# # ChangeLog for /MPI # # Generated by Trac 0.10.4 # 11/24/09 04:07:12 # 11/19/09 10:09:08 cholt [283] * MPI/mpi_iprscan (modified) * lib/iprscan/runlog.pm (modified) * lib/runlog.pm (modified) mpi_iprscan fixes 11/04/09 09:39:38 cholt [277] * MPI/mpi_maker (modified) * bin/maker (modified) * lib/GI.pm (modified) * lib/PhatHit_utils.pm (modified) * lib/Process/MpiChunk.pm (modified) * lib/Widget/exonerate/est2genome.pm (modified) * lib/runlog.pm (modified) attempt to fix exonerate holdover errors 09/08/09 16:43:05 cholt [259] * MPI/mpi_iprscan (modified) * lib/Process/IPRchunk.pm (modified) * lib/Process/MpiTiers.pm (modified) * lib/basiclog.pm (added) * lib/iprscan/runlog.pm (modified) mpi_iprscan more maker like behavior 09/08/09 11:32:56 cholt [258] * MPI/mpi_iprscan (modified) * lib/Process/IPRchunk.pm (modified) * lib/Process/MpiTiers.pm (modified) * lib/iprscan (added) * lib/iprscan/runlog.pm (added) better iprscan wrapper 09/04/09 10:45:29 cholt [256] * MPI/mpi_iprscan (modified) * MPI/mpi_maker (modified) * bin/maker (modified) * lib/Process/IPRchunk.pm (modified) * lib/Process/IPRtiers.pm (deleted) * lib/Process/MpiChunk.pm (modified) * lib/Process/MpiTiers.pm (modified) Update tiers 08/21/09 16:52:11 cholt [244] * INSTALL (modified) * MPI/mpi_evaluator (modified) * MPI/mpi_maker (modified) * README (modified) * bin/maker (modified) * lib/GI.pm (modified) * lib/PhatHit_utils.pm (modified) * lib/Widget/fgenesh.pm (modified) * lib/Widget/genemark/gmhmm_wrap (modified) bug in repeat mask cause by prok upgrade 07/14/09 23:35:46 cholt [236] * MPI/mpi_maker (modified) * bin/maker (modified) fix usage 07/07/09 15:20:38 cholt [228] * MPI/mpi_iprscan (modified) * lib/Process/IPRtiers.pm (modified) * lib/shadow_AED.pm (modified) update mpi_iprscan 06/22/09 17:04:45 cholt [226] * MPI/Install.PL (modified) updated intall 06/22/09 16:20:18 cholt [225] * MPI/mpi_iprscan (modified) * lib/Process/IPRchunk.pm (modified) * lib/Widget/iprscan.pm (modified) fix more mpi_iprscan 06/22/09 12:44:51 cholt [224] * MPI/mpi_iprscan (modified) * bin/fix_fasta (added) update mpi_iprscan 06/22/09 12:33:44 cholt [221] * MPI/mpi_iprscan (added) * bin/add_utr_start_stop_gff (modified) * lib/Process/IPRchunk.pm (added) * lib/Process/IPRtiers.pm (added) * lib/Process/MpiChunk.pm (modified) * lib/Widget/iprscan.pm (added) * lib/basiclog.pm (added) mpi_iprscan added 05/04/09 16:40:07 cholt [212] * MPI/Install.PL (modified) * MPI/threads-1.71 (deleted) * perl/Install.PL (modified) * perl/threads-1.71 (added) * perl/threads-1.71/Changes (added) * perl/threads-1.71/MANIFEST (added) * perl/threads-1.71/META.yml (added) * perl/threads-1.71/Makefile.PL (added) * perl/threads-1.71/README (added) * perl/threads-1.71/examples (added) * perl/threads-1.71/examples/pool.pl (added) * perl/threads-1.71/hints (added) * perl/threads-1.71/hints/hpux.pl (added) * perl/threads-1.71/hints/linux.pl (added) * perl/threads-1.71/ppport.h (added) * perl/threads-1.71/t (added) * perl/threads-1.71/t/basic.t (added) * perl/threads-1.71/t/blocks.t (added) * perl/threads-1.71/t/context.t (added) * perl/threads-1.71/t/end.t (added) * perl/threads-1.71/t/err.t (added) * perl/threads-1.71/t/exit.t (added) * perl/threads-1.71/t/free.t (added) * perl/threads-1.71/t/free2.t (added) * perl/threads-1.71/t/join.t (added) * perl/threads-1.71/t/kill.t (added) * perl/threads-1.71/t/libc.t (added) * perl/threads-1.71/t/list.t (added) * perl/threads-1.71/t/pod.t (added) * perl/threads-1.71/t/problems.t (added) * perl/threads-1.71/t/stack.t (added) * perl/threads-1.71/t/stack_env.t (added) * perl/threads-1.71/t/state.t (added) * perl/threads-1.71/t/stress_cv.t (added) * perl/threads-1.71/t/stress_re.t (added) * perl/threads-1.71/t/stress_string.t (added) * perl/threads-1.71/t/test.pl (added) * perl/threads-1.71/t/thread.t (added) * perl/threads-1.71/threads.h (added) * perl/threads-1.71/threads.pm (added) * perl/threads-1.71/threads.xs (added) changed install process 04/28/09 19:21:50 bmoore [210] * MPI/mpi_maker (modified) Just a bit of whitespace cleanup on mpi_maker 04/28/09 15:01:45 cholt [209] * INSTALL (modified) * MPI/mpi_maker (modified) * README (modified) * lib/File/NFSLock.pm (modified) * lib/GI.pm (modified) * lib/ds_utility.pm (modified) * lib/runlog.pm (modified) lock file update 04/08/09 14:42:34 cholt [198] * MPI/Install.PL (modified) * MPI/mpi_evaluator (added) * MPI/mpi_maker (modified) * bin/evaluator (modified) * bin/maker (modified) * lib/GI.pm (modified) Changed back to three control files, and added mpi_evaluator 04/07/09 16:36:40 cholt [195] * MPI/mpi_maker (modified) * bin/maker (modified) * lib/GFFDB.pm (modified) * lib/GI.pm (modified) * lib/runlog.pm (modified) fix dumper GFFDB, and added again option to maker 03/25/09 11:11:26 cholt [177] * MPI/Install.PL (modified) * MPI/MPIcar/Makefile.PL (modified) * MPI/threads-1.71/Makefile.PL (modified) update Intall for MPI 03/25/09 10:52:13 cholt [176] * MPI/mpi_maker (modified) * bin/maker (modified) update use lib in maker 03/24/09 15:08:16 cholt [173] * MPI/mpi_maker (modified) * README (modified) * lib/Dumper/GFF/GFFV3.pm (modified) * lib/GFFDB.pm (modified) * lib/GI.pm (modified) * lib/Widget/RepeatMasker.pm (modified) * lib/Widget/fgenesh.pm (modified) * lib/runlog.pm (modified) update README 03/16/09 14:18:16 cholt [160] * MPI/mpi_maker (modified) * lib/GI.pm (modified) * lib/Process/MpiChunk.pm (modified) * lib/maker/auto_annotator.pm (modified) * lib/maker/join.pm (modified) * lib/runlog.pm (modified) * lib/shadow_AED.pm (modified) Maker Updates for OOmycete genome, clone hsps, hits in join.pm 03/09/09 00:50:16 cholt [159] * MPI/mpi_maker (modified) * bin/fasta_merge (modified) * bin/gff3_preds2models (added) * bin/maker (modified) * lib/Dumper/GFF/GFFV3.pm (modified) * lib/File (added) * lib/File/NFSLock.pm (added) * lib/GFFDB.pm (modified) * lib/GI.pm (modified) * lib/Process/MpiChunk.pm (modified) * lib/Process/MpiTiers.pm (modified) * lib/Widget/RepeatMasker.pm (modified) * lib/Widget/fgenesh.pm (modified) * lib/cluster.pm (modified) * lib/evaluator/evaluate.pm (modified) * lib/runlog.pm (modified) maker update for all oomycete 02/20/09 12:38:14 cholt [151] * Apollo/gff3.tiers (modified) * MPI/mpi_maker (modified) * bin/gff3_merge (modified) * bin/maker (modified) * lib/Bio/Search/Hit/PhatHit/Base.pm (modified) * lib/CGL/TranslationMachine.pm (modified) * lib/Dumper/GFF/GFFV3.pm (modified) * lib/Fasta.pm (modified) * lib/GFFDB.pm (modified) * lib/GI.pm (modified) * lib/Process/MpiChunk.pm (modified) * lib/Widget/augustus.pm (modified) * lib/clean.pm (modified) * lib/cluster.pm (modified) * lib/evaluator/funs.pm (modified) * lib/evaluator/quality_index.pm (modified) * lib/maker/auto_annotator.pm (modified) * lib/maker/join.pm (modified) * lib/shadow_AED.pm (modified) maker update CDS has stop codon and other opts 02/10/09 12:07:42 cholt [149] * MPI/threads-1.71/Makefile (deleted) * MPI/threads-1.71/blib (deleted) * MPI/threads-1.71/pm_to_blib (deleted) * MPI/threads-1.71/threads.bs (deleted) * MPI/threads-1.71/threads.c (deleted) remove extra thinks in makefiles 02/10/09 12:03:54 cholt [148] * MPI/threads-1.71/Makefile (modified) update of maker 02/09/09 16:49:11 cholt [146] * MPI/mpi_maker (modified) * bin/maker (modified) * lib/Dumper/GFF/GFFV3.pm (modified) * lib/GI.pm (modified) * lib/Process/MpiChunk.pm (modified) * lib/evaluator/evaluate.pm (modified) * lib/maker/auto_annotator.pm (modified) * lib/shadow_AED.pm (added) temporarily disabled evaluator AED 02/06/09 23:23:19 cholt [144] * MPI/mpi_maker (modified) * bin/maker (modified) * bin/mpi_maker (deleted) * lib/FastaChunker.pm (modified) * lib/GFFDB.pm (modified) * lib/GI.pm (modified) * lib/Process/MpiChunk.pm (modified) * lib/Process/MpiTiers.pm (modified) mpi maker updated 01/23/09 12:58:16 cholt [127] * MPI/threads-1.71/Makefile (added) * MPI/threads-1.71/blib (added) * MPI/threads-1.71/blib/arch (added) * MPI/threads-1.71/blib/arch/.exists (added) * MPI/threads-1.71/blib/arch/auto (added) * MPI/threads-1.71/blib/arch/auto/threads (added) * MPI/threads-1.71/blib/arch/auto/threads/.exists (added) * MPI/threads-1.71/blib/arch/auto/threads/threads.bs (added) * MPI/threads-1.71/blib/arch/auto/threads/threads.bundle (added) * MPI/threads-1.71/blib/bin (added) * MPI/threads-1.71/blib/bin/.exists (added) * MPI/threads-1.71/blib/lib (added) * MPI/threads-1.71/blib/lib/.exists (added) * MPI/threads-1.71/blib/lib/auto (added) * MPI/threads-1.71/blib/lib/auto/threads (added) * MPI/threads-1.71/blib/lib/auto/threads/.exists (added) * MPI/threads-1.71/blib/lib/threads.pm (added) * MPI/threads-1.71/blib/man1 (added) * MPI/threads-1.71/blib/man1/.exists (added) * MPI/threads-1.71/blib/man3 (added) * MPI/threads-1.71/blib/man3/.exists (added) * MPI/threads-1.71/blib/script (added) * MPI/threads-1.71/blib/script/.exists (added) * MPI/threads-1.71/pm_to_blib (added) * MPI/threads-1.71/threads.bs (added) * bin/add_utr_gff (deleted) * bin/add_utr_gff.pl (added) * bin/evaluator (added) * bin/gff3_merge (modified) * bin/maker (modified) * bin/maker2zff (deleted) * bin/maker2zff.pl (added) * bin/mpi_maker (added) * bin/split_fasta (deleted) * lib/Bio/Search/HSP/PhatHSP/Base.pm (modified) * lib/Bio/Search/HSP/PhatHSP/augustus.pm (added) * lib/Bio/Search/HSP/PhatHSP/est2genome.pm (added) * lib/Bio/Search/HSP/PhatHSP/fgenesh.pm (added) * lib/Bio/Search/HSP/PhatHSP/gff3.pm (added) * lib/Bio/Search/HSP/PhatHSP/protein2genome.pm (added) * lib/Bio/Search/HSP/PhatHSP/repeatmasker.pm (added) * lib/Bio/Search/HSP/PhatHSP/snap.pm (added) * lib/Bio/Search/Hit/PhatHit/Base.pm (modified) * lib/Bio/Search/Hit/PhatHit/augustus.pm (added) * lib/Bio/Search/Hit/PhatHit/est2genome.pm (added) * lib/Bio/Search/Hit/PhatHit/fgenesh.pm (added) * lib/Bio/Search/Hit/PhatHit/gff3.pm (added) * lib/Bio/Search/Hit/PhatHit/protein2genome.pm (added) * lib/Bio/Search/Hit/PhatHit/repeatmasker.pm (added) * lib/Bio/Search/Hit/PhatHit/snap.pm (added) * lib/Datastore/docs (deleted) * lib/Dumper/GFF/GFF3.pm (deleted) * lib/Dumper/GFF/GFF3_DEF.pm (deleted) * lib/Dumper/GFF/GFFV3.pm (modified) * lib/Dumper/SpaceBase.pm (deleted) * lib/Error/docs (deleted) * lib/Fasta.pm (modified) * lib/FastaChunker.pm (modified) * lib/FastaFile.pm (modified) * lib/GFFDB.pm (added) * lib/GI.pm (added) * lib/Iterator.pm (modified) * lib/Iterator/Any.pm (added) * lib/Iterator/Fasta.pm (modified) * lib/Iterator/GFF3.pm (added) * lib/PhatHit.pm (deleted) * lib/PhatHit_utils.pm (modified) * lib/PhatHsp.pm (deleted) * lib/Process/MakerChunk.pm (deleted) * lib/Process/MakerTiers.pm (deleted) * lib/Process/MpiChunk.pm (added) * lib/Process/MpiTiers.pm (added) * lib/Shared_Functions.pm (deleted) * lib/Widget/.snap.pm.swp (deleted) * lib/Widget/RepeatMasker.pm (modified) * lib/Widget/augustus.pm (modified) * lib/Widget/blastn.pm (modified) * lib/Widget/blastx.pm (modified) * lib/Widget/exonerate/est2genome.pm (modified) * lib/Widget/exonerate/est2genome.pm_orig (deleted) * lib/Widget/exonerate/est2genome.pm_rev (deleted) * lib/Widget/exonerate/protein2genome.pm (modified) * lib/Widget/exonerate/protein2genome.pm_orig (deleted) * lib/Widget/exonerate/protein2genome.pm_rev (deleted) * lib/Widget/fgenesh.pm (modified) * lib/Widget/formatdb.pm (added) * lib/Widget/pressdb.pm (added) * lib/Widget/setdb.pm (added) * lib/Widget/snap.pm (modified) * lib/Widget/tblastx.pm (modified) * lib/Widget/xdformat.pm (modified) * lib/augustus (deleted) * lib/clean.pm (modified) * lib/cluster.pm (modified) * lib/compare.pm (modified) * lib/ds_utility.pm (added) * lib/evaluator/evaluate.pm (modified) * lib/evaluator/funs.pm (modified) * lib/evaluator/gff3_to_phatHit (added) * lib/evaluator/gff3_to_phatHit/FlyBase.pm (added) * lib/evaluator/gff3_to_phatHit/Maker.pm (added) * lib/evaluator/gff3_to_phatHit/WormBase.pm (added) * lib/evaluator/gff3_to_phatHit/gff3_classifier.pm (added) * lib/evaluator/hey_gff3_to_phatHit.pm (added) * lib/evaluator/maker_gff.pm (added) * lib/evaluator/master_codes (added) * lib/evaluator/quality_index.pm (added) * lib/evaluator/quality_seq.pm (modified) * lib/exonerate/PhatHSP (deleted) * lib/exonerate/PhatHit (deleted) * lib/exonerate/splice_info.pm (modified) * lib/external_gff (added) * lib/external_gff/PhatHit.pm (added) * lib/external_gff/PhatHsp.pm (added) * lib/fgenesh (deleted) * lib/maker/auto_annotator.pm (modified) * lib/maker/join.pm (modified) * lib/maker/quality_index.pm (modified) * lib/polisher.pm (modified) * lib/polisher/exonerate/est.pm (modified) * lib/polisher/exonerate/protein.pm (modified) * lib/repeat_mask_seq.pm (modified) * lib/repeatmasker (deleted) * lib/runlog.pm (modified) * lib/snap (deleted) major maker update, gff passthrough, evaluator integration, tblastx, ncbi, error control 11/21/08 14:57:37 hao [122] * MPI/mpi_maker (modified) * lib/Process/MakerChunk.pm (modified) * lib/Shared_Functions.pm (modified) * lib/evaluator/Widget (added) * lib/evaluator/Widget/blast.pm (added) * lib/evaluator/evaluate.pm (modified) * lib/evaluator/funs.pm (modified) * lib/maker/auto_annotator.pm (modified) 10/03/08 14:38:02 cholt [115] * MPI/MPIcar/MPIcar.c (deleted) MPI Install fix 10/03/08 14:28:35 cholt [114] * MPI/MPIcar/MANIFEST (modified) * MPI/MPIcar/Makefile.PL (modified) * MPI/MPIcar/t/01_mpi_init (added) * MPI/MPIcar/t/01_mpi_init.PL (deleted) * MPI/MPIcar/t/02_mpi_finalize (added) * MPI/MPIcar/t/02_mpi_finalize.PL (deleted) * MPI/MPIcar/t/03_mpi_comm_rank (added) * MPI/MPIcar/t/03_mpi_comm_rank.PL (deleted) * MPI/MPIcar/t/04_mpi_comm_size (added) * MPI/MPIcar/t/04_mpi_comm_size.PL (deleted) * MPI/MPIcar/t/05_mpi_initialized (added) * MPI/MPIcar/t/05_mpi_initialized.PL (deleted) * MPI/MPIcar/t/06_mpi_sendrecv (added) * MPI/MPIcar/t/06_mpi_sendrecv.PL (deleted) * MPI/MPIcar/t/06_sendrecv_dbl (added) * MPI/MPIcar/t/06_sendrecv_dbl.PL (deleted) * MPI/MPIcar/t/06_sendrecv_dblarray (added) * MPI/MPIcar/t/06_sendrecv_dblarray.PL (deleted) * MPI/MPIcar/t/06_sendrecv_flt (added) * MPI/MPIcar/t/06_sendrecv_flt.PL (deleted) * MPI/MPIcar/t/06_sendrecv_fltarray (added) * MPI/MPIcar/t/06_sendrecv_fltarray.PL (deleted) * MPI/MPIcar/t/06_sendrecv_int (added) * MPI/MPIcar/t/06_sendrecv_int.PL (deleted) * MPI/MPIcar/t/06_sendrecv_intarray (added) * MPI/MPIcar/t/06_sendrecv_intarray.PL (deleted) * MPI/MPIcar/t/07_mpi_bcast (added) * MPI/MPIcar/t/07_mpi_bcast.PL (deleted) * MPI/MPIcar/t/07_mpi_bcastarray (added) * MPI/MPIcar/t/07_mpi_bcastarray.PL (deleted) * MPI/MPIcar/t/08_mpi_reduce (added) * MPI/MPIcar/t/08_mpi_reduce.PL (deleted) * MPI/MPIcar/t/09_mpi_barrier (added) * MPI/MPIcar/t/09_mpi_barrier.PL (deleted) * MPI/MPIcar/t/10_mpi_wtime (added) * MPI/MPIcar/t/10_mpi_wtime.PL (deleted) * MPI/MPIcar/t/11_mpi_scattergather (added) * MPI/MPIcar/t/11_mpi_scattergather.PL (deleted) * MPI/MPIcar/t/11_mpi_scattergatherarray (added) * MPI/MPIcar/t/11_mpi_scattergatherarray.PL (deleted) * MPI/MPIcar/t/12_mpi_allreduce (added) * MPI/MPIcar/t/12_mpi_allreduce.PL (deleted) * MPI/MPIcar/t/13_mpi_sendrecv (added) * MPI/MPIcar/t/13_mpi_sendrecv.PL (deleted) * lib/perllocal.pod (deleted) MPI install fixes 10/03/08 12:04:06 cholt [111] * MPI/mpi_maker (modified) * bin/maker (modified) * lib/Process/MakerChunk.pm (modified) * lib/Process/MakerTiers.pm (modified) * lib/Shared_Functions.pm (modified) * lib/runlog.pm (modified) tblastx mpi_maker 09/15/08 13:35:22 cholt [101] * MPI/mpi_maker (modified) * bin/maker (modified) * lib/Process/MakerChunk.pm (modified) * lib/Shared_Functions.pm (modified) clean up temp automatically 09/15/08 11:57:35 cholt [100] * MPI/mpi_maker (modified) * lib/Process/MakerChunk.pm (modified) * lib/Shared_Functions.pm (modified) attempt to fix fasta index error 09/09/08 13:02:30 cholt [97] * MPI/mpi_maker (modified) * lib/Process/MakerTiers.pm (modified) * lib/perllocal.pod (modified) fix mpi related issues 09/03/08 14:14:48 cholt [96] * INSTALL (modified) * MPI/MPIcar/MPIcar.bs (deleted) * MPI/MPIcar/Makefile.PL (modified) * MPI/MPIcar/mpi_maker (deleted) * MPI/MPIcar/pm_to_blib (deleted) * README (modified) documentation update 09/03/08 14:13:00 cholt [95] * MPI/threads-1.71/pm_to_blib (deleted) * MPI/threads-1.71/threads.bs (deleted) update to mpi install 09/03/08 14:05:39 cholt [94] * MPI/Install.PL (added) * MPI/MANIFEST (deleted) * MPI/MANIFEST.SKIP (deleted) * MPI/MPIcar (added) * MPI/MPIcar.pm (deleted) * MPI/MPIcar.xs (deleted) * MPI/MPIcar/MANIFEST (added) * MPI/MPIcar/MANIFEST.SKIP (added) * MPI/MPIcar/MPIcar.bs (added) * MPI/MPIcar/MPIcar.c (added) * MPI/MPIcar/MPIcar.pm (added) * MPI/MPIcar/MPIcar.xs (added) * MPI/MPIcar/Makefile.PL (added) * MPI/MPIcar/contrib (added) * MPI/MPIcar/contrib/cpi (added) * MPI/MPIcar/contrib/cpi/Makefile (added) * MPI/MPIcar/contrib/cpi/cpi.PL (added) * MPI/MPIcar/contrib/cpi/cpi.c (added) * MPI/MPIcar/contrib/heat (added) * MPI/MPIcar/contrib/heat/Makefile (added) * MPI/MPIcar/contrib/heat/heat_plate_mpi.PL (added) * MPI/MPIcar/contrib/heat/heat_plate_mpi.f (added) * MPI/MPIcar/contrib/perf (added) * MPI/MPIcar/contrib/perf/Makefile (added) * MPI/MPIcar/contrib/perf/mpi_timing.PL (added) * MPI/MPIcar/contrib/perf/mpi_timing.c (added) * MPI/MPIcar/contrib/perf/runtiming.pl (added) * MPI/MPIcar/docs (added) * MPI/MPIcar/docs/MPI-C-Bindings.txt (added) * MPI/MPIcar/docs/README (added) * MPI/MPIcar/docs/TODO (added) * MPI/MPIcar/docs/paper.tex (added) * MPI/MPIcar/mpi_maker (added) * MPI/MPIcar/pm_to_blib (added) * MPI/MPIcar/t (added) * MPI/MPIcar/t/00_use_mpi.t (added) * MPI/MPIcar/t/01_mpi_init.PL (added) * MPI/MPIcar/t/01_mpi_init.t (added) * MPI/MPIcar/t/02_mpi_finalize.PL (added) * MPI/MPIcar/t/02_mpi_finalize.t (added) * MPI/MPIcar/t/03_mpi_comm_rank.PL (added) * MPI/MPIcar/t/03_mpi_comm_rank.t (added) * MPI/MPIcar/t/04_mpi_comm_size.PL (added) * MPI/MPIcar/t/04_mpi_comm_size.t (added) * MPI/MPIcar/t/05_mpi_initialized.PL (added) * MPI/MPIcar/t/05_mpi_initialized.t (added) * MPI/MPIcar/t/06_mpi_sendrecv.PL (added) * MPI/MPIcar/t/06_mpi_sendrecv.t (added) * MPI/MPIcar/t/06_sendrecv_dbl.PL (added) * MPI/MPIcar/t/06_sendrecv_dbl.t (added) * MPI/MPIcar/t/06_sendrecv_dblarray.PL (added) * MPI/MPIcar/t/06_sendrecv_dblarray.t (added) * MPI/MPIcar/t/06_sendrecv_flt.PL (added) * MPI/MPIcar/t/06_sendrecv_flt.t (added) * MPI/MPIcar/t/06_sendrecv_fltarray.PL (added) * MPI/MPIcar/t/06_sendrecv_fltarray.t (added) * MPI/MPIcar/t/06_sendrecv_int.PL (added) * MPI/MPIcar/t/06_sendrecv_int.t (added) * MPI/MPIcar/t/06_sendrecv_intarray.PL (added) * MPI/MPIcar/t/06_sendrecv_intarray.t (added) * MPI/MPIcar/t/07_mpi_bcast.PL (added) * MPI/MPIcar/t/07_mpi_bcast.t (added) * MPI/MPIcar/t/07_mpi_bcastarray.PL (added) * MPI/MPIcar/t/07_mpi_bcastarray.t (added) * MPI/MPIcar/t/08_mpi_reduce.PL (added) * MPI/MPIcar/t/08_mpi_reduce.t (added) * MPI/MPIcar/t/09_mpi_barrier.PL (added) * MPI/MPIcar/t/09_mpi_barrier.t (added) * MPI/MPIcar/t/10_mpi_wtime.PL (added) * MPI/MPIcar/t/10_mpi_wtime.t (added) * MPI/MPIcar/t/11_mpi_scattergather.PL (added) * MPI/MPIcar/t/11_mpi_scattergather.t (added) * MPI/MPIcar/t/11_mpi_scattergatherarray.PL (added) * MPI/MPIcar/t/11_mpi_scattergatherarray.t (added) * MPI/MPIcar/t/12_mpi_allreduce.PL (added) * MPI/MPIcar/t/12_mpi_allreduce.t (added) * MPI/MPIcar/t/13_mpi_sendrecv.PL (added) * MPI/MPIcar/t/13_mpi_sendrecv.t (added) * MPI/MPIcar/t/greetings.c (added) * MPI/MPIcar/t/machinefile (added) * MPI/MPIcar/typemap (added) * MPI/MPIcar/utils.c (added) * MPI/Makefile.PL (deleted) * MPI/contrib (deleted) * MPI/docs (deleted) * MPI/t (deleted) * MPI/threads-1.71 (added) * MPI/threads-1.71/Changes (added) * MPI/threads-1.71/MANIFEST (added) * MPI/threads-1.71/META.yml (added) * MPI/threads-1.71/Makefile.PL (added) * MPI/threads-1.71/README (added) * MPI/threads-1.71/examples (added) * MPI/threads-1.71/examples/pool.pl (added) * MPI/threads-1.71/hints (added) * MPI/threads-1.71/hints/hpux.pl (added) * MPI/threads-1.71/hints/linux.pl (added) * MPI/threads-1.71/pm_to_blib (added) * MPI/threads-1.71/ppport.h (added) * MPI/threads-1.71/t (added) * MPI/threads-1.71/t/basic.t (added) * MPI/threads-1.71/t/blocks.t (added) * MPI/threads-1.71/t/context.t (added) * MPI/threads-1.71/t/end.t (added) * MPI/threads-1.71/t/err.t (added) * MPI/threads-1.71/t/exit.t (added) * MPI/threads-1.71/t/free.t (added) * MPI/threads-1.71/t/free2.t (added) * MPI/threads-1.71/t/join.t (added) * MPI/threads-1.71/t/kill.t (added) * MPI/threads-1.71/t/libc.t (added) * MPI/threads-1.71/t/list.t (added) * MPI/threads-1.71/t/pod.t (added) * MPI/threads-1.71/t/problems.t (added) * MPI/threads-1.71/t/stack.t (added) * MPI/threads-1.71/t/stack_env.t (added) * MPI/threads-1.71/t/state.t (added) * MPI/threads-1.71/t/stress_cv.t (added) * MPI/threads-1.71/t/stress_re.t (added) * MPI/threads-1.71/t/stress_string.t (added) * MPI/threads-1.71/t/test.pl (added) * MPI/threads-1.71/t/thread.t (added) * MPI/threads-1.71/threads.bs (added) * MPI/threads-1.71/threads.c (added) * MPI/threads-1.71/threads.h (added) * MPI/threads-1.71/threads.pm (added) * MPI/threads-1.71/threads.xs (added) * MPI/typemap (deleted) * MPI/utils.c (deleted) threads added to package, changed mpi install 08/26/08 17:15:30 cholt [89] * Apollo (added) * Apollo/fly.tiers (added) * Apollo/gff3.tiers (added) * INSTALL (added) * MPI (added) * MPI/MANIFEST (added) * MPI/MANIFEST.SKIP (added) * MPI/MPIcar.pm (added) * MPI/MPIcar.xs (added) * MPI/Makefile.PL (added) * MPI/contrib (added) * MPI/contrib/cpi (added) * MPI/contrib/cpi/Makefile (added) * MPI/contrib/cpi/cpi.PL (added) * MPI/contrib/cpi/cpi.c (added) * MPI/contrib/heat (added) * MPI/contrib/heat/Makefile (added) * MPI/contrib/heat/heat_plate_mpi.PL (added) * MPI/contrib/heat/heat_plate_mpi.f (added) * MPI/contrib/perf (added) * MPI/contrib/perf/Makefile (added) * MPI/contrib/perf/mpi_timing.PL (added) * MPI/contrib/perf/mpi_timing.c (added) * MPI/contrib/perf/runtiming.pl (added) * MPI/docs (added) * MPI/docs/MPI-C-Bindings.txt (added) * MPI/docs/README (added) * MPI/docs/TODO (added) * MPI/docs/paper.tex (added) * MPI/mpi_maker (added) * MPI/t (added) * MPI/t/00_use_mpi.t (added) * MPI/t/01_mpi_init.PL (added) * MPI/t/01_mpi_init.t (added) * MPI/t/02_mpi_finalize.PL (added) * MPI/t/02_mpi_finalize.t (added) * MPI/t/03_mpi_comm_rank.PL (added) * MPI/t/03_mpi_comm_rank.t (added) * MPI/t/04_mpi_comm_size.PL (added) * MPI/t/04_mpi_comm_size.t (added) * MPI/t/05_mpi_initialized.PL (added) * MPI/t/05_mpi_initialized.t (added) * MPI/t/06_mpi_sendrecv.PL (added) * MPI/t/06_mpi_sendrecv.t (added) * MPI/t/06_sendrecv_dbl.PL (added) * MPI/t/06_sendrecv_dbl.t (added) * MPI/t/06_sendrecv_dblarray.PL (added) * MPI/t/06_sendrecv_dblarray.t (added) * MPI/t/06_sendrecv_flt.PL (added) * MPI/t/06_sendrecv_flt.t (added) * MPI/t/06_sendrecv_fltarray.PL (added) * MPI/t/06_sendrecv_fltarray.t (added) * MPI/t/06_sendrecv_int.PL (added) * MPI/t/06_sendrecv_int.t (added) * MPI/t/06_sendrecv_intarray.PL (added) * MPI/t/06_sendrecv_intarray.t (added) * MPI/t/07_mpi_bcast.PL (added) * MPI/t/07_mpi_bcast.t (added) * MPI/t/07_mpi_bcastarray.PL (added) * MPI/t/07_mpi_bcastarray.t (added) * MPI/t/08_mpi_reduce.PL (added) * MPI/t/08_mpi_reduce.t (added) * MPI/t/09_mpi_barrier.PL (added) * MPI/t/09_mpi_barrier.t (added) * MPI/t/10_mpi_wtime.PL (added) * MPI/t/10_mpi_wtime.t (added) * MPI/t/11_mpi_scattergather.PL (added) * MPI/t/11_mpi_scattergather.t (added) * MPI/t/11_mpi_scattergatherarray.PL (added) * MPI/t/11_mpi_scattergatherarray.t (added) * MPI/t/12_mpi_allreduce.PL (added) * MPI/t/12_mpi_allreduce.t (added) * MPI/t/13_mpi_sendrecv.PL (added) * MPI/t/13_mpi_sendrecv.t (added) * MPI/t/greetings.c (added) * MPI/t/machinefile (added) * MPI/typemap (added) * MPI/utils.c (added) * README (added) * bin (added) * bin/add_utr_gff.pl (added) * bin/maker (added) * bin/maker2zff.pl (added) * bin/maker_manager (added) * bin/special_apps (added) * bin/special_apps/convert-hmm.pl (added) * bin/special_apps/exonerate_debugger (added) * bin/special_apps/maker_ngasp (added) * bin/special_apps/transposon_masker (added) * data (added) * data/dpp_contig.fasta (added) * data/dpp_proteins.fasta (added) * data/dpp_transcripts.fasta (added) * data/te_proteins.fasta (added) * lib (added) * lib/Bio (added) * lib/Bio/Search (added) * lib/Bio/Search/HSP (added) * lib/Bio/Search/HSP/PhatHSP (added) * lib/Bio/Search/HSP/PhatHSP.pod (added) * lib/Bio/Search/HSP/PhatHSP/Base.pm (added) * lib/Bio/Search/HSP/PhatHSP/blastn.pm (added) * lib/Bio/Search/HSP/PhatHSP/blastp.pm (added) * lib/Bio/Search/HSP/PhatHSP/blastx.pm (added) * lib/Bio/Search/HSP/PhatHSP/tblastn.pm (added) * lib/Bio/Search/HSP/PhatHSP/tblastx.pm (added) * lib/Bio/Search/Hit (added) * lib/Bio/Search/Hit/PhatHit (added) * lib/Bio/Search/Hit/PhatHit.pod (added) * lib/Bio/Search/Hit/PhatHit/Base.pm (added) * lib/Bio/Search/Hit/PhatHit/blastn.pm (added) * lib/Bio/Search/Hit/PhatHit/blastp.pm (added) * lib/Bio/Search/Hit/PhatHit/blastx.pm (added) * lib/Bio/Search/Hit/PhatHit/tblastn.pm (added) * lib/Bio/Search/Hit/PhatHit/tblastx.pm (added) * lib/Bio/SearchIO (added) * lib/Bio/SearchIO/wublasttable.pm (added) * lib/CGL (added) * lib/CGL/Annotation (added) * lib/CGL/Annotation.pm (added) * lib/CGL/Annotation/Feature (added) * lib/CGL/Annotation/Feature.pm (added) * lib/CGL/Annotation/Feature/Contig.pm (added) * lib/CGL/Annotation/Feature/Exon.pm (added) * lib/CGL/Annotation/Feature/Gene.pm (added) * lib/CGL/Annotation/Feature/Intron.pm (added) * lib/CGL/Annotation/Feature/Protein.pm (added) * lib/CGL/Annotation/Feature/Sequence_variant.pm (added) * lib/CGL/Annotation/Feature/Transcript.pm (added) * lib/CGL/Annotation/FeatureLocation.pm (added) * lib/CGL/Annotation/FeatureRelationship.pm (added) * lib/CGL/Annotation/GFF3 (added) * lib/CGL/Annotation/GFF3/DictyBase.pm (added) * lib/CGL/Annotation/GFF3/FlyBase.pm (added) * lib/CGL/Annotation/GFF3/Maker.pm (added) * lib/CGL/Annotation/GFF3/Maker_snap.pm (added) * lib/CGL/Annotation/GFF3/WormBase.pm (added) * lib/CGL/Annotation/GFF3/nGASP.pm (added) * lib/CGL/Annotation/GFF3/nGASP2.pm (added) * lib/CGL/Annotation/Iterator.pm (added) * lib/CGL/Annotation/Trace.pm (added) * lib/CGL/Clone.pm (added) * lib/CGL/Ontology (added) * lib/CGL/Ontology/GO.pm (added) * lib/CGL/Ontology/Node.pm (added) * lib/CGL/Ontology/NodeRelationship.pm (added) * lib/CGL/Ontology/Ontology.pm (added) * lib/CGL/Ontology/Parser (added) * lib/CGL/Ontology/Parser/OBO.pm (added) * lib/CGL/Ontology/SO.pm (added) * lib/CGL/Ontology/Trace.pm (added) * lib/CGL/Revcomp.pm (added) * lib/CGL/TranslationMachine.pm (added) * lib/CGL/Version.pm (added) * lib/CGL/gene_ontology.obo (added) * lib/CGL/so.new.obo (added) * lib/CGL/so.obo (added) * lib/CGL/sofa.obo (added) * lib/Datastore (added) * lib/Datastore/Base.pm (added) * lib/Datastore/CG.pm (added) * lib/Datastore/MD5.pm (added) * lib/Datastore/bin (added) * lib/Datastore/bin/ds_dir (added) * lib/Datastore/bin/ds_do (added) * lib/Datastore/docs (added) * lib/Datastore/docs/Datastore::Base.3pm (added) * lib/Datastore/docs/Datastore::CG.3pm (added) * lib/Datastore/docs/Datastore::MD5.3pm (added) * lib/Datastore/docs/ds_dir.1 (added) * lib/Datastore/docs/ds_do.1 (added) * lib/Dumper (added) * lib/Dumper/GFF (added) * lib/Dumper/GFF/GFF3.pm (added) * lib/Dumper/GFF/GFF3_DEF.pm (added) * lib/Dumper/GFF/GFFV3.pm (added) * lib/Dumper/SpaceBase.pm (added) * lib/Dumper/XML (added) * lib/Dumper/XML/Game.pm (added) * lib/Dumper/XML/Game_Xml.pm (added) * lib/Error (added) * lib/Error.pm (added) * lib/Error/Simple.pm (added) * lib/Error/docs (added) * lib/Error/docs/Error.3pm (added) * lib/Error/docs/Error::Simple.3pm (added) * lib/Fasta.pm (added) * lib/FastaChunk.pm (added) * lib/FastaChunker.pm (added) * lib/FastaFile.pm (added) * lib/Iterator (added) * lib/Iterator.pm (added) * lib/Iterator/Fasta.pm (added) * lib/PhatHit.pm (added) * lib/PhatHit_utils.pm (added) * lib/PhatHsp.pm (added) * lib/PostData.pm (added) * lib/Process (added) * lib/Process/MakerChunk.pm (added) * lib/Process/MakerTiers.pm (added) * lib/Shadower.pm (added) * lib/Shared_Functions.pm (added) * lib/SimpleCluster.pm (added) * lib/SpaceBase.pm (added) * lib/Widget (added) * lib/Widget.pm (added) * lib/Widget/.snap.pm.swp (added) * lib/Widget/PolyBayes.pm (added) * lib/Widget/RepeatMasker.pm (added) * lib/Widget/TblastN.pm (added) * lib/Widget/augustus.pm (added) * lib/Widget/blastn.pm (added) * lib/Widget/blastp.pm (added) * lib/Widget/blastx.pm (added) * lib/Widget/exonerate (added) * lib/Widget/exonerate.pm (added) * lib/Widget/exonerate/est2genome.pm (added) * lib/Widget/exonerate/est2genome.pm_orig (added) * lib/Widget/exonerate/est2genome.pm_rev (added) * lib/Widget/exonerate/protein2genome.pm (added) * lib/Widget/exonerate/protein2genome.pm_orig (added) * lib/Widget/exonerate/protein2genome.pm_rev (added) * lib/Widget/geneid.pm (added) * lib/Widget/genscan.pm (added) * lib/Widget/primer3.pm (added) * lib/Widget/qrna.pm (added) * lib/Widget/snap.pm (added) * lib/Widget/tblastx.pm (added) * lib/Widget/xdformat.pm (added) * lib/augustus (added) * lib/augustus/PhatHit.pm (added) * lib/augustus/PhatHsp.pm (added) * lib/auto (added) * lib/auto/Datastore (added) * lib/auto/Datastore/.packlist (added) * lib/auto/Datastore/Base (added) * lib/auto/Datastore/Base/autosplit.ix (added) * lib/auto/Datastore/CG (added) * lib/auto/Datastore/CG/autosplit.ix (added) * lib/auto/Datastore/MD5 (added) * lib/auto/Datastore/MD5/autosplit.ix (added) * lib/auto/Error (added) * lib/auto/Error/.packlist (added) * lib/clean.pm (added) * lib/cluster.pm (added) * lib/compare.pm (added) * lib/evaluator (added) * lib/exonerate (added) * lib/exonerate/PhatHSP (added) * lib/exonerate/PhatHSP/est2genome.pm (added) * lib/exonerate/PhatHSP/protein2genome.pm (added) * lib/exonerate/PhatHit (added) * lib/exonerate/PhatHit/est2genome.pm (added) * lib/exonerate/PhatHit/protein2genome.pm (added) * lib/exonerate/splice_info.pm (added) * lib/maker (added) * lib/maker/auto_annotator.pm (added) * lib/maker/join.pm (added) * lib/maker/quality_index.pm (added) * lib/maker/sens_spec.pm (added) * lib/perllocal.pod (added) * lib/polisher (added) * lib/polisher.pm (added) * lib/polisher/exonerate (added) * lib/polisher/exonerate.pm (added) * lib/polisher/exonerate/est.pm (added) * lib/polisher/exonerate/protein.pm (added) * lib/repeat_mask_seq.pm (added) * lib/repeatmasker (added) * lib/repeatmasker/PhatHit.pm (added) * lib/repeatmasker/PhatHsp.pm (added) * lib/runlog.pm (added) * lib/snap (added) * lib/snap/PhatHit.pm (added) * lib/snap/PhatHsp.pm (added) * lib/verifier (added) error