Updating tools/augustus to 3.5.0

tools/augustus/augustus.xml

@@ -246,6 +246,28 @@
                     <option value="Fistulifera_solaris">Fistulifera solaris</option>
                     <option value="Bathycoccus_prasinos">Bathycoccus prasinos</option>
                     <option value="Chloropicon_primus">Chloropicon primus</option>
+                    <option value="Vitis_vinfera">Vitis vinfera</option>
+                    <option value="Berviolum_minutum">Berviolum minutum</option>
+                    <option value="Hydra_vulgaris">Hydra vulgaris</option>
+                    <option value="Skeletonema_costatum">Skeletonema costatum</option>
+                    <option value="Pediculus_humanus">Pediculus humanus</option>
+                    <option value="Pycnopodia_helianthoides">Pycnopodia helianthoides</option>
+                    <option value="Dermasterias_imbricata">Dermasterias imbricata</option>
+                    <option value="Ricinus_communis">Ricinus communis</option>
+                    <option value="Taeniopygia_guttata">Taeniopygia guttata</option>
+                    <option value="Branchiostoma_floridae">Branchiostoma floridae</option>
+                    <option value="Anopheles_gambiae">Anopheles gambiae</option>
+                    <option value="Cryptosporidium_hominis">Cryptosporidium hominis</option>
+                    <option value="Physcomitrium_patens">Physcomitrium patens</option>
+                    <option value="Loa_loa">Loa loa</option>
+                    <option value="Trypanosoma_cruzi">Trypanosoma cruzi</option>
+                    <option value="Naegleria_gruberi">Naegleria gruberi</option>
+                    <option value="Monosiga_brevicollis">Monosiga brevicollis</option>
+                    <option value="Cyclotella_cryptica">Cyclotella cryptica</option>
+                    <option value="Sclerotinia_sclerotiorum">Sclerotinia sclerotiorum</option>
+                    <option value="Paramecium_tetraurelia">Paramecium tetraurelia</option>
+                    <option value="Xenopus_tropicalis">Xenopus tropicalis</option>
+                    <option value="sunflower">sunflower</option>
                 </param>
             </when>
         </conditional>
@@ -473,4 +495,4 @@ Running this tool will produce this:
 ]]>
     </help>
     <expand macro="citations"/>
-</tool>
+</tool>

tools/augustus/augustus_training.xml

@@ -8,7 +8,7 @@
         <xref type="bio.tools">augustus</xref>
     </xrefs>
     <expand macro="requirements">
-        <requirement type="package" version="2.31.10">maker</requirement>
+        <requirement type="package" version="3.01.03">maker</requirement>
     </expand>
     <command><![CDATA[
         cp -r `command -v augustus | xargs dirname`/../config/ augustus_dir/ &&

tools/augustus/macros.xml

@@ -7,8 +7,8 @@
         </requirements>
     </xml>
 
-    <token name="@TOOL_VERSION@">3.4.0</token>
-    <token name="@VERSION_SUFFIX@">2</token>
+    <token name="@TOOL_VERSION@">3.5.0</token>
+    <token name="@VERSION_SUFFIX@">0</token>
     <token name="@PROFILE@">23.1</token>
 
 

tools/augustus/test-data/augustus.hints.output.gtf

@@ -1,17 +1,17 @@
-# This output was generated with AUGUSTUS (version 3.4.0).
+# This output was generated with AUGUSTUS (version 3.5.0).
 # AUGUSTUS is a gene prediction tool written by M. Stanke ([email protected]),
-# O. Keller, S. König, L. Gerischer, L. Romoth and Katharina Hoff.
+# O. Keller, S. König, L. Gerischer, L. Romoth, Katharina Hoff, Henry Mehlan and Daniel Honsel.
 # Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008),
 # Using native and syntenically mapped cDNA alignments to improve de novo gene finding
 # Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013
 # Sources of extrinsic information: M RM E W 
 # Setting CDSpart local malus: 0.985
 # Setting UTRpart local malus: 0.973
-# reading in the file /tmp/tmpb49zmbej/files/6/4/3/dataset_64360fd3-ce82-407d-a499-79ac51decbd9.dat ...
+# reading in the file /tmp/tmppoq4flrj/files/9/3/2/dataset_9324eb55-2768-47e7-810a-f6b680ce991c.dat ...
 # Have extrinsic information about 1 sequences (in the specified range). 
 # Initializing the parameters using config directory /usr/local/config/ ...
 # fly version. Using default transition matrix.
-# Looks like /tmp/tmpb49zmbej/files/0/c/6/dataset_0c6b001d-370e-42cf-be92-b3435bd212c5.dat is in fasta format.
+# Looks like /tmp/tmppoq4flrj/files/1/5/a/dataset_15a2d256-bf11-48b4-b436-22f4c66d8c5a.dat is in fasta format.
 # We have hints for 1 sequence and for 1 of the sequences in the input set.
 #
 # ----- prediction on sequence number 1 (length = 9950, name = chr2R) -----
@@ -59,4 +59,4 @@ chr2R	AUGUSTUS	start_codon	9301	9303	.	-	0	transcript_id "chr2R.g1.t1"; gene_id
 # end gene chr2R.g1
 ###
 # command line:
-# augustus --strand=both --noInFrameStop=false --gff3=off --uniqueGeneId=true --protein=off --codingseq=off --introns=off --stop=off --stop=off --cds=off --singlestrand=false /tmp/tmpb49zmbej/files/0/c/6/dataset_0c6b001d-370e-42cf-be92-b3435bd212c5.dat --UTR=off --genemodel=complete --softmasking=0 --hintsfile=/tmp/tmpb49zmbej/files/6/4/3/dataset_64360fd3-ce82-407d-a499-79ac51decbd9.dat --extrinsicCfgFile=/tmp/tmpb49zmbej/files/8/6/b/dataset_86b0a149-1d37-4615-9915-2c48586e3ca1.dat --species=fly
+# augustus --strand=both --noInFrameStop=false --gff3=off --uniqueGeneId=true --protein=off --codingseq=off --introns=off --stop=off --stop=off --cds=off --singlestrand=false /tmp/tmppoq4flrj/files/1/5/a/dataset_15a2d256-bf11-48b4-b436-22f4c66d8c5a.dat --UTR=off --genemodel=complete --softmasking=0 --hintsfile=/tmp/tmppoq4flrj/files/9/3/2/dataset_9324eb55-2768-47e7-810a-f6b680ce991c.dat --extrinsicCfgFile=/tmp/tmppoq4flrj/files/1/f/a/dataset_1fa5c464-019f-4a97-8759-0b44332f4963.dat --species=fly

tools/augustus/test-data/augustus.hints_and_range.output.gtf

@@ -1,17 +1,17 @@
-# This output was generated with AUGUSTUS (version 3.4.0).
+# This output was generated with AUGUSTUS (version 3.5.0).
 # AUGUSTUS is a gene prediction tool written by M. Stanke ([email protected]),
-# O. Keller, S. König, L. Gerischer, L. Romoth and Katharina Hoff.
+# O. Keller, S. König, L. Gerischer, L. Romoth, Katharina Hoff, Henry Mehlan and Daniel Honsel.
 # Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008),
 # Using native and syntenically mapped cDNA alignments to improve de novo gene finding
 # Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013
 # Sources of extrinsic information: M RM E W 
 # Setting CDSpart local malus: 0.985
 # Setting UTRpart local malus: 0.973
-# reading in the file /tmp/tmpb49zmbej/files/f/a/8/dataset_fa8684ad-0602-4c00-9999-b998db931a6e.dat ...
+# reading in the file /tmp/tmppoq4flrj/files/9/c/0/dataset_9c0c03c0-7d1a-4b5f-86dd-0ce3d861e601.dat ...
 # Have extrinsic information about 1 sequences (in the specified range). 
 # Initializing the parameters using config directory /usr/local/config/ ...
 # fly version. Using default transition matrix.
-# Looks like /tmp/tmpb49zmbej/files/4/c/8/dataset_4c80a809-791b-4afe-a497-698a7460ac31.dat is in fasta format.
+# Looks like /tmp/tmppoq4flrj/files/5/2/c/dataset_52ca6132-4c8f-4bb1-8edc-a985c1310790.dat is in fasta format.
 # We have hints for 1 sequence and for 1 of the sequences in the input set.
 #
 # ----- prediction on sequence number 1 (length = 2001, name = chr2R) -----
@@ -53,4 +53,4 @@ chr2R	AUGUSTUS	start_codon	8929	8931	.	-	0	transcript_id "chr2R.g1.t1"; gene_id
 # end gene chr2R.g1
 ###
 # command line:
-# augustus --strand=both --noInFrameStop=false --gff3=off --uniqueGeneId=true --protein=off --codingseq=off --introns=off --stop=off --stop=off --cds=off --singlestrand=false /tmp/tmpb49zmbej/files/4/c/8/dataset_4c80a809-791b-4afe-a497-698a7460ac31.dat --UTR=off --genemodel=complete --softmasking=0 --hintsfile=/tmp/tmpb49zmbej/files/f/a/8/dataset_fa8684ad-0602-4c00-9999-b998db931a6e.dat --extrinsicCfgFile=/tmp/tmpb49zmbej/files/3/3/5/dataset_335e9fec-9340-42e6-97ce-af35d5220fcc.dat --predictionStart=7000 --predictionEnd=9000 --species=fly
+# augustus --strand=both --noInFrameStop=false --gff3=off --uniqueGeneId=true --protein=off --codingseq=off --introns=off --stop=off --stop=off --cds=off --singlestrand=false /tmp/tmppoq4flrj/files/5/2/c/dataset_52ca6132-4c8f-4bb1-8edc-a985c1310790.dat --UTR=off --genemodel=complete --softmasking=0 --hintsfile=/tmp/tmppoq4flrj/files/9/c/0/dataset_9c0c03c0-7d1a-4b5f-86dd-0ce3d861e601.dat --extrinsicCfgFile=/tmp/tmppoq4flrj/files/f/6/0/dataset_f6046d74-eb33-4cb6-9062-0955336c2672.dat --predictionStart=7000 --predictionEnd=9000 --species=fly

tools/augustus/test-data/human_augustus_protein_codingseq_introns_cds_main.gtf

@@ -1,13 +1,13 @@
-# This output was generated with AUGUSTUS (version 3.4.0).
+# This output was generated with AUGUSTUS (version 3.5.0).
 # AUGUSTUS is a gene prediction tool written by M. Stanke ([email protected]),
-# O. Keller, S. König, L. Gerischer, L. Romoth and Katharina Hoff.
+# O. Keller, S. König, L. Gerischer, L. Romoth, Katharina Hoff, Henry Mehlan and Daniel Honsel.
 # Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008),
 # Using native and syntenically mapped cDNA alignments to improve de novo gene finding
 # Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013
 # No extrinsic information on sequences given.
 # Initializing the parameters using config directory /usr/local/config/ ...
 # human version. Using default transition matrix.
-# Looks like /tmp/tmpb49zmbej/files/c/d/6/dataset_cd6650af-fd36-4176-b9f1-e38bb118655f.dat is in fasta format.
+# Looks like /tmp/tmppoq4flrj/files/b/9/e/dataset_b9eb8c49-e040-4f55-b476-56080cc0c7ac.dat is in fasta format.
 # We have hints for 0 sequences and for 0 of the sequences in the input set.
 #
 # ----- prediction on sequence number 1 (length = 9453, name = HS04636) -----
@@ -98,4 +98,4 @@ HS08198	AUGUSTUS	stop_codon	1846	1848	.	+	0	transcript_id "HS08198.g2.t1"; gene_
 # end gene HS08198.g2
 ###
 # command line:
-# augustus --strand=both --noInFrameStop=false --gff3=off --uniqueGeneId=true --protein=on --codingseq=on --introns=on --start=on --stop=on --cds=on --singlestrand=false /tmp/tmpb49zmbej/files/c/d/6/dataset_cd6650af-fd36-4176-b9f1-e38bb118655f.dat --UTR=off --genemodel=complete --softmasking=0 --species=human
+# augustus --strand=both --noInFrameStop=false --gff3=off --uniqueGeneId=true --protein=on --codingseq=on --introns=on --start=on --stop=on --cds=on --singlestrand=false /tmp/tmppoq4flrj/files/b/9/e/dataset_b9eb8c49-e040-4f55-b476-56080cc0c7ac.dat --UTR=off --genemodel=complete --softmasking=0 --species=human

tools/augustus/test-data/human_augustus_utr-on.gff

@@ -1,14 +1,14 @@
 ##gff-version 3
-# This output was generated with AUGUSTUS (version 3.4.0).
+# This output was generated with AUGUSTUS (version 3.5.0).
 # AUGUSTUS is a gene prediction tool written by M. Stanke ([email protected]),
-# O. Keller, S. König, L. Gerischer, L. Romoth and Katharina Hoff.
+# O. Keller, S. König, L. Gerischer, L. Romoth, Katharina Hoff, Henry Mehlan and Daniel Honsel.
 # Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008),
 # Using native and syntenically mapped cDNA alignments to improve de novo gene finding
 # Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013
 # No extrinsic information on sequences given.
 # Initializing the parameters using config directory /usr/local/config/ ...
 # human version. Using default transition matrix.
-# Looks like /tmp/tmpb49zmbej/files/e/0/1/dataset_e0109fd4-ac59-4275-90d3-25691349bc0c.dat is in fasta format.
+# Looks like /tmp/tmppoq4flrj/files/3/4/a/dataset_34aeff85-4867-4ac0-a3b5-57c9af2f6d41.dat is in fasta format.
 # We have hints for 0 sequences and for 0 of the sequences in the input set.
 #
 # ----- prediction on sequence number 1 (length = 9453, name = HS04636) -----
@@ -103,4 +103,4 @@ HS08198	AUGUSTUS	transcription_end_site	2105	2105	.	+	.	Parent=HS08198.g2.t1
 # end gene HS08198.g2
 ###
 # command line:
-# augustus --strand=both --noInFrameStop=false --gff3=on --uniqueGeneId=true --protein=on --codingseq=on --introns=off --stop=off --stop=off --cds=on --singlestrand=false /tmp/tmpb49zmbej/files/e/0/1/dataset_e0109fd4-ac59-4275-90d3-25691349bc0c.dat --UTR=on --genemodel=complete --softmasking=0 --species=human
+# augustus --strand=both --noInFrameStop=false --gff3=on --uniqueGeneId=true --protein=on --codingseq=on --introns=off --stop=off --stop=off --cds=on --singlestrand=false /tmp/tmppoq4flrj/files/3/4/a/dataset_34aeff85-4867-4ac0-a3b5-57c9af2f6d41.dat --UTR=on --genemodel=complete --softmasking=0 --species=human

tools/augustus/test-data/human_augustus_utr-on.gtf

@@ -1,13 +1,13 @@
-# This output was generated with AUGUSTUS (version 3.4.0).
+# This output was generated with AUGUSTUS (version 3.5.0).
 # AUGUSTUS is a gene prediction tool written by M. Stanke ([email protected]),
-# O. Keller, S. König, L. Gerischer, L. Romoth and Katharina Hoff.
+# O. Keller, S. König, L. Gerischer, L. Romoth, Katharina Hoff, Henry Mehlan and Daniel Honsel.
 # Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008),
 # Using native and syntenically mapped cDNA alignments to improve de novo gene finding
 # Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013
 # No extrinsic information on sequences given.
 # Initializing the parameters using config directory /usr/local/config/ ...
 # human version. Using default transition matrix.
-# Looks like /tmp/tmpb49zmbej/files/6/0/5/dataset_605b6f62-4302-4e11-b378-848be921c4e4.dat is in fasta format.
+# Looks like /tmp/tmppoq4flrj/files/9/2/f/dataset_92f269da-33a0-4419-9ebb-402fb31a679e.dat is in fasta format.
 # We have hints for 0 sequences and for 0 of the sequences in the input set.
 #
 # ----- prediction on sequence number 1 (length = 9453, name = HS04636) -----
@@ -102,4 +102,4 @@ HS08198	AUGUSTUS	tts	2105	2105	.	+	.	transcript_id "HS08198.g2.t1"; gene_id "HS0
 # end gene HS08198.g2
 ###
 # command line:
-# augustus --strand=both --noInFrameStop=false --gff3=off --uniqueGeneId=true --protein=on --codingseq=on --introns=off --stop=off --stop=off --cds=on --singlestrand=false /tmp/tmpb49zmbej/files/6/0/5/dataset_605b6f62-4302-4e11-b378-848be921c4e4.dat --UTR=on --genemodel=complete --softmasking=0 --species=human
+# augustus --strand=both --noInFrameStop=false --gff3=off --uniqueGeneId=true --protein=on --codingseq=on --introns=off --stop=off --stop=off --cds=on --singlestrand=false /tmp/tmppoq4flrj/files/9/2/f/dataset_92f269da-33a0-4419-9ebb-402fb31a679e.dat --UTR=on --genemodel=complete --softmasking=0 --species=human

tools/augustus/test-data/human_augustus_utr-on_softmasking.gtf

@@ -1,14 +1,14 @@
-# This output was generated with AUGUSTUS (version 3.4.0).
+# This output was generated with AUGUSTUS (version 3.5.0).
 # AUGUSTUS is a gene prediction tool written by M. Stanke ([email protected]),
-# O. Keller, S. König, L. Gerischer, L. Romoth and Katharina Hoff.
+# O. Keller, S. König, L. Gerischer, L. Romoth, Katharina Hoff, Henry Mehlan and Daniel Honsel.
 # Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008),
 # Using native and syntenically mapped cDNA alignments to improve de novo gene finding
 # Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013
 # No extrinsic information on sequences given.
 # Sources of extrinsic information: M RM 
 # Initializing the parameters using config directory /usr/local/config/ ...
 # human version. Using default transition matrix.
-# Looks like /tmp/tmpb49zmbej/files/1/1/4/dataset_11447207-979d-4b84-a63d-14dd1e776f0e.dat is in fasta format.
+# Looks like /tmp/tmppoq4flrj/files/8/9/9/dataset_8998cdab-ae1a-4630-be3b-51ec04b35598.dat is in fasta format.
 # We have hints for 0 sequences and for 0 of the sequences in the input set.
 #
 # ----- prediction on sequence number 1 (length = 9453, name = HS04636) -----
@@ -21,4 +21,4 @@
 # Predicted genes for sequence number 2 on both strands
 # (none)
 # command line:
-# augustus --strand=both --noInFrameStop=false --gff3=off --uniqueGeneId=true --protein=on --codingseq=on --introns=off --stop=off --stop=off --cds=on --singlestrand=false /tmp/tmpb49zmbej/files/1/1/4/dataset_11447207-979d-4b84-a63d-14dd1e776f0e.dat --UTR=on --genemodel=complete --softmasking=1 --species=human
+# augustus --strand=both --noInFrameStop=false --gff3=off --uniqueGeneId=true --protein=off --codingseq=off --introns=off --stop=off --stop=off --cds=off --singlestrand=false /tmp/tmppoq4flrj/files/8/9/9/dataset_8998cdab-ae1a-4630-be3b-51ec04b35598.dat --UTR=on --genemodel=complete --softmasking=1 --species=human