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avoid conflicts with other taxonomy-based tools and keep script names consistent (also create taxonomy-directory during installation if not already existing) #106

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avoid conflicts with other taxonomy-based tools and keep script names consistent (also create taxonomy-directory during installation if not already existing) #106

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25 changes: 21 additions & 4 deletions KronaTools/install.pl
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Original file line number Diff line number Diff line change
Expand Up @@ -35,6 +35,7 @@
}

my $scriptPath = abs_path('scripts');
my $currentPath = abs_path('.');

createDir($path);
createDir("$path/bin");
Expand Down Expand Up @@ -74,11 +75,24 @@
}
}

foreach my $script
(qw(
updateTaxonomy
updateAccessions
))
{
if ( system('ln', '-sf', "$currentPath/$script.sh", "$path/bin/kt$script") )
{
linkFail("$path/bin");
}
}

if ( defined $taxonomyDir )
{
if ( ! -e $taxonomyDir )
{
ktDie("$taxonomyDir does not exist.");
print "\n $taxonomyDir does not exist. --> creating it.\n";
createDir("$taxonomyDir");
}

if ( -e 'taxonomy')
Expand All @@ -89,19 +103,22 @@
print "Linking taxonomy to $taxonomyDir...\n";
system('ln -s -f -F ' . $taxonomyDir . ' taxonomy');
}

else
{
createDir("$currentPath/taxonomy");
}
print '
Installation complete.

Run ./updateTaxonomy.sh to use scripts that rely on NCBI taxonomy:
Run ktupdateTaxonomy to use scripts that rely on NCBI taxonomy:
ktClassifyBLAST
ktGetLCA
ktGetTaxInfo
ktImportBLAST
ktImportTaxonomy
ktImportMETAREP-BLAST

Run ./updateAccessions.sh to use scripts that get taxonomy IDs from accessions:
Run ktupdateAccessions to use scripts that get taxonomy IDs from accessions:
ktClassifyBLAST
ktGetTaxIDFromAcc
ktImportBLAST
Expand Down
12 changes: 6 additions & 6 deletions KronaTools/lib/KronaTools.pm
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Expand Up @@ -1229,7 +1229,7 @@ sub getTaxInfo

if ( ! open TAX, "<$options{'taxonomy'}/$fileTaxonomy" )
{
print "ERROR: Taxonomy not found in $options{'taxonomy'}. Was updateTaxonomy.sh run?\n";
print "ERROR: Taxonomy not found in $options{'taxonomy'}. Was ktupdateTaxonomy run?\n";
exit 1;
}

Expand Down Expand Up @@ -1348,7 +1348,7 @@ sub getTaxIDFromAcc

if ( ! open ACC, "<$options{'taxonomy'}/$fileTaxByAcc" )
{
print "ERROR: Sorted accession to taxID list not found. Was updateAccessions.sh run?\n";
print "ERROR: Sorted accession to taxID list not found. Was ktupdateAccessions run?\n";
exit 1;
}

Expand Down Expand Up @@ -1527,7 +1527,7 @@ sub loadMagnitudes
sub loadTaxonomy
{
open INFO, "<$options{'taxonomy'}/$fileTaxonomy" or die
"Taxonomy not found in $options{'taxonomy'}. Was updateTaxonomy.sh run?";
"Taxonomy not found in $options{'taxonomy'}. Was ktupdateTaxonomy run?";

while ( my $line = <INFO> )
{
Expand All @@ -1545,7 +1545,7 @@ sub loadTaxonomy
ktDie
(
"Local taxonomy database is out of date and does not support the
-$optionFormats{'noRank'} option. Update using updateTaxonomy.sh."
-$optionFormats{'noRank'} option. Update using ktupdateTaxonomy."
);
}
close INFO;
Expand Down Expand Up @@ -1678,7 +1678,7 @@ sub printWarnings
{
ktWarn
(
"The following accessions were not found in the local database (if they were recently added to NCBI, use updateAccessions.sh to update the local database):\n" .
"The following accessions were not found in the local database (if they were recently added to NCBI, use ktupdateAccessions to update the local database):\n" .
join ' ', (keys %missingAccs)
);

Expand All @@ -1689,7 +1689,7 @@ sub printWarnings
{
ktWarn
(
"The following taxonomy IDs were not found in the local database and were set to root (if they were recently added to NCBI, use updateTaxonomy.sh to update the local database):\n" .
"The following taxonomy IDs were not found in the local database and were set to root (if they were recently added to NCBI, use ktupdateTaxonomy to update the local database):\n" .
join ' ', (keys %missingTaxIDs)
);

Expand Down
7 changes: 6 additions & 1 deletion KronaTools/updateAccessions.sh
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Expand Up @@ -6,6 +6,11 @@
#
# See the LICENSE.txt file included with this software for license information.

ktPath="$( cd "$( dirname "${BASH_SOURCE[0]}" )" > /dev/null && pwd )"
# This would not resolve symlink:
# ktPath="$( cd "$( dirname "${BASH_SOURCE[0]}" )" > /dev/null && pwd )"
# Therefore this:
# perl function to resolve symlinks that will function on Linux and OSX (since 'readlink -f' is different under OSX)
readlink_f(){ perl -MCwd -e 'print Cwd::abs_path shift' "$1";}
ktPath=$(dirname $(readlink_f $0))

$ktPath/updateTaxonomy.sh --accessions $@
2 changes: 2 additions & 0 deletions KronaTools/updateTaxonomy.sh
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Expand Up @@ -20,6 +20,8 @@ fi
readlink_f(){ perl -MCwd -e 'print Cwd::abs_path shift' "$1";}
ktPath=$(dirname $(readlink_f $0))

echo $ktPATH

makefileAcc2taxid="scripts/accession2taxid.make"
makefileTaxonomy="scripts/taxonomy.make"

Expand Down