[Bioperl-l] Production scripts

[Brian Osborne]

Bioperl-l,

The idea that we've tacitly agreed upon is that there will be scripts in
bioperl that are available for installation, should the user choose to
install them. These scripts would be labeled *PLS and be kept in scripts/,
all other scripts would be kept in examples/. Scripts destined for scripts/
should:

-Do something useful
-Be non-trivial
-Be sufficiently flexible and accept command-line arguments
-Be documented

My opinion is that "documented" should mean documented by POD, such that the
various POD-equivalents like man pages, HTML, etc. can be created. I like
the man page particularly because it allows 'man -k', so that someone like
myself who knows that a script that probably does something-or-other has
been installed but whose name I can't recall can find the script. Your
thoughts? Should production scripts be POD-documented?

Here's list of scripts that are PODded and could be considered scripts
destined for installation:

scripts/graphics/feature_draw.pl
scripts/index/bpfetch.pl
scripts/index/bpindex.pl
scripts/tools/remote_blast.pl
scripts/taxa/taxid4species.PLS
scripts/seq/extract_feature_seq.PLS
scripts/taxa/taxid4species.PLS
scripts/utilities/bp_mrtrans.PLS
scripts/utilities/bp_nrdb.PLS
scripts/utilities/bp_sreformat.PLS
scripts/utilities/pairwise_kaks.PLS
scripts/seq_length.pl
scripts/Bio-DB-GFF/generate_histogram.pl
scripts/Bio-DB-GFF/process_gadfly.pl
scripts/Bio-DB-GFF/process_ncbi_human.pl
scripts/Bio-DB-GFF/process_sgd.pl
scripts/Bio-DB-GFF/process_wormbase.pl
scripts/tools/remote_blast.pl
scripts/tree/blast2tree.pl

Here's a list of scripts that could be installable scripts except that they
aren't PODded:

scripts/make_mrna_protein.pl
Bio-DB-GFF/bulk_load_gff
Bio-DB-GFF/fast_load_gff
Bio-DB-GFF/load_gff
Bio-DB-GFF/ucsc2gff
scripts/DB/blast_fetch.pl
scripts/DB/blast_fetch_local.pl
scripts/DB/get_seqs.pl
scripts/align/align_on_codons.pl
scripts/align/clustalw.pl
scripts/biblio/biblio.pl

Only my opinions, you understand. If I don't hear complaints I'll go ahead
and rearrange the scripts/ and examples/ directories as proposed above. I
don't know what the actual dir names would be, perhaps "tools" would become
"utilities". And we'll need to test these, as Peter suggested.

Brian O.