-
Notifications
You must be signed in to change notification settings - Fork 2
/
lncRNApipeline.pl
1797 lines (1352 loc) · 70.4 KB
/
lncRNApipeline.pl
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
#!/usr/bin/env perl
use strict;
use warnings;
use Getopt::Long;
use File::Temp;
use File::Basename;
use Cwd qw (abs_path cwd);
use Term::ANSIColor qw(:constants);
Getopt::Long::Configure('prefix=--');
my ($LASTCHANGEDBY) = q$LastChangedBy: konganti $ =~ m/.+?\:(.+)/;
my ($LASTCHANGEDDATE) = q$LastChangedDate: 2015-07-08 11:45:27 -0500 (Fri, 08 May 2015) $ =~ m/.+?\:(.+)/;
my ($VERSION) = q$LastChangedRevision: 0.7.9 $ =~ m/.+?\:\s*(.*)\s*.*/;
my $AUTHORFULLNAME = 'Kranti Konganti';
my ($help, $quiet, $setup, $get_uq_sc_opts,
$fetch_sc_opts, $categorize_sc_opts,
$cuffcmp_opts, $deps, $out, $start_cpc,
$start_rnafold, $rm_int_plots, $start_infernal,
$num_cpu, $local_lib, $inf_cov, $skip_cpc_core,
$skip_rnafold_core, $skip_cmscan_core,
$lncRNApipe_ver_info, $no_update_check,
$skip_get_uq, $lncRNApipe_succ, $num_cpu_by_2,
$skip_cpc, $debug);
my $is_valid_option = GetOptions('help:s' => \$help,
'quiet' => \$quiet,
'setup' => \$setup,
'run=s' => \$out,
'cuffcompare|cuffcmp=s' => \$cuffcmp_opts,
'cat-ncRNAs=s' => \$categorize_sc_opts,
'fetch-seq:s' => \$fetch_sc_opts,
'get-uq-feat=s' => \$get_uq_sc_opts,
'cpc' => \$start_cpc,
'rnafold:s' => \$start_rnafold,
'rm-int-plots' => \$rm_int_plots,
'infernal:s' => \$start_infernal,
'cpu=i' => \$num_cpu,
'skip-blastall-core' => \$skip_cpc_core,
'skip-rnafold-core' => \$skip_rnafold_core,
'skip-cmscan-core' => \$skip_cmscan_core,
'coverage-infernal|cov-inf=f' => \$inf_cov,
'local-lib=s' => \$local_lib,
'version' => \$lncRNApipe_ver_info,
'no-update-chk|noup|d' => \$no_update_check,
'skip-get|skip-get-uq' => \$skip_get_uq,
'skip-cpc' => \$skip_cpc,
'send-run-report=s' => \$debug);
# Initialize known defaults
my $CAT_SC = 'categorize_ncRNAs.pl';
my $FETCH_SC = 'fetch_seq_from_ucsc.pl';
my $GET_UQ_SC = 'get_unique_features.pl';
my $CPC_SH_SC = 'CPC.sh';
my $ANN_INF_SC = 'annotate_final_ncRNAs.sh';
my $RELPLOT_MOD_SC = 'relplot_mod.pl';
my $SEND_MAIL_SC = 'send_lncRNApipe_log.pl';
my $USER_HOME = dirname(abs_path($0));
if (defined $num_cpu) {
$num_cpu_by_2 = sprintf("%.0f", $num_cpu / 2) - 1;
}
else {
$num_cpu_by_2 = 1;
}
$inf_cov = 10 if (!defined $inf_cov);
$skip_get_uq = 1 if (defined $skip_get_uq || (!defined $get_uq_sc_opts && defined $fetch_sc_opts));
if (!$is_valid_option) {
die "\nInvalid / No Option(s) Provided:$! See $0 --help for valid options.\n\n";
}
elsif (defined $lncRNApipe_ver_info) {
my $io = run_lncRNApipe('version');
$io->this_script_info('lncRNApipe',
$VERSION,
$AUTHORFULLNAME,
$LASTCHANGEDBY,
$LASTCHANGEDDATE, 'gnu');
exit 0;
}
elsif (defined $setup) {
setup_lncRNApipe(`pwd`)
}
elsif (defined $out || (defined $help && $help eq '')) {
run_lncRNApipe();
}
elsif (defined $debug) {
my $depconf_fh = read_conf('/.lncRNApipe.depconf');
my $pl_dep_paths_fh = read_conf('/.lncRNApipe.PERLLIBS');
my $pl_inc_string = source_env($pl_dep_paths_fh);
get_deps($depconf_fh);
system("$deps->{'email'} $debug");
}
elsif (defined $help && $help ne '') {
my $depconf_fh = read_conf('/.lncRNApipe.depconf');
my $pl_dep_paths_fh = read_conf('/.lncRNApipe.PERLLIBS');
my $pl_inc_string = source_env($pl_dep_paths_fh);
get_deps($depconf_fh);
system("$deps->{'cuffcompare'} -h") if ($help =~ m/cuff|cuffcompare/i);
system("perl $pl_inc_string $deps->{'cat'} -h") if ($help =~ m/cat|cat-ncRNAs/i);
system("perl $pl_inc_string $deps->{'get'} -h") if ($help =~ m/get|get-uq-feat/i);
system("perl $pl_inc_string $deps->{'fetch'} -h") if ($help =~ m/fetch|fetch-seq/i);
system("$deps->{'RNAfold'} --detailed-help") if ($help =~ m/rnafold|rna|fold/i);
system("$deps->{'cmscan'} -h") if ($help =~m /infernal|inf/i);
print "\nSee http://cpc.cbi.pku.edu.cn/docs/install_guide.jsp for help documentation.\n\n" if ($help =~ m/cpc/i);
close $depconf_fh;
close $pl_dep_paths_fh;
}
else {
################################################################################################
# #
# Check for updates first, unless disabled as some serious bugs may have been fixed #
# ================================================================================= #
# #
################################################################################################
check_for_updates();
}
################################################################################################
# #
# Run the pipeline #
# ================ #
# #
################################################################################################
sub run_lncRNApipe {
my $shall_I_run = shift;
my $outdir;
my $pl_dep_paths_fh = read_conf('/.lncRNApipe.PERLLIBS');
my $pl_inc_string = source_env($pl_dep_paths_fh);
$shall_I_run = '' if (!defined $shall_I_run);
# We will quit, if the setup was unsuccessful.
require IO::Routine;
IO::Routine->import();
my $io = IO::Routine->new($help, $quiet);
return $io if ($shall_I_run eq 'version');
$io->verify_options([$out, $is_valid_option]) if (defined $help && $help eq '');
if (!defined $out) {
$outdir = $io->validate_create_path($out, 'do not create',
'lncRNApipe pipeline output directory');
}
else {
$outdir = $io->validate_create_path($out, 'create',
'lncRNApipe pipeline output directory')
}
my $s_time = $io->start_timer;
binmode(STDOUT, ":utf8");
# Validate options here after help documentation is printed
$io->c_time('Validating options...');
$io->c_time("Starting \x{2632}\x{2634} lncRNApipe Pipeline...");
my $dep_tools_fh = $io->open_file('<', $USER_HOME . '/.lncRNApipe.depconf');
get_deps($dep_tools_fh);
$io->exist_sys_cmd(['mkdir']);
my $cuffcmp_dir = $outdir . 'cuffcompare';
# Run cuffcompare ################################################################################
do {
module_header($io, 'Module 1: Running cuffcompare...');
$io->execute_system_command("mkdir -p $cuffcmp_dir",
'Making output directory for cuffcompare [ ' . $cuffcmp_dir . ' ]')
if (!-d $cuffcmp_dir);
# Check if -i is provided with cuffcompare and adjust accordingly.
(my $cuffcmp_opts_trs_in_file) = ($cuffcmp_opts =~ m/-i\s+([^\s]*)/);
if ($cuffcmp_opts_trs_in_file) {
my $i_fh = $io->open_file('<', $cuffcmp_opts_trs_in_file);
my $i_files = do {local $/; <$i_fh>};
my $i_file_str = join(' ', split(/\n|\r/, $i_files));
$cuffcmp_opts =~ s/-i\s+[^\s]*/$i_file_str/;
}
$io->execute_system_command($deps->{'cuffcompare'} .
" -T -o $cuffcmp_dir/lncRNApipe_cuffcmp " .
join('-', split(/\-/, $cuffcmp_opts)),
"Command call:\n" .
"-------------\n" . $deps->{'cuffcompare'} .
" -T -o $cuffcmp_dir/lncRNApipe_cuffcmp " .
join('-', split(/\-/, $cuffcmp_opts)));
} if (defined($cuffcmp_opts) && $cuffcmp_opts ne '');
# Run categorize_ncRNAs.pl ########################################################################
do {
module_header($io, 'Module 2: Running categorize_ncRNAs.pl');
my $is_failed = '';
my $cat_dir = $outdir . 'categorize_ncRNAs';
if (!-e "$cuffcmp_dir/lncRNApipe_cuffcmp.tracking" || !-s "$cuffcmp_dir/lncRNApipe_cuffcmp.tracking") {
print "\nCannot find Cuffcompare tracking [ $cuffcmp_dir/lncRNApipe_cuffcmp.tracking ] file...\n";
$lncRNApipe_succ = pipeline_status($io, 'ERROR');
}
$io->execute_system_command("mkdir -p $cat_dir",
'Making output directory for ' .
$io->file_basename($deps->{'cat'}, 'suffix') .
' [ ' . $cat_dir . ' ]')
if (!-d $cat_dir);
if (defined $cuffcmp_opts && $cuffcmp_opts ne '') {
$lncRNApipe_succ = pipeline_status($io, 'ERROR!', "Required options not mentioned for -cat module.\nSee '" .
"$0 -h cat" . "' for required options.") if ($categorize_sc_opts !~ m/sample/);
my ($tr_files, $tr_size) = get_num_tr_files($cuffcmp_opts);
my $annot_for_cat = '';
if ($categorize_sc_opts !~ m/-ann.*?\s+.+/) {
my $annot = get_annot($cuffcmp_opts);
$io->c_time('Converting annotation file supplied with cuffcompare to gene prediction format [ GTF -> genePred ]');
$annot_for_cat = '-annot ' . $cat_dir . '/' . $io->file_basename($annot) . '.txt';
my $gtfToGenePred_failed = $is_failed = $io->execute_get_sys_cmd_output($deps->{'bin-gtfToGenePred'} . ' -genePredExt -geneNameAsName2 ' .
$annot . ' ' . $cat_dir . '/' . $io->file_basename($annot) . '.txt',
"Command call:\n" .
"-------------\n" .
$deps->{'bin-gtfToGenePred'} . ' -genePredExt -geneNameAsName2 ' .
$annot . ' ' . $cat_dir . '/' . $io->file_basename($annot) . '.txt');
$gtfToGenePred_failed =~ s/[\s\r\n]+//g;
$io->error('gtfToGenePred quit with the following error:' . "\n\n$is_failed\nBailing out!"),
$lncRNApipe_succ = 0
if ($gtfToGenePred_failed =~ m/invalid|error|not/i);
}
$categorize_sc_opts .= " -cpu $num_cpu" if (defined $num_cpu);
$is_failed = $io->execute_get_sys_cmd_output('perl' . $pl_inc_string . $deps->{'cat'} . ' ' .
join('-', split(/\-|\--/, $categorize_sc_opts)) .
" -cuffcmp $cuffcmp_dir/lncRNApipe_cuffcmp.tracking -out $cat_dir " .
"-bin $deps->{'bin-gtfToGenePred'} " . $annot_for_cat . ' ' .
$tr_files,
"Command call:\n" .
"-------------\n" . $deps->{'cat'} . ' ' .
join('-', split(/\-|\--/, $categorize_sc_opts)) .
" -cuffcmp $cuffcmp_dir/lncRNApipe_cuffcmp.tracking -out $cat_dir " .
"-bin $deps->{'bin-gtfToGenePred'} " . $annot_for_cat . ' ' .
$tr_files);
}
else {
$lncRNApipe_succ = pipeline_status($io, 'ERROR!', "Required options not mentioned for -cat module.\nSee '" .
"$0 -h cat" . "' for required options.") if ($categorize_sc_opts !~ m/cuff|annot|out|sample/);
$deps->{'cat'} .= " -cpu $num_cpu" if (defined $num_cpu);
$is_failed = $io->execute_get_sys_cmd_output('perl' . $pl_inc_string . $deps->{'cat'} . ' ' .
"-cuffcmp $cuffcmp_dir/lncRNApipe_cuffcmp.tracking -out $cat_dir " .
"-bin $deps->{'bin-gtfToGenePred'} " .
join('-', split(/\-|\--/, $categorize_sc_opts)),
"Command call:\n" .
"-------------\n" . $deps->{'cat'} . ' ' .
"-cuffcmp $cuffcmp_dir/lncRNApipe_cuffcmp.tracking -out $cat_dir " .
"-bin $deps->{'bin-gtfToGenePred'} " .
join('-', split(/\-|\--/, $categorize_sc_opts)));
}
$lncRNApipe_succ = pipeline_status($io, $is_failed);
} if (defined($categorize_sc_opts) && $categorize_sc_opts ne '');
# Run get_unique_features.pl ######################################################################
do {
my $cpu = do_parallel($num_cpu) if (defined $num_cpu);
$lncRNApipe_succ = get_pipeline_status_code($cpu) if (defined $num_cpu);
module_header($io, 'Module 3: Running get_unique_features.pl');
my $is_failed = '';
my $cat_dir = $outdir . 'get_unique_features';
$io->execute_system_command("mkdir -p $cat_dir",
'Making output directory for ' .
$io->file_basename($deps->{'get'}, 'suffix') .
' [ ' . $cat_dir . ' ]')
if (!-d $cat_dir);
opendir (lncRNApipe_categorize_mod, $outdir . 'categorize_ncRNAs') ||
$io->error("Cannot open directory $outdir" .
'categorize_ncRNAs to read lncRNApipe class files.');
push my @lncRNApipe_class_files, grep {/putative\.class\.lncRNAs\.gtf$/} readdir lncRNApipe_categorize_mod;
if ($#lncRNApipe_class_files < 0) {
$lncRNApipe_succ = pipeline_status($io, 'ERROR', "Cannot find output in $cat_dir ...");
}
$lncRNApipe_succ = pipeline_status($io, 'ERROR!', "Required options not mentioned for -get module.\nSee '" .
"$0 -h get" . "' for required options.") if ($get_uq_sc_opts !~ m/sf|cf/);
foreach my $lncRNApipe_class_file (@lncRNApipe_class_files) {
$cpu->start and next if (defined $num_cpu);
$lncRNApipe_class_file = $outdir . 'categorize_ncRNAs/' . $lncRNApipe_class_file;
my $unique_ncRNAs = $cat_dir . '/' . $io->file_basename($lncRNApipe_class_file) . '.unique.gtf';
unlink $unique_ncRNAs if (-e $unique_ncRNAs);
my $sff_opt = '';
if ($get_uq_sc_opts !~ m/-sff/) {
$io->c_time("Assuming supplied known ncRNAs to be in BED format...\n" .
'You can change this option with -sff. Ex: -sff gtf');
$sff_opt = '-sff bed';
}
$is_failed = $io->execute_get_sys_cmd_output('perl' . $pl_inc_string . $deps->{'get'} . ' ' .
'-q -cf ' . $lncRNApipe_class_file . " -cff gtf $sff_opt ".
join('-', split(/\-|\--/, $get_uq_sc_opts)) .
' -unique -out ' .
$unique_ncRNAs,
"Command call:\n" .
"-------------\n" . $deps->{'get'} . ' ' .
'-q -cf ' . $lncRNApipe_class_file . " -cff gtf $sff_opt ".
join('-', split(/\-|\--/, $get_uq_sc_opts)) .
' -unique -out ' .
$unique_ncRNAs);
$lncRNApipe_succ = pipeline_status($io, $is_failed);
if (-e $unique_ncRNAs && !-s $unique_ncRNAs) {
$lncRNApipe_succ = pipeline_status($io, 'ERROR', "No unique features found. In fact, this is not an error.\n" .
'It just means that any putative lncRNAs that have been extracted from -cat module are all known ncRNAs.');
$io->warning("No unique features found. In fact, this is not an error.\n" .
'It just means that any putative ncRNAs that have been extracted from -cat module are all known ncRNAs.');
$io->warning('Proceeding with files from "categorize_ncRNAs" module.', 'INFO!!');
$skip_get_uq = 1;
}
disp_ncRNA_counts($io, $unique_ncRNAs, 'Total number of putative unique ncRNAs');
$cpu->finish(0, {'lncRNApipe_succ' => $lncRNApipe_succ}) if (defined $num_cpu);
}
$cpu->wait_all_children if (defined $num_cpu);
close lncRNApipe_categorize_mod;
} if (defined($get_uq_sc_opts) && $get_uq_sc_opts ne '');
# Find out if local FASTA mentioned with cuffcompare before running fetch_seq_from_ucsc.pl ########
my $local_ref_seq = '';
# Use local reference FASTA instead of fetching, if provided with cuffcompare
# This needs to be outside do {}, to guarantee parsing, even if -fetch-seq does not have any options.
($local_ref_seq) = ($cuffcmp_opts =~ m/-s\s+([^\s]*)/) if ($cuffcmp_opts);
if ($local_ref_seq && -s $local_ref_seq && -e $local_ref_seq) {
$io->warning('Using local FASTA reference [ ' . $io->file_basename($local_ref_seq, 'suffix') . ' ] to fetch sequences to maintain consistency.' .
"\n** Requires Bio::SeqIO module to be installed and available **", 'INFO!!');
$fetch_sc_opts = "-local $local_ref_seq";
}
elsif( ($local_ref_seq eq '' || !-s $local_ref_seq || !-e $local_ref_seq) && !defined $fetch_sc_opts) {
$io->error("We need to know where to fetch FASTA sequences from [ -local or -db or -ncbi ] ??\n\nSee $0 --h fetch for options.");
}
# Run fetch_seq_from_ucsc.pl ######################################################################
do {
my $cpu = do_parallel($num_cpu) if (defined $num_cpu);
$lncRNApipe_succ = get_pipeline_status_code($cpu) if (defined $num_cpu);
my $uq_tr_feat_dir = 'get_unique_features';
my $tr_feat_here_suffix = 'putative\.class\.lncRNAs\.unique\.gtf$';
module_header($io, 'Module 4: Running fetch_seq_from_ucsc.pl');
my $is_failed = '';
my $cat_dir = $outdir . 'fetch_seq_from_ucsc';
$io->execute_system_command("mkdir -p $cat_dir",
'Making output directory for ' . $io->file_basename($deps->{'fetch'}, 'suffix') . ' [ ' . $cat_dir . ' ]')
if (!-d $cat_dir);
if (defined $skip_get_uq) {
$uq_tr_feat_dir = 'categorize_ncRNAs';
$tr_feat_here_suffix = 'putative\.class\.lncRNAs\.gtf$';
}
opendir (lncRNApipe_get_unique_mod, $outdir . $uq_tr_feat_dir) ||
$io->error("Cannot open directory $outdir" . $uq_tr_feat_dir .
' to read unique ncRNA features.');
push my @lncRNApipe_unique_files, grep {/$tr_feat_here_suffix$/} readdir lncRNApipe_get_unique_mod;
if ($#lncRNApipe_unique_files < 0) {
$lncRNApipe_succ = pipeline_status($io, 'ERROR', "Cannot find output in $cat_dir ...");
}
foreach my $lncRNApipe_unique_file (@lncRNApipe_unique_files) {
$cpu->start and next if (defined $num_cpu);
$lncRNApipe_unique_file = $outdir . $uq_tr_feat_dir . '/' . $lncRNApipe_unique_file;
$is_failed = $io->execute_get_sys_cmd_output('perl' . $pl_inc_string . $deps->{'fetch'} . ' ' .
join('-', split(/\-|\--/, $fetch_sc_opts)) .
' -tmap ' . $lncRNApipe_unique_file .
" -out $cat_dir -ff gtf -id 'transcript_id\\s+\\\"(.+?)\\\"' -skip '\\ttranscript\\t'",
"Command call:\n" .
"-------------\n" . $deps->{'fetch'} . ' ' .
join('-', split(/\-|\--/, $fetch_sc_opts)) .
' -tmap ' . $lncRNApipe_unique_file .
" -out $cat_dir -ff gtf -id 'transcript_id\\s+\\\"(.+?)\\\"' -skip '\\ttranscript\\t'");
$lncRNApipe_succ = pipeline_status($io, $is_failed);
$cpu->finish(0, {'lncRNApipe_succ' => $lncRNApipe_succ}) if (defined $num_cpu);
}
$cpu->wait_all_children if (defined $num_cpu);
close lncRNApipe_get_unique_mod;
} if (defined $fetch_sc_opts);
# Finally Run CPC, RNAfold and Infernal ##############################################################
do {
my $cpu = do_parallel($num_cpu) if (defined $num_cpu);
$lncRNApipe_succ = get_pipeline_status_code($cpu) if (defined $num_cpu);
opendir (lncRNApipe_fetch_seq_mod, $outdir . 'fetch_seq_from_ucsc') ||
$io->error("Cannot open directory $outdir" .
'fetch_seq_from_ucsc to read unique ncRNA features.');
push my @lncRNApipe_unique_seq_files, grep {/putative\.class\.lncRNAs.*?\.fa$/} readdir lncRNApipe_fetch_seq_mod;
my $blastall_path = sub {
my @file_parts = $io->file_basename(shift, 'all');
chop $file_parts[1] if ($file_parts[1] =~ m/\/$/);
return $file_parts[1]
};
$io->exist_sys_cmd(['cut']);
my $lncRNApipe_final = $outdir . 'lncRNApipe.final';
my $cat_dir = $outdir . 'CPC';
$io->execute_system_command("mkdir -p $lncRNApipe_final",
'Making output directory to store final list of ncRNAs [ ' . $io->file_basename($lncRNApipe_final) . ' ]')
if (!-d $lncRNApipe_final);
foreach my $lncRNApipe_unique_seq_file (@lncRNApipe_unique_seq_files) {
$cpu->start and next if (defined $num_cpu);
$num_cpu_by_2 = sprintf("%.0f", $num_cpu / scalar(@lncRNApipe_unique_seq_files)) - 1 if (defined $num_cpu);
$num_cpu_by_2 = 1 if ($num_cpu_by_2 == 0);
$lncRNApipe_unique_seq_file = $outdir . 'fetch_seq_from_ucsc/' . $lncRNApipe_unique_seq_file;
my $lncRNApipe_unique_seq_noncoding_file = $outdir . 'fetch_seq_from_ucsc/' .
$io->file_basename($lncRNApipe_unique_seq_file) . '.noncoding.FASTA';
my $CPC_out_file = $cat_dir . '/' . $io->file_basename($lncRNApipe_unique_seq_file) . '.CPC.predict.txt';
my $cpc_work_dir = $cat_dir . '/' . $io->file_basename($lncRNApipe_unique_seq_file) . '.CPC.out' ;
my $lncRNApipe_final_trs = $lncRNApipe_final . '/' . $io->file_basename($lncRNApipe_unique_seq_file) . '.final.gtf';
my $lncRNApipe_allInfernal_trs = $lncRNApipe_final . '/' . $io->file_basename($lncRNApipe_unique_seq_file) . '.allInfernalHits.gtf';
my $RNAfold_dir = $lncRNApipe_final . '/' . $io->file_basename($lncRNApipe_unique_seq_file) . '.pre.RNAfold';
my $RNAfold_dir_final = $lncRNApipe_final . '/' . $io->file_basename($lncRNApipe_unique_seq_file) . '.final.RNAfold';
my $RNAfold_mfe = $RNAfold_dir . '/' . $io->file_basename($lncRNApipe_unique_seq_file) . '.mfe';
my $unique_gtf = $outdir . 'get_unique_features/' . $io->file_basename($lncRNApipe_unique_seq_file) . '.gtf';
my $pre_infernal = $lncRNApipe_final . '/' . $io->file_basename($lncRNApipe_unique_seq_file) . '.pre.infernal';
my $final_infernal = $lncRNApipe_final . '/' . $io->file_basename($lncRNApipe_unique_seq_file) . '.final.infernal';
if ($skip_get_uq || !-e $unique_gtf) {
$unique_gtf = $outdir . 'categorize_ncRNAs/' . $io->file_basename($lncRNApipe_unique_seq_file) . '.gtf';
}
# Run CPC ####################################################################################
do {
module_header($io, 'Module 5: Running CPC.sh' . ' [ on ' . $io->file_basename($lncRNApipe_unique_seq_file, 'suffix') . ' ] ...');
unlink $lncRNApipe_final_trs if (-e $lncRNApipe_final_trs);
$ENV{'CPC_HOME'} = $deps->{'cpc_home'} if (!exists $ENV{'CPC_HOME'});
if (!-d $ENV{'CPC_HOME'} || $ENV{'CPC_HOME'} eq '') {
$io->error("Environment variable CPC_HOME must be set pointing to CPC directory before running CPC.\n" .
'See CPC installation instructions (http://cpc.cbi.pku.edu.cn/docs/install_guide.jsp)');
}
$io->execute_system_command("mkdir -p $cat_dir",
'Making output directory for ' . $io->file_basename($deps->{'cpc'}, 'suffix') . ' [ ' . $cat_dir . ' ]')
if (!-d $cat_dir);
$io->execute_system_command("mkdir -p $cpc_work_dir") if (!-d $cpc_work_dir);
my $cpc_cpu = 1;
$cpc_cpu = $num_cpu_by_2 if (defined $num_cpu);
if (!defined $skip_cpc_core) {
$io->execute_system_command('NUM_CPU=' . $cpc_cpu . ' ' . $deps->{'cpc'} .
' "' . $lncRNApipe_unique_seq_file . ' ' . $CPC_out_file . ' ' . $cpc_work_dir . ' ' . $cpc_work_dir . '" ' .
$blastall_path->($deps->{'blastall'}),
"Command call:\n" .
"-------------\n" . 'NUM_CPU=' . $cpc_cpu . ' ' . $deps->{'cpc'} .
' "' . $lncRNApipe_unique_seq_file . ' ' . $CPC_out_file . ' ' . $cpc_work_dir . ' ' . $cpc_work_dir . '" ' .
$blastall_path->($deps->{'blastall'}));
}
} if (defined $start_cpc);
# To resume the remaining 2 modules, we need to check for CPC prediction file and adjust the file.
if (!defined $skip_cpc) {
if (-e $CPC_out_file && -s $CPC_out_file) {
$io->c_time('Getting noncoding "only" transcripts [ from ' .
$io->file_basename($unique_gtf, 'suffix') .
" ] ...");
$io->execute_system_command("grep noncoding $CPC_out_file | cut -f 1 | " .
'while read trid; do grep -P "${trid//\./\\\.}\W" ' .
"$unique_gtf; done &> $lncRNApipe_final_trs");
$io->c_time('Creating FASTA for noncoding "only" transcripts [ from ' .
$io->file_basename($unique_gtf, 'suffix') .
" ] ...");
$io->execute_system_command("grep noncoding $CPC_out_file | cut -f 1 | ".
'while read trid; do grep -A 1 -P "${trid//\./\\\.}\W" ' .
"$lncRNApipe_unique_seq_file; done &> $lncRNApipe_unique_seq_noncoding_file");
$lncRNApipe_unique_seq_file = $lncRNApipe_unique_seq_noncoding_file;
}
else {
$lncRNApipe_succ = 0;
$io->error("CPC prediction step seems to have failed... \n" .
"See --skip-cpc if you do not want to run CPC altogether\n\nBailing out!");
}
}
elsif (defined $skip_cpc) {
$io->c_time('Creating a place holder [ --skip-cpc requested ] ...');
$CPC_out_file = $lncRNApipe_final . '/.' . $io->file_basename($lncRNApipe_unique_seq_file) . '.ph';
$io->execute_system_command('grep -oP ">.+?\\s+" ' . $lncRNApipe_unique_seq_file . " | sed -e 's/>//g' | sed -e 's/\\s+\$//g' " .
'| while read trid; do echo -e "${trid}\tnoncoding"; done > ' . $CPC_out_file);
$io->execute_system_command("cp $unique_gtf $lncRNApipe_final_trs");
}
# Do RNAfold and draw entropy plot ############################################################
do {
module_header($io, 'Module 6: Running RNAfold predictions [ on ' . $io->file_basename($lncRNApipe_unique_seq_file, 'suffix') . ' ] ...');
$io->execute_system_command("mkdir -p $RNAfold_dir") if (!-d $RNAfold_dir);
chdir $RNAfold_dir;
$io->c_time('Making directory for RNAfold predictions [ ' . $io->file_basename($RNAfold_dir_final, 'suffix') . ' ] ...');
$io->execute_system_command("mkdir -p $RNAfold_dir_final")
if (!-d $RNAfold_dir_final);
$io->warning('CPC was not run! Will run RNAfold on all transcript models.') if (defined $skip_cpc);
if (!defined $skip_rnafold_core) {
$io->c_time('Running RNAfold with -p flag [ on ' . $io->file_basename($lncRNApipe_unique_seq_file, 'suffix') .
' ]. This may take very long time ...');
$io->execute_system_command($deps->{'RNAfold'} .
' -p ' . $start_rnafold . ' < ' . $lncRNApipe_unique_seq_file . ' &> ' . $RNAfold_mfe,
"Command call:\n" .
"-------------\n" . $deps->{'RNAfold'} .
' -p ' . $start_rnafold . ' < ' . $lncRNApipe_unique_seq_file . ' &> ' . $RNAfold_mfe);
}
$io->c_time('Now generating RNAfold color plots ...');
opendir (RNAfold_pl, $RNAfold_dir) ||
$io->error("Cannot open directory $RNAfold_dir to generate plots");
push my @RNA_relPlots, grep {/\_dp\.ps$/} readdir RNAfold_pl;
$io->error('Cannot find _dp PostScript files. Bailing out!')
if (scalar(@RNA_relPlots) == 0);
foreach my $dp_ (@RNA_relPlots) {
$dp_ = $RNAfold_dir . '/' . $dp_;
my $ss_ = $RNAfold_dir . '/' . $io->file_basename($dp_, 'suffix');
$ss_ =~ s/\_dp\.ps$/\_ss\.ps/i;
my $ps = $ss_;
$ps =~ s/\_ss\.ps$/\_fstruct\.ps/;
my $pre_ps = $ps;
$io->error('Cannot find corresponding _dp or _ss PostScript file(s) [ for transcript ' .
$io->file_basename($ps) . ' ] or any content in it. Bailing out!')
if (!-e $ss_ || !-e $dp_ || !-s $ss_ || !-s $dp_);
$ss_ = esc_tr_id($ss_);
$dp_ = esc_tr_id($dp_);
$ps = esc_tr_id($pre_ps);
$io->execute_system_command($deps->{'relplot'} . ' ' . $ss_ . ' ' . $dp_ . ' > ' . $ps,
"Command call:\n" .
"-------------\n" .
$deps->{'relplot'} . ' ' . $ss_ . ' ' . $dp_ . ' > ' . $ps);
$io->c_time('Cleaning up *_ss.ps and *_dp.ps files ...'),
$io->execute_system_command("rm $dp_"),
$io->execute_system_command("rm $ss_")
if ($rm_int_plots);
$io->error('RNAfold prediction step failed. Cannot generate final PostScript file from _ss.ps and _dp.ps.' . "\nBailing out!")
if (!-e $pre_ps || !-s $pre_ps);
$io->execute_system_command("mv $ps $RNAfold_dir_final/.");
}
close RNAfold_pl;
if (-e $CPC_out_file && -s $CPC_out_file) {
$io->c_time('Filtering transcripts [ ' . $io->file_basename($unique_gtf, 'suffix') . ' ] ...');
$io->execute_system_command("grep noncoding $CPC_out_file | cut -f 1 | " .
"while read trid; do find $RNAfold_dir -type f -name \${trid//\\./\\\\.}_fstruct.ps" .
" -exec mv -t $RNAfold_dir_final" . "/\ {} \\;; done;");
}
$io->c_time('Moving around files and cleaning up directories ...');
$io->execute_system_command("mv $RNAfold_dir/*.mfe $RNAfold_dir_final/.")
if (-e $RNAfold_mfe);
# All possible checks complete, RNAfold has finished.
$lncRNApipe_succ = 1;
} if (defined $start_rnafold);
# Start Infernal and edit final GTF #############################################################
do {
my $tbl = $final_infernal . '/' . $io->file_basename($lncRNApipe_unique_seq_file) . '.txt';
my $raw = $final_infernal . '/' . $io->file_basename($lncRNApipe_unique_seq_file) . '.cmscan';
$io->execute_system_command("mkdir -p $final_infernal")
if (!-d $final_infernal);
module_header($io, 'Module 7: Running cmscan from Infernal [ on ' . $io->file_basename($lncRNApipe_unique_seq_file, 'suffix') . ' ] ...');
$deps->{'cmscan'} .= " --cpu $num_cpu_by_2" if (defined $num_cpu);
if (!defined $skip_cmscan_core) {
$io->execute_system_command($deps->{'cmscan'} . ' ' . $start_infernal . ' --tblout ' .
$tbl . ' ' . $deps->{'rfam_cm'} . ' ' . $lncRNApipe_unique_seq_file . ' &> ' . $raw,
"Command call:\n" .
"-------------\n" . $deps->{'cmscan'} . ' ' . $start_infernal . ' --tblout ' .
$tbl . ' ' . $deps->{'rfam_cm'} . ' ' . $lncRNApipe_unique_seq_file . ' &> ' . $raw);
}
$io->warning('CPC was not run! Will run Infernal on all transcript models.') if (defined $skip_cpc);
if (-e $CPC_out_file && -s $CPC_out_file) {
$io->exist_sys_cmd(['sort', 'head', 'awk', 'uniq', 'mv', 'bc']);
$io->c_time('Updating final GTF file with Infernal annotations...');
my $tmp_annot = $io->open_file('>', $lncRNApipe_final_trs . '.tmp');
unlink $lncRNApipe_allInfernal_trs if (-e $lncRNApipe_allInfernal_trs);
my $infernal_run = $io->execute_get_sys_cmd_output("INF_GTF=$lncRNApipe_allInfernal_trs FINAL_GTF=$lncRNApipe_final_trs" .
" CM_TXT_OUT=$tbl CPC_TXT_OUT=$CPC_out_file COV=$inf_cov" .
' ' . $deps->{'ann-inf'},
"Command call:\n" .
"-------------\n" .
"INF_GTF=$lncRNApipe_allInfernal_trs FINAL_GTF=$lncRNApipe_final_trs" .
" CM_TXT_OUT=$tbl CPC_TXT_OUT=$CPC_out_file COV=$inf_cov" .
' ' . $deps->{'ann-inf'});
$lncRNApipe_succ = pipeline_status($io, 'ERROR!', 'Cannot get annotation from Infernal run') if (!$infernal_run ||
$infernal_run =~ m/could not capture/i ||
!-e $tbl || !-e $raw || !-s $tbl || !-s $raw);
print $tmp_annot $infernal_run;
close $tmp_annot;
$io->c_time('Moving around files...');
$io->execute_system_command("mv $lncRNApipe_final_trs" . '.tmp ' . $lncRNApipe_final_trs);
}
} if (defined $start_infernal);
chomp (my $final_nc_tr_count = $io->execute_get_sys_cmd_output('grep -oP \'transcript_id\\s+\\".+?\\"\' ' . $lncRNApipe_final_trs .
' | grep -oP \'\\".+\\"\' | sed -e \'s/\\"//g\' | sort -n | uniq | wc -l'));
if (!$final_nc_tr_count) {
$io->execute_system_command( "cat $cat_dir/*.CPC.predict.txt | head",
"Truncated output from $cat_dir/*.CPC.predict.txt");
$io->error("Could not get final putative lncRNA count.\n" .
"Try re-running the final module. Take a look at --skip-blastall-core, --skip-rnafold-core and --skip-cmscan-core options." .
"\nThis may also mean that the putative lncRNAs that were used with CPC may have all been flagged as \"coding\".");
}
else {
# Since we will have some transcripts by now that are filtered and passed all stages of the pipeline
$lncRNApipe_succ = 1;
}
disp_ncRNA_counts($io, $lncRNApipe_final_trs, 'Final putative novel lncRNA count');
$cpu->finish(0, {'lncRNApipe_test' => $lncRNApipe_succ}) if (defined $num_cpu);
unlink $CPC_out_file if (defined $skip_cpc);
}
$cpu->wait_all_children if (defined $cpu);
close lncRNApipe_fetch_seq_mod;
} if (defined $start_cpc || defined $start_rnafold || defined $start_infernal || defined $skip_cpc);
close $dep_tools_fh;
close $pl_dep_paths_fh;
# \x{2633}
if ($lncRNApipe_succ) {
$io->c_time("\x{2632}\x{2634} lncRNApipe Pipeline finished!");
}
else {
$io->c_time("\x{2632}\x{2634} lncRNApipe Pipeline aborted(?)");
}
$io->end_timer($s_time);
}
################################################################################################
# #
# Install the pipeline #
# ==================== #
# #
################################################################################################
sub setup_lncRNApipe {
chomp(my $install_dir = shift);
chomp(my $dl_util = `which wget 2>&1`);
binmode(STDOUT, ":utf8");
print "\n\x{1f473} Hi! I am Vayu and I will attempt to install lncRNApipe for you.";
print "\nChecking for platform independent prerequisites on UNIX based machines...\n";
# Wget or Curl
if ($dl_util !~ m/.+?wget$/i) {
chomp ($dl_util = `which curl 2>&1`);
succ_or_fail(0, 'Curl|Wget')
if ($dl_util !~ m/.+?curl$/i);
succ_or_fail(1, 'curl');
$dl_util .= ' -LkO ';
}
elsif ($dl_util =~ m/.+?(wget)$/i) {
succ_or_fail(1, $1);
$dl_util .= ' --no-check-certificate ';
}
else{
succ_or_fail(0, 'Curl|Wget');
}
# Unzip
check_util('unzip');
# Make
check_util('make');
# Echo
check_util('echo');
# Uname
check_util('uname');
# bunzip2
check_util('bunzip2');
# gunzip
check_util('gunzip');
# rm
check_util('rm');
# cp
check_util('cp');
# mkdir
check_util('mkdir');
# touch
check_util('touch');
# mv
check_util('mv');
# find
check_util('find');
# bc
check_util('bc');
print "\n\nWe definetely need the custom module, IO::Routine.\n" .
"We also need good grace of cpanm to install remaining modules.\n\n" .
"Attempting to fetch IO::Routine from Perl-for-Bioinformatics repository on github...\n";
if (-d "$install_dir/.build") {
system("rm -rf $install_dir/.build");
}
if (-d '.build') {
system("rm -rf .build");
}
system("mkdir $install_dir/.build");
succ_or_fail(0, '.build dir') if (!-d "$install_dir/.build");
system("rm $install_dir/master.zip") if (-e "$install_dir/master.zip");
my $dl_util_slave = '';
if ($dl_util =~ m/.*?wget\s+/i) {
$dl_util_slave = $dl_util . '-O master.zip';
}
else {
$dl_util_slave = $dl_util;
}
print "\n$dl_util_slave https://github.com/biocoder/Perl-for-Bioinformatics/archive/master.zip\n\n";
system("$dl_util_slave https://github.com/biocoder/Perl-for-Bioinformatics/archive/master.zip > /dev/null 2>&1");
system("mv $install_dir/master.zip $install_dir/.build/master.zip");
succ_or_fail(0, 'master.zip')
if (!-e "$install_dir/.build/master.zip");
print "Inflating master.zip...\n";
print "\nunzip -d $install_dir/.build $install_dir/.build/master.zip\n";
system("unzip -d $install_dir/.build $install_dir/.build/master.zip > /dev/null 2>&1");
# Use cpanm to install Set::IntervalTree
system("$dl_util https://raw.githubusercontent.com/miyagawa/cpanminus/master/cpanm > /dev/null 2>&1");
succ_or_fail(0, 'cpanm') if (!-e 'cpanm');
system("mv cpanm $install_dir/.build");
system("chmod 755 $install_dir/.build/cpanm");
my $pm_install_dir = $install_dir;
if (defined $local_lib) {
chop $local_lib if ($local_lib =~ m/\/$/);
$pm_install_dir = $local_lib;
}
cpanm_status($pm_install_dir, 'Module::Load', $install_dir);
cpanm_status($pm_install_dir, 'Set::IntervalTree', $install_dir);
cpanm_status($pm_install_dir, 'LWP::Simple', $install_dir);
cpanm_status($pm_install_dir, 'XML::XPath', $install_dir);
cpanm_status($pm_install_dir, 'XML::XPath::XMLParser', $install_dir);
cpanm_status($pm_install_dir, 'Parallel::ForkManager', $install_dir);
cpanm_status($pm_install_dir, 'MIME::Lite', $install_dir);
cpanm_status($pm_install_dir, 'Email::Valid', $install_dir);
if (!ask_user("\n\nDo you already have BioPerl installed?")) {
print "\nOK ... This may take a while ... Grab a snack or coffee!\n";
cpanm_status($pm_install_dir, 'BioPerl', $install_dir);
}
print "\nThank you cpanm!\n";
my $pm_path = "$pm_install_dir/PERLLIBS:$pm_install_dir/PERLLIBS/lib:$pm_install_dir/PERLLIBS/lib/perl5";
print "\nInstalling IO::Routine...\n\n";
system("mkdir $pm_install_dir/PERLLIBS") if (!-d "$pm_install_dir/PERLLIBS");
my $custom_pm_log = `cd $install_dir/.build/Perl-for-Bioinformatics-master/IO-Routine;perl Makefile.PL PREFIX=$pm_install_dir/PERLLIBS LIB=$pm_install_dir/PERLLIBS/lib && make && make test && make install; 2>&1`;
if ($custom_pm_log =~ m/fail|error|cannot/i) {
succ_or_fail(0, 'IO::Routine');
}
else {
succ_or_fail(1, 'IO::Routine');
}
require "$pm_install_dir/PERLLIBS/lib/IO/Routine.pm";
my $io = IO::Routine->new($help, $quiet);
chomp(my $lncRNApipe_root = dirname(abs_path($0)));
if (!-d "$lncRNApipe_root/.lncRNApipe.depbin") {
print "\n\nMoving required tools and scripts to current install path...\n";
system("mkdir $install_dir/.lncRNApipe.depbin");
system("mv $install_dir/.build/Perl-for-Bioinformatics-master/NGS-Utils/.lncRNApipe.depbin/* $install_dir/.lncRNApipe.depbin/.");
system("mv $install_dir/.build/Perl-for-Bioinformatics-master/NGS-Utils/* $install_dir/.");
}
print "\n\nCleaning up build directory...\n";
system("rm -rf $install_dir/.build");
$io->execute_system_command(0, 'Detecting system architecture...');
my $sys_arch_info = $io->execute_get_sys_cmd_output('uname -a');
$io->error('This is not a UNIX based machine ... Aborting installation!')
if (!$sys_arch_info ||
$sys_arch_info !~ m/linux|darwin/i);
$io->error('It is not a 64-bit machine!' .
"\nIt is your responsibility to make sure that you have the following tools" .
" installed for your system architecture and also must be found in \$PATH:\n" .
"\nblastall, gtfToGenePred, cuffcompare and RNAfold\n\nBailing out!")
if ($sys_arch_info !~ m/x86\_64/i);
my $sys_arch = '';
if ($sys_arch_info =~ m/darwin/i) {
$sys_arch = 'darwin';
$io->execute_system_command(0, 'Skipping version requirement check for system level commands [ tar ], [ cut ] and [ wc ].' .
"\nFreeBSD's tools does not provide version numbers (?)");
check_util('tar');
check_util('cut');
check_util('wc');
# Darwin special case...
chomp(my $darwin_sed = `sed --version 2>&1`);
chomp(my $darwin_grep = `grep --version 2>&1`);
if ($darwin_sed !~ m/gnu/i || $darwin_grep !~ m/gnu/i) {
print "\n";
$io->warning("We need GNU's grep and sed instead of FreeBSD's.");
chomp(my $homebrew = `which brew 2>&1`);
print "Looking to see if you have homebrew to install GNU tools [ grep and sed ] ...\n";
if ($homebrew =~ m/.*brew$/i) {
succ_or_fail(1, 'homebrew');
}
else {
$io->error('Please install homebrew. See installation instructions at http://brew.sh/' .
"\nThen, do the following:\n\nbrew update\nbrew tap homebrew/dupes\n" .
"brew install grep\nbrew install gnu-sed\n" .
"ln -s /usr/local/bin/ggrep /usr/local/bin/grep\n" .
"ln -s /usr/local/bin/gsed /usr/local/bin/sed\n\n" .
"Then, rerun the setup procedure to successfully install lncRNApipe pipeline.");
}
print "\n\nPlease execute the following commands in order and" .
" rerun the setup procedure to successfully install lncRNApipe pipeline.\n";
$io->execute_system_command(0,
"brew update\nbrew tap homebrew/dupes\n" .
"brew install grep\nbrew install gnu-sed\n" .
"ln -s /usr/local/bin/ggrep /usr/local/bin/grep\n" .
"ln -s /usr/local/bin/gsed /usr/local/bin/sed");
print "Skipping version check for GNU grep and GNU sed...\n";
succ_or_fail(2, 'sed');
succ_or_fail(2, 'grep');
print "\n\nAborting setup...\n\n";
exit;
}
else {
$io->check_sys_level_cmds(['grep', 'sed'],
['2.6.3', '4.2.1']);
succ_or_fail(1, 'grep');
succ_or_fail(1, 'sed');
}
}
else {
$sys_arch = 'linux';
$io->check_sys_level_cmds(['grep', 'sed', 'tar', 'cut', 'wc'],
['2.6.3', '4.2.1', '0', '8', '8']);
succ_or_fail(1, 'grep');
succ_or_fail(1, 'sed');
succ_or_fail(1, 'tar');
succ_or_fail(1, 'cut');
succ_or_fail(1, 'wc');
}
print "\n\nSetting up PERL5LIB paths...\n";
unlink "$USER_HOME/.lncRNApipe.PERLLIBS" if (-e "$USER_HOME/.lncRNApipe.PERLLIBS");
my $pl_dep_fh = $io->open_file('>', "$USER_HOME/.lncRNApipe.PERLLIBS");
print $pl_dep_fh $pm_path;
$io->execute_system_command(0,
"\nChecking for lncRNApipe pipeline tool dependencies..." .
"\n\nWriting tool dependency chain to $USER_HOME/.lncRNApipe.depconf");
my $dep_fh = $io->open_file('>', "$USER_HOME/.lncRNApipe.depconf");
# We will figure out if user is installing at a different location other than
# from the cloned repo.
$install_dir = $lncRNApipe_root if (-d "$lncRNApipe_root/.lncRNApipe.depbin" && $lncRNApipe_root !~ m/^\./);
if (-e "$install_dir/.lncRNApipe.depbin/Rfam.cm.1_1.bz2" &&
-e "$install_dir/.lncRNApipe.depbin/Rfam.cm.1_1.i1m.bz2") {
print "Decompressing Rfam CM files...\n\n";
system("bunzip2 $install_dir/.lncRNApipe.depbin/Rfam.cm.1_1.bz2");
system("bunzip2 $install_dir/.lncRNApipe.depbin/Rfam.cm.1_1.i1m.bz2");
}
print $dep_fh check_bio_util('cuffcompare', $install_dir, $sys_arch), "\n";
print $dep_fh check_bio_util('blastall', $install_dir, $sys_arch), "\n";
print $dep_fh check_bio_util('RNAfold', $install_dir, $sys_arch), "\n";
print $dep_fh check_bio_util('gtfToGenePred', $install_dir, $sys_arch), "\n";
print $dep_fh check_bio_util('cmscan', $install_dir, $sys_arch), "\n";
print $dep_fh check_bio_util('formatdb', $install_dir, $sys_arch), "\n";
print $dep_fh "$install_dir/" . $CAT_SC, "\n" if (check_native("$install_dir/" . $CAT_SC));
print $dep_fh "$install_dir/" . $FETCH_SC, "\n" if (check_native("$install_dir/" . $FETCH_SC));
print $dep_fh "$install_dir/" . $GET_UQ_SC, "\n" if (check_native("$install_dir/" . $GET_UQ_SC));
print $dep_fh "$install_dir/" . $RELPLOT_MOD_SC, "\n" if (check_native("$install_dir/" . $RELPLOT_MOD_SC));
print $dep_fh "$install_dir/" . $CPC_SH_SC, "\n" if (check_native("$install_dir/" . $CPC_SH_SC));
print $dep_fh "$install_dir/" . $ANN_INF_SC, "\n" if (check_native("$install_dir/" . $ANN_INF_SC));
print $dep_fh "$install_dir/" . $SEND_MAIL_SC, "\n" if (check_native("$install_dir/" . $SEND_MAIL_SC));