[Bioperl-l] Production scripts

Hilmar Lapp hlapp at gnf.org
Mon Jan 27 10:08:31 EST 2003


Brian I second this. -hilmar

On Monday, January 27, 2003, at 06:49  AM, Brian Osborne wrote:

> 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.
>
>
>
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>
-- 
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------



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