Changeset 89

Timestamp:

08/26/08 17:15:30 (1 year ago)

Author:

cholt

Message:

error

Files:

• 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)