Science packages

rudi · 2005-02-14 21:04:53

Hi,

Why is it that there are so few science packages available for Arch? I've read in another topic that one of the package maintainers uses his computer for sequence alignment:

dp wrote:

i effectively _work_ on computer ~1h/d + short times that are difficult to count ... but the computer runs for ~6h/d because of compilings and computing for my studies (sequence alignment, ...)

Why are there are so few bioinformatics packages? Is it possible that there could be more science tools added like ncbi tools, clustalW, clustalX, njplot, phylip, seaview, scilab.......well you get the idea

Rudi

sarah31 · 2005-02-14 21:08:28

probably because no one other than dp has ever bothered to make or request any? In this case i would say if you need them or want them then you may have to start reading on how to build packages. If you build any and get them working maybe you can talk dp into maintaining them

rudi · 2005-02-14 21:24:31

Well, i'll start reading the wiki about ABS then

Make a note that next to dp, i also have made a request, that's two allready! (how much are needed to get them into the repositories? )

sarah31 · 2005-02-14 21:36:27

rudi wrote:

Well, i'll start reading the wiki about ABS then
Make a note that next to dp, i also have made a request, that's two allready! (how much are needed to get them into the repositories? )

Well how many requests to get something in the repos is very hard to guage. There are always packages that can be added that will get alot of use but people will not think about them until they do exist in the repos.

You are right that there are not enough science apps in the arch repos and if you endevour to make some it would be nice to see them added. Then we can see how they do.

phrakture · 2005-02-14 22:22:48

i thought I saw scilab somewhere.....

Snowman · 2005-02-14 23:20:14

phrakture wrote:

i thought I saw scilab somewhere.....

I have scilab in my repo.

dp · 2005-02-15 00:26:55

rudi wrote:

Hi,
Why is it that there are so few science packages available for Arch? I've read in another topic that one of the package maintainers uses his computer for sequence alignment:
dp wrote:
i effectively _work_ on computer ~1h/d + short times that are difficult to count ... but the computer runs for ~6h/d because of compilings and computing for my studies (sequence alignment, ...)
Why are there are so few bioinformatics packages? Is it possible that there could be more science tools added like ncbi tools, clustalW, clustalX, njplot, phylip, seaview, scilab.......well you get the idea
Rudi

clustal{X,W}, fasta and phylip i have on my local machine ... and i would include them to [extra]::science but there is one small trouble: licences! i have no idea if these tools are free to be providen as binary

if you can find that out for me, it would be a good start - feel free to contact me per email, if you find something out

rudi · 2005-02-15 09:15:30

* Edit *
Phylip added
FASTA added
******

NJPlot - License: not mentioned on the website (http://pbil.univ-lyon1.fr/software/njplot.html)
Binary files:
* njplot.linux
* njplot.help
* test.ph
NCBI Toolbox - License: gpl
Source: ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/ncbi.tar.gz
(I only occasionally have compiled packages, so I don't know to much about make. I couldn't compile this. It uses csh)
ClustalW - I have contacted Toby Gibson and asked if ClustalW can be added to the repos of Archlinux. This is his reply:

Anything that is freely available to end users is acceptable to us without restriction.
Best,
Toby

I think, because ClustalX has the same license description, that ClustalX can also be included (i wouldn't mind asking those developers also btw to be completely sure).

Phylip - License: (http://evolution.genetics.washington.ed … #copyright)
Phylip may be distributed freely, not on commercial products (charged CD's)

FASTA - License: (ftp://ftp.virginia.edu/pub/fasta/COPYRIGHT)
Archlinux is free and non-commercial, so i guess FASTA can be included. It is included with biobrew btw.

dp · 2005-02-15 14:19:51

rudi,

many thanx for checking this licences

NJPlot: there is only the binary around, right? it would be much better to build it from source. the alternative is treeview but this will not build somehow

ncbi-toolbox: as the original pkg i made is over 150mb i try to build it now with shared libs enabled ... hope it works ;-) - i didn't know that this is gpl - great news!!!

clustal{w,x}: is scheduled after the ncbi-toolbox - THANX!

phylip, fasta: i lost the pkgbuilds in the last cleanup of my harddisk i realized but reconstructing is no problem (and the things work fine):

[damir@Asteraceae /]$ fasta34
# fasta34
FASTA searches a protein or DNA sequence data bank
 version 3.4t23 Oct 30, 2003
Please cite:
 W.R. Pearson & D.J. Lipman PNAS (1988) 85:2444-2448

 test sequence file name: 
[damir@Asteraceae /]$

thanx for checking! expect most of them to go to extra very soon (now it's only a matter of free cpu cycles on my machine ;-) )

dp · 2005-02-15 14:50:43

update:

ncbi-toolbox is not able to be built with shared libs ... static results in a really big pkg :-(
http://bbs.archlinux.org/viewtopic.php?p=67607

clustalw is compiled and commited ... and soon available in extra

clustalx: -lvibrant -lncbi are not available (yet)

rudi · 2005-02-15 15:22:28

Great that those packages are commited! Thanks!!!

Weird that the NCBI toolkit is so big... I've downloaded and installed the debian version some time ago when i was still working with debian.......
(http://packages.debian.org/cgi-bin/sear … elease=all)

About the gpl license, maybe i've mistakenly interpreted the statement from the NCBI website:

This software/database is "United States Government Work" under the *
* terms of the United States Copyright Act. It was written as part of *
* the author's official duties as a Government employee and thus cannot *
* be copyrighted. This software/database is freely available to the *
* public for use without a copyright notice. Restrictions cannot be *
* placed on its present or future use. *

dp · 2005-02-15 18:24:55

pkgdb2: inserting clustalw
pkgdb2: inserting fasta
pkgdb2: inserting phylip

enjoy!

clustalx is needing -Ivibrant and -Incbi (both should be part of ncbi-toolbox) --- however: i never used clustalx but always was fine with clustalw for me
ncbi-toolbox is not yet working the way i want it to work

about the licence of ncbi-toolbox: i'm not american and do not know in detail, what this means about copyright. the thing is: there is nowhere GPL mentioned ... that's why i in the first run stopped on this

dp · 2005-02-15 19:11:39

forgot to ask: do you have any details on the licence of seaview? i have the pkg for it and would with pleasure include it to extra

# $Id: PKGBUILD,v 1.1 2005/01/02 17:53:36 damir Exp $
# Maintainer: damir <damir@archlinux.org>
pkgname=seaview
pkgver=0.0.20041220
pkgrel=1
pkgdesc="graphical multiple sequence alignment editor"
url="http://pbil.univ-lyon1.fr/software/seaview.html"
depends=('clustalw' 'x-server' 'bash')
source=(ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/$pkgname.tar)

build() {
  cd $startdir/src/
  make || return 1
  mkdir -p $startdir/pkg/usr/bin
  cp $startdir/src/$pkgname $startdir/pkg/usr/bin
  cp $startdir/src/seaview_align.sh $startdir/pkg/usr/bin
}

rudi · 2005-02-15 20:56:11

Hi,

I have contacted Manolo Gouy for licensing information about SeaView. If I get a response I will let you know. Where have you downloaded the source for SeaView? I can only find the binaries on the website (just like NJPlot).

dp · 2005-02-15 21:19:42

rudi wrote:

Hi,
I have contacted Manolo Gouy for licensing information about SeaView. If I get a response I will let you know.

ok, thx

rudi wrote:

Where have you downloaded the source for SeaView? I can only find the binaries on the website (just like NJPlot).

on the ftp-server:

ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/

Arch Linux

#1 2005-02-14 21:04:53

Science packages

#2 2005-02-14 21:08:28

Re: Science packages

#3 2005-02-14 21:24:31

Re: Science packages

#4 2005-02-14 21:36:27

Re: Science packages

#5 2005-02-14 22:22:48

Re: Science packages

#6 2005-02-14 23:20:14

Re: Science packages

#7 2005-02-15 00:26:55

Re: Science packages

#8 2005-02-15 09:15:30

Re: Science packages

#9 2005-02-15 14:19:51

Re: Science packages

#10 2005-02-15 14:50:43

Re: Science packages

#11 2005-02-15 15:22:28

Re: Science packages

#12 2005-02-15 18:24:55

Re: Science packages

#13 2005-02-15 19:11:39

Re: Science packages

#14 2005-02-15 20:56:11

Re: Science packages

#15 2005-02-15 21:19:42

Re: Science packages

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