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Prefix auxiliary executables with kraken2_ #91

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Prefix auxiliary executables with kraken2_ #91

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10 changes: 5 additions & 5 deletions .gitignore
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
*.o
src/build_db
src/classify
src/estimate_capacity
src/dump_table
src/lookup_accession_numbers
src/kraken2_build_db
src/kraken2_classify
src/kraken2_estimate_capacity
src/kraken2_dump_table
src/kraken2_lookup_accession_numbers
2 changes: 1 addition & 1 deletion install_kraken2.sh
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Expand Up @@ -44,7 +44,7 @@ echo "Kraken 2 installation complete."
echo
echo "To make things easier for you, you may want to copy/symlink the following"
echo "files into a directory in your PATH:"
for file in $KRAKEN2_DIR/kraken2*
for file in $KRAKEN2_DIR/kraken2 $KRAKEN2_DIR/kraken2-*
do
if [ -x "$file" ]
then
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6 changes: 3 additions & 3 deletions scripts/build_kraken2_db.sh
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Expand Up @@ -81,7 +81,7 @@ else
grep "^TAXID" taxonomy/prelim_map.txt | cut -f 2- > $seqid2taxid_map_file.tmp || true
if grep "^ACCNUM" taxonomy/prelim_map.txt | cut -f 2- > accmap_file.tmp; then
if compgen -G "taxonomy/*.accession2taxid" > /dev/null; then
lookup_accession_numbers accmap_file.tmp taxonomy/*.accession2taxid > seqid2taxid_acc.tmp
kraken2_lookup_accession_numbers accmap_file.tmp taxonomy/*.accession2taxid > seqid2taxid_acc.tmp
cat seqid2taxid_acc.tmp >> $seqid2taxid_map_file.tmp
rm seqid2taxid_acc.tmp
else
Expand All @@ -98,7 +98,7 @@ fi
echo "Estimating required capacity (step 2)..."

step_time=$(get_current_time)
estimate=$(list_sequence_files | xargs -0 cat | estimate_capacity -k $KRAKEN2_KMER_LEN -l $KRAKEN2_MINIMIZER_LEN -S $KRAKEN2_SEED_TEMPLATE -p $KRAKEN2_THREAD_CT $KRAKEN2XFLAG )
estimate=$(list_sequence_files | xargs -0 cat | kraken2_estimate_capacity -k $KRAKEN2_KMER_LEN -l $KRAKEN2_MINIMIZER_LEN -S $KRAKEN2_SEED_TEMPLATE -p $KRAKEN2_THREAD_CT $KRAKEN2XFLAG )
required_capacity=$(perl -le 'print int(shift() / 0.7)' $estimate);

echo "Estimated hash table requirement: $(( required_capacity * 4 )) bytes"
Expand All @@ -123,7 +123,7 @@ then
else
step_time=$(get_current_time)
list_sequence_files | xargs -0 cat | \
build_db -k $KRAKEN2_KMER_LEN -l $KRAKEN2_MINIMIZER_LEN -S $KRAKEN2_SEED_TEMPLATE $KRAKEN2XFLAG \
kraken2_build_db -k $KRAKEN2_KMER_LEN -l $KRAKEN2_MINIMIZER_LEN -S $KRAKEN2_SEED_TEMPLATE $KRAKEN2XFLAG \
-H hash.k2d.tmp -t taxo.k2d.tmp -o opts.k2d.tmp -n taxonomy/ -m $seqid2taxid_map_file \
-c $required_capacity -p $KRAKEN2_THREAD_CT $max_db_flag
finalize_file taxo.k2d
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4 changes: 2 additions & 2 deletions scripts/kraken2
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Expand Up @@ -16,7 +16,7 @@ my $PROG = basename $0;
my $KRAKEN2_DIR = "#####=KRAKEN2_DIR=#####";

# Test to see if the executables got moved, try to recover if we can
if (! -e "$KRAKEN2_DIR/classify") {
if (! -e "$KRAKEN2_DIR/kraken2_classify") {
use Cwd 'abs_path';
$KRAKEN2_DIR = dirname abs_path($0);
}
Expand All @@ -25,7 +25,7 @@ require "$KRAKEN2_DIR/kraken2lib.pm";
$ENV{"KRAKEN2_DIR"} = $KRAKEN2_DIR;
$ENV{"PATH"} = "$KRAKEN2_DIR:$ENV{PATH}";

my $CLASSIFY = "$KRAKEN2_DIR/classify";
my $CLASSIFY = "$KRAKEN2_DIR/kraken2_classify";
my $GZIP_MAGIC = chr(hex "1f") . chr(hex "8b");
my $BZIP2_MAGIC = "BZ";

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2 changes: 1 addition & 1 deletion scripts/kraken2-build
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Expand Up @@ -15,7 +15,7 @@ my $PROG = basename $0;
my $KRAKEN2_DIR = "#####=KRAKEN2_DIR=#####";

# Test to see if the executables got moved, try to recover if we can
if (! -e "$KRAKEN2_DIR/classify") {
if (! -e "$KRAKEN2_DIR/kraken2_classify") {
use Cwd 'abs_path';
$KRAKEN2_DIR = dirname abs_path($0);
}
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2 changes: 1 addition & 1 deletion scripts/kraken2-inspect
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Expand Up @@ -25,7 +25,7 @@ require "$KRAKEN2_DIR/kraken2lib.pm";
$ENV{"KRAKEN2_DIR"} = $KRAKEN2_DIR;
$ENV{"PATH"} = "$KRAKEN2_DIR:$ENV{PATH}";

my $DUMP_TABLE = "$KRAKEN2_DIR/dump_table";
my $DUMP_TABLE = "$KRAKEN2_DIR/kraken2_dump_table";

my $db_prefix;
my $names_in_output = 0;
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17 changes: 11 additions & 6 deletions src/Makefile
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Expand Up @@ -4,7 +4,7 @@ CXXFLAGS += -DLINEAR_PROBING

.PHONY: all clean install

PROGS = estimate_capacity build_db classify dump_table lookup_accession_numbers
PROGS = kraken2_estimate_capacity kraken2_build_db kraken2_classify kraken2_dump_table kraken2_lookup_accession_numbers

all: $(PROGS)

Expand All @@ -24,12 +24,17 @@ reports.o: reports.cc reports.h
aa_translate.o: aa_translate.cc aa_translate.h
utilities.o: utilities.cc utilities.h

build_db: build_db.cc mmap_file.o compact_hash.o taxonomy.o seqreader.o mmscanner.o omp_hack.o utilities.o
kraken2_build_db: build_db.cc mmap_file.o compact_hash.o taxonomy.o seqreader.o mmscanner.o omp_hack.o utilities.o
$(CXX) $(CPPFLAGS) $(CXXFLAGS) $^ -o $@

classify: classify.cc reports.o mmap_file.o compact_hash.o taxonomy.o seqreader.o mmscanner.o omp_hack.o aa_translate.o utilities.o
kraken2_classify: classify.cc reports.o mmap_file.o compact_hash.o taxonomy.o seqreader.o mmscanner.o omp_hack.o aa_translate.o utilities.o
$(CXX) $(CPPFLAGS) $(CXXFLAGS) $^ -o $@

estimate_capacity: estimate_capacity.cc seqreader.o mmscanner.o omp_hack.o utilities.o
kraken2_estimate_capacity: estimate_capacity.cc seqreader.o mmscanner.o omp_hack.o utilities.o
$(CXX) $(CPPFLAGS) $(CXXFLAGS) $^ -o $@

dump_table: dump_table.cc mmap_file.o compact_hash.o omp_hack.o taxonomy.o reports.o
kraken2_dump_table: dump_table.cc mmap_file.o compact_hash.o omp_hack.o taxonomy.o reports.o
$(CXX) $(CPPFLAGS) $(CXXFLAGS) $^ -o $@

lookup_accession_numbers: lookup_accession_numbers.cc mmap_file.o omp_hack.o utilities.o
kraken2_lookup_accession_numbers: lookup_accession_numbers.cc mmap_file.o omp_hack.o utilities.o
$(CXX) $(CPPFLAGS) $(CXXFLAGS) $^ -o $@
2 changes: 1 addition & 1 deletion src/build_db.cc
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Expand Up @@ -311,7 +311,7 @@ void ParseCommandLine(int argc, char **argv, Options &opts) {
}

void usage(int exit_code) {
cerr << "Usage: build_db <options>\n"
cerr << "Usage: kraken2_build_db <options>\n"
<< "\n"
<< "Options (*mandatory):\n"
<< "* -H FILENAME Kraken 2 hash table filename\n"
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2 changes: 1 addition & 1 deletion src/estimate_capacity.cc
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Expand Up @@ -154,7 +154,7 @@ void ParseCommandLine(int argc, char **argv, Options &opts) {
}

void usage(int exit_code) {
cerr << "Usage: estimate_capacity <options>" << endl
cerr << "Usage: kraken2_estimate_capacity <options>" << endl
<< endl
<< "Options (*mandatory):" << endl
<< "* -k INT Set length of k-mers" << endl
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2 changes: 1 addition & 1 deletion src/lookup_accession_numbers.cc
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Expand Up @@ -15,7 +15,7 @@ using std::vector;

int main(int argc, char **argv) {
if (argc < 3)
errx(EX_USAGE, "Usage: lookup_accession_numbers <lookup file> <accmaps>");
errx(EX_USAGE, "Usage: kraken2_lookup_accession_numbers <lookup file> <accmaps>");

unordered_map<string, vector<string>> target_lists;
std::ifstream lookup_list_file(argv[1]);
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