[Cdd-commits] r850 - in projects/med/trunk/debian-med: debian tasks
CDD Subversion Commit
noreply at alioth.debian.org
Mon Jun 23 06:49:54 UTC 2008
Author: tille
Date: Mon Jun 23 06:49:54 2008
New Revision: 850
Modified:
projects/med/trunk/debian-med/debian/changelog
projects/med/trunk/debian-med/tasks/bio
projects/med/trunk/debian-med/tasks/bio-dev
projects/med/trunk/debian-med/tasks/cms
projects/med/trunk/debian-med/tasks/epi
projects/med/trunk/debian-med/tasks/imaging
projects/med/trunk/debian-med/tasks/imaging-dev
projects/med/trunk/debian-med/tasks/pharmacy
projects/med/trunk/debian-med/tasks/physics
projects/med/trunk/debian-med/tasks/practice
projects/med/trunk/debian-med/tasks/tools
projects/med/trunk/debian-med/tasks/typesetting
Log:
Added seqan to bio-dev; Changed all "Depends" to "Recommends" because this is
done by current cdd-dev anyway and it seems logical to express what is finally
implemented.
Modified: projects/med/trunk/debian-med/debian/changelog
==============================================================================
--- projects/med/trunk/debian-med/debian/changelog (original)
+++ projects/med/trunk/debian-med/debian/changelog Mon Jun 23 06:49:54 2008
@@ -35,6 +35,10 @@
* debian/control.stub: XS-DM-Upload-Allowed -> DM-Upload-Allowed
* Standards-Version: 3.8.0 (no changes needed)
* Fixed typing of Debian Med: sed -i 's/Debian-Med/Debian Med/' *
+ * tasks/*: s/Depends/Recommens/ - this is done by current cdd-dev anyway
+ The rationale for this behaviour is explained there. It seems logical
+ to state in the tasks files what finally is implemented. We might think
+ about enabling real Depends later if there might be reasons for this.
-- Andreas Tille <tille at debian.org> Mon, 31 Mar 2008 16:21:25 +0200
Modified: projects/med/trunk/debian-med/tasks/bio
==============================================================================
--- projects/med/trunk/debian-med/tasks/bio (original)
+++ projects/med/trunk/debian-med/tasks/bio Mon Jun 23 06:49:54 2008
@@ -3,36 +3,36 @@
This meta package will install Debian packages related to molecular biology,
structural biology and bioinformatics for use in life sciences.
-Depends: altree, fastdnaml, njplot, tree-puzzle | tree-ppuzzle, treeviewx
+Recommends: altree, fastdnaml, njplot, tree-puzzle | tree-ppuzzle, treeviewx
Why: Phylogenetic analysis.
-Depends: molphy, phylip, treetool
+Recommends: molphy, phylip, treetool
Why: Phylogenetic analysis (Non-free, thus only suggested).
-Depends: fastlink, loki, r-cran-qtl
+Recommends: fastlink, loki, r-cran-qtl
Why: Genetics
-Depends: amap-align, blast2, boxshade, dialign, gff2aplot, emboss, hmmer, kalign, mummer, muscle, poa, probcons, proda, seaview, sim4, sibsim4, sigma-align, t-coffee, wise, exonerate
+Recommends: amap-align, blast2, boxshade, dialign, gff2aplot, emboss, hmmer, kalign, mummer, muscle, poa, probcons, proda, seaview, sim4, sibsim4, sigma-align, t-coffee, wise, exonerate
Why: Sequence alignments and related programs.
-Depends: arb, clustalw | clustalw-mpi, clustalx
+Recommends: arb, clustalw | clustalw-mpi, clustalx
Why: Sequence alignments and related programs (Non-free, thus only suggested).
-Depends: adun.app, garlic, gdpc, ghemical, gromacs, pymol, rasmol, autodock, autogrid
+Recommends: adun.app, garlic, gdpc, ghemical, gromacs, pymol, rasmol, autodock, autogrid
Why: Molecular modelling and molecular dynamics.
-Depends: plasmidomics
+Recommends: plasmidomics
Why: Presentation
-Depends: biosquid, gff2ps, mipe, melting, ncbi-epcr, ncbi-tools-bin, ncbi-tools-x11, perlprimer, primer3, readseq, tigr-glimmer
+Recommends: biosquid, gff2ps, mipe, melting, ncbi-epcr, ncbi-tools-bin, ncbi-tools-x11, perlprimer, primer3, readseq, tigr-glimmer
Why: Tools for the molecular biologist.
Suggests: mozilla-biofox
Why: Tools for the molecular biologist. Because of the dependency from firefox we only suggest this package to not bloat the system of the user.
-Depends: dialign-tx
+Recommends: dialign-tx
-Depends: glam2
+Recommends: glam2
Suggests: pdb2pqr
@@ -42,7 +42,7 @@
work under Mac OSX only and it is not really maintained (Debian QA group).
We want to keep track of it anyway.
-Depends: meme
+Recommends: meme
Homepage: http://meme.nbcr.net/meme/
Responsible: Steffen Moeller <moeller at debian.org>
License: non-free for commercial purpose (http://meme.nbcr.net/meme/COPYRIGHT.html)
@@ -61,7 +61,7 @@
techniques to automatically choose the best width, number of occurrences,
and description for each motif.
-Depends: vienna-rna
+Recommends: vienna-rna
Homepage: http://www.tbi.univie.ac.at/~ivo/RNA/
Responsible: Steffen Moeller <moeller at debian.org>
License: non-free but redistributable
@@ -71,7 +71,7 @@
stand-alone programs for the prediction and comparison of RNA secondary
structures.
-Depends: cytoscape
+Recommends: cytoscape
Homepage: http://cytoscape.org/
Responsible: Mike Smoot <mes at aescon.com>
License: LGPL
@@ -81,7 +81,7 @@
interaction networks and integrating these interactions with gene expression
profiles and other state data. Additional features are available as plugins.
-Depends: ballview
+Recommends: ballview
Homepage: http://www.ballview.org
Responsible: Andreas Moll <kerosin at gmx.de>
Pkg-URL: http://mentors.debian.net/debian/pool/main/b/ballview/
@@ -102,7 +102,7 @@
for Molecular Mechanics, advanced solvation methods, comparison and
analysis of protein structures, file import/export, and visualization.
-Depends: raxml
+Recommends: raxml
Homepage: http://icwww.epfl.ch/~stamatak/index-Dateien/Page443.htm
License: GPL
Pkg-Description: Randomized Axelerated Maximum Likelihood
@@ -114,7 +114,7 @@
http://phylobench.vital-it.ch/raxml-bb/ and
http://8ball.sdsc.edu:8889/cipres-web/Bootstrap.do .
-Depends: axparafit
+Recommends: axparafit
Homepage: http://icwww.epfl.ch/~stamatak/AxParafit.html
Responsible: David Paleino <d.paleino at gmail.com>
License: GPL
@@ -126,7 +126,7 @@
for compute clusters and was used to carry out the largest
co-evolutionary analysis to date for the paper describing the software.
-Depends: axpcoords
+Recommends: axpcoords
Homepage: http://icwww.epfl.ch/~stamatak/AxParafit.html
Responsible: David Paleino <d.paleino at gmail.com>
License: GPL
@@ -139,7 +139,7 @@
This program is required for the pipeline that conducts a full host-parasite
co-phylogenetic analysis in combination with AxParafit.
-Depends: copycat
+Recommends: copycat
Homepage: http://www-ab.informatik.uni-tuebingen.de/software/copycat/welcome.html
License: Use of the program is free for academic purposes at an academic institute. For all other uses, please contact the authors.
Pkg-Description: fast access to cophylogenetic analyses
@@ -150,7 +150,7 @@
creation of customized host-parasite association data and the
computation of phylogenetic host/parasite trees based on the NCBI taxonomy.
-Depends: mustang
+Recommends: mustang
Homepage: http://www.cs.mu.oz.au/~arun/mustang/
Responsible: Morten Kjeldgaard <mok at bioxray.au.dk>
License: 3 clause BSD
@@ -164,7 +164,7 @@
reports the multiple sequence alignment and the corresponding
superposition of structures.
-Depends: btk-core
+Recommends: btk-core
Homepage: http://sourceforge.net/projects/btk/
Responsible: Morten Kjeldgaard <mok at bioxray.au.dk>
License: GPL
@@ -175,7 +175,7 @@
for common tasks in structural biology to facilitate the development of
molecular modeling, design and analysis tools.
-Depends: tacg
+Recommends: tacg
Homepage: http://sourceforge.net/projects/tacg
Responsible: Charles Plessy <plessy at debian.org>
License: GPL and others
@@ -201,7 +201,7 @@
The use of tacg may be cited as: Mangalam, HJ. (2002) tacg, a grep for DNA.
BMC Bioinformatics. 3:8 http://www.biomedcentral.com/1471-2105/3/8
-Depends: treeplot
+Recommends: treeplot
Responsible: Charles Plessy <plessy at debian.org>
License: GPL
WNPP: 461508
@@ -220,7 +220,7 @@
package.' So this package should probably be delisted in favour of
populations (see http://lists.debian.org/debian-med/2008/03/msg00124.html).
-Depends: treevolve
+Recommends: treevolve
Homepage: http://evolve.zoo.ox.ac.uk/software.html?id=Treevolve
Responsible: Charles Plessy <plessy at debian.org>
License: has to be verified
@@ -242,7 +242,7 @@
Citation: Population dynamics of HIV-1 inferred from gene sequences
Grassly NC, Harvey PH & Holmes EC (1999) Genetics 151, 427-438.
-Depends: infernal
+Recommends: infernal
Homepage: http://infernal.janelia.org/
Responsible: Steffen Moeller <moeller at debian.org>
License: GPL
@@ -264,7 +264,7 @@
"Query-Dependent Banding (QDB) for Faster RNA Similarity Searches."
E. P. Nawrocki, S. R. Eddy. PLoS Comput. Biol., 3:e56, 2007.
-Depends: mauvealigner
+Recommends: mauvealigner
Homepage: http://asap.ahabs.wisc.edu/mauve/
Responsible: Andreas Tille <tille at debian.org>
License: GPL
@@ -294,7 +294,7 @@
Note: There are instructions for compiling Mauve from source available at
http://asap.ahabs.wisc.edu/mauve/mauve-developer-guide/compiling-mauvealigner-from-source.html
-Depends: asap
+Recommends: asap
Homepage: http://asap.ahabs.wisc.edu/software/asap/
Responsible: Andreas Tille <tille at debian.org>
License: GPL
@@ -321,7 +321,7 @@
installations come to pass, ASAP will be further extended to be
inter-operable between sites.
-Depends: emboss-kaptain
+Recommends: emboss-kaptain
Homepage: http://userpage.fu-berlin.de/~sgmd/download.html
Responsible: Charles Plessy <plessy at debian.org>
License: GPL-2+
@@ -334,7 +334,7 @@
analysis. With EMBOSS.kaptn it integrates nicely into X window based
desktops like KDE.
-Depends: agdbnet
+Recommends: agdbnet
Homepage: http://pubmlst.org/software/database/agdbnet/
Responsible: Andreas Tille <tille at debian.org>
License: GPL
@@ -356,7 +356,7 @@
* Campylobacter flaA
* Streptococcus equi seM
-Depends: gamgi
+Recommends: gamgi
Homepage: http://www.gamgi.org/
Responsible: Steffen Moeller <moeller at debian.org>
License: Free
@@ -366,7 +366,7 @@
GAMGI provides a graphical user interface for the handling
of molecular structures.
-Depends: martj
+Recommends: martj
Homepage: http://www.ebi.ac.uk/biomart/
Responsible: Steffen Moeller <moeller at debian.org>
License: GPL
@@ -377,7 +377,7 @@
to the following data sources: UniProt Proteomes, Macromolecular
Structure Database (MSD), Ensembl, Vega, and dbSNP.
-Depends: cluster3
+Recommends: cluster3
Homepage: http://bonsai.ims.u-tokyo.ac.jp/~mdehoon/software/cluster/software.htm#ctv
License: non-free
WNPP: #286167
@@ -393,7 +393,7 @@
distance and the city-block distance were added to the available
measures of similarity.
-Depends: jmol
+Recommends: jmol
Homepage: http://jmol.sourceforge.net/
Responsible: Daniel Leidert <daniel.leidert.spam at gmx.net>
License: LGPL
@@ -410,7 +410,7 @@
For more detailed information about packaging status please see
http://lists.debian.org/debian-med/2008/03/msg00097.html
-Depends: jtreeview
+Recommends: jtreeview
Homepage: http://jtreeview.sourceforge.net/
Responsible: Steffen Moeller <moeller at debian.org>
License: GPL
@@ -427,7 +427,7 @@
Java TreeView is an extensible viewer for microarray data in
PCL or CDT format.
-Depends: smile
+Recommends: smile
Homepage: http://www-igm.univ-mlv.fr/~marsan/smile_english.html
Responsible: Steffen Moeller <moeller at debian.org>
WNPP: 221492
@@ -442,7 +442,7 @@
The specificity of SMILE is to allow to deal with what we call structured
motifs, which are motifs associated by some distance constraints.
-Depends: cactus
+Recommends: cactus
Homepage: http://www.cactuscode.org/Community/Biology.html
License: GPL
Pkg-Description:
@@ -456,7 +456,7 @@
Metacomputing Toolkit, HDF5 parallel file I/O, the PETSc scientific library,
adaptive mesh refinement, web interfaces, and advanced visualization tools.
-Depends: contralign
+Recommends: contralign
Homepage: http://contra.stanford.edu/contralign/
License: Public Domain
Pkg-Description: parameter learning framework for protein pairwise sequence alignment
@@ -467,7 +467,7 @@
previously unseen sequences and avoid overfitting by controlling model
complexity through regularization.
-Depends: galaxy
+Recommends: galaxy
Homepage: http://g2.trac.bx.psu.edu/
License: MIT
WNPP: 432472
@@ -478,7 +478,7 @@
strong ties with the UCSC genome browser, and makes it easy to
visualise modified annotation files as a custom track.
-Depends: genographer
+Recommends: genographer
Homepage: http://hordeum.oscs.montana.edu/genographer/
License: GPL
Pkg-Description: read data and reconstruct them into a gel image
@@ -490,7 +490,7 @@
The program is written in Java and uses the Java 1.3 API. Therefore,
it should run on any machine that can run java.
-Depends: molekel
+Recommends: molekel
Homepage: http://bioinformatics.org/molekel/wiki/Main/HomePage
License: GPL
Pkg-Description: multiplatform molecular visualization
@@ -498,7 +498,7 @@
program being developed at the Swiss National Supercomputing Centre
(CSCS).
-Depends: pftools
+Recommends: pftools
Homepage: ftp://us.expasy.org/databases/prosite/tools/ps_scan/sources
License: GPL
Pkg-Description: tools to handle patterns from PROSITE
@@ -507,7 +507,7 @@
in Swiss-Prot or FASTA format. It requires two compiled external
programs from the PFTOOLS, which are also distributed with the sources.
-Depends: proalign
+Recommends: proalign
Homepage: http://evol-linux1.ulb.ac.be/ueg/ProAlign/
License: GPL
Responsible: Charles Plessy <plessy at debian.org>
@@ -527,7 +527,7 @@
characters according to an evolutionary model. It has been published in
Bioinformatics. 2003 Aug 12;19(12):1505-13.
-Depends: ssaha
+Recommends: ssaha
Homepage: http://www.sanger.ac.uk/Software/analysis/SSAHA/
License: GPL
Responsible: Charles Plessy <plessy at debian.org>
@@ -547,7 +547,7 @@
http://www.sanger.ac.uk/Software/analysis/SSAHA2/
does not seem to be available.
-Depends: ngila
+Recommends: ngila
Homepage: http://scit.us/projects/ngila/
License: GPLv3
Responsible: Charles Plessy <plessy at debian.org>
@@ -572,7 +572,7 @@
Ngila is published in Cartwright RA Bioinformatics 2007
23(11):1427-1428; doi:10.1093/bioinformatics/btm095
-Depends: tm-align
+Recommends: tm-align
Homepage: http://zhang.bioinformatics.ku.edu/TM-align/
License: free to change and redistribute
Responsible: Steffen Moeller <moeller at debian.org>
@@ -586,14 +586,14 @@
TM-align performs a structural alignment of protein sequences. It is
said to be 10 times faster than DALI and no worse in accuracy.
-Depends: staden
+Recommends: staden
Homepage: http://staden.sourceforge.net/
License: BSD
Pkg-Description: DNA sequence assembly (Gap4), editing and analysis tools
A fully developed set of DNA sequence assembly (Gap4), editing and
analysis tools (Spin).
-Depends: dazzle
+Recommends: dazzle
Homepage: http://www.biojava.org/dazzle
Responsible: Steffen Moeller <moeller at debian.org>
License: LGPL
@@ -608,7 +608,7 @@
.
Information on DAS is available from http://www.biodas.org/
-Depends: mgltools
+Recommends: mgltools
Homepage: http://mgltools.scripps.edu
Responsible: Steffen Moeller <moeller at debian.org>
WNPP: 458811
@@ -626,7 +626,7 @@
third party. This set of tools is well known across biochemistry and
computational/structural biology.
-Depends: ecell
+Recommends: ecell
Homepage: http://www.e-cell.org/
Responsible: Steffen Moeller <moeller at debian.org>
WNPP: 241195
@@ -651,7 +651,7 @@
* E-Cell Modeling Environment (or E-Cell ME)
* E-Cell Analysis Toolkit.
-Depends: ncoils
+Recommends: ncoils
Homepage: http://www.russell.embl.de/cgi-bin/coils-svr.pl
Responsible: Steffen Moeller <moeller at debian.org>
WNPP: 299856
@@ -663,7 +663,7 @@
Lupas, van Dyke & Stock, Predicting coiled coils from
protein sequences Science, 252, 1162-1164, 1991.
-Depends: haploview
+Recommends: haploview
Homepage: http://www.broad.mit.edu/mpg/haploview/
Responsible: Steffen Moeller <moeller at debian.org>
WNPP: 311421
@@ -675,7 +675,7 @@
to determine genes and genetic pathways that are associated
with diseases. This is an early stage in the quest for new drugs.
-Depends: mauvealigner
+Recommends: mauvealigner
Homepage: http://asap.ahabs.wisc.edu/mauve/
Responsible: Andreas Tille <tille at debian.org>
License: GPL
@@ -707,7 +707,7 @@
.
Mauve is developed at the University of Wisconsin.
-Depends: gbrowse
+Recommends: gbrowse
Homepage: http://www.gmod.org/wiki/index.php/GBrowse
Responsible: Charles Plessy <plessy at debian.org>
WNPP: 429610
@@ -731,7 +731,7 @@
* Customizable plug-in architecture (e.g. run BLAST, dump & import many formats,
find oligonucleotides, design primers, create restriction maps, edit features)
-Depends: mira
+Recommends: mira
Homepage: http://chevreux.org/projects_mira.html
Responsible: Charles Plessy <plessy at debian.org>
WNPP: 435915
@@ -750,7 +750,7 @@
between organisms, and pristine assembly of sequences from various
sources for oligo design in clinical microarray experiments.
-Depends: phylographer
+Recommends: phylographer
Homepage: http://www.atgc.org/PhyloGrapher/PhyloGrapher_Welcome.html
Responsible: Charles Plessy <plessy at debian.org>
WNPP: 426489
@@ -769,7 +769,7 @@
biological sequence alignment reports (BLAST is provided by Debian's
blast2 package).
-Depends: phylowin
+Recommends: phylowin
Homepage: http://pbil.univ-lyon1.fr/software/phylowin.html
Responsible: Charles Plessy <plessy at debian.org>
WNPP: 395840
@@ -788,7 +788,7 @@
its use for profit. Therfore, Phylo_win will unfortunately have to be
distributed in contrib or non-free.
-Depends: seq-gen
+Recommends: seq-gen
Homepage: http://tree.bio.ed.ac.uk/software/seqgen/
License: Free
Pkg-Description: simulate the evolution of nucleotide or amino acid sequences
@@ -804,7 +804,7 @@
incorporates most of the commonly used (and computationally tractable)
models of molecular sequence evolution.
-Depends: wgs-assembler
+Recommends: wgs-assembler
Homepage: http://wgs-assembler.sourceforge.net/
Responsible: Charles Plessy <plessy at debian.org>
WNPP: 395843
@@ -848,7 +848,7 @@
See also: http://www.jcvi.org/cms/research/software/celera-assembler/overview/
Note: Genome assembly and large-scale genome alignment (http://www.cbcb.umd.edu/software/)
-Depends: gbioseq
+Recommends: gbioseq
Homepage: http://www.bioinformatics.org/project/?group_id=94
License: GPL
Pkg-Description: DNA sequence editor for Linux
@@ -856,7 +856,7 @@
The goal is to provide an easy to use software to edit DNA sequences under
Linux, Windows, MacOsX, using GTK C# (Mono).
-Depends: populations
+Recommends: populations
Homepage: http://bioinformatics.org/~tryphon/populations/
License: GPL
Pkg-Description: individuals or populations distances based on allelic frequencies
@@ -873,14 +873,14 @@
* Converts data files from Genepop to different formats (Genepop, Genetix, Msat,
Populations...)
-Depends: phpphylotree
+Recommends: phpphylotree
Homepage: http://www.bioinformatics.org/project/?group_id=372
License: GPL
Pkg-Description: draw phylogenetic trees
PhpPhylotree is a web application that is able to draw phylogenetic trees.
It produces an SVG (Scalable Vector Graphic) file from phylip/newick tree files.
-Depends: tracetuner
+Recommends: tracetuner
Homepage: http://www.jcvi.org/cms/research/software/tracetuner/overview
License: GPL; but US Patent #6,681,186
Pkg-Description: DNA sequencing and trace processing
@@ -909,7 +909,7 @@
and conditions of the GNU General Public License, version 2, as published by the
Free Software Foundation (the "GNU General Public License").
-Depends: plink
+Recommends: plink
Homepage: http://pngu.mgh.harvard.edu/~purcell/plink/
License: GPL
Responsible: Steffen Moeller <moeller at debian.org>
@@ -922,7 +922,7 @@
variations with a phenotype and can retrieve
SNP annotation from an online source.
-Depends: twain
+Recommends: twain
Homepage: http://cbcb.umd.edu/software/pirate/twain/twain.shtml
License: Open Source
Pkg-Description: syntenic genefinder employing a Generalized Pair Hidden Markov Model
@@ -945,7 +945,7 @@
Slides from a talk at Computational Genomics 2004 are now available.
Note: Computational Gene Finding (http://www.cbcb.umd.edu/software/)
-Depends: rose
+Recommends: rose
Homepage: http://www.cbcb.umd.edu/software/rose/Rose.html
License: Open Source
Pkg-Description: Region-Of-Synteny Extractor
@@ -964,7 +964,7 @@
boundaries of the output region.
Note: Computational Gene Finding (http://www.cbcb.umd.edu/software/)
-Depends: glimmerhmm
+Recommends: glimmerhmm
Homepage: http://www.cbcb.umd.edu/software/glimmerhmm/
License: Artistic
Pkg-Description: Eukaryotic Gene-Finding System
@@ -979,7 +979,7 @@
user manual can be consulted here.
Note: Computational Gene Finding (http://www.cbcb.umd.edu/software/)
-Depends: genezilla
+Recommends: genezilla
Homepage: http://www.genezilla.org/
License: Artistic
Pkg-Description: eukaryotic gene finder
@@ -1006,7 +1006,7 @@
for the comparative gene finder TWAIN.
Note: Computational Gene Finding (http://www.cbcb.umd.edu/software/)
-Depends: exalt
+Recommends: exalt
Homepage: http://www.cbcb.umd.edu/software/exalt/
License: Artistic
Pkg-Description: phylogenetic generalized hidden Markov model for predicting alternatively spliced exons
@@ -1020,7 +1020,7 @@
run on other species.
Note: Computational Gene Finding (http://www.cbcb.umd.edu/software/)
-Depends: jigsaw
+Recommends: jigsaw
Homepage: http://www.cbcb.umd.edu/software/jigsaw/
License: Artistic
Pkg-Description: gene prediction using multiple sources of evidence
@@ -1048,7 +1048,7 @@
custom tracks in the UCSC Human Genome Browser
Note: Computational Gene Finding (http://www.cbcb.umd.edu/software/)
-Depends: genesplicer
+Recommends: genesplicer
Homepage: http://www.cbcb.umd.edu/software/GeneSplicer/
License: Artistic
Pkg-Description: computational method for splice site prediction
@@ -1115,7 +1115,7 @@
packaging effort is stalled. Feel free to tell us, if you are
interested in turning this into an official package.
-Depends: mummergpu
+Recommends: mummergpu
Homepage: http://mummergpu.sourceforge.net/
License: Artistic
Pkg-Description: High-throughput sequence alignment using Graphics Processing Units
@@ -1143,7 +1143,7 @@
technologies.
Note: Genome assembly and large-scale genome alignment (http://www.cbcb.umd.edu/software/)
-Depends: amos-assembler
+Recommends: amos-assembler
Homepage: http://amos.sourceforge.net/
License: Artistic
Pkg-Description: modular whole genome assembler
@@ -1160,7 +1160,7 @@
design philosophy and a software system.
Note: Genome assembly and large-scale genome alignment (http://www.cbcb.umd.edu/software/)
-Depends: amoscmp
+Recommends: amoscmp
Homepage: http://amos.sourceforge.net/docs/pipeline/AMOScmp.html
License: Artistic
Pkg-Description: comparative genome assembly package
@@ -1189,7 +1189,7 @@
modular open-source framework for assembly development.
Note: Genome assembly and large-scale genome alignment (http://www.cbcb.umd.edu/software/)
-Depends: minimus
+Recommends: minimus
Homepage: http://amos.sourceforge.net/docs/pipeline/minimus.html
License: Artistic
Pkg-Description: AMOS lightweight assembler
@@ -1281,7 +1281,7 @@
Note: Found at
http://gforge.nci.nih.gov/softwaremap/trove_list.php?form_cat=337
-Depends: mage2tab
+Recommends: mage2tab
Homepage: https://www.cbil.upenn.edu/magewiki/index.php/mage2tab
License: CBIL Software and Data License (Apache-like)
WNPP: 476209
@@ -1293,7 +1293,7 @@
MINiML) from or into databases like GUS (the Genomics Unified Schema,
www.gusdb.org).
-Depends: bambus
+Recommends: bambus
Homepage: http://amos.sourceforge.net/docs/bambus/
License: Artistic
Pkg-Description: hierarchical approach to building contig scaffolds
@@ -1308,7 +1308,7 @@
integrated with the AMOS package (see http://amos.sourceforge.net/)
Note: Genome assembly and large-scale genome alignment (http://www.cbcb.umd.edu/software/)
-Depends: hawkeye
+Recommends: hawkeye
Homepage: http://amos.sourceforge.net/hawkeye/
License: Artistic
Pkg-Description: Interactive Visual Analytics Tool for Genome Assemblies
@@ -1341,7 +1341,7 @@
assemblies. Genome Biology 8:R34.
Note: Genome assembly and large-scale genome alignment (http://www.cbcb.umd.edu/software/)
-Depends: murasaki
+Recommends: murasaki
Homepage: http://murasaki.dna.bio.keio.ac.jp/
License: GPL
Pkg-URL: http://svn.debian.org/wsvn/debian-med/trunk/packages/murasaki/trunk/?rev=0&sc=0
@@ -1360,7 +1360,7 @@
* repeat tolerant
* intelligent noise reduction
-Depends: gmv
+Recommends: gmv
Homepage: http://murasaki.dna.bio.keio.ac.jp/wiki/index.php?GMV
License: GPL
Pkg-Description: comparative genome browser for Murasaki
@@ -1368,14 +1368,14 @@
anchors from Murasaki, annotation data from GenBank files, and
expression / prediction score from GFF files.
-Depends: pyrophosphate_tools
+Recommends: pyrophosphate_tools
Homepage: http://www-naweb.iaea.org/nafa/ipc/public/d4_pbl_6a.html
License: not specified
Pkg-Description: for assembling and searching pyrophosphate sequence data
Simple tools for assembling and searching high-density picolitre
pyrophosphate sequence data.
-Depends: figaro
+Recommends: figaro
Homepage: http://amos.sourceforge.net/Figaro/Figaro.html
License: Artistic
Pkg-Description: novel vector trimming software
@@ -1388,7 +1388,7 @@
part of the AMOS suite.
Note: Genome assembly and large-scale genome alignment (http://www.cbcb.umd.edu/software/)
-Depends: velvet
+Recommends: velvet
Homepage: http://www.ebi.ac.uk/~zerbino/velvet/
License: GPL
Pkg-Description: genomic assembler specially designed for short read sequencing
@@ -1405,7 +1405,7 @@
the GPL-2. It also contain a PDF manual whose sources are missing.
The final package would depend on zlib.
-Depends: mirbase
+Recommends: mirbase
Homepage: http://microrna.sanger.ac.uk/
License: Public Domain
WNPP: 420938
@@ -1428,7 +1428,7 @@
It is possible that mirbase will not be a package from the main archive, but
will be autogenerated as part of a larger data packaging effort.
-Depends: elph
+Recommends: elph
Homepage: http://www.cbcb.umd.edu/software/ELPH/
License: Artistic
Pkg-Description: motif finder that can find ribosome binding sites, exon splicing enhancers, or regulatory sites
@@ -1446,7 +1446,7 @@
http://www.cbcb.umd.edu/software/SeeEse/index.html .
Note: Other sequence analysis tools (http://www.cbcb.umd.edu/software/)
-Depends: repeatfinder
+Recommends: repeatfinder
Homepage: http://www.cbcb.umd.edu/software/RepeatFinder/
License: Artistic
Pkg-Description: finding repetitive sequences complete and draft genomes
@@ -1460,7 +1460,7 @@
Kurtz's REPuter.
Note: Other sequence analysis tools (http://www.cbcb.umd.edu/software/)
-Depends: reputer
+Recommends: reputer
Homepage: http://citeseer.ist.psu.edu/kurtz95reputer.html
License: to be clarified
Pkg-Description: fast computation of maximal repeats in complete genomes
@@ -1468,7 +1468,7 @@
palindromes in entire genomes very efficiently.
Note: Download site (temporarily) not available - try to contact author
-Depends: transtermhp
+Recommends: transtermhp
Homepage: http://transterm.cbcb.umd.edu/index.php
License: Free
Pkg-Description: finds rho-independent transcription terminators in bacterial genomes
@@ -1481,7 +1481,7 @@
relationship to DNA uptake. Genome Biology 8:R22 (2007).
Note: Other sequence analysis tools (http://www.cbcb.umd.edu/software/)
-Depends: patman
+Recommends: patman
Homepage: http://bioinf.eva.mpg.de/patman/
License: GPL-2+
WNPP: 482555
@@ -1491,7 +1491,7 @@
for approximate matches. It is optimized for searching for many small
pattern at the same time, for example microarray probes.
-Depends: uniprime
+Recommends: uniprime
Homepage: http://code.google.com/p/uniprime/
License: GPL-3+
Responsible: Charles Plessy <plessy at debian.org>
@@ -1507,7 +1507,7 @@
generates successful cross-species primers that take into account the
biological aspects of the PCR.
-Depends: genetrack
+Recommends: genetrack
Homepage: http://sysbio.bx.psu.edu/genetrack.html
License: MIT
Responsible: Charles Plessy <plessy at debian.org>
@@ -1517,7 +1517,7 @@
analyze data obtained via high-throughput rapid sequencing platforms such as
the 454 and Solexa as well as tiling array data based on various platforms.
-Depends: operondb
+Recommends: operondb
Homepage: http://www.cbcb.umd.edu/cgi-bin/operons/operons.cgi
License: to be clarified
Pkg-Description: detect and analyze conserved gene pairs
@@ -1546,7 +1546,7 @@
no info about license or downloadable code found, but tried to
contact authors.
-Depends: velvet
+Recommends: velvet
Homepage: http://www.ebi.ac.uk/~zerbino/velvet/
License: GPL-2+
WNPP: 487026
Modified: projects/med/trunk/debian-med/tasks/bio-dev
==============================================================================
--- projects/med/trunk/debian-med/tasks/bio-dev (original)
+++ projects/med/trunk/debian-med/tasks/bio-dev Mon Jun 23 06:49:54 2008
@@ -3,26 +3,26 @@
This meta package will install Debian packages which might be helpful
for development of applications for micro-biological research.
-Depends: bioperl, libncbi6-dev, mcl
+Recommends: bioperl, libncbi6-dev, mcl
Suggests: biomode, r-base-core
Recommends: libvibrant6-dev
Why: libmotif-dev conflicts lesstif-dev, so if someone wants to install libmotif-dev it must be possible to deinstall libvibrant6-dev without beeing forced to deinstall med-bio-dev as well
-Depends: python-biopython
+Recommends: python-biopython
-Depends: libbio-ruby
+Recommends: libbio-ruby
Recommends: libqsearch-dev
-Depends: libgenome-1.3-1
+Recommends: libgenome-1.3-1
-Depends: libbio-mage-perl
+Recommends: libbio-mage-perl
Why: Useful for the submission of microarray data to public repositories.
-Depends: libajax5-dev, libnucleus5-dev
+Recommends: libajax5-dev, libnucleus5-dev
-Depends: bioconductor
+Recommends: bioconductor
Homepage: http://www.bioconductor.org/
Responsible: Debian CRAN/BioConductor/Omegahat packaging team <pkg-bioc-devel at lists.alioth.debian.org>
License: GPL/LGPL
@@ -48,7 +48,7 @@
* provide training in computational and statistical methods for the analysis
of genomic data.
-Depends: bioclipse
+Recommends: bioclipse
Homepage: http://www.bioclipse.net/
License: Eclipse Public License (EPL) + exception
Pkg-Description: platform for chemo- and bioinformatics based on Eclipse
@@ -69,7 +69,7 @@
followed on the Bioclipse Wiki where we document the progress and
ideas of the development on a daily basis.
-Depends: aceperl
+Recommends: aceperl
Homepage: http://stein.cshl.org/AcePerl/
Responsible: David Paleino <d.paleino at gmail.com>
License: GPL-1+ | Artistic
@@ -86,7 +86,7 @@
Institute). It was originally developed for the C.elegans genome
project , from which its name was derived (A C. elegans DataBase).
-Depends: libgff-perl
+Recommends: libgff-perl
Homepage: http://www.sanger.ac.uk/Software/formats/GFF/
Responsible: David Paleino <d.paleino at gmail.com>
License: GPL-1+
@@ -97,7 +97,7 @@
.
This package provides a Perl module to use GFF objects.
-Depends: libmems-1.5-1
+Recommends: libmems-1.5-1
Homepage: http://asap.ahabs.wisc.edu/software/software-development-libraries/libmems.html
Responsible: Andreas Tille <tille at debian.org>
License: GPL
@@ -112,7 +112,7 @@
input sequence, and this data can be stored externally (i.e. on disk) to
further reduce memory requirements.
-Depends: libbio-das-perl
+Recommends: libbio-das-perl
Homepage: http://www.biodas.org/
Responsible: Steffen Moeller <moeller at debian.org>
License: Perl Artistic License
@@ -123,7 +123,7 @@
version 1.5. Both unencrypted (http:) and SSL-encrypted (https:)
DAS servers are supported.
-Depends: libbiojava-java
+Recommends: libbiojava-java
Homepage: http://www.biojava.org
Responsible: Steffen Moeller <moeller at debian.org>
License: LGPL
@@ -135,7 +135,7 @@
and Ensembl databases, and powerful analysis and statistical routines
including a dynamic programming toolkit.
-Depends: limma
+Recommends: limma
Homepage: http://bioinf.wehi.edu.au/limma
Responsible: Steffen Moeller <moeller at debian.org>
WNPP: 293320
@@ -145,7 +145,7 @@
investigate gene expression data from microarrays with the
statistical package R.
-Depends: libtfbs-perl
+Recommends: libtfbs-perl
Homepage: http://forkhead.cgb.ki.se/TFBS/
Responsible: Steffen Moeller <moeller at debian.org>
WNPP: 320777
@@ -179,7 +179,7 @@
The modules within the TFBS set are fully integrated and compatible with
Bioperl.
-Depends: libgo-perl
+Recommends: libgo-perl
Homepage: http://geneontology.sourceforge.net/
Responsible: Charles Plessy <plessy at debian.org>
WNPP: 452923
@@ -192,7 +192,7 @@
contains both scripts (which can be used with no knowledge of perl),
and libraries which will be of use to perl programmers using GO or OBO.
-Depends: libbio-mage-utils-perl
+Recommends: libbio-mage-utils-perl
Homepage: http://mged.sourceforge.net/
License: MIT/X
WNPP: 476202
@@ -207,3 +207,18 @@
.
Bio-MAGE-Utils contains extra modules for handling MAGE XML and MGED ontology,
as well as SQL utilities.
+
+Recommends: seqan
+Homepage: http://www.seqan.de/
+License: LGPL
+WNPP: 487361
+Responsible: Soeren Sonnenburg <bugreports at nn7.de>
+Pkg-Description: C++ template library for the analysis of sequences.
+ SeqAn is a C++ template library of efficient algorithms and data
+ structures for the analysis of sequences with the focus on
+ biological data. This library applies a unique generic design that
+ guarantees high performance, generality, extensibility, and
+ integration with other libraries. SeqAn is easy to use and
+ simplifies the development of new software tools with a minimal loss
+ of performance.
+
Modified: projects/med/trunk/debian-med/tasks/cms
==============================================================================
--- projects/med/trunk/debian-med/tasks/cms (original)
+++ projects/med/trunk/debian-med/tasks/cms Mon Jun 23 06:49:54 2008
@@ -3,4 +3,4 @@
This meta package will install packages which are useful to build a
content management system for medical care.
-Depends: zope-zms
+Suggests: zope-zms
Modified: projects/med/trunk/debian-med/tasks/epi
==============================================================================
--- projects/med/trunk/debian-med/tasks/epi (original)
+++ projects/med/trunk/debian-med/tasks/epi Mon Jun 23 06:49:54 2008
@@ -3,9 +3,9 @@
This meta package will install tools that are useful in epidemiological
research.
-Depends: epigrass
+Recommends: epigrass
-Depends: netepi-analysis
+Recommends: netepi-analysis
Homepage: http://www.netepi.org/
Responsible: Andreas Tille <tille at debian.org>
License: free
@@ -29,7 +29,7 @@
.
The software was developed by New South Wales Department of Health.
-Depends: netepi-collection
+Recommends: netepi-collection
Homepage: http://www.netepi.org/
Responsible: Andreas Tille <tille at debian.org>
License: free
Modified: projects/med/trunk/debian-med/tasks/imaging
==============================================================================
--- projects/med/trunk/debian-med/tasks/imaging (original)
+++ projects/med/trunk/debian-med/tasks/imaging Mon Jun 23 06:49:54 2008
@@ -13,17 +13,17 @@
or download the current DICOM standard as PDF files from
http://www.dclunie.com/dicom-status/status.html .
-Depends: amide, ctsim, ctn, dicomnifti, imagej, minc-tools, medcon, python-nifti, xmedcon, dcmtk
+Recommends: amide, ctsim, ctn, dicomnifti, imagej, minc-tools, medcon, python-nifti, xmedcon, dcmtk
Suggests: imagemagick, pngquant, imview
-Depends: nifti-bin, dicomnifti, libvolpack1
+Recommends: nifti-bin, dicomnifti, libvolpack1
-Depends: aeskulap
+Recommends: aeskulap
-Depends: fslview, fsl
+Recommends: fslview, fsl
-Depends: bioimagesuite
+Recommends: bioimagesuite
Homepage: http://www.bioimagesuite.org/
License: GPL
Pkg-Description: integrated image analysis software suite
@@ -44,7 +44,7 @@
compiling it from source and packaging issues at
http://research.yale.edu/bioimagesuite/forum/index.php?board=12.0
-Depends: drjekyll
+Recommends: drjekyll
Homepage: http://drjekyll.sourceforge.net
License: GPL
Pkg-Description: interactive voxel editor for viewing and editing three-dimensional images
@@ -55,7 +55,7 @@
a final polishing process.
Why: Hint given by Petter Reinholdtsen
-Depends: libvista2
+Recommends: libvista2
Homepage: http://mia.sourceforge.net/
License: GPL
Pkg-Description: software environment for computer vision research
@@ -73,7 +73,7 @@
Max Planck Institute of Cognitive Neuroscience
(http://www.cns.mpg.de/).
-Depends: dcm4che
+Recommends: dcm4che
Homepage: http://www.dcm4che.org/
License: LGPL, MPL, Apache, other (also non-free)
Pkg-Description: collection of open source applications and utilities healthcare enterprise
@@ -92,9 +92,9 @@
role of several IHE actors for the sake of interoperability, the
application provides many robust and scalable services.
-Depends: gwyddion
+Recommends: gwyddion
-Depends: piano
+Recommends: piano
Homepage: http://mbi.dkfz-heidelberg.de/mbi/software/
License: BSD
Pkg-Description: medical image processing library for surgical planning
@@ -102,7 +102,7 @@
multi-dimensional medical image processing, analysis and visualization.
It is used in the field of surgical planning.
-Depends: pixelmed
+Recommends: pixelmed
Homepage: http://www.pixelmed.com/index.html#PixelMedJavaDICOMToolkit
License: Free
Pkg-Description: PixelMed Java DICOM Toolkit
@@ -111,7 +111,7 @@
support for display of directories, images, reports and spectra, and DICOM object
validation.
-Depends: slicer
+Recommends: slicer
Homepage: http://www.slicer.org/
License: BSD like
Pkg-Description: visualization, registration, segmentation, and quantification of medical data
@@ -122,7 +122,7 @@
The license statement can be seen at
http://www.slicer.org/cgi-bin/License/SlicerLicenseForm.pl
-Depends: sofa
+Recommends: sofa
Homepage: http://www.sofa-framework.org/
License: LGPL
Pkg-Description: Simulation Open Framework Architecture
@@ -143,7 +143,7 @@
SOFA version 1.0 beta 1 was released during the Medicine Meets Virtual
Reality 2007 conference in Long Beach, California.
-Depends: mesa-test-tools
+Recommends: mesa-test-tools
Homepage: http://ihedoc.wustl.edu/mesasoftware/
License: free
Pkg-Description: IHE Test Software for Radiology
@@ -176,7 +176,7 @@
of CTN software in those tools does not have a separate release number
but is more current than version 3.0.6."
-Depends: gdcm
+Recommends: gdcm
Homepage: http://sourceforge.net/project/showfiles.php?group_id=137895
License: BSD
Pkg-URL: http://sourceforge.net/project/showfiles.php?group_id=137895&package_id=197047
@@ -187,13 +187,13 @@
Supports currently RAW,JPEG,J2K,JPEG lossless,RLE, deflate(zlib) but
not JPEG-LS,MPEG for now.
-Depends: dicom4j
+Recommends: dicom4j
Homepage: http://dicom4j.sourceforge.net/
License: GPL
Pkg-Description: Java framework for Dicom
Java framework for Dicom
-Depends: opendicom.net
+Recommends: opendicom.net
Homepage: http://opendicom.sourceforge.net/
License: LGPL
Responsible: Albert Gnandt <agnandt at users.sourceforge.net>
@@ -242,7 +242,7 @@
All GUI applications focus the popular GNOME desktop, but are 100%
platform independent by relying on Mono.
-Depends: afni
+Recommends: afni
Homepage: http://afni.nimh.nih.gov/
WNPP: 409849
Responsible: Michael Hanke <michael.hanke at gmail.com>
@@ -255,7 +255,7 @@
In addition to its own format AFNI understands the NIfTI format and is
therefore easily usable in combination with FSL and Freesurfer.
-Depends: blox
+Recommends: blox
Homepage: http://sourceforge.net/projects/blox/
License: GPL
Pkg-Description: medical imaging and visualization program
@@ -265,7 +265,7 @@
Johns Hopkins University, Psychiatric Neuroimaging Lab
(http://pni.med.jhu.edu/methods/morph.htm).
-Depends: conquest-dicom-server
+Recommends: conquest-dicom-server
Homepage: http://www.xs4all.nl/~ingenium/dicom.html
License: Public domain
Pkg-Description: full featured DICOM server
@@ -280,7 +280,7 @@
* Advanced automatic image forwarding and (de)compression
* DICOM caching and archive merging
-Depends: dicomscope
+Recommends: dicomscope
Homepage: http://dicom.offis.de/dscope.php.en
License: Has to be clarified
Pkg-Description:
@@ -303,7 +303,7 @@
presentation states. The program is not appropriate to be used in a
clinical environment, e.g. for reporting.
-Depends: dicom3tools
+Recommends: dicom3tools
Homepage: http://www.dclunie.com/dicom3tools.html
License: BSD
Pkg-Description: handling offline files of DICOM 3 attributes
@@ -315,7 +315,7 @@
It has extremely limited X display capability and no networking
code that is why this is not a complete DICOM implementation.
-Depends: ecg2png
+Recommends: ecg2png
X-Homepage-old: http://www.cardiothink.com/downloads
License: GPL
Pkg-Description: convert scanned electrocardiograms into PNG format
@@ -339,7 +339,7 @@
can be downloaded fro instance from
http://www.freshports.org/graphics/ecg2png/ .
-Depends: kradview
+Recommends: kradview
Homepage: http://www.orcero.org/irbis/kradview/
License: GPLv3
Pkg-Description: the free DICOM viewer for Linux
@@ -355,7 +355,7 @@
and the graphical interface has been developed in C++ and includes
the former routines with "extern C" for fast use.
-Depends: opensourcepacs
+Recommends: opensourcepacs
Homepage: http://www.mii.ucla.edu/index.php/MainSite:OpenSourcePacsHome
License: GPL
Pkg-Description: medical image referral, archiving, routing and viewing system
@@ -373,7 +373,7 @@
OpenSourcePACS is a product of the UCLA Medical Imaging Informatics
group (http://www.mii.ucla.edu/).
-Depends: pixelmed-dicom-toolkit
+Recommends: pixelmed-dicom-toolkit
Homepage: http://www.pixelmed.com/index.html#PixelMedJavaDICOMToolkit
License: BSD
Pkg-Description:
@@ -404,7 +404,7 @@
VisIt was designed to handle very large data set sizes in the terascale
range and yet can also handle small data sets in the kilobyte range.
-Depends: caret
+Recommends: caret
Homepage: http://brainmap.wustl.edu/caret/
WNPP: 421703
License: GPL
@@ -419,7 +419,7 @@
Caret can download and use stereotaxic atlases (human, monkey, mouse
and rat) from an open online database.
-Depends: mni-autoreg
+Recommends: mni-autoreg
Homepage: http://www.bic.mni.mcgill.ca/software/mni_autoreg/
License: no-free, but GPLed parts
Responsible: Michael Hanke <michael.hanke at gmail.com>
@@ -440,7 +440,7 @@
http://mentors.debian.net/cgi-bin/sponsor-pkglist?action=details;package=mni-autoreg-model
to Debian Med svn and start group maintenance.
-Depends: mni-n3
+Recommends: mni-n3
Homepage: http://www.bic.mni.mcgill.ca/software/N3/
License: BSDish
Responsible: Michael Hanke <michael.hanke at gmail.com>
@@ -456,7 +456,7 @@
http://mentors.debian.net/cgi-bin/sponsor-pkglist?action=details;package=mni-n3
to Debian Med svn and start group maintenance.
-Depends: brainvisa
+Recommends: brainvisa
Homepage: http://brainvisa.info/
License: Free? (CeCill License)
Pkg-Description: image processing factory for MR images
@@ -475,7 +475,7 @@
labeling of the cortical folds according to a nomenclature of the
main sulci.
-Depends: maris
+Recommends: maris
Homepage: http://maris.homelinux.org/
License: GPL
Pkg-Description: package suite for Radiological Workflow
@@ -486,7 +486,7 @@
that is an ensamble of single pieces that cooperate together using
IHE profiles.
-Depends: lipsia
+Recommends: lipsia
Homepage: http://www.cbs.mpg.de/institute/software/lipsia
License: GPL
Responsible: Felix Botner <botner at cbs.mpg.de>
Modified: projects/med/trunk/debian-med/tasks/imaging-dev
==============================================================================
--- projects/med/trunk/debian-med/tasks/imaging-dev (original)
+++ projects/med/trunk/debian-med/tasks/imaging-dev Mon Jun 23 06:49:54 2008
@@ -3,11 +3,11 @@
This meta package will install Debian packages which might be useful
for developing applications for medical image processing.
-Depends: ctn-dev, cimg-dev, libminc-dev, libmdc2-dev
+Recommends: ctn-dev, cimg-dev, libminc-dev, libmdc2-dev
-Depends: libnifti1-dev
+Recommends: libnifti1-dev
-Depends: libinsighttoolkit3-dev
+Recommends: libinsighttoolkit3-dev
Suggests: insighttoolkit3-examples
@@ -15,9 +15,9 @@
Suggests: libvtk5
-Depends: libvolpack1-dev
+Recommends: libvolpack1-dev
-Depends: odin
+Recommends: odin
Homepage: http://od1n.sourceforge.net/
License: GPL
WNPP: 410318
@@ -44,7 +44,7 @@
write: The sequences that come with ODIN are easy to understand and
modify.
-Depends: libvista2-dev
+Recommends: libvista2-dev
Homepage: http://mia.sourceforge.net/
License: GPL
Pkg-Description: software environment for computer vision research
@@ -64,7 +64,7 @@
.
This is the development package.
-Depends: libmni-perllib-perl
+Recommends: libmni-perllib-perl
Homepage: http://packages.bic.mni.mcgill.ca/tgz/
License: Artistic License
Responsible: Michael Hanke <michael.hanke at gmail.com>
@@ -77,7 +77,7 @@
http://mentors.debian.net/cgi-bin/sponsor-pkglist?action=details;package=libmni-perllib-perl
to Debian Med svn and start group maintenance.
-Depends: rumba
+Recommends: rumba
Homepage: http://www.rumba.rutgers.edu/soft/
License: Artistic
Pkg-URL: http://itanix.rutgers.edu/rumba/dists/unstable/perspect/source/science/
@@ -92,7 +92,7 @@
Remark: There seems to be a lot of packaging stuff just done by upstream
guessed from http://itanix.rutgers.edu/rumba/ and the project homepage.
-Depends: nipy
+Recommends: nipy
Homepage: http://neuroimaging.scipy.org/
License: Free
Pkg-Description: development platform for neuroimaging research
Modified: projects/med/trunk/debian-med/tasks/pharmacy
==============================================================================
--- projects/med/trunk/debian-med/tasks/pharmacy (original)
+++ projects/med/trunk/debian-med/tasks/pharmacy Mon Jun 23 06:49:54 2008
@@ -4,4 +4,4 @@
collection of software and documentation which is useful for
pharmaceutical research.
-Depends: chemtool
+Recommends: chemtool
Modified: projects/med/trunk/debian-med/tasks/physics
==============================================================================
--- projects/med/trunk/debian-med/tasks/physics (original)
+++ projects/med/trunk/debian-med/tasks/physics Mon Jun 23 06:49:54 2008
@@ -5,7 +5,7 @@
medical physicists in radiation oncology, diagnostics imaging
and related fields.
-Depends: paw++
+Recommends: paw++
Why: Just depend from the user friendly version because it is easier to
povide a menu item
@@ -14,8 +14,8 @@
Suggests: paw-demos
-Depends: octave3.0
+Recommends: octave3.0
-Depends: r-base | r-base-core
+Recommends: r-base | r-base-core
Why: "r-base" is a meta package and it is better to have a default
alternative -- Dirk Eddelbuettel <edd at debian.org>
Modified: projects/med/trunk/debian-med/tasks/practice
==============================================================================
--- projects/med/trunk/debian-med/tasks/practice (original)
+++ projects/med/trunk/debian-med/tasks/practice Mon Jun 23 06:49:54 2008
@@ -3,12 +3,12 @@
This meta package contains dependencies for a collection of software
which might be helpful for practitioners to manage their practice.
-Depends: gnumed-client
+Recommends: gnumed-client
Recommends: libchipcardc2, libchipcardd0
Why: Reading German "Gesundheitskarte"
-Depends: mirth
+Recommends: mirth
Homepage: http://www.mirthproject.org/
License: MPL 1.1
Pkg-Description: HL7 integration engine
@@ -23,7 +23,7 @@
Mirth also supports filters written in Java if you require more complex
filtering options.
-Depends: tinyheb
+Recommends: tinyheb
Homepage: http://tinyheb.sourceforge.net/
License: GPL
Pkg-URL: http://home.arcor.de/thomas.baum/tinyheb/source/
@@ -31,7 +31,7 @@
This billing system enables midwives to exchange data with health
insurances in Germany (compliant to §302 SGB V).
-Depends: gnumed-server
+Recommends: gnumed-server
Homepage: http://gnumed.org/
Responsible: Andreas Tille <tille at debian.org>
License: GPL
Modified: projects/med/trunk/debian-med/tasks/tools
==============================================================================
--- projects/med/trunk/debian-med/tasks/tools (original)
+++ projects/med/trunk/debian-med/tasks/tools Mon Jun 23 06:49:54 2008
@@ -3,12 +3,12 @@
This meta package will install tools for several purposes in health care.
Currently it contains some simple programs for Personal Health.
-Depends: mencal, cycle, pondus
+Recommends: mencal, cycle, pondus
Suggests: cl-pubmed
Why: Strong dependency would cost installing a large amount of Common Lisp tools which in most cases is not worth the effort
-Depends: mssstest
+Recommends: mssstest
-Depends: wgerman-medical, hunspell-de-med
+Recommends: wgerman-medical, hunspell-de-med
Modified: projects/med/trunk/debian-med/tasks/typesetting
==============================================================================
--- projects/med/trunk/debian-med/tasks/typesetting (original)
+++ projects/med/trunk/debian-med/tasks/typesetting Mon Jun 23 06:49:54 2008
@@ -4,4 +4,4 @@
for typesetting and publishing in medical care and structural
biology.
-Depends: texlive-science, texlive-latex-extra
+Recommends: texlive-science, texlive-latex-extra
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