[Bioperl-l] Production scripts

[Ewan Birney]

On Mon, 27 Jan 2003, 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.

This all sounds great. Lots of encouragement from this end... ;)




> 
> Brian O.
> 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at bioperl.org
> http://bioperl.org/mailman/listinfo/bioperl-l
> 

-----------------------------------------------------------------
Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
<birney at ebi.ac.uk>. 
-----------------------------------------------------------------