Merge pull request #739 from Gaius-Augustus/compleasm

Compleasm

example/docker-tests/test1.sh

@@ -8,8 +8,11 @@ fi
 
 # --gm_max_intergenic 10000 option is used here only to make the test run faster.
 # It is not recommended to use this option in real BRAKER runs. The speed increase
-# achieved by adjusting this option is negligible on full-sized genomes.
+# achieved by adjusting this option is negligible on full-sized genomes. Also,
+# --skipOptimize is used here only to make the test run faster.
+# Use an appropriate BUSCO lineage in real life use case. eukaryota_odb10 is used here
+# only to make the test run faster.
 
 export GENEMARK_PATH=$GENEMARK_PATH/gmes
 
-( time braker.pl --genome=/opt/BRAKER/example/genome.fa --bam=/opt/BRAKER/example/RNAseq.bam --workingdir=$wd --threads 8 --gm_max_intergenic 10000 --skipOptimize ) &> test1.log
+( time braker.pl --genome=/opt/BRAKER/example/genome.fa --bam=/opt/BRAKER/example/RNAseq.bam --workingdir=$wd --threads 8 --gm_max_intergenic 10000 --skipOptimize --busco_lineage eukaryota_odb10 ) &> test1.log

example/docker-tests/test2.sh

@@ -8,11 +8,14 @@ fi
 
 # --gm_max_intergenic 10000 option is used here only to make the test run faster.
 # It is not recommended to use this option in real BRAKER runs. The speed increase
-# achieved by adjusting this option is negligible on full-sized genomes.
+# achieved by adjusting this option is negligible on full-sized genomes. Also,
+# --skipOptimize is used here only to make the test run faster.
+# Use an appropriate BUSCO lineage in real life use case. eukaryota_odb10 is used here
+# only to make the test run faster.
 
 # For instructions on how to prepare the proteins.fa input file from OrthoDB,
 # see https://github.com/gatech-genemark/ProtHint#protein-database-preparation
 
 export GENEMARK_PATH=$GENEMARK_PATH/gmes
 
-( time braker.pl --genome=/opt/BRAKER/example/genome.fa --prot_seq=/opt/BRAKER/example/proteins.fa --workingdir=$wd --threads=8 --gm_max_intergenic 10000 --skipOptimize ) &> test2.log
+( time braker.pl --genome=/opt/BRAKER/example/genome.fa --prot_seq=/opt/BRAKER/example/proteins.fa --workingdir=$wd --threads=8 --gm_max_intergenic 10000 --skipOptimize --busco_lineage eukaryota_odb10 ) &> test2.log

example/docker-tests/test3.sh

@@ -15,9 +15,12 @@ fi
 
 # --gm_max_intergenic 10000 option is used here only to make the test run faster.
 # It is not recommended to use this option in real BRAKER runs. The speed increase
-# achieved by adjusting this option is negligible on full-sized genomes.
+# achieved by adjusting this option is negligible on full-sized genomes. Also,
+# --skipOptimize is used here only to make the test run faster.
+# Use an appropriate BUSCO lineage in real life use case. eukaryota_odb10 is used here
+# only to make the test run faster.
 
 # For instructions on how to prepare the proteins.fa input file from OrthoDB,
 # see https://github.com/gatech-genemark/ProtHint#protein-database-preparation
 
-( time braker.pl --genome=/opt/BRAKER/example/genome.fa --prot_seq=/opt/BRAKER/example/proteins.fa --bam=/opt/BRAKER/example/RNAseq.bam --workingdir=$wd --threads 8 --skipOptimize ) &> test3.log
+( time braker.pl --genome=/opt/BRAKER/example/genome.fa --prot_seq=/opt/BRAKER/example/proteins.fa --bam=/opt/BRAKER/example/RNAseq.bam --workingdir=$wd --threads 8 --skipOptimize --busco_lineage eukaryota_odb10 ) &> test3.log

example/singularity-tests/test1.sh

@@ -45,7 +45,7 @@ if [ -d $wd ]; then
     rm -r $wd
 fi
 
-singularity exec -B ${PWD}:${PWD} ${BRAKER_SIF} braker.pl --genome=/opt/BRAKER/example/genome.fa --bam=/opt/BRAKER/example/RNAseq.bam --workingdir=${wd} --GENEMARK_PATH=${ETP}/gmes --threads 8 --gm_max_intergenic 10000 --skipOptimize
+singularity exec -B ${PWD}:${PWD} ${BRAKER_SIF} braker.pl --genome=/opt/BRAKER/example/genome.fa --bam=/opt/BRAKER/example/RNAseq.bam --workingdir=${wd} --GENEMARK_PATH=${ETP}/gmes --threads 8 --gm_max_intergenic 10000 --skipOptimize --busco_lineage eukaryota_odb10 &> test1.log
 
 	    # Important: the options --gm_max_intergenic 10000 --skipOptimize should never be applied to a real life run!!!
 	    # They were only introduced to speed up the test. Please delete them from the script if you use it for real data analysis.

example/singularity-tests/test2.sh

@@ -47,7 +47,7 @@ if [ -d $wd ]; then
     rm -r $wd
 fi
 
-singularity exec -B ${PWD}:${PWD} ${BRAKER_SIF} braker.pl --genome=/opt/BRAKER/example/genome.fa --prot_seq=/opt/BRAKER/example/proteins.fa --workingdir=${wd} --threads 8 --gm_max_intergenic 10000 --skipOptimize
+singularity exec -B ${PWD}:${PWD} ${BRAKER_SIF} braker.pl --genome=/opt/BRAKER/example/genome.fa --prot_seq=/opt/BRAKER/example/proteins.fa --workingdir=${wd} --threads 8 --gm_max_intergenic 10000 --skipOptimize --busco_lineage eukaryota_odb10 &> test2.log
             # Important: the options --gm_max_intergenic 10000 --skipOptimize should never be applied to a real life run!!!
             # They were only introduced to speed up the test. Please delete them from the script if you use it for real data analysis.
 

example/singularity-tests/test3.sh

@@ -46,7 +46,7 @@ if [ -d $wd ]; then
 fi
 
 singularity exec -B ${PWD}:${PWD} ${BRAKER_SIF} braker.pl --genome=/opt/BRAKER/example/genome.fa --prot_seq=/opt/BRAKER/example/proteins.fa --bam=/opt/BRAKER/example/RNAseq.bam --workingdir=${wd} \
-	    --threads 8 --gm_max_intergenic 10000 --skipOptimize
+	    --threads 8 --gm_max_intergenic 10000 --skipOptimize --busco_lineage eukaryota_odb10 &> test3.log
 
 	    # Important: the options --gm_max_intergenic 10000 --skipOptimize should never be applied to a real life run!!!                                   
-            # They were only introduced to speed up the test. Please delete them from the script if you use it for real data analysis. 
+        # They were only introduced to speed up the test. Please delete them from the script if you use it for real data analysis.