Hi! > > fasta, fasta3, > Here we have probably to do some further investigation: We have the blast2 > package which also seems to contain a version of fasta. Could anybody more > educated than me please comment on this?
>From my emails changed with upstream author William R. Pearson <[EMAIL >PROTECTED]> (this is what he said): [EMAIL 1] I am nervous about distributing FASTA with a Linux distribution, because there is always a chance that the version of FASTA that is distributed would have a bug, which, by the time someone installed it from the distribution, would probably be fixed. I am more comfortable including a script that would automatically download the current version from ftp.virginia.edu/pub/fasta/fasta3.shar.Z, and compile it. [EMAIL 2]: It did not occur to me that you would only want to distribute binaries, since they are not very useful without DNA and/or protein sequence databases (which are considerably larger). Are you planning on a distribution that includes sequence databases? I can certainly see an advantage to a distribution that has pre-compiled versions of the programs (possibly pre-configured to recognize the databases). [THE LAST ONE]: I do not think there is much reason to distribute only my program, because compiling my program is the smallest of the several steps required to having a working FASTA system. Downloading the databases and editing configuration files to find the databases is much more time consuming and confusing. So, I would prefer that FASTA not be included in your distribution, though I encourage you to include a script that would allow people to download and compile FASTA. [END] "your distribution" = Debian So, I think that fasta is out of Debian, right? > > gff2ps, (...) > Here the reasons are given in the mails of the thread above: It is just > duplicated functionality with a worse implementation. As Steffen Moeller said: "BioPerl does not offer the example as a ready-to-use application." Bioperl's version is different from the one that I cited. And I found the error on gff2ps. It is something with locales. Using LC_ALL=pt_BR, it fails to build the PS file. LC_ALL=C works OK. I have contacted upstream author and said about that. Also, from TODO list of gff2ps: "Full re-write in Perl..." I can release a gff2ps version, using a wrapper with something like /usr/bin/gff2ps = #!/bin/sh LC_ALL=C /usr/share/gff2ps/gff2ps.real Or something like that. This is a workaround until upstream releases a new version. Or we could wait to the new version, without releasing a version before. > > gperiodic, grappa, kinemage, lamarc, > > libgenome, lsysexp, migrate, nab, > Missing. Gperiodic is on Debian! :-) > Matt Hope, who is an official Debian developer maintains a private archive > of biological software. I have heard that the reason for this is that he > has not enough time to bring the packages into a shape which is fit for > official Debian (Matt, please correct me if I'm wrong). My idea would be > to start group maintainance of these packages. If somebody would be able > to offer Matt the help he needs we might quickly be able to move all his > packages to the Debian mirror. I would also spend some time on some of > these > packages (perhaps tagging myself as "Uploader" for the packages). If there is something that I could help, let me know, please. Cheers, Nelson A. de Oliveira __________________________________________________________________________ UOL Fone: Fale com o Brasil e o Mundo com at� 90% de economia. http://www.uol.com.br/fone
