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Danpf/fix install deps #80

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merged 2 commits into from
Jun 11, 2019
Merged

Danpf/fix install deps #80

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b4d8e34
fixed install deps
danpf Jun 10, 2019
bb37c57
missing my
danpf Jun 10, 2019
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40 changes: 29 additions & 11 deletions fragment_tools/install_dependencies.pl
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Original file line number Diff line number Diff line change
Expand Up @@ -266,10 +266,18 @@
if (!$skip_nr && $database eq "nr" && ($overwrite || !-s "$datdir/nr.pal")) {
chdir($datdir);
print "Fetching NR database from NCBI. Be very patient ......\n";
system("wget -N http://www.ncbi.nlm.nih.gov/blast/docs/update_blastdb.pl");
die "ERROR! wget http://www.ncbi.nlm.nih.gov/blast/docs/update_blastdb.pl failed.\n" if (!-s "$datdir/update_blastdb.pl");
system("rm $datdir/nr*"); # clean up interrupted attempts
$SIG{INT} = \&clean_nr_tgz;
system("wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.9.0+-src.tar.gz");
system("tar -zxf ncbi-blast-2.9.0+-src.tar.gz");
system("cp ncbi-blast-2.9.0+-src/c++/src/app/blast/update_blastdb.pl .");
die "ERROR! wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-1.9.0+-src.tar.gz failed.\n" if (!-s "$datdir/update_blastdb.pl");
if ( -d "$datdir/nr" ) {
system("rm -rf $datdir/nr*"); # clean up interrupted attempts
$SIG{INT} = \&clean_nr_tgz;
}
# Sometimes fails randomly, run multiple times (sorry horrible hack)
system("perl $datdir/update_blastdb.pl nr");
system("perl $datdir/update_blastdb.pl nr");
system("perl $datdir/update_blastdb.pl nr");
(system("perl $datdir/update_blastdb.pl nr") == 0) or do { &clean_nr_tgz; };
$SIG{INT} = \&clean_nr;
foreach my $f (glob("$datdir/nr.*tar.gz")) {
Expand All @@ -288,16 +296,26 @@
# p_filt NR database from installed nr
if (!$skip_nr && ($overwrite || !-s "$datdir/nr_pfilt.pal")) {
chdir($datdir);
print "Generating nr fasta. Be very patient ......\n";
my $cmd = "$Bin/blast/bin/fastacmd -D 1 > $datdir/nr";
(system($cmd) == 0) or die "ERROR! $cmd failed.\n";
print "Generating nr_pfilt fasta. Be very very patient ......\n";
$cmd = "$Bin/psipred/bin/pfilt $datdir/nr > $datdir/nr_pfilt";
(system($cmd) == 0) or die "ERROR! $cmd failed.\n";
if (!-s "$datdir/nr") {
print "Generating nr fasta. Be very patient ......\n";
my $cmd = "$Bin/blast/bin/fastacmd -D 1 > $datdir/nr";
print $cmd;
(system($cmd) == 0) or die "ERROR! $cmd failed.\n";
}

if (!-s "$datdir/nr_pfilt") {
print "Generating nr_pfilt fasta. Be very very patient ......\n";
my $cmd = "$Bin/psipred/bin/pfilt $datdir/nr > $datdir/nr_pfilt";
print $cmd;
(system($cmd) == 0) or die "ERROR! $cmd failed.\n";
}

print "Formatting nr_pfilt fasta. Be very very very patient ......\n";
system("rm $datdir/nr_pfilt.*"); # clean up interrupted attempts
$SIG{INT} = \&clean_nr_pfilt;
(system("$Bin/blast/bin/formatdb -o T -i $datdir/nr_pfilt") == 0) or do { &clean_nr_pfilt; };
my $cmd = "$Bin/blast/bin/formatdb -o T -i $datdir/nr_pfilt -v 10000";
print $cmd;
(system($cmd) == 0) or do { &clean_nr_pfilt; };
$SIG{INT} = 'DEFAULT';
(-s "$datdir/nr_pfilt.pal") or die "ERROR! $datdir/nr_pfilt database installation failed!\n";
}
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