5be70caf
   - 989f7c061f35
+  - 0ffe5be70caf
+  - 30fb23d4c31c
   - a230ea445788
   - 73428a792541
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: funannotate_compare
   owner: iuc
   revisions:
-  - 30f08d74024f
-  - 5a5ae61da69c
   - 494f0bb4a993
   - 563a19373357
+  - 30f08d74024f
+  - 5a5ae61da69c
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: funannotate_predict
   owner: iuc
   revisions:
-  - f31125bb85ea
   - 2bba2ff070d9
+  - f31125bb85ea
   - d6c7106b7b2e
   - 7abc5f6dd595
   - 1bc5a03faf2e
@@ -157,11 +163,11 @@ tools:
 - name: funannotate_sort
   owner: iuc
   revisions:
-  - 52af33194019
-  - d3af38b9c7e1
   - 520e30695ec3
-  - b3cf4684e9c7
   - 54961e026fe4
+  - b3cf4684e9c7
+  - 52af33194019
+  - d3af38b9c7e1
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: get_orfs_or_cdss
@@ -188,8 +194,8 @@ tools:
   owner: iuc
   revisions:
   - 43798b4caee0
-  - ef2ad746b589
   - 602de62d995b
+  - ef2ad746b589
   - 8b3e3657034e
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
@@ -208,16 +214,16 @@ tools:
 - name: infernal
   owner: bgruening
   revisions:
-  - c9e29ac5d099
   - 477d829d3250
+  - c9e29ac5d099
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: interproscan
   owner: bgruening
   revisions:
   - 74810db257cc
-  - c55643c3d813
   - 98cafcbd2578
+  - c55643c3d813
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: jcvi_gff_stats
@@ -235,16 +241,16 @@ tools:
 - name: maker_map_ids
   owner: iuc
   revisions:
-  - e906fa778440
   - 326f9c294b09
+  - e906fa778440
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: maker
   owner: iuc
   revisions:
   - 3c1a01127868
-  - d46d803ca6cc
   - 370c210d9541
+  - d46d803ca6cc
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: mitos2
@@ -275,11 +281,11 @@ tools:
 - name: prokka
   owner: crs4
   revisions:
-  - d643e3b03500
-  - eaee459f3d69
   - bf68eb663bc3
-  - 8a22554cdde2
+  - eaee459f3d69
   - a17498c603ec
+  - d643e3b03500
+  - 8a22554cdde2
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: red
@@ -291,15 +297,15 @@ tools:
 - name: repeat_masker
   owner: bgruening
   revisions:
-  - ba6d2c32f797
   - 3f987772e283
+  - ba6d2c32f797
   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: snap_training
@@ -311,22 +317,22 @@ tools:
 - name: snpeff
   owner: iuc
   revisions:
-  - 5c7b70713fb5
-  - 268d162b9c49
-  - cfcf33df7fc0
   - 5a29ab10dba6
+  - 9473cd297a76
   - 68693743661e
+  - 5c7b70713fb5
+  - cfcf33df7fc0
   - 8f92c2b26e6d
-  - 9473cd297a76
+  - 268d162b9c49
   - 5b80f544c67f
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: snpsift
   owner: iuc
   revisions:
   - 2b3e65a4252f
-  - 5fab4f81391d
   - 09d6806c609e
+  - 5fab4f81391d
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: snptools
@@ -338,8 +344,8 @@ tools:
 - name: sortmerna
   owner: rnateam
   revisions:
-  - 10b84b577117
   - eb35257d2e29
+  - 10b84b577117
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: tbl2gff3
@@ -351,15 +357,15 @@ tools:
 - name: tbprofiler
   owner: iuc
   revisions:
-  - ba6f87115e13
-  - 45083d070fb8
   - 37213cf56392
-  - 2c68b0c38785
-  - 200c378d85f3
-  - ac8250086ac3
+  - ba6f87115e13
+  - 809dfc93d593
   - e1a9d6fd258d
   - 037a11682176
-  - 809dfc93d593
+  - 200c378d85f3
+  - 45083d070fb8
+  - ac8250086ac3
+  - 2c68b0c38785
   tool_panel_section_label: Annotation
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: transit_gumbel