Merge pull request galaxyproject#6497 from SaimMomin12/busco_update

Updating BUSCO to 5.8.0
SaimMomin12 · Oct 29, 2024 · 8565e82 · 8565e82
2 parents 90275e5 + d63591a
commit 8565e82
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Showing 17 changed files with 115 additions and 114 deletions.
diff --git a/tools/busco/busco.xml b/tools/busco/busco.xml
diff --git a/tools/busco/macros.xml b/tools/busco/macros.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <macros>
-    <token name="@TOOL_VERSION@">5.7.1</token>
+    <token name="@TOOL_VERSION@">5.8.0</token>
     <token name="@VERSION_SUFFIX@">0</token>
 
     <xml name="citations">

diff --git a/tools/busco/test-data/genome_results/full_table b/tools/busco/test-data/genome_results/full_table
@@ -1,4 +1,4 @@
-# BUSCO version is: 5.7.1 
+# BUSCO version is: 5.8.0 
 # The lineage dataset is: arthropoda_odb10 (Creation date: 2024-01-08, number of genomes: 90, number of BUSCOs: 1013)
 # Busco id	Status	Sequence	Gene Start	Gene End	Strand	Score	Length	OrthoDB url	Description
 774at6656	Missing
@@ -509,7 +509,7 @@
 93535at6656	Missing
 93797at6656	Missing
 94054at6656	Missing
-94238at6656	Complete	sample	38486	34764	-	60.7	116	https://v10-1.orthodb.org/?query=94238at6656	Checkpoint protein HUS1
+94238at6656	Complete	sample	38486	34764	-	60.7	117	https://v10-1.orthodb.org/?query=94238at6656	Checkpoint protein HUS1
 94263at6656	Missing
 94304at6656	Missing
 94473at6656	Missing

diff --git a/tools/busco/test-data/genome_results/missing_buscos_list b/tools/busco/test-data/genome_results/missing_buscos_list
@@ -1,4 +1,4 @@
-# BUSCO version is: 5.7.1 
+# BUSCO version is: 5.8.0 
 # The lineage dataset is: arthropoda_odb10 (Creation date: 2024-01-08, number of genomes: 90, number of BUSCOs: 1013)
 # Busco id
 100070at6656

diff --git a/tools/busco/test-data/genome_results/short_summary b/tools/busco/test-data/genome_results/short_summary
@@ -1,6 +1,6 @@
-# BUSCO version is: 5.7.1 
+# BUSCO version is: 5.8.0 
 # The lineage dataset is: arthropoda_odb10 (Creation date: 2024-01-08, number of genomes: 90, number of BUSCOs: 1013)
-# Summarized benchmarking in BUSCO notation for file /tmp/tmpl5l1blpe/files/7/a/3/dataset_7a33f452-1064-4b4a-943f-b0efef6a4a4a.dat
+# Summarized benchmarking in BUSCO notation for file /tmp/tmpmwpuw5w8/files/f/d/6/dataset_fd6995c7-d1df-43b9-b8be-7e62043550f0.dat
 # BUSCO was run in mode: euk_genome_aug
 # Gene predictor used: augustus
 
@@ -24,13 +24,13 @@ Assembly Statistics:
 
 
 Dependencies and versions:
-	hmmsearch: 3.1
-	bbtools: 39.06
-	makeblastdb: 2.15.0+
-	tblastn: 2.15.0+
+	hmmsearch: 3.4
+	bbtools: None
+	makeblastdb: 2.16.0+
+	tblastn: 2.16.0+
 	augustus: 3.5.0
 	gff2gbSmallDNA.pl: None
 	new_species.pl: None
 	etraining: None
-	python: sys.version_info(major=3, minor=9, micro=19, releaselevel='final', serial=0)
-	busco: 5.7.1
+	python: sys.version_info(major=3, minor=10, micro=14, releaselevel='final', serial=0)
+	busco: 5.8.0
diff --git a/tools/busco/test-data/genome_results_metaeuk/full_table b/tools/busco/test-data/genome_results_metaeuk/full_table
@@ -1,4 +1,4 @@
-# BUSCO version is: 5.7.1 
+# BUSCO version is: 5.8.0 
 # The lineage dataset is: arthropoda_odb10 (Creation date: 2024-01-08, number of genomes: 90, number of BUSCOs: 1013)
 # Busco id	Status	Sequence	Gene Start	Gene End	Strand	Score	Length	OrthoDB url	Description
 774at6656	Missing
@@ -340,7 +340,7 @@
 68939at6656	Missing
 68961at6656	Missing
 68981at6656	Missing
-68987at6656	Complete	sample	40255	42070	+	122.8	266	https://v10-1.orthodb.org/?query=68987at6656	Nucleotidyl transferase domain
+68987at6656	Complete	sample	40255	42070	+	122.8	267	https://v10-1.orthodb.org/?query=68987at6656	Nucleotidyl transferase domain
 69201at6656	Missing
 69238at6656	Missing
 69284at6656	Missing
@@ -509,7 +509,7 @@
 93535at6656	Missing
 93797at6656	Missing
 94054at6656	Missing
-94238at6656	Complete	sample	35693	34845	-	60.6	116	https://v10-1.orthodb.org/?query=94238at6656	Checkpoint protein HUS1
+94238at6656	Complete	sample	35693	34845	-	60.6	117	https://v10-1.orthodb.org/?query=94238at6656	Checkpoint protein HUS1
 94263at6656	Missing
 94304at6656	Missing
 94473at6656	Missing

diff --git a/tools/busco/test-data/genome_results_metaeuk/missing_buscos_list b/tools/busco/test-data/genome_results_metaeuk/missing_buscos_list
@@ -1,4 +1,4 @@
-# BUSCO version is: 5.7.1 
+# BUSCO version is: 5.8.0 
 # The lineage dataset is: arthropoda_odb10 (Creation date: 2024-01-08, number of genomes: 90, number of BUSCOs: 1013)
 # Busco id
 100070at6656

diff --git a/tools/busco/test-data/genome_results_metaeuk/summary.png b/tools/busco/test-data/genome_results_metaeuk/summary.png
diff --git a/tools/busco/test-data/genome_results_metaeuk_auto/summary.png b/tools/busco/test-data/genome_results_metaeuk_auto/summary.png
diff --git a/tools/busco/test-data/genome_results_miniprot/full_table b/tools/busco/test-data/genome_results_miniprot/full_table
@@ -1,4 +1,4 @@
-# BUSCO version is: 5.7.1 
+# BUSCO version is: 5.8.0 
 # The lineage dataset is: arthropoda_odb10 (Creation date: 2024-01-08, number of genomes: 90, number of BUSCOs: 1013)
 # Busco id	Status	Sequence	Gene Start	Gene End	Strand	Score	Length	OrthoDB url	Description
 774at6656	Missing
@@ -509,7 +509,7 @@
 93535at6656	Missing
 93797at6656	Missing
 94054at6656	Missing
-94238at6656	Complete	sample	35679	34845	-	60.7	116	https://v10-1.orthodb.org/?query=94238at6656	Checkpoint protein HUS1
+94238at6656	Complete	sample	35679	34845	-	60.7	117	https://v10-1.orthodb.org/?query=94238at6656	Checkpoint protein HUS1
 94263at6656	Missing
 94304at6656	Missing
 94473at6656	Missing

diff --git a/tools/busco/test-data/genome_results_miniprot/out.gff b/tools/busco/test-data/genome_results_miniprot/out.gff
@@ -0,0 +1,4 @@
+##gff-version 3
+sample	miniprot	mRNA	34843	35679	1341	-	.	ID=MP000459;Rank=1;Identity=0.9640;Positive=0.9856;Target=94238at6656_7220_0:000926 1 278
+sample	miniprot	CDS	34843	35679	1341	-	0	Parent=MP000459;Rank=1;Identity=0.9640;Target=94238at6656_7220_0:000926 1 278
+sample	miniprot	stop_codon	34843	34845	0	-	0	Parent=MP000459;Rank=1
diff --git a/tools/busco/test-data/proteome_results/full_table b/tools/busco/test-data/proteome_results/full_table
@@ -1,4 +1,4 @@
-# BUSCO version is: 5.7.1 
+# BUSCO version is: 5.8.0 
 # The lineage dataset is: arthropoda_odb10 (Creation date: 2024-01-08, number of genomes: 90, number of BUSCOs: 1013)
 # Busco id	Status	Sequence	Score	Length	OrthoDB url	Description
 774at6656	Missing
@@ -86,7 +86,7 @@
 22098at6656	Missing
 22148at6656	Missing
 22358at6656	Missing
-22364at6656	Complete	BUSCOaEOG7B0HST	1355.6	788	https://v10-1.orthodb.org/?query=22364at6656	Importin repeat 4
+22364at6656	Complete	BUSCOaEOG7B0HST	1355.6	789	https://v10-1.orthodb.org/?query=22364at6656	Importin repeat 4
 22468at6656	Missing
 22611at6656	Missing
 22887at6656	Missing

diff --git a/tools/busco/test-data/proteome_results/missing_buscos_list b/tools/busco/test-data/proteome_results/missing_buscos_list
@@ -1,4 +1,4 @@
-# BUSCO version is: 5.7.1 
+# BUSCO version is: 5.8.0 
 # The lineage dataset is: arthropoda_odb10 (Creation date: 2024-01-08, number of genomes: 90, number of BUSCOs: 1013)
 # Busco id
 100070at6656

diff --git a/tools/busco/test-data/proteome_results/summary.png b/tools/busco/test-data/proteome_results/summary.png
diff --git a/tools/busco/test-data/transcriptome_results/full_table b/tools/busco/test-data/transcriptome_results/full_table
@@ -1,4 +1,4 @@
-# BUSCO version is: 5.7.1 
+# BUSCO version is: 5.8.0 
 # The lineage dataset is: arthropoda_odb10 (Creation date: 2024-01-08, number of genomes: 90, number of BUSCOs: 1013)
 # Busco id	Status	Sequence	Score	Length	OrthoDB url	Description
 774at6656	Missing
@@ -86,7 +86,7 @@
 22098at6656	Missing
 22148at6656	Missing
 22358at6656	Missing
-22364at6656	Complete	BUSCOaEOG7B0HST:0-2699	1355.6	788	https://v10-1.orthodb.org/?query=22364at6656	Importin repeat 4
+22364at6656	Complete	BUSCOaEOG7B0HST:0-2699	1355.6	789	https://v10-1.orthodb.org/?query=22364at6656	Importin repeat 4
 22468at6656	Missing
 22611at6656	Missing
 22887at6656	Missing

diff --git a/tools/busco/test-data/transcriptome_results/missing_buscos_list b/tools/busco/test-data/transcriptome_results/missing_buscos_list
@@ -1,4 +1,4 @@
-# BUSCO version is: 5.7.1 
+# BUSCO version is: 5.8.0 
 # The lineage dataset is: arthropoda_odb10 (Creation date: 2024-01-08, number of genomes: 90, number of BUSCOs: 1013)
 # Busco id
 100070at6656

diff --git a/tools/busco/test-data/transcriptome_results/summary.png b/tools/busco/test-data/transcriptome_results/summary.png