maint: 644 permissions for almost all files
commitad0159e71e9f24686641816a26949b9e21cd2906
authorCarnë Draug <carandraug+dev@gmail.com>
Sun, 16 Sep 2018 22:04:31 +0000 (16 23:04 +0100)
committerCarnë Draug <carandraug+dev@gmail.com>
Sun, 16 Sep 2018 22:04:31 +0000 (16 23:04 +0100)
tree0b37a1f7cb16e639bc396ac07e4501a96b325308
parent89aa88420658f837094e5da74862c5dd963782f7
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).
126 files changed:
Bio/CodonUsage/IO.pm [changed mode: 0755->0644]
Bio/CodonUsage/Table.pm [changed mode: 0755->0644]
Bio/DB/CUTG.pm [changed mode: 0755->0644]
Bio/Index/Qual.pm [changed mode: 0755->0644]
Bio/Map/Contig.pm [changed mode: 0755->0644]
Bio/Map/EntityI.pm [changed mode: 0755->0644]
Bio/Map/Gene.pm [changed mode: 0755->0644]
Bio/Map/GenePosition.pm [changed mode: 0755->0644]
Bio/Map/GeneRelative.pm [changed mode: 0755->0644]
Bio/Map/Mappable.pm [changed mode: 0755->0644]
Bio/Map/Physical.pm [changed mode: 0755->0644]
Bio/Map/PositionHandler.pm [changed mode: 0755->0644]
Bio/Map/PositionHandlerI.pm [changed mode: 0755->0644]
Bio/Map/Relative.pm [changed mode: 0755->0644]
Bio/Map/RelativeI.pm [changed mode: 0755->0644]
Bio/Matrix/PSM/IO/masta.pm [changed mode: 0755->0644]
Bio/OntologyIO/simplehierarchy.pm [changed mode: 0755->0644]
Bio/Search/BlastStatistics.pm [changed mode: 0755->0644]
Bio/Search/GenericStatistics.pm [changed mode: 0755->0644]
Bio/Search/HSP/PullHSPI.pm [changed mode: 0755->0644]
Bio/Search/Hit/PullHitI.pm [changed mode: 0755->0644]
Bio/Search/Result/PullResultI.pm [changed mode: 0755->0644]
Bio/Search/StatisticsI.pm [changed mode: 0755->0644]
Bio/Search/Tiling/MapTileUtils.pm [changed mode: 0755->0644]
Bio/Search/Tiling/MapTiling.pm [changed mode: 0755->0644]
Bio/Search/Tiling/TilingI.pm [changed mode: 0755->0644]
Bio/Seq/SequenceTrace.pm [changed mode: 0755->0644]
Bio/Seq/TraceI.pm [changed mode: 0755->0644]
Bio/Tools/Alignment/Trim.pm [changed mode: 0755->0644]
Bio/Tools/Analysis/Protein/ELM.pm [changed mode: 0755->0644]
Bio/Tools/Blat.pm [changed mode: 0755->0644]
Bio/Tools/Coil.pm [changed mode: 0755->0644]
Bio/Tools/Fgenesh.pm [changed mode: 0755->0644]
Bio/Tools/Match.pm [changed mode: 0755->0644]
Bio/Tools/Phylo/Gerp.pm [changed mode: 0755->0644]
Bio/Tools/Primer3.pm [changed mode: 0755->0644]
Bio/Tools/Prints.pm [changed mode: 0755->0644]
Bio/Tools/Run/GenericParameters.pm [changed mode: 0755->0644]
Bio/Tools/Run/ParametersI.pm [changed mode: 0755->0644]
Bio/Tools/Seg.pm [changed mode: 0755->0644]
Bio/Tools/Signalp.pm [changed mode: 0755->0644]
Bio/Tools/Spidey/Exon.pm [changed mode: 0755->0644]
Bio/Tools/Spidey/Results.pm [changed mode: 0755->0644]
Bio/Tools/Tmhmm.pm [changed mode: 0755->0644]
Bio/Tools/isPcr.pm [changed mode: 0755->0644]
Bio/Tools/pICalculator.pm [changed mode: 0755->0644]
examples/Bio-DB-GFF/load_ucsc.pl [changed mode: 0755->0644]
examples/align/align_on_codons.pl [changed mode: 0755->0644]
examples/align/aligntutorial.pl [changed mode: 0755->0644]
examples/align/simplealign.pl [changed mode: 0755->0644]
examples/cluster/dbsnp.pl [changed mode: 0755->0644]
examples/contributed/nmrpdb_parse.pl [changed mode: 0755->0644]
examples/contributed/prosite2perl.pl [changed mode: 0755->0644]
examples/contributed/rebase2list.pl [changed mode: 0755->0644]
examples/db/dbfetch [changed mode: 0755->0644]
examples/db/est_tissue_query.pl [changed mode: 0755->0644]
examples/db/gb2features.pl [changed mode: 0755->0644]
examples/db/getGenBank.pl [changed mode: 0755->0644]
examples/db/get_seqs.pl [changed mode: 0755->0644]
examples/db/rfetch.pl [changed mode: 0755->0644]
examples/db/use_registry.pl [changed mode: 0755->0644]
examples/generate_random_seq.pl [changed mode: 0755->0644]
examples/liveseq/change_gene.pl [changed mode: 0755->0644]
examples/longorf.pl [changed mode: 0755->0644]
examples/quality/svgtrace.pl [changed mode: 0755->0644]
examples/rev_and_trans.pl [changed mode: 0755->0644]
examples/revcom_dir.pl [changed mode: 0755->0644]
examples/root/README [changed mode: 0755->0644]
examples/root/exceptions1.pl [changed mode: 0755->0644]
examples/root/exceptions2.pl [changed mode: 0755->0644]
examples/root/exceptions3.pl [changed mode: 0755->0644]
examples/root/exceptions4.pl [changed mode: 0755->0644]
examples/searchio/blast_example.pl [changed mode: 0755->0644]
examples/searchio/custom_writer.pl [changed mode: 0755->0644]
examples/searchio/hitwriter.pl [changed mode: 0755->0644]
examples/searchio/hspwriter.pl [changed mode: 0755->0644]
examples/searchio/htmlwriter.pl [changed mode: 0755->0644]
examples/searchio/psiblast_features.pl [changed mode: 0755->0644]
examples/searchio/psiblast_iterations.pl [changed mode: 0755->0644]
examples/searchio/rawwriter.pl [changed mode: 0755->0644]
examples/searchio/resultwriter.pl [changed mode: 0755->0644]
examples/searchio/waba2gff.pl [changed mode: 0755->0644]
examples/searchio/waba2gff3.pl [changed mode: 0755->0644]
examples/sirna/rnai_finder.cgi [changed mode: 0755->0644]
examples/tk/gsequence.pl [changed mode: 0755->0644]
examples/tk/hitdisplay.pl [changed mode: 0755->0644]
examples/tools/extract_genes.pl [changed mode: 0755->0644]
examples/tools/gb_to_gff.pl [changed mode: 0755->0644]
examples/tools/gff2ps.pl [changed mode: 0755->0644]
examples/tools/parse_codeml.pl [changed mode: 0755->0644]
examples/tools/psw.pl [changed mode: 0755->0644]
examples/tools/reverse-translate.pl [changed mode: 0755->0644]
examples/tools/run_genscan.pl [changed mode: 0755->0644]
examples/tools/run_primer3.pl [changed mode: 0755->0644]
examples/tools/seq_pattern.pl [changed mode: 0755->0644]
examples/tools/standaloneblast.pl [changed mode: 0755->0644]
examples/tree/paup2phylip.pl [changed mode: 0755->0644]
maintenance/dependencies.pl [changed mode: 0644->0755]
maintenance/deprecated.pl [changed mode: 0644->0755]
maintenance/module_usage.pl [changed mode: 0644->0755]
scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_load.pl [changed mode: 0755->0644]
scripts/README [changed mode: 0755->0644]
scripts/seq/bp_seqpart.pl [changed mode: 0755->0644]
t/LocalDB/Registry.t [changed mode: 0755->0644]
t/Map/MicrosatelliteMarker.t [changed mode: 0755->0644]
t/Matrix/IO/masta.t [changed mode: 0755->0644]
t/Ontology/GraphAdaptor.t [changed mode: 0755->0644]
t/Ontology/IO/go.t [changed mode: 0755->0644]
t/RemoteDB/CUTG.t [changed mode: 0755->0644]
t/RemoteDB/EntrezGene.t [changed mode: 0755->0644]
t/RemoteDB/GenBank.t [changed mode: 0755->0644]
t/RemoteDB/GenPept.t [changed mode: 0755->0644]
t/RemoteDB/Query/GenBank.t [changed mode: 0755->0644]
t/RemoteDB/SwissProt.t [changed mode: 0755->0644]
t/SearchIO/Writer/HSPTableWriter.t [changed mode: 0755->0644]
t/Seq/PrimedSeq.t [changed mode: 0755->0644]
t/SeqIO/scf.t [changed mode: 0755->0644]
t/SeqIO/tinyseq.t [changed mode: 0755->0644]
t/Tools/Alignment/Consed.t [changed mode: 0755->0644]
t/Tools/Analysis/Protein/ELM.t [changed mode: 0755->0644]
t/Tools/Analysis/Protein/Scansite.t [changed mode: 0755->0644]
t/Tools/Lucy.t [changed mode: 0755->0644]
t/Tools/Primer3.t [changed mode: 0755->0644]
t/Tools/Pseudowise.t [changed mode: 0755->0644]
t/Tools/pICalculator.t [changed mode: 0755->0644]
t/Tree/Compatible.t [changed mode: 0755->0644]