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BRAKER_testing.md

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Load modules

module load GCC/7.3.0-2.30 module load GCCcore/7.3.0 module load OpenMPI/3.1.1 module load BRAKER/2.1.2 module load AUGUSTUS/3.3 module load GeneMark-ET/4.46 module load BamTools/2.5.1 module load SAMtools/1.9 module load GenomeThreader/1.7.1-Linux_x86_64-64bit module load BLAST+/2.9.0

Missing modules Spaln 2.3.1 Exonerate 2.2.0 DIAMOND cdbfasta cdbyank

########################

BRAKER

########################

cd /sonas-hs/ware/hpc_norepl/data/diniz/analysis/braker

module load Anaconda2/5.3.0

conda create -n braker #only once source activate braker

conda install -c anaconda perl conda install -c bioconda perl-app-cpanminus conda install -c bioconda perl-hash-merge conda install -c bioconda perl-parallel-forkmanager conda install -c bioconda perl-scalar-util-numeric conda install -c bioconda perl-yaml conda install -c bioconda perl-class-data-inheritable conda install -c bioconda perl-exception-class conda install -c bioconda perl-test-pod conda install -c anaconda biopython #conda install -c bioconda perl-file-homedir conda install -c bioconda perl-file-which # skip if you are not comparing to reference annotation cpanm Logger::Simple

module load GCCcore/7.3.0 module load GCC/7.3.0-2.30 module load OpenMPI/3.1.1 module load git/2.19.1 module load BamTools/2.5.1 module load SAMtools/1.9 module load CMake/3.13.4 module load Python/3.6.6

git clone https://github.com/Gaius-Augustus/BRAKER.git

#Install GeneMark cd /sonas-hs/ware/hpc_norepl/data/diniz/analysis/braker wget http://topaz.gatech.edu/GeneMark/tmp/GMtool_Zid0r/gm_et_linux_64.tar.gz tar xvzf gm_et_linux_64.tar.gz cd gm_et_linux_64 wget http://topaz.gatech.edu/GeneMark/tmp/GMtool_Zid0r/gm_key_64.gz gunzip gm_key_64.gz cp gm_key_64 ~/.gm_key

for f in bet_to_gff.pl bp_seq_select.pl build_mod.pl calc_introns_from_gtf.pl
change_path_in_perl_scripts.pl gc_distr.pl get_sequence_from_GTF.pl
gmes_petap.pl histogram.pl hmm_to_gtf.pl make_nt_freq_mat.pl
parse_by_introns.pl parse_ET.pl parse_gibbs.pl parse_set.pl predict_genes.pl
reformat_fasta.pl reformat_gff.pl rescale_gff.pl rnaseq_introns_to_gff.pl
run_es.pl run_hmm_pbs.pl scan_for_bp.pl star_to_gff.pl verify_evidence_gmhmm.pl; do cat $f | perl -pe 's//usr/bin/perl//usr/bin/env perl/' > $f.tmp mv $f.tmp $f chmod u+x $f done

#Install Augustus cd /sonas-hs/ware/hpc_norepl/data/diniz/analysis/braker git clone https://github.com/Gaius-Augustus/Augustus.git cd Augustus/ make

#Install diamond cd /sonas-hs/ware/hpc_norepl/data/diniz/analysis/braker conda install -c bioconda diamond conda update diamond

#Install cdbfasta cd /sonas-hs/ware/hpc_norepl/data/diniz/analysis/braker git clone https://github.com/gpertea/cdbfasta.git

#Example cd /sonas-hs/ware/hpc_norepl/data/diniz/analysis/braker/BRAKER/example wget http://bioinf.uni-greifswald.de/bioinf/braker/RNAseq.bam

export GENEMARK_PATH=/sonas-hs/ware/hpc_norepl/data/diniz/analysis/braker/gm_et_linux_64 export CDBTOOLS_PATH=/sonas-hs/ware/hpc_norepl/data/diniz/analysis/braker/cdbfasta

braker.pl --genome=genome.fa --bam=RNAseq.bam --softmasking

PATH=/sonas-hs/ware/hpc_norepl/data/diniz/analysis/braker/BRAKER/scripts:$PATH export PATH

export AUGUSTUS_CONFIG_PATH=/sonas-hs/ware/hpc_norepl/data/diniz/analysis/braker/Augustus/config export AUGUSTUS_BIN_PATH=/sonas-hs/ware/hpc_norepl/data/diniz/analysis/braker/Augustus/bin export AUGUSTUS_SCRIPTS_PATH=/sonas-hs/ware/hpc_norepl/data/diniz/analysis/braker/Augustus/scripts export BAMTOOLS_BIN_PATH=/sonas-hs/it/hpc/home/easybuild/install_prod/software/MPI/GCC/7.3.0-2.30/OpenMPI/3.1.1/BamTools/2.5.1/bin export SAMTOOLS_PATH=/sonas-hs/it/hpc/home/easybuild/install_prod/software/MPI/GCC/7.3.0-2.30/OpenMPI/3.1.1/SAMtools/1.9/bin export DIAMOND_PATH=/sonas-hs/ware/hpc/home/bwang/software/diamond export PYTHON3_PATH=/sonas-hs/it/hpc/home/easybuild/install_prod/software/MPI/GCC/7.3.0-2.30/OpenMPI/3.1.1/Python/3.6.6/bin

########################

BRAKER 2

########################

cd /sonas-hs/ware/hpc_norepl/data/diniz/analysis/braker2

module load Anaconda2/5.3.0

#conda create -n braker2-2.1.2 -c conda-forge -c bioconda -c defaults braker2=2.1.2=2 conda create -n braker2 -c conda-forge -c bioconda -c defaults braker2

To activate this environment, use:

source activate braker2

which perl which braker.pl ls ~/.conda/envs/braker2/bin/helpMod.pm

To deactivate an active environment, use:

conda deactivate

module load GCCcore/7.3.0 module load GCC/7.3.0-2.30 module load OpenMPI/3.1.1 module load git/2.19.1

#Install Braker cd /sonas-hs/ware/hpc_norepl/data/diniz/analysis/braker2 git clone https://github.com/Gaius-Augustus/BRAKER.git

#Install GeneMark cd /sonas-hs/ware/hpc_norepl/data/diniz/analysis/braker2 wget http://topaz.gatech.edu/GeneMark/tmp/GMtool_Zid0r/gm_et_linux_64.tar.gz tar xvzf gm_et_linux_64.tar.gz cd gm_et_linux_64 wget http://topaz.gatech.edu/GeneMark/tmp/GMtool_Zid0r/gm_key_64.gz gunzip gm_key_64.gz cp gm_key_64 .gm_key

for f in bet_to_gff.pl bp_seq_select.pl build_mod.pl calc_introns_from_gtf.pl
change_path_in_perl_scripts.pl gc_distr.pl get_sequence_from_GTF.pl
gmes_petap.pl histogram.pl hmm_to_gtf.pl make_nt_freq_mat.pl
parse_by_introns.pl parse_ET.pl parse_gibbs.pl parse_set.pl predict_genes.pl
reformat_fasta.pl reformat_gff.pl rescale_gff.pl rnaseq_introns_to_gff.pl
run_es.pl run_hmm_pbs.pl scan_for_bp.pl star_to_gff.pl verify_evidence_gmhmm.pl; do cat $f | perl -pe 's//usr/bin/perl//usr/bin/env perl/' > $f.tmp mv $f.tmp $f chmod u+x $f done

#Install Augustus cd /sonas-hs/ware/hpc_norepl/data/diniz/analysis/braker2 git clone https://github.com/Gaius-Augustus/Augustus.git cd Augustus/ make

#Install diamond cd /sonas-hs/ware/hpc_norepl/data/diniz/analysis/braker2 conda install -c bioconda diamond conda update diamond

#Install cdbfasta cd /sonas-hs/ware/hpc_norepl/data/diniz/analysis/braker2 git clone https://github.com/gpertea/cdbfasta.git cd cdbfasta make all

########################

Wed Dec 11 18:10:17 2019: ERROR: in file /sonas-hs/ware/hpc_norepl/data/diniz/analysis/braker2/BRAKER/scripts/braker.pl at line 3153

Perl module 'Logger::Simple' is required but not installed yet. ########################

#trying conda install -c bioconda perl-logger-simple

######################## ==> WARNING: A newer version of conda exists. <== current version: 4.5.11 latest version: 4.8.0

Please update conda by running

$ conda update -n base -c defaults conda

########################

#trying conda update -n base -c defaults conda

#Peter's hint export PERL5LIB=/sonas-hs/ware/hpc/home/diniz/perl5/lib/perl5:$PERL5LIB perl -MLogger::Simple -e 1 #no output means it is ok

#Example module load Anaconda2/5.3.0

source activate braker2

module load GCC/7.3.0-2.30 module load OpenMPI/3.1.1 module load Python/3.6.6

cd /sonas-hs/ware/hpc_norepl/data/diniz/analysis/braker2/BRAKER/example

wget http://bioinf.uni-greifswald.de/bioinf/braker/RNAseq.bam

source activate braker2 cd /sonas-hs/ware/hpc_norepl/data/diniz/analysis/braker2/BRAKER/example

export CDBTOOLS_PATH=/sonas-hs/ware/hpc_norepl/data/diniz/analysis/braker2/cdbfasta export GENEMARK_PATH=/sonas-hs/ware/hpc_norepl/data/diniz/analysis/braker2/gm_et_linux_64

/sonas-hs/ware/hpc_norepl/data/diniz/analysis/braker2/BRAKER/scripts/braker.pl
--genome=genome.fa
--bam=RNAseq.bam
--softmasking
--AUGUSTUS_CONFIG_PATH=/sonas-hs/ware/hpc_norepl/data/diniz/analysis/braker2/Augustus/config
--AUGUSTUS_BIN_PATH=/sonas-hs/ware/hpc_norepl/data/diniz/analysis/braker2/Augustus/bin
--AUGUSTUS_SCRIPTS_PATH=/sonas-hs/ware/hpc_norepl/data/diniz/analysis/braker2/Augustus/scripts
--CDBTOOLS_PATH=/sonas-hs/ware/hpc_norepl/data/diniz/analysis/braker2/cdbfasta
--GENEMARK_PATH=/sonas-hs/ware/hpc_norepl/data/diniz/analysis/braker2/gm_et_linux_64

########################

BRAKER 2 on Mac

########################

cd /Users/diniz/braker2 #conda create -n braker2 -c conda-forge -c bioconda -c defaults braker2

To activate this environment, use:

source activate braker2

which perl which braker.pl ls ~/miniconda3/envs/braker2/bin/helpMod.pm #testing braker braker.pl

#Install GeneMark cd /Users/diniz/braker2 curl http://topaz.gatech.edu/GeneMark/tmp/GMtool_aNOK4/gm_et_macosx.tar.gz --output gm_et_macosx.tar.gz tar xvzf gm_et_macosx.tar.gz rm -rf gm_et_macosx.tar.gz cd gm_et_macosx/gmes_petap curl http://topaz.gatech.edu/GeneMark/tmp/GMtool_aNOK4/gm_key_64.gz --output gm_key_64.gz gunzip gm_key_64.gz cp gm_key_64 ~/.gm_key

#Install diamond conda install -c bioconda diamond conda update diamond

#Install cdbfasta git clone https://github.com/gpertea/cdbfasta.git

git clone braker

git clone https://github.com/Gaius-Augustus/BRAKER.git cd cdbfasta/ make

example

cd /Users/diniz/braker2/BRAKER/example curl http://bioinf.uni-greifswald.de/bioinf/braker/RNAseq.bam --output RNAseq.bam

export GENEMARK_PATH=/Users/diniz/braker2/gm_et_macosx/gmes_petap export CDBTOOLS_PATH=/Users/diniz/braker2/cdbfasta

braker.pl
--genome=genome.fa
--bam=RNAseq.bam
--softmasking

braker.pl --genome=genome.fa --softmasking --esmode

export DIAMOND_PATH=/sonas-hs/ware/hpc/home/bwang/software/diamond

########################

BRAKER 2 on helix

########################

cd /projects/augustold/CSHL/braker2

#conda create -n braker2 -c conda-forge -c bioconda -c defaults braker2 conda activate braker2

which perl which braker.pl ls ~/./miniconda3/envs/braker2/bin/helpMod.pm

To deactivate an active environment, use:

conda deactivate

#Install Braker cd /projects/augustold/CSHL/braker2 git clone https://github.com/Gaius-Augustus/BRAKER.git

#Install GeneMark cd /projects/augustold/CSHL/braker2 wget http://topaz.gatech.edu/GeneMark/tmp/GMtool_Zid0r/gm_et_linux_64.tar.gz tar xvzf gm_et_linux_64.tar.gz rm -rf gm_et_linux_64.tar.gz cd gm_et_linux_64 wget http://topaz.gatech.edu/GeneMark/tmp/GMtool_Zid0r/gm_key_64.gz gunzip gm_key_64.gz cp gm_key_64 ~/.gm_key

for f in bet_to_gff.pl bp_seq_select.pl build_mod.pl calc_introns_from_gtf.pl
change_path_in_perl_scripts.pl gc_distr.pl get_sequence_from_GTF.pl
gmes_petap.pl histogram.pl hmm_to_gtf.pl make_nt_freq_mat.pl
parse_by_introns.pl parse_ET.pl parse_gibbs.pl parse_set.pl predict_genes.pl
reformat_fasta.pl reformat_gff.pl rescale_gff.pl rnaseq_introns_to_gff.pl
run_es.pl run_hmm_pbs.pl scan_for_bp.pl star_to_gff.pl verify_evidence_gmhmm.pl; do cat $f | perl -pe 's//usr/bin/perl//usr/bin/env perl/' > $f.tmp mv $f.tmp $f chmod u+x $f done

#Install diamond conda install -c bioconda diamond conda update diamond

#Install cdbfasta git clone https://github.com/gpertea/cdbfasta.git cd cdbfasta make all

#Example

source activate braker2

cd /projects/augustold/CSHL/braker2/BRAKER/example #wget http://bioinf.uni-greifswald.de/bioinf/braker/RNAseq.bam

export GENEMARK_PATH=/projects/augustold/CSHL/braker2/gm_et_linux_64 export CDBTOOLS_PATH=/projects/augustold/CSHL/braker2/cdbfasta

braker.pl
--genome=genome.fa
--bam=RNAseq.bam
--softmasking