From ad0159e71e9f24686641816a26949b9e21cd2906 Mon Sep 17 00:00:00 2001 From: =?utf8?q?Carn=C3=AB=20Draug?= Date: Sun, 16 Sep 2018 23:04:31 +0100 Subject: [PATCH] maint: 644 permissions for almost all files All files permissions set to 644. Exception are scripts in maintenance and travis_scripts (all set to 755) since they are meant to be run after clone. Even stuff in scripts/ is set to 644 because it's only meant to be run after the installation, and never from the git repository (the release and install steps both modify the scripts). --- Bio/CodonUsage/IO.pm | 0 Bio/CodonUsage/Table.pm | 0 Bio/DB/CUTG.pm | 0 Bio/Index/Qual.pm | 0 Bio/Map/Contig.pm | 0 Bio/Map/EntityI.pm | 0 Bio/Map/Gene.pm | 0 Bio/Map/GenePosition.pm | 0 Bio/Map/GeneRelative.pm | 0 Bio/Map/Mappable.pm | 0 Bio/Map/Physical.pm | 0 Bio/Map/PositionHandler.pm | 0 Bio/Map/PositionHandlerI.pm | 0 Bio/Map/Relative.pm | 0 Bio/Map/RelativeI.pm | 0 Bio/Matrix/PSM/IO/masta.pm | 0 Bio/OntologyIO/simplehierarchy.pm | 0 Bio/Search/BlastStatistics.pm | 0 Bio/Search/GenericStatistics.pm | 0 Bio/Search/HSP/PullHSPI.pm | 0 Bio/Search/Hit/PullHitI.pm | 0 Bio/Search/Result/PullResultI.pm | 0 Bio/Search/StatisticsI.pm | 0 Bio/Search/Tiling/MapTileUtils.pm | 0 Bio/Search/Tiling/MapTiling.pm | 0 Bio/Search/Tiling/TilingI.pm | 0 Bio/Seq/SequenceTrace.pm | 0 Bio/Seq/TraceI.pm | 0 Bio/Tools/Alignment/Trim.pm | 0 Bio/Tools/Analysis/Protein/ELM.pm | 0 Bio/Tools/Blat.pm | 0 Bio/Tools/Coil.pm | 0 Bio/Tools/Fgenesh.pm | 0 Bio/Tools/Match.pm | 0 Bio/Tools/Phylo/Gerp.pm | 0 Bio/Tools/Primer3.pm | 0 Bio/Tools/Prints.pm | 0 Bio/Tools/Run/GenericParameters.pm | 0 Bio/Tools/Run/ParametersI.pm | 0 Bio/Tools/Seg.pm | 0 Bio/Tools/Signalp.pm | 0 Bio/Tools/Spidey/Exon.pm | 0 Bio/Tools/Spidey/Results.pm | 0 Bio/Tools/Tmhmm.pm | 0 Bio/Tools/isPcr.pm | 0 Bio/Tools/pICalculator.pm | 0 examples/Bio-DB-GFF/load_ucsc.pl | 0 examples/align/align_on_codons.pl | 0 examples/align/aligntutorial.pl | 0 examples/align/simplealign.pl | 0 examples/cluster/dbsnp.pl | 0 examples/contributed/nmrpdb_parse.pl | 0 examples/contributed/prosite2perl.pl | 0 examples/contributed/rebase2list.pl | 0 examples/db/dbfetch | 0 examples/db/est_tissue_query.pl | 0 examples/db/gb2features.pl | 0 examples/db/getGenBank.pl | 0 examples/db/get_seqs.pl | 0 examples/db/rfetch.pl | 0 examples/db/use_registry.pl | 0 examples/generate_random_seq.pl | 0 examples/liveseq/change_gene.pl | 0 examples/longorf.pl | 0 examples/quality/svgtrace.pl | 0 examples/rev_and_trans.pl | 0 examples/revcom_dir.pl | 0 examples/root/README | 0 examples/root/exceptions1.pl | 0 examples/root/exceptions2.pl | 0 examples/root/exceptions3.pl | 0 examples/root/exceptions4.pl | 0 examples/searchio/blast_example.pl | 0 examples/searchio/custom_writer.pl | 0 examples/searchio/hitwriter.pl | 0 examples/searchio/hspwriter.pl | 0 examples/searchio/htmlwriter.pl | 0 examples/searchio/psiblast_features.pl | 0 examples/searchio/psiblast_iterations.pl | 0 examples/searchio/rawwriter.pl | 0 examples/searchio/resultwriter.pl | 0 examples/searchio/waba2gff.pl | 0 examples/searchio/waba2gff3.pl | 0 examples/sirna/rnai_finder.cgi | 0 examples/tk/gsequence.pl | 0 examples/tk/hitdisplay.pl | 0 examples/tools/extract_genes.pl | 0 examples/tools/gb_to_gff.pl | 0 examples/tools/gff2ps.pl | 0 examples/tools/parse_codeml.pl | 0 examples/tools/psw.pl | 0 examples/tools/reverse-translate.pl | 0 examples/tools/run_genscan.pl | 0 examples/tools/run_primer3.pl | 0 examples/tools/seq_pattern.pl | 0 examples/tools/standaloneblast.pl | 0 examples/tree/paup2phylip.pl | 0 maintenance/dependencies.pl | 0 maintenance/deprecated.pl | 0 maintenance/module_usage.pl | 0 scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_load.pl | 0 scripts/README | 0 scripts/seq/bp_seqpart.pl | 0 t/LocalDB/Registry.t | 0 t/Map/MicrosatelliteMarker.t | 0 t/Matrix/IO/masta.t | 0 t/Ontology/GraphAdaptor.t | 0 t/Ontology/IO/go.t | 0 t/RemoteDB/CUTG.t | 0 t/RemoteDB/EntrezGene.t | 0 t/RemoteDB/GenBank.t | 0 t/RemoteDB/GenPept.t | 0 t/RemoteDB/Query/GenBank.t | 0 t/RemoteDB/SwissProt.t | 0 t/SearchIO/Writer/HSPTableWriter.t | 0 t/Seq/PrimedSeq.t | 0 t/SeqIO/scf.t | 0 t/SeqIO/tinyseq.t | 0 t/Tools/Alignment/Consed.t | 0 t/Tools/Analysis/Protein/ELM.t | 0 t/Tools/Analysis/Protein/Scansite.t | 0 t/Tools/Lucy.t | 0 t/Tools/Primer3.t | 0 t/Tools/Pseudowise.t | 0 t/Tools/pICalculator.t | 0 t/Tree/Compatible.t | 0 126 files changed, 0 insertions(+), 0 deletions(-) mode change 100755 => 100644 Bio/CodonUsage/IO.pm mode change 100755 => 100644 Bio/CodonUsage/Table.pm mode change 100755 => 100644 Bio/DB/CUTG.pm mode change 100755 => 100644 Bio/Index/Qual.pm mode change 100755 => 100644 Bio/Map/Contig.pm mode change 100755 => 100644 Bio/Map/EntityI.pm mode change 100755 => 100644 Bio/Map/Gene.pm mode change 100755 => 100644 Bio/Map/GenePosition.pm mode change 100755 => 100644 Bio/Map/GeneRelative.pm mode change 100755 => 100644 Bio/Map/Mappable.pm mode change 100755 => 100644 Bio/Map/Physical.pm mode change 100755 => 100644 Bio/Map/PositionHandler.pm mode change 100755 => 100644 Bio/Map/PositionHandlerI.pm mode change 100755 => 100644 Bio/Map/Relative.pm mode change 100755 => 100644 Bio/Map/RelativeI.pm mode change 100755 => 100644 Bio/Matrix/PSM/IO/masta.pm mode change 100755 => 100644 Bio/OntologyIO/simplehierarchy.pm mode change 100755 => 100644 Bio/Search/BlastStatistics.pm mode change 100755 => 100644 Bio/Search/GenericStatistics.pm mode change 100755 => 100644 Bio/Search/HSP/PullHSPI.pm mode change 100755 => 100644 Bio/Search/Hit/PullHitI.pm mode change 100755 => 100644 Bio/Search/Result/PullResultI.pm mode change 100755 => 100644 Bio/Search/StatisticsI.pm mode change 100755 => 100644 Bio/Search/Tiling/MapTileUtils.pm mode change 100755 => 100644 Bio/Search/Tiling/MapTiling.pm mode change 100755 => 100644 Bio/Search/Tiling/TilingI.pm mode change 100755 => 100644 Bio/Seq/SequenceTrace.pm mode change 100755 => 100644 Bio/Seq/TraceI.pm mode change 100755 => 100644 Bio/Tools/Alignment/Trim.pm mode change 100755 => 100644 Bio/Tools/Analysis/Protein/ELM.pm mode change 100755 => 100644 Bio/Tools/Blat.pm mode change 100755 => 100644 Bio/Tools/Coil.pm mode change 100755 => 100644 Bio/Tools/Fgenesh.pm mode change 100755 => 100644 Bio/Tools/Match.pm mode change 100755 => 100644 Bio/Tools/Phylo/Gerp.pm mode change 100755 => 100644 Bio/Tools/Primer3.pm mode change 100755 => 100644 Bio/Tools/Prints.pm mode change 100755 => 100644 Bio/Tools/Run/GenericParameters.pm mode change 100755 => 100644 Bio/Tools/Run/ParametersI.pm mode change 100755 => 100644 Bio/Tools/Seg.pm mode change 100755 => 100644 Bio/Tools/Signalp.pm mode change 100755 => 100644 Bio/Tools/Spidey/Exon.pm mode change 100755 => 100644 Bio/Tools/Spidey/Results.pm mode change 100755 => 100644 Bio/Tools/Tmhmm.pm mode change 100755 => 100644 Bio/Tools/isPcr.pm mode change 100755 => 100644 Bio/Tools/pICalculator.pm mode change 100755 => 100644 examples/Bio-DB-GFF/load_ucsc.pl mode change 100755 => 100644 examples/align/align_on_codons.pl mode change 100755 => 100644 examples/align/aligntutorial.pl mode change 100755 => 100644 examples/align/simplealign.pl mode change 100755 => 100644 examples/cluster/dbsnp.pl mode change 100755 => 100644 examples/contributed/nmrpdb_parse.pl mode change 100755 => 100644 examples/contributed/prosite2perl.pl mode change 100755 => 100644 examples/contributed/rebase2list.pl mode change 100755 => 100644 examples/db/dbfetch mode change 100755 => 100644 examples/db/est_tissue_query.pl mode change 100755 => 100644 examples/db/gb2features.pl mode change 100755 => 100644 examples/db/getGenBank.pl mode change 100755 => 100644 examples/db/get_seqs.pl mode change 100755 => 100644 examples/db/rfetch.pl mode change 100755 => 100644 examples/db/use_registry.pl mode change 100755 => 100644 examples/generate_random_seq.pl mode change 100755 => 100644 examples/liveseq/change_gene.pl mode change 100755 => 100644 examples/longorf.pl mode change 100755 => 100644 examples/quality/svgtrace.pl mode change 100755 => 100644 examples/rev_and_trans.pl mode change 100755 => 100644 examples/revcom_dir.pl mode change 100755 => 100644 examples/root/README mode change 100755 => 100644 examples/root/exceptions1.pl mode change 100755 => 100644 examples/root/exceptions2.pl mode change 100755 => 100644 examples/root/exceptions3.pl mode change 100755 => 100644 examples/root/exceptions4.pl mode change 100755 => 100644 examples/searchio/blast_example.pl mode change 100755 => 100644 examples/searchio/custom_writer.pl mode change 100755 => 100644 examples/searchio/hitwriter.pl mode change 100755 => 100644 examples/searchio/hspwriter.pl mode change 100755 => 100644 examples/searchio/htmlwriter.pl mode change 100755 => 100644 examples/searchio/psiblast_features.pl mode change 100755 => 100644 examples/searchio/psiblast_iterations.pl mode change 100755 => 100644 examples/searchio/rawwriter.pl mode change 100755 => 100644 examples/searchio/resultwriter.pl mode change 100755 => 100644 examples/searchio/waba2gff.pl mode change 100755 => 100644 examples/searchio/waba2gff3.pl mode change 100755 => 100644 examples/sirna/rnai_finder.cgi mode change 100755 => 100644 examples/tk/gsequence.pl mode change 100755 => 100644 examples/tk/hitdisplay.pl mode change 100755 => 100644 examples/tools/extract_genes.pl mode change 100755 => 100644 examples/tools/gb_to_gff.pl mode change 100755 => 100644 examples/tools/gff2ps.pl mode change 100755 => 100644 examples/tools/parse_codeml.pl mode change 100755 => 100644 examples/tools/psw.pl mode change 100755 => 100644 examples/tools/reverse-translate.pl mode change 100755 => 100644 examples/tools/run_genscan.pl mode change 100755 => 100644 examples/tools/run_primer3.pl mode change 100755 => 100644 examples/tools/seq_pattern.pl mode change 100755 => 100644 examples/tools/standaloneblast.pl mode change 100755 => 100644 examples/tree/paup2phylip.pl mode change 100644 => 100755 maintenance/dependencies.pl mode change 100644 => 100755 maintenance/deprecated.pl mode change 100644 => 100755 maintenance/module_usage.pl mode change 100755 => 100644 scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_load.pl mode change 100755 => 100644 scripts/README mode change 100755 => 100644 scripts/seq/bp_seqpart.pl mode change 100755 => 100644 t/LocalDB/Registry.t mode change 100755 => 100644 t/Map/MicrosatelliteMarker.t mode change 100755 => 100644 t/Matrix/IO/masta.t mode change 100755 => 100644 t/Ontology/GraphAdaptor.t mode change 100755 => 100644 t/Ontology/IO/go.t mode change 100755 => 100644 t/RemoteDB/CUTG.t mode change 100755 => 100644 t/RemoteDB/EntrezGene.t mode change 100755 => 100644 t/RemoteDB/GenBank.t mode change 100755 => 100644 t/RemoteDB/GenPept.t mode change 100755 => 100644 t/RemoteDB/Query/GenBank.t mode change 100755 => 100644 t/RemoteDB/SwissProt.t mode change 100755 => 100644 t/SearchIO/Writer/HSPTableWriter.t mode change 100755 => 100644 t/Seq/PrimedSeq.t mode change 100755 => 100644 t/SeqIO/scf.t mode change 100755 => 100644 t/SeqIO/tinyseq.t mode change 100755 => 100644 t/Tools/Alignment/Consed.t mode change 100755 => 100644 t/Tools/Analysis/Protein/ELM.t mode change 100755 => 100644 t/Tools/Analysis/Protein/Scansite.t mode change 100755 => 100644 t/Tools/Lucy.t mode change 100755 => 100644 t/Tools/Primer3.t mode change 100755 => 100644 t/Tools/Pseudowise.t mode change 100755 => 100644 t/Tools/pICalculator.t mode change 100755 => 100644 t/Tree/Compatible.t diff --git a/Bio/CodonUsage/IO.pm b/Bio/CodonUsage/IO.pm old mode 100755 new mode 100644 diff --git a/Bio/CodonUsage/Table.pm b/Bio/CodonUsage/Table.pm old mode 100755 new mode 100644 diff --git a/Bio/DB/CUTG.pm b/Bio/DB/CUTG.pm old mode 100755 new mode 100644 diff --git a/Bio/Index/Qual.pm b/Bio/Index/Qual.pm old mode 100755 new mode 100644 diff --git a/Bio/Map/Contig.pm b/Bio/Map/Contig.pm old mode 100755 new mode 100644 diff --git a/Bio/Map/EntityI.pm b/Bio/Map/EntityI.pm old mode 100755 new mode 100644 diff --git a/Bio/Map/Gene.pm b/Bio/Map/Gene.pm old mode 100755 new mode 100644 diff --git a/Bio/Map/GenePosition.pm b/Bio/Map/GenePosition.pm old mode 100755 new mode 100644 diff --git a/Bio/Map/GeneRelative.pm b/Bio/Map/GeneRelative.pm old mode 100755 new mode 100644 diff --git a/Bio/Map/Mappable.pm b/Bio/Map/Mappable.pm old mode 100755 new mode 100644 diff --git a/Bio/Map/Physical.pm b/Bio/Map/Physical.pm old mode 100755 new mode 100644 diff --git a/Bio/Map/PositionHandler.pm b/Bio/Map/PositionHandler.pm old mode 100755 new mode 100644 diff --git a/Bio/Map/PositionHandlerI.pm b/Bio/Map/PositionHandlerI.pm old mode 100755 new mode 100644 diff --git a/Bio/Map/Relative.pm b/Bio/Map/Relative.pm old mode 100755 new mode 100644 diff --git a/Bio/Map/RelativeI.pm b/Bio/Map/RelativeI.pm old mode 100755 new mode 100644 diff --git a/Bio/Matrix/PSM/IO/masta.pm b/Bio/Matrix/PSM/IO/masta.pm old mode 100755 new mode 100644 diff --git a/Bio/OntologyIO/simplehierarchy.pm b/Bio/OntologyIO/simplehierarchy.pm old mode 100755 new mode 100644 diff --git a/Bio/Search/BlastStatistics.pm b/Bio/Search/BlastStatistics.pm old mode 100755 new mode 100644 diff --git a/Bio/Search/GenericStatistics.pm b/Bio/Search/GenericStatistics.pm old mode 100755 new mode 100644 diff --git a/Bio/Search/HSP/PullHSPI.pm b/Bio/Search/HSP/PullHSPI.pm old mode 100755 new mode 100644 diff --git a/Bio/Search/Hit/PullHitI.pm b/Bio/Search/Hit/PullHitI.pm old mode 100755 new mode 100644 diff --git a/Bio/Search/Result/PullResultI.pm b/Bio/Search/Result/PullResultI.pm old mode 100755 new mode 100644 diff --git a/Bio/Search/StatisticsI.pm b/Bio/Search/StatisticsI.pm old mode 100755 new mode 100644 diff --git a/Bio/Search/Tiling/MapTileUtils.pm b/Bio/Search/Tiling/MapTileUtils.pm old mode 100755 new mode 100644 diff --git a/Bio/Search/Tiling/MapTiling.pm b/Bio/Search/Tiling/MapTiling.pm old mode 100755 new mode 100644 diff --git a/Bio/Search/Tiling/TilingI.pm b/Bio/Search/Tiling/TilingI.pm old mode 100755 new mode 100644 diff --git a/Bio/Seq/SequenceTrace.pm b/Bio/Seq/SequenceTrace.pm old mode 100755 new mode 100644 diff --git a/Bio/Seq/TraceI.pm b/Bio/Seq/TraceI.pm old mode 100755 new mode 100644 diff --git a/Bio/Tools/Alignment/Trim.pm b/Bio/Tools/Alignment/Trim.pm old mode 100755 new mode 100644 diff --git a/Bio/Tools/Analysis/Protein/ELM.pm b/Bio/Tools/Analysis/Protein/ELM.pm old mode 100755 new mode 100644 diff --git a/Bio/Tools/Blat.pm b/Bio/Tools/Blat.pm old mode 100755 new mode 100644 diff --git a/Bio/Tools/Coil.pm b/Bio/Tools/Coil.pm old mode 100755 new mode 100644 diff --git a/Bio/Tools/Fgenesh.pm b/Bio/Tools/Fgenesh.pm old mode 100755 new mode 100644 diff --git a/Bio/Tools/Match.pm b/Bio/Tools/Match.pm old mode 100755 new mode 100644 diff --git a/Bio/Tools/Phylo/Gerp.pm b/Bio/Tools/Phylo/Gerp.pm old mode 100755 new mode 100644 diff --git a/Bio/Tools/Primer3.pm b/Bio/Tools/Primer3.pm old mode 100755 new mode 100644 diff --git a/Bio/Tools/Prints.pm b/Bio/Tools/Prints.pm old mode 100755 new mode 100644 diff --git a/Bio/Tools/Run/GenericParameters.pm b/Bio/Tools/Run/GenericParameters.pm old mode 100755 new mode 100644 diff --git a/Bio/Tools/Run/ParametersI.pm b/Bio/Tools/Run/ParametersI.pm old mode 100755 new mode 100644 diff --git a/Bio/Tools/Seg.pm b/Bio/Tools/Seg.pm old mode 100755 new mode 100644 diff --git a/Bio/Tools/Signalp.pm b/Bio/Tools/Signalp.pm old mode 100755 new mode 100644 diff --git a/Bio/Tools/Spidey/Exon.pm b/Bio/Tools/Spidey/Exon.pm old mode 100755 new mode 100644 diff --git a/Bio/Tools/Spidey/Results.pm b/Bio/Tools/Spidey/Results.pm old mode 100755 new mode 100644 diff --git a/Bio/Tools/Tmhmm.pm b/Bio/Tools/Tmhmm.pm old mode 100755 new mode 100644 diff --git a/Bio/Tools/isPcr.pm b/Bio/Tools/isPcr.pm old mode 100755 new mode 100644 diff --git a/Bio/Tools/pICalculator.pm b/Bio/Tools/pICalculator.pm old mode 100755 new mode 100644 diff --git a/examples/Bio-DB-GFF/load_ucsc.pl b/examples/Bio-DB-GFF/load_ucsc.pl old mode 100755 new mode 100644 diff --git a/examples/align/align_on_codons.pl b/examples/align/align_on_codons.pl old mode 100755 new mode 100644 diff --git a/examples/align/aligntutorial.pl b/examples/align/aligntutorial.pl old mode 100755 new mode 100644 diff --git a/examples/align/simplealign.pl b/examples/align/simplealign.pl old mode 100755 new mode 100644 diff --git a/examples/cluster/dbsnp.pl b/examples/cluster/dbsnp.pl old mode 100755 new mode 100644 diff --git a/examples/contributed/nmrpdb_parse.pl b/examples/contributed/nmrpdb_parse.pl old mode 100755 new mode 100644 diff --git a/examples/contributed/prosite2perl.pl b/examples/contributed/prosite2perl.pl old mode 100755 new mode 100644 diff --git a/examples/contributed/rebase2list.pl b/examples/contributed/rebase2list.pl old mode 100755 new mode 100644 diff --git a/examples/db/dbfetch b/examples/db/dbfetch old mode 100755 new mode 100644 diff --git a/examples/db/est_tissue_query.pl b/examples/db/est_tissue_query.pl old mode 100755 new mode 100644 diff --git a/examples/db/gb2features.pl b/examples/db/gb2features.pl old mode 100755 new mode 100644 diff --git a/examples/db/getGenBank.pl b/examples/db/getGenBank.pl old mode 100755 new mode 100644 diff --git a/examples/db/get_seqs.pl b/examples/db/get_seqs.pl old mode 100755 new mode 100644 diff --git a/examples/db/rfetch.pl b/examples/db/rfetch.pl old mode 100755 new mode 100644 diff --git a/examples/db/use_registry.pl b/examples/db/use_registry.pl old mode 100755 new mode 100644 diff --git a/examples/generate_random_seq.pl b/examples/generate_random_seq.pl old mode 100755 new mode 100644 diff --git a/examples/liveseq/change_gene.pl b/examples/liveseq/change_gene.pl old mode 100755 new mode 100644 diff --git a/examples/longorf.pl b/examples/longorf.pl old mode 100755 new mode 100644 diff --git a/examples/quality/svgtrace.pl b/examples/quality/svgtrace.pl old mode 100755 new mode 100644 diff --git a/examples/rev_and_trans.pl b/examples/rev_and_trans.pl old mode 100755 new mode 100644 diff --git a/examples/revcom_dir.pl b/examples/revcom_dir.pl old mode 100755 new mode 100644 diff --git a/examples/root/README b/examples/root/README old mode 100755 new mode 100644 diff --git a/examples/root/exceptions1.pl b/examples/root/exceptions1.pl old mode 100755 new mode 100644 diff --git a/examples/root/exceptions2.pl b/examples/root/exceptions2.pl old mode 100755 new mode 100644 diff --git a/examples/root/exceptions3.pl b/examples/root/exceptions3.pl old mode 100755 new mode 100644 diff --git a/examples/root/exceptions4.pl b/examples/root/exceptions4.pl old mode 100755 new mode 100644 diff --git a/examples/searchio/blast_example.pl b/examples/searchio/blast_example.pl old mode 100755 new mode 100644 diff --git a/examples/searchio/custom_writer.pl b/examples/searchio/custom_writer.pl old mode 100755 new mode 100644 diff --git a/examples/searchio/hitwriter.pl b/examples/searchio/hitwriter.pl old mode 100755 new mode 100644 diff --git a/examples/searchio/hspwriter.pl b/examples/searchio/hspwriter.pl old mode 100755 new mode 100644 diff --git a/examples/searchio/htmlwriter.pl b/examples/searchio/htmlwriter.pl old mode 100755 new mode 100644 diff --git a/examples/searchio/psiblast_features.pl b/examples/searchio/psiblast_features.pl old mode 100755 new mode 100644 diff --git a/examples/searchio/psiblast_iterations.pl b/examples/searchio/psiblast_iterations.pl old mode 100755 new mode 100644 diff --git a/examples/searchio/rawwriter.pl b/examples/searchio/rawwriter.pl old mode 100755 new mode 100644 diff --git a/examples/searchio/resultwriter.pl b/examples/searchio/resultwriter.pl old mode 100755 new mode 100644 diff --git a/examples/searchio/waba2gff.pl b/examples/searchio/waba2gff.pl old mode 100755 new mode 100644 diff --git a/examples/searchio/waba2gff3.pl b/examples/searchio/waba2gff3.pl old mode 100755 new mode 100644 diff --git a/examples/sirna/rnai_finder.cgi b/examples/sirna/rnai_finder.cgi old mode 100755 new mode 100644 diff --git a/examples/tk/gsequence.pl b/examples/tk/gsequence.pl old mode 100755 new mode 100644 diff --git a/examples/tk/hitdisplay.pl b/examples/tk/hitdisplay.pl old mode 100755 new mode 100644 diff --git a/examples/tools/extract_genes.pl b/examples/tools/extract_genes.pl old mode 100755 new mode 100644 diff --git a/examples/tools/gb_to_gff.pl b/examples/tools/gb_to_gff.pl old mode 100755 new mode 100644 diff --git a/examples/tools/gff2ps.pl b/examples/tools/gff2ps.pl old mode 100755 new mode 100644 diff --git a/examples/tools/parse_codeml.pl b/examples/tools/parse_codeml.pl old mode 100755 new mode 100644 diff --git a/examples/tools/psw.pl b/examples/tools/psw.pl old mode 100755 new mode 100644 diff --git a/examples/tools/reverse-translate.pl b/examples/tools/reverse-translate.pl old mode 100755 new mode 100644 diff --git a/examples/tools/run_genscan.pl b/examples/tools/run_genscan.pl old mode 100755 new mode 100644 diff --git a/examples/tools/run_primer3.pl b/examples/tools/run_primer3.pl old mode 100755 new mode 100644 diff --git a/examples/tools/seq_pattern.pl b/examples/tools/seq_pattern.pl old mode 100755 new mode 100644 diff --git a/examples/tools/standaloneblast.pl b/examples/tools/standaloneblast.pl old mode 100755 new mode 100644 diff --git a/examples/tree/paup2phylip.pl b/examples/tree/paup2phylip.pl old mode 100755 new mode 100644 diff --git a/maintenance/dependencies.pl b/maintenance/dependencies.pl old mode 100644 new mode 100755 diff --git a/maintenance/deprecated.pl b/maintenance/deprecated.pl old mode 100644 new mode 100755 diff --git a/maintenance/module_usage.pl b/maintenance/module_usage.pl old mode 100644 new mode 100755 diff --git a/scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_load.pl b/scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_load.pl old mode 100755 new mode 100644 diff --git a/scripts/README b/scripts/README old mode 100755 new mode 100644 diff --git a/scripts/seq/bp_seqpart.pl b/scripts/seq/bp_seqpart.pl old mode 100755 new mode 100644 diff --git a/t/LocalDB/Registry.t b/t/LocalDB/Registry.t old mode 100755 new mode 100644 diff --git a/t/Map/MicrosatelliteMarker.t b/t/Map/MicrosatelliteMarker.t old mode 100755 new mode 100644 diff --git a/t/Matrix/IO/masta.t b/t/Matrix/IO/masta.t old mode 100755 new mode 100644 diff --git a/t/Ontology/GraphAdaptor.t b/t/Ontology/GraphAdaptor.t old mode 100755 new mode 100644 diff --git a/t/Ontology/IO/go.t b/t/Ontology/IO/go.t old mode 100755 new mode 100644 diff --git a/t/RemoteDB/CUTG.t b/t/RemoteDB/CUTG.t old mode 100755 new mode 100644 diff --git a/t/RemoteDB/EntrezGene.t b/t/RemoteDB/EntrezGene.t old mode 100755 new mode 100644 diff --git a/t/RemoteDB/GenBank.t b/t/RemoteDB/GenBank.t old mode 100755 new mode 100644 diff --git a/t/RemoteDB/GenPept.t b/t/RemoteDB/GenPept.t old mode 100755 new mode 100644 diff --git a/t/RemoteDB/Query/GenBank.t b/t/RemoteDB/Query/GenBank.t old mode 100755 new mode 100644 diff --git a/t/RemoteDB/SwissProt.t b/t/RemoteDB/SwissProt.t old mode 100755 new mode 100644 diff --git a/t/SearchIO/Writer/HSPTableWriter.t b/t/SearchIO/Writer/HSPTableWriter.t old mode 100755 new mode 100644 diff --git a/t/Seq/PrimedSeq.t b/t/Seq/PrimedSeq.t old mode 100755 new mode 100644 diff --git a/t/SeqIO/scf.t b/t/SeqIO/scf.t old mode 100755 new mode 100644 diff --git a/t/SeqIO/tinyseq.t b/t/SeqIO/tinyseq.t old mode 100755 new mode 100644 diff --git a/t/Tools/Alignment/Consed.t b/t/Tools/Alignment/Consed.t old mode 100755 new mode 100644 diff --git a/t/Tools/Analysis/Protein/ELM.t b/t/Tools/Analysis/Protein/ELM.t old mode 100755 new mode 100644 diff --git a/t/Tools/Analysis/Protein/Scansite.t b/t/Tools/Analysis/Protein/Scansite.t old mode 100755 new mode 100644 diff --git a/t/Tools/Lucy.t b/t/Tools/Lucy.t old mode 100755 new mode 100644 diff --git a/t/Tools/Primer3.t b/t/Tools/Primer3.t old mode 100755 new mode 100644 diff --git a/t/Tools/Pseudowise.t b/t/Tools/Pseudowise.t old mode 100755 new mode 100644 diff --git a/t/Tools/pICalculator.t b/t/Tools/pICalculator.t old mode 100755 new mode 100644 diff --git a/t/Tree/Compatible.t b/t/Tree/Compatible.t old mode 100755 new mode 100644 -- 2.11.4.GIT