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fix braker to work with docker, update to v1.1.1
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Jon Palmer committed Jan 29, 2018
1 parent 92f3f90 commit 056cb21
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Showing 2 changed files with 98 additions and 98 deletions.
2 changes: 1 addition & 1 deletion funannotate.py
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Original file line number Diff line number Diff line change
Expand Up @@ -31,7 +31,7 @@ def fmtcols(mylist, cols):
for i in range(0,num_lines))
return "\n".join(lines)

version = '1.1.0'
version = '1.1.1'

default_help = """
Usage: funannotate <command> <arguments>
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194 changes: 97 additions & 97 deletions util/BRAKER/braker.pl
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Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,8 @@
# #
# This script is under the Artistic Licence #
# (http://www.opensource.org/licenses/artistic-license.php) #
# #
#
# Edited Jan 29th, 2018 by Jon Palmer, remove calls to ln -s as fails in virtual env, fix --version#
####################################################################################################

use Getopt::Long;
Expand Down Expand Up @@ -212,7 +213,7 @@



my $version = 2.0.3; # braker.pl version number
my $version = "2.0.3b"; # braker.pl version number
my $logString; # stores log messages produced before opening log file
my $printString;
my $alternatives_from_evidence = "true"; # output alternative transcripts based on explicit evidence from hints
Expand All @@ -221,60 +222,11 @@
my $augustus_bin_path; # path to augustus folder binaries folder
my $augustus_scripts_path; # path to augustus scripts folder
my $AUGUSTUS_CONFIG_PATH;
if(defined($ENV{'AUGUSTUS_CONFIG_PATH'})){
if(-e $ENV{'AUGUSTUS_CONFIG_PATH'}){
$printString = "\# ".(localtime).": Found environment variable \$AUGUSTUS_CONFIG_PATH.\n";
print STDOUT $printString;
$logString .= $printString;
$AUGUSTUS_CONFIG_PATH = $ENV{'AUGUSTUS_CONFIG_PATH'};
}
}else{
$printString = "\# ".(localtime).": Did not find environment variable \$AUGUSTUS_CONFIG_PATH (either variable does not exist, or the path given in variable does not exist). Will try to set this variable in a different way, later.\n";
print STDOUT $printString;
$logString .= $printString;
}
my $AUGUSTUS_BIN_PATH;
if(defined($ENV{'AUGUSTUS_BIN_PATH'})){
if(-e $ENV{'AUGUSTUS_BIN_PATH'}){
$printString = "\# ".(localtime).": Found environment variable \$AUGUSTUS_BIN_PATH.\n";
print STDOUT $printString;
$logString .= $printString;
$AUGUSTUS_BIN_PATH = $ENV{'AUGUSTUS_BIN_PATH'};
}
}else{
$printString = "\# ".(localtime).": Did not find environment variable \$AUGUSTUS_BIN_PATH (either variable does not exist, or the path given in variable does not exist). Will try to set this variable in a different way, later.\n";
print STDOUT $printString;
$logString .= $printString;
}

my $AUGUSTUS_SCRIPTS_PATH;
if(defined($ENV{'$AUGUSTUS_SCRIPTS_PATH'})){
if(-e $ENV{'$AUGUSTUS_SCRIPTS_PATH'}){
$printString = "\# ".(localtime).": Found environment variable \$AUGUSTUS_SCRIPTS_PATH.\n";
print STDOUT $printString;
$logString .= $printString;
$AUGUSTUS_SCRIPTS_PATH = $ENV{'AUGUSTUS_SCRIPTS_PATH'};
}
}else{
$printString = "\# ".(localtime).": Did not find environment variable \$AUGUSTUS_SCRIPTS_PATH (either variable does not exist, or the path given in variable does not exist). Will try to set this variable in a different way, later.\n";
print STDOUT $printString;
$logString .= $printString;
}
my @bam; # bam file names
my $bamtools_path;
my $BAMTOOLS_BIN_PATH;
if(defined($ENV{'BAMTOOLS_PATH'})){
if(-e $ENV{'BAMTOOLS_PATH'}){ # path to bamtools executable, higher priority than $BAMTOOLS_BIN_PATH on system
$printString = "\# ".(localtime).": Found environment variable \$BAMTOOLS_PATH.\n";
print STDOUT $printString;
$logString .= $printString;
$BAMTOOLS_BIN_PATH = $ENV{'BAMTOOLS_PATH'}; # bamtools environment variable
}
}else{
$printString = "\# ".(localtime).": Did not find environment variable \$BAMTOOLS_PATH (either variable does not exist, or the path given in variable does not exist). Will try to set this variable in a different way, later.\n";
print STDOUT $printString;
$logString .= $printString;
}
my @bonus; # array of bonus values for extrinsic file
my $bool_species = "true"; # false, if $species contains forbidden words (e.g. chmod)
my $cmdString; # to store shell commands
Expand All @@ -291,18 +243,6 @@
my $genbank; # genbank file name
my $genemarkDir; # directory for GeneMark-ET output
my $GENEMARK_PATH;
if(defined($ENV{'GENEMARK_PATH'})){
if(-e $ENV{'GENEMARK_PATH'}){
$printString = "\# ".(localtime).": Found environment variable \$GENEMARK_PATH.\n";
print STDOUT $printString;
$logString .= $printString;
$GENEMARK_PATH = $ENV{'GENEMARK_PATH'}; # path to 'gmes_petap.pl' script on system, environment variable
}
}else{
$printString = "\# ".(localtime).": Did not find environment variable \$GENEMARK_PATH (either variable does not exist, or the path given in variable does not exist). Will try to set this variable in a different way, later.\n";
print STDOUT $printString;
$logString .= $printString;
}
my $GMET_path; # GeneMark-ET path, higher priority than $GENEMARK_PATH; will use the same variable for GeneMark-EP path
my $genome; # name of sequence file
my $genome_length = 0; # length of genome file
Expand All @@ -322,18 +262,6 @@
my $perlCmdString; # stores perl commands
my $printVersion = 0; # print version number, if set
my $SAMTOOLS_PATH;
if(defined($ENV{'SAMTOOLS_PATH'})){
if(-e $ENV{'SAMTOOLS_PATH'}){
$printString = "\# ".(localtime).": Found environment variable \$SAMTOOLS_PATH.\n";
print STDOUT $printString;
$logString .= $printString;
my $SAMTOOLS_PATH = $ENV{'SAMTOOLS_PATH'}; # samtools environment variable
}
}else{
$printString = "\# ".(localtime).": Did not find environment variable \$SAMTOOLS_PATH (either variable does not exist, or the path given in variable does not exist). Will try to set this variable in a different way, later.\n";
print STDOUT $printString;
$logString .= $printString;
}
my $SAMTOOLS_PATH_OP; # path to samtools executable, higher priority than $SAMTOOLS_PATH on system
my $scriptPath=dirname($0); # path of directory where this script is located
my $skipGeneMarkET = 0; # skip GeneMark-ET and use provided GeneMark-ET output (e.g. from a different source)
Expand Down Expand Up @@ -368,18 +296,6 @@
my @prot_seq_files; # variable to store protein sequence file name
my @prot_aln_files; # variable to store protein alingment file name
my $ALIGNMENT_TOOL_PATH; # stores path to binary of gth, spaln or exonerate for running protein alignments
if(defined($ENV{'ALIGNMENT_TOOL_PATH'})){
if(-e $ENV{'ALIGNMENT_TOOL_PATH'}){
$printString = "\# ".(localtime).": Found environment variable \$ALIGNMENT_TOOL_PATH.\n";
print STDOUT $printString;
$logString .= $printString;
$ALIGNMENT_TOOL_PATH = $ENV{'ALIGNMENT_TOOL_PATH'};
}
}else{
$printString = "\# ".(localtime).": Did not find environment variable \$ALIGNMENT_TOOL_PATH (either variable does not exist, or the path given in variable does not exist). Will try to set this variable in a different way, later.\n";
print STDOUT $printString;
$logString .= $printString;
}
my $ALIGNMENT_TOOL_PATH_OP; # higher priority than environment variable
my %hintTypes; # stores hint types occuring over all generated and supplied hints for comparison
my $rnaseq2utr_args; # additional parameters to be passed to rnaseq2utr
Expand Down Expand Up @@ -505,6 +421,91 @@
print "braker.pl version $version\n";
exit(0);
}
#move installation checks here so if you print version you don't pollute the terminal
if(defined($ENV{'AUGUSTUS_CONFIG_PATH'})){
if(-e $ENV{'AUGUSTUS_CONFIG_PATH'}){
$printString = "\# ".(localtime).": Found environment variable \$AUGUSTUS_CONFIG_PATH.\n";
print STDOUT $printString;
$logString .= $printString;
$AUGUSTUS_CONFIG_PATH = $ENV{'AUGUSTUS_CONFIG_PATH'};
}
}else{
$printString = "\# ".(localtime).": Did not find environment variable \$AUGUSTUS_CONFIG_PATH (either variable does not exist, or the path given in variable does not exist). Will try to set this variable in a different way, later.\n";
print STDOUT $printString;
$logString .= $printString;
}
if(defined($ENV{'AUGUSTUS_BIN_PATH'})){
if(-e $ENV{'AUGUSTUS_BIN_PATH'}){
$printString = "\# ".(localtime).": Found environment variable \$AUGUSTUS_BIN_PATH.\n";
print STDOUT $printString;
$logString .= $printString;
$AUGUSTUS_BIN_PATH = $ENV{'AUGUSTUS_BIN_PATH'};
}
}else{
$printString = "\# ".(localtime).": Did not find environment variable \$AUGUSTUS_BIN_PATH (either variable does not exist, or the path given in variable does not exist). Will try to set this variable in a different way, later.\n";
print STDOUT $printString;
$logString .= $printString;
}
if(defined($ENV{'$AUGUSTUS_SCRIPTS_PATH'})){
if(-e $ENV{'$AUGUSTUS_SCRIPTS_PATH'}){
$printString = "\# ".(localtime).": Found environment variable \$AUGUSTUS_SCRIPTS_PATH.\n";
print STDOUT $printString;
$logString .= $printString;
$AUGUSTUS_SCRIPTS_PATH = $ENV{'AUGUSTUS_SCRIPTS_PATH'};
}
}else{
$printString = "\# ".(localtime).": Did not find environment variable \$AUGUSTUS_SCRIPTS_PATH (either variable does not exist, or the path given in variable does not exist). Will try to set this variable in a different way, later.\n";
print STDOUT $printString;
$logString .= $printString;
}
if(defined($ENV{'BAMTOOLS_PATH'})){
if(-e $ENV{'BAMTOOLS_PATH'}){ # path to bamtools executable, higher priority than $BAMTOOLS_BIN_PATH on system
$printString = "\# ".(localtime).": Found environment variable \$BAMTOOLS_PATH.\n";
print STDOUT $printString;
$logString .= $printString;
$BAMTOOLS_BIN_PATH = $ENV{'BAMTOOLS_PATH'}; # bamtools environment variable
}
}else{
$printString = "\# ".(localtime).": Did not find environment variable \$BAMTOOLS_PATH (either variable does not exist, or the path given in variable does not exist). Will try to set this variable in a different way, later.\n";
print STDOUT $printString;
$logString .= $printString;
}
if(defined($ENV{'GENEMARK_PATH'})){
if(-e $ENV{'GENEMARK_PATH'}){
$printString = "\# ".(localtime).": Found environment variable \$GENEMARK_PATH.\n";
print STDOUT $printString;
$logString .= $printString;
$GENEMARK_PATH = $ENV{'GENEMARK_PATH'}; # path to 'gmes_petap.pl' script on system, environment variable
}
}else{
$printString = "\# ".(localtime).": Did not find environment variable \$GENEMARK_PATH (either variable does not exist, or the path given in variable does not exist). Will try to set this variable in a different way, later.\n";
print STDOUT $printString;
$logString .= $printString;
}
if(defined($ENV{'SAMTOOLS_PATH'})){
if(-e $ENV{'SAMTOOLS_PATH'}){
$printString = "\# ".(localtime).": Found environment variable \$SAMTOOLS_PATH.\n";
print STDOUT $printString;
$logString .= $printString;
my $SAMTOOLS_PATH = $ENV{'SAMTOOLS_PATH'}; # samtools environment variable
}
}else{
$printString = "\# ".(localtime).": Did not find environment variable \$SAMTOOLS_PATH (either variable does not exist, or the path given in variable does not exist). Will try to set this variable in a different way, later.\n";
print STDOUT $printString;
$logString .= $printString;
}
if(defined($ENV{'ALIGNMENT_TOOL_PATH'})){
if(-e $ENV{'ALIGNMENT_TOOL_PATH'}){
$printString = "\# ".(localtime).": Found environment variable \$ALIGNMENT_TOOL_PATH.\n";
print STDOUT $printString;
$logString .= $printString;
$ALIGNMENT_TOOL_PATH = $ENV{'ALIGNMENT_TOOL_PATH'};
}
}else{
$printString = "\# ".(localtime).": Did not find environment variable \$ALIGNMENT_TOOL_PATH (either variable does not exist, or the path given in variable does not exist). Will try to set this variable in a different way, later.\n";
print STDOUT $printString;
$logString .= $printString;
}

if($skipAllTraining){ # if no training is performed, existing parameters must be used
$useexisting=1;
Expand Down Expand Up @@ -534,7 +535,6 @@
}



# check the write permission of $workDir before building of the work directory
if(! -w $workDir){
$printString = "\# ".(localtime).":ERROR: Do not have write permission for $workDir.\nPlease use command 'chmod' to reset permissions, or specify another working directory with option --workingdir=...\n";
Expand Down Expand Up @@ -1400,7 +1400,7 @@

if(defined($geneMarkGtf)){
print LOG "\# ".(localtime).": creating softlink of $geneMarkGtf to $genemarkDir/genemark.gtf.\n";
$cmdString = "ln -s $geneMarkGtf $genemarkDir/genemark.gtf";
$cmdString = "cp $geneMarkGtf $genemarkDir/genemark.gtf";
print LOG "$cmdString\n";
system($cmdString)==0 or die("failed to execute: $cmdString!\n");
}
Expand Down Expand Up @@ -1471,8 +1471,8 @@
if(@prot_seq_files or @prot_aln_files or @hints){
separateHints();
}else{
print LOG "\# ".(localtime).": Creating softlink from $genemark_hintsfile to $hintsfile\n";
$cmdString = "ln -s $hintsfile $genemark_hintsfile";
print LOG "\# ".(localtime).": Copying $genemark_hintsfile to $hintsfile\n";
$cmdString = "cp $hintsfile $genemark_hintsfile";
print LOG "$cmdString\n";
system($cmdString)==0 or die("failed to execute: $cmdString!\n");
}
Expand Down Expand Up @@ -1813,8 +1813,8 @@ sub separateHints{
print LOG "$cmdString\n\n";
system($cmdString)==0 or die("Failed to execute: $cmdString\n");
}else{
print LOG "\n\# ".(localtime).": No other hint types found. Creating softlink from $genemark_hintsfile to $hintsfile\n";
$cmdString = "ln -s $hintsfile $genemark_hintsfile";
print LOG "\n\# ".(localtime).": No other hint types found. Copying $genemark_hintsfile to $hintsfile\n";
$cmdString = "cp $hintsfile $genemark_hintsfile";
print LOG "$cmdString\n";
system($cmdString)==0 or die("Failed to execute: $cmdString\n");
}
Expand Down Expand Up @@ -2394,7 +2394,7 @@ sub training{
}
close(FILTEREDGTH) or die ("Could not close file $gthTrainGeneFile.f!\n");
}else{
$cmdString = "ln -s $gthTrainGeneFile $gthTrainGeneFile.f";
$cmdString = "cp $gthTrainGeneFile $gthTrainGeneFile.f";
print LOG "$cmdString\n\n";
system("$cmdString")==0 or die("Failed to execute: $cmdString\n");
}
Expand Down Expand Up @@ -2438,14 +2438,14 @@ sub training{
if(not($trainFromGth) && not($gth2traingenes)){
# make genemark gb final
print LOG "\# ".(localtime).": creating softlink of $geneMarkGb to $otherfilesDir/genbank.good.gb.\n";
$cmdString = "ln -s $geneMarkGb $otherfilesDir/genbank.good.gb";
$cmdString = "cp $geneMarkGb $otherfilesDir/genbank.good.gb";
print LOG "$cmdString\n";
system($cmdString)==0 or die("failed to execute: $cmdString!\n");

}elsif($trainFromGth){
# make gth gb final
print LOG "\# ".(localtime).": creating softlink of $gthGb to $otherfilesDir/genbank.good.gb.\n";
$cmdString = "ln -s $gthGb $otherfilesDir/genbank.good.gb";
$cmdString = "cp $gthGb $otherfilesDir/genbank.good.gb";
print LOG "$cmdString\n";
system($cmdString)==0 or die("failed to execute: $cmdString!\n");

Expand Down Expand Up @@ -3756,7 +3756,7 @@ sub train_utr{
system("$cmdString") or die ("Failed to execute: $cmdString!\n");
}else{
print LOG "\# ".(localtime).": Creating softlink to bam file $bam[0]...\n";
$cmdString = "ln -s $bam[0] merged.bam";
$cmdString = "cp $bam[0] merged.bam";
print LOG "$cmdString\n";
system($cmdString)==0 or die("Failed to exectute: $cmdString!\n");
}
Expand Down

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