[Blends-commit] [SCM] med branch, master, updated. dc9b2005772cbcfb1662e6dc83e5d3f3bc3b1af3

Fri Dec 1 18:53:02 UTC 2017

The following commit has been merged in the master branch:
commit dc9b2005772cbcfb1662e6dc83e5d3f3bc3b1af3
Author: Andreas Tille <tille at debian.org>
Date:   Fri Dec 1 19:51:57 2017 +0100

    Lamarc was added as packaging skeleton to Git thus removed extra information from task.  All other lamarc related software vanished from the web and from biolinux - so remove it from the task

diff --git a/tasks/bio b/tasks/bio
index 14421d0..e2c3f1a 100644
--- a/tasks/bio
+++ b/tasks/bio
@@ -2007,31 +2007,6 @@ Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
 Recommends: blixem, dotter, belvu
 Comment: These packages are all from source package seqtools
 
-Recommends: coalesce
-Homepage: http://evolution.gs.washington.edu/lamarc/coalesce.html
-License: not specified
-Responsible: BioLinux - Nathan S Haigh <n.haigh at sheffield.ac.uk>
-Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
-Pkg-Description: outdated program to estimate population-genetic parameters
- COALESCE fits the model which has a single population of constant
- size, and estimates 4Nu, where N is the effective population size and
- u is the neutral mutation rate per site. You may also want the
- Postscript or the TeX file of the preprint version of the Kuhner,
- Yamato, and Felsenstein 1995 paper.
-Remark: This software is probably outdated
- The homepage contains the explicite link: "We are no longer
- supporting COALESCE as its functions can be done just as well by
- LAMARC and it's easier for us to support just one program. You may
- still want the paper, however."  So this is actually no target for
- the Debian Med distribution but just a hint for users about the
- existence of this program and the even better alternative even if
- BioLinux distribution http://envgen.nox.ac.uk/biolinux.html contains
- a package.
-
-Comment: BioLinux contains a dendroscope package which is available
- at http://www.dendroscope.org but this project has only a
- "free as in beer" binary download - so this is not for us ...
-
 Recommends: estferret
 Homepage: http://legr.liv.ac.uk/EST-ferret/index.htm
 License: to be clarified
@@ -2133,42 +2108,8 @@ Pkg-Description: searching DNA and protein databases
  several nearby hits.
 Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
 
-Recommends: fluctuate
-Homepage: http://evolution.gs.washington.edu/lamarc/fluctuate.html
-License: not specified
-Responsible: BioLinux - Nathan S Haigh <n.haigh at sheffield.ac.uk>
-Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
-Pkg-Description: outdated program to model a single population
- FLUCTUATE fits the model which has a single population which has been
- growing (or shrinking) according to an exponential growth law. It
- estimates 4Nu and g, where N is the effective population size, u is
- the neutral mutation rate per site, and g is the growth rate of the
- population.
-Remark: This software is probably outdated
- The homepage contains the explicite link: "We are no longer
- supporting FLUCTUATE as its functions can be done just as well by
- LAMARC and it's easier for us to support just one program. You may
- still want the paper, however."  So this is actually no target for
- the Debian Med distribution but just a hint for users about the
- existence of this program and the even better alternative even if
- BioLinux distribution http://envgen.nox.ac.uk/biolinux.html contains
- a package.
-
 Recommends: lamarc
-Homepage: http://evolution.gs.washington.edu/lamarc/
-License: Apache V2.0
-Responsible: BioLinux - Nathan S Haigh <n.haigh at sheffield.ac.uk>
 Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
-Pkg-Description: estimate population-genetic parameters
- LAMARC is a program which estimates population-genetic parameters
- such as population size, population growth rate, recombination rate,
- and migration rates. It approximates a summation over all possible
- genealogies that could explain the observed sample, which may be
- sequence, SNP, microsatellite, or electrophoretic data. LAMARC and
- its sister program Migrate are successor programs to the older
- programs Coalesce, Fluctuate, and Recombine, which are no longer
- being supported. The programs are memory-intensive but can run
- effectively on workstations.
 Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
 
 Recommends: lucy
@@ -2391,28 +2332,6 @@ Pkg-Description: find ribosome binding sites(RBS)
  http://nbc11.biologie.uni-kl.de/docbook/doc_userguide_bioinformatics_server/chunk/ch01s06.html
 Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
 
-Recommends: recombine
-Homepage: http://evolution.genetics.washington.edu/lamarc/recombine.html
-License: not specified
-Responsible: BioLinux - Nathan S Haigh <n.haigh at sheffield.ac.uk>
-Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
-Pkg-Description: effective population size of populations
- RECOMBINE fits a model which has a single population of constant size
- with a single recombination rate across all sites. It can accomodate
- either plain DNA or RNA data or SNP (Single Nucleotide Polymorphism)
- data. It estimates 4Nu and r, where N is the effective population
- size, u is the neutral mutation rate per site, and r is the ratio of
- the per-site recombination rate to the per-site mutation rate.
-Remark: This software might be outdated
- The homepage contains the explicite link: "We are no longer
- supporting RECOMBINE as its functions can be done just as well by
- LAMARC and it's easier for us to support just one program. You may
- still want the paper, however."  So this is actually no target for
- the Debian Med distribution but just a hint for users about the
- existence of this program and the even better alternative even if
- BioLinux distribution http://envgen.nox.ac.uk/biolinux.html contains
- a package.
-
 Recommends: splitstree
 Homepage: http://www-ab.informatik.uni-tuebingen.de/software/splitstree3/welcome.html
 License: to be clarified

-- 
Debian Med metapackages

