[Bioperl-guts-l] [bioperl/bioperl-live] f84488: rename *.PLS to *.pl; Module::Build reworks the sh...

noreply at github.com noreply at github.com
Thu Aug 4 17:51:45 EDT 2011


  Branch: refs/heads/topic/scripts_to_pl
  Home:   https://github.com/bioperl/bioperl-live

  Commit: f844883dff28771046e38941b72fb00d1ac7b3a0
      https://github.com/bioperl/bioperl-live/commit/f844883dff28771046e38941b72fb00d1ac7b3a0
  Author: Chris Fields <cjfields at bioperl.org>
  Date:   2011-08-04 (Thu, 04 Aug 2011)

  Changed paths:
    R scripts/Bio-DB-EUtilities/bp_einfo.PLS
  A scripts/Bio-DB-EUtilities/bp_einfo.pl
  R scripts/Bio-DB-GFF/bp_bulk_load_gff.PLS
  A scripts/Bio-DB-GFF/bp_bulk_load_gff.pl
  R scripts/Bio-DB-GFF/bp_fast_load_gff.PLS
  A scripts/Bio-DB-GFF/bp_fast_load_gff.pl
  R scripts/Bio-DB-GFF/bp_genbank2gff.PLS
  A scripts/Bio-DB-GFF/bp_genbank2gff.pl
  R scripts/Bio-DB-GFF/bp_genbank2gff3.PLS
  A scripts/Bio-DB-GFF/bp_genbank2gff3.pl
  R scripts/Bio-DB-GFF/bp_generate_histogram.PLS
  A scripts/Bio-DB-GFF/bp_generate_histogram.pl
  R scripts/Bio-DB-GFF/bp_load_gff.PLS
  A scripts/Bio-DB-GFF/bp_load_gff.pl
  R scripts/Bio-DB-GFF/bp_meta_gff.PLS
  A scripts/Bio-DB-GFF/bp_meta_gff.pl
  R scripts/Bio-DB-GFF/bp_process_gadfly.PLS
  A scripts/Bio-DB-GFF/bp_process_gadfly.pl
  R scripts/Bio-DB-GFF/bp_process_sgd.PLS
  A scripts/Bio-DB-GFF/bp_process_sgd.pl
  R scripts/Bio-DB-GFF/bp_process_wormbase.PLS
  A scripts/Bio-DB-GFF/bp_process_wormbase.pl
  R scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_delete.PLS
  A scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_delete.pl
  R scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_gff3.PLS
  A scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_gff3.pl
  R scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_load.PLS
  A scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_load.pl
  R scripts/DB-HIV/bp_hivq.PLS
  A scripts/DB-HIV/bp_hivq.pl
  R scripts/DB/bp_biofetch_genbank_proxy.PLS
  A scripts/DB/bp_biofetch_genbank_proxy.pl
  R scripts/DB/bp_bioflat_index.PLS
  A scripts/DB/bp_bioflat_index.pl
  R scripts/DB/bp_biogetseq.PLS
  A scripts/DB/bp_biogetseq.pl
  R scripts/DB/bp_flanks.PLS
  A scripts/DB/bp_flanks.pl
  R scripts/biblio/bp_biblio.PLS
  A scripts/biblio/bp_biblio.pl
  R scripts/index/bp_fetch.PLS
  A scripts/index/bp_fetch.pl
  R scripts/index/bp_index.PLS
  A scripts/index/bp_index.pl
  R scripts/index/bp_seqret.PLS
  A scripts/index/bp_seqret.pl
  R scripts/popgen/bp_composite_LD.PLS
  A scripts/popgen/bp_composite_LD.pl
  R scripts/popgen/bp_heterogeneity_test.PLS
  A scripts/popgen/bp_heterogeneity_test.pl
  R scripts/searchio/bp_fastam9_to_table.PLS
  A scripts/searchio/bp_fastam9_to_table.pl
  R scripts/searchio/bp_filter_search.PLS
  A scripts/searchio/bp_filter_search.pl
  R scripts/searchio/bp_hmmer_to_table.PLS
  A scripts/searchio/bp_hmmer_to_table.pl
  R scripts/searchio/bp_parse_hmmsearch.PLS
  A scripts/searchio/bp_parse_hmmsearch.pl
  R scripts/searchio/bp_search2table.PLS
  A scripts/searchio/bp_search2table.pl
  R scripts/seq/bp_extract_feature_seq.PLS
  A scripts/seq/bp_extract_feature_seq.pl
  R scripts/seq/bp_make_mrna_protein.PLS
  A scripts/seq/bp_make_mrna_protein.pl
  R scripts/seq/bp_seqconvert.PLS
  A scripts/seq/bp_seqconvert.pl
  R scripts/seq/bp_seqretsplit.PLS
  A scripts/seq/bp_seqretsplit.pl
  R scripts/seq/bp_split_seq.PLS
  A scripts/seq/bp_split_seq.pl
  R scripts/seq/bp_translate_seq.PLS
  A scripts/seq/bp_translate_seq.pl
  R scripts/seq/bp_unflatten_seq.PLS
  A scripts/seq/bp_unflatten_seq.pl
  R scripts/seqstats/bp_aacomp.PLS
  A scripts/seqstats/bp_aacomp.pl
  R scripts/seqstats/bp_chaos_plot.PLS
  A scripts/seqstats/bp_chaos_plot.pl
  R scripts/seqstats/bp_gccalc.PLS
  A scripts/seqstats/bp_gccalc.pl
  R scripts/seqstats/bp_oligo_count.PLS
  A scripts/seqstats/bp_oligo_count.pl
  R scripts/taxa/bp_classify_hits_kingdom.PLS
  A scripts/taxa/bp_classify_hits_kingdom.pl
  R scripts/taxa/bp_local_taxonomydb_query.PLS
  A scripts/taxa/bp_local_taxonomydb_query.pl
  R scripts/taxa/bp_query_entrez_taxa.PLS
  A scripts/taxa/bp_query_entrez_taxa.pl
  R scripts/taxa/bp_taxid4species.PLS
  A scripts/taxa/bp_taxid4species.pl
  R scripts/taxa/bp_taxonomy2tree.PLS
  A scripts/taxa/bp_taxonomy2tree.pl
  R scripts/tree/bp_blast2tree.PLS
  A scripts/tree/bp_blast2tree.pl
  R scripts/tree/bp_nexus2nh.PLS
  A scripts/tree/bp_nexus2nh.pl
  R scripts/tree/bp_tree2pag.PLS
  A scripts/tree/bp_tree2pag.pl
  R scripts/utilities/bp_dbsplit.PLS
  A scripts/utilities/bp_dbsplit.pl
  R scripts/utilities/bp_download_query_genbank.PLS
  A scripts/utilities/bp_download_query_genbank.pl
  R scripts/utilities/bp_mask_by_search.PLS
  A scripts/utilities/bp_mask_by_search.pl
  R scripts/utilities/bp_mrtrans.PLS
  A scripts/utilities/bp_mrtrans.pl
  R scripts/utilities/bp_mutate.PLS
  A scripts/utilities/bp_mutate.pl
  R scripts/utilities/bp_netinstall.PLS
  A scripts/utilities/bp_netinstall.pl
  R scripts/utilities/bp_nrdb.PLS
  A scripts/utilities/bp_nrdb.pl
  R scripts/utilities/bp_pairwise_kaks.PLS
  A scripts/utilities/bp_pairwise_kaks.pl
  R scripts/utilities/bp_remote_blast.PLS
  A scripts/utilities/bp_remote_blast.pl
  R scripts/utilities/bp_revtrans-motif.PLS
  A scripts/utilities/bp_revtrans-motif.pl
  R scripts/utilities/bp_search2BSML.PLS
  A scripts/utilities/bp_search2BSML.pl
  R scripts/utilities/bp_search2alnblocks.PLS
  A scripts/utilities/bp_search2alnblocks.pl
  R scripts/utilities/bp_search2gff.PLS
  A scripts/utilities/bp_search2gff.pl
  R scripts/utilities/bp_search2tribe.PLS
  A scripts/utilities/bp_search2tribe.pl
  R scripts/utilities/bp_seq_length.PLS
  A scripts/utilities/bp_seq_length.pl
  R scripts/utilities/bp_sreformat.PLS
  A scripts/utilities/bp_sreformat.pl

  Log Message:
  -----------
  rename *.PLS to *.pl; Module::Build reworks the shebang line accordingly anyway, so the *.PLS distinction is obsolete


  Commit: e1bfea1cf646e2d4626de4d4d2a839db61ae2fd1
      https://github.com/bioperl/bioperl-live/commit/e1bfea1cf646e2d4626de4d4d2a839db61ae2fd1
  Author: Chris Fields <cjfields at bioperl.org>
  Date:   2011-08-04 (Thu, 04 Aug 2011)

  Changed paths:
    M Bio/Root/Build.pm

  Log Message:
  -----------
  remove script code that is obsolete


Compare: https://github.com/bioperl/bioperl-live/compare/f844883^...e1bfea1


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