[Blends-commit] [SCM] med branch, historic, updated. 6c0b338c229d6163381015383ea1a8ab646c33e2
Andreas Tille
tille at debian.org
Wed Feb 21 13:36:49 UTC 2018
The following commit has been merged in the historic branch:
commit b0a51476449d07638c4fd4f3beca147e9902a985
Author: Andreas Tille <tille at debian.org>
Date: Wed Feb 21 14:30:49 2018 +0100
Commit status of debian/0.8
diff --git a/VERSION b/VERSION
index eb49d7c..aec258d 100644
--- a/VERSION
+++ b/VERSION
@@ -1 +1 @@
-0.7
+0.8
diff --git a/common/conf b/common/conf
index a665e5a..f7dd169 100644
--- a/common/conf
+++ b/common/conf
@@ -1,4 +1,9 @@
## This is a configuration file for Debian-med Custom Debian Distribution
## It is read after /etc/cdd/cdd.conf and can override or add variables
-UPDATEUSERMENU=yes
+## This variable is replaced by a debconf question
+## UPDATEUSERMENU=yes
+
+## Some CDDs do not build their name generic like Debian-#CDD# so
+## we need the correct name here
+CDDNAME=Debian-Med
diff --git a/debian/changelog b/debian/changelog
index 757e07d..91a0c53 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,10 @@
+debian-med (0.8) unstable; urgency=low
+
+ * Added med-physics, med-pharmacy, med-bio-dev
+ * Overworked menus of meta packages
+
+ -- Andreas Tille <tille at debian.org> Fri, 4 Jun 2004 14:44:36 +0200
+
debian-med (0.7) unstable; urgency=low
* Switched to new version of cdd package (0.3) which has many
diff --git a/debian/control b/debian/control
index f8d3d96..cabc02c 100644
--- a/debian/control
+++ b/debian/control
@@ -2,7 +2,7 @@ Source: debian-med
Section: misc
Priority: extra
Maintainer: Andreas Tille <tille at debian.org>
-Build-Depends-Indep: debhelper (>= 4), cdd-dev (>= 0.3)
+Build-Depends-Indep: debhelper (>= 4), cdd-dev (>= 0.3.2)
Standards-Version: 3.6.1
Package: med-common
@@ -18,22 +18,30 @@ Description: Debian-Med Project common package
Package: med-bio
Architecture: all
-Depends: bioperl, blast2, boxshade, bugsx, fastdnaml, fastlink, garlic, ghemical, hmmer, loki, ncbi-epcr, ncbi-tools-bin, ncbi-tools-x11, njplot, pymol, r-cran-qtl, rasmol, readseq, tigr-glimmer, tree-puzzle, med-common (>= 0.8.3)
-Suggests: biomode, clustalw, clustalw-mpi, clustalx, molphy, phylip, r-base-core, seaview, treetool
+Depends: blast2, boxshade, bugsx, fastdnaml, fastlink, garlic, ghemical, hmmer, loki, ncbi-epcr, ncbi-tools-bin, ncbi-tools-x11, njplot, pymol, r-cran-qtl, rasmol, readseq, tigr-glimmer, tree-puzzle, med-common (>= ${binary:Version})
+Suggests: clustalw, clustalw-mpi, clustalx, molphy, phylip, seaview, treetool
Description: Debian-Med micro-biology packages
This meta package will install micro-biology related Debian packages
for use in medical research.
+Package: med-bio-dev
+Architecture: all
+Depends: bioperl, libncbi6-dev, libvibrant6-dev, mcl, med-common (>= ${binary:Version})
+Suggests: biomode, r-base-core
+Description: Debian-Med packages for development of micro-biology applications
+ This meta package will install Debian packages which might be helpful
+ for development of applications for micro-biological research.
+
Package: med-cms
Architecture: all
-Depends: zope-zms, med-common (>= 0.8.3)
+Depends: zope-zms, med-common (>= ${binary:Version})
Description: Debian-Med content management systems
This meta package will install packages which are useful to build a
content management system for medical care.
Package: med-dent
Architecture: all
-Depends: mozilla-browser, med-common (>= 0.8.3)
+Depends: mozilla-browser, med-common (>= ${binary:Version})
Suggests: debconf (>= 1.2), debianutils (>= 2.6.2), www-browser
Description: Debian-Med package for dental practice client
This meta package will configure your system to act as client for the
@@ -41,7 +49,7 @@ Description: Debian-Med package for dental practice client
Package: med-imaging
Architecture: all
-Depends: ctn, ctsim, medcon, minc-tools, paul, xmedcon, med-common (>= 0.8.3)
+Depends: ctn, ctsim, medcon, minc-tools, paul, xmedcon, med-common (>= ${binary:Version})
Suggests: imagemagick
Description: Debian-Med imaging packages
This meta package will install Debian packages which might be useful in medical
@@ -49,14 +57,33 @@ Description: Debian-Med imaging packages
Package: med-imaging-dev
Architecture: all
-Depends: ctn-dev, libgtkimreg-dev, libmdc2-dev, libminc0-dev, med-common (>= 0.8.3)
+Depends: ctn-dev, libgtkimreg-dev, libmdc2-dev, libminc0-dev, med-common (>= ${binary:Version})
Description: Debian-Med packages for medical image development
This meta package will install Debian packages which might be useful
for developing applications for medical image processing.
+Package: med-pharmacy
+Architecture: all
+Depends: chemtool, med-common (>= ${binary:Version})
+Description: Debian-Med packages for pharmaceutical research
+ This meta package contains dependencies for a
+ collection of software and documentation which is useful for
+ pharmaceutical research.
+
+Package: med-physics
+Architecture: all
+Depends: octave, paw++, r-base, med-common (>= ${binary:Version})
+Recommends: paw
+Suggests: paw-demos
+Description: Debian-Med packages for medical physicists
+ This meta package contains dependencies for a
+ collection of software and documentation which is useful for
+ medical physicists in radiation oncology, diagnostics imaging
+ and related fields.
+
Package: med-tools
Architecture: all
-Depends: mencal, med-common (>= 0.8.3)
+Depends: mencal, med-common (>= ${binary:Version})
Description: Debian-Med several tools
This meta package will install tools for several purposes in health care.
Currently it just depends from mencal.
diff --git a/debian/control.stub b/debian/control.stub
index 0af5a18..a6c819f 100644
--- a/debian/control.stub
+++ b/debian/control.stub
@@ -2,7 +2,7 @@ Source: debian-med
Section: misc
Priority: extra
Maintainer: Andreas Tille <tille at debian.org>
-Build-Depends-Indep: debhelper (>= 4), cdd-dev (>= 0.3)
+Build-Depends-Indep: debhelper (>= 4), cdd-dev (>= 0.3.2)
Standards-Version: 3.6.1
Package: med
diff --git a/debian/rules b/debian/rules
index 47f7aef..f6cd24d 100755
--- a/debian/rules
+++ b/debian/rules
@@ -5,7 +5,8 @@
# Uncomment this to turn on verbose mode.
#export DH_VERBOSE=1
-pkgsrc=debian-med
+cdd=med
+pkgsrc=debian-$(cdd)
control: gen-control debian/control.stub tasks/* control-stamp
control-stamp:
@@ -16,9 +17,18 @@ control-stamp:
build: control-stamp build-stamp
build-stamp:
+ # Fix *.dsc file to mention all binary targets
+ TASKS="" ; \
+ if [ -d common ] ; then TASKS="$(cdd)-common" ; fi ; \
+ for task in `ls -1 tasks | sort` ; do \
+ if [ "$${TASKS}" != "" ] ; then TASKS="$${TASKS}, " ; fi ; \
+ TASKS="$${TASKS}$(cdd)-$${task}" ; \
+ done ; \
+ sed "s/^\(Binary: \)$(cdd)/\1$${TASKS}/" ../$(pkgsrc)_*.dsc > tmp.dsc ; \
+ mv tmp.dsc ../$(pkgsrc)_*.dsc
dh_testdir
- #/usr/bin/docbook-to-man debian/meta-med.sgml > meta-med.1
+ #/usr/bin/docbook-to-man debian/meta-$(cdd).sgml > meta-$(cdd).1
touch build-stamp
@@ -28,8 +38,8 @@ clean: debian/control
rm -f build-stamp control-stamp
rm -rf tmp
rm -f tasks/*~
- [ -d menu ] && rm -f debian/med-*.post{inst,rm}
- rm -f debian/med-common.{templates,config}
+ [ -d menu ] && rm -f debian/$(cdd)-*.post{inst,rm}
+ rm -f debian/$(cdd)-common.{templates,config,install} debian/90$(cdd)-common
rm -rf debian/po
if [ -f debian/control ] ; then dh_clean ; fi
@@ -43,12 +53,12 @@ install: control-stamp build
dh_clean -k
dh_installdirs
-# Build architecture-independent files here.
-binary-indep: build install
-# We have nothing to do by default.
-
# Build architecture-dependent files here.
binary-arch: build install
+# We have nothing to do by default.
+
+# Build architecture-independent files here.
+binary-indep: build install
dh_testdir
dh_testroot
dh_installdocs
@@ -62,6 +72,7 @@ binary-arch: build install
dh_installcron
dh_installman
cdd-install-helper
+ dh_install
dh_installdebconf
# dh_installinfo
dh_installchangelogs
diff --git a/docs/bio/#biomode.txt b/docs/bio-dev/#biomode.txt
similarity index 100%
copy from docs/bio/#biomode.txt
copy to docs/bio-dev/#biomode.txt
diff --git a/docs/bio/bioperl.txt b/docs/bio-dev/bioperl.txt
similarity index 100%
copy from docs/bio/bioperl.txt
copy to docs/bio-dev/bioperl.txt
diff --git a/docs/bio-dev/libvibrant6-dev.txt b/docs/bio-dev/libvibrant6-dev.txt
new file mode 100644
index 0000000..90e1ce1
--- /dev/null
+++ b/docs/bio-dev/libvibrant6-dev.txt
@@ -0,0 +1,13 @@
+libvibrant6-dev: NCBI libraries for graphic biology applications
+ (development files)
+
+Some information about libvibrant6-dev from the Debian-Med project.
+
+ Vibrant allows you to develop portable (Motif, MS-Windows, Mac-OS) graphic
+ biological applications.
+
+The Homepage is http://www.ncbi.nlm.nih.gov/
+
+You can get a good overview by reading
+
+ zless /usr/share/doc/libvibrant6-dev/README.gz
diff --git a/docs/bio-dev/mcl.txt b/docs/bio-dev/mcl.txt
new file mode 100644
index 0000000..e7feacd
--- /dev/null
+++ b/docs/bio-dev/mcl.txt
@@ -0,0 +1,33 @@
+MCL: Markov Cluster algorithm
+
+Some information about mcl from the Debian-Med project.
+
+ The MCL package is an implementation of the MCL algorithm, and offers
+ utilities for manipulating sparse matrices (the essential data
+ structure in the MCL algorithm) and conducting cluster experiments.
+
+ MCL is currently being used in sciences like biology (protein family
+ detection, genomics), computer sciense (node clustering in
+ Peer-to-Peer networks), and linguistics (text analysis).
+
+ Homepage: http://micans.org/mcl/
+
+An overview about the various tools are given by the following manpages:
+
+ man mcx
+ man clmimac
+ man clmmate
+ man clmmeet
+ man clmformat
+ man clmdist
+ man clminfo
+ man mcxconvert
+ man mcxassemble
+ man mcxmap
+ man mcxsubs
+ man mcxarray
+ man mcxdeblast
+ man mclblastline
+ man mcl
+ man clmresidue
+ man mclpipeline
diff --git a/docs/bio/r-cran-qtl.txt b/docs/bio/r-cran-qtl.txt
new file mode 100644
index 0000000..390f415
--- /dev/null
+++ b/docs/bio/r-cran-qtl.txt
@@ -0,0 +1,23 @@
+r-cran-qtl: GNU R package for genetic marker linkage analysis
+
+Some information about r-cran-qtl from the Debian-Med project.
+
+ R/qtl is an extensible, interactive environment for
+ mapping quantitative trait loci (QTLs) in experimental crosses. It is
+ implemented as an add-on-package for the freely available and widely used
+ statistical language/software R (see http://www.r-project.org). The
+ user will benefit from the seamless integration of the QTL mapping
+ software into a general statistical analysis program.
+
+ The current version of R/qtl includes facilities for estimating
+ genetic maps, identifying genotyping errors, and performing single-QTL
+ genome scans and two-QTL, two-dimensional genome scans, by interval
+ mapping (with EM algorithm), Haley-Knott regression, and multiple
+ imputation. All of this may be done in the presence of covariates
+ (such as sex, age or treatment). The fit of higher-order QTL models,
+ with sophisticated techniques for model comparisons and model search,
+ will be incorporated soon.
+
+More information can be found at
+
+ Homepage: http://www.biostat.jhsph.edu/~kbroman/qtl/index.html
diff --git a/docs/cms/zope-zms.txt b/docs/cms/zope-zms.txt
new file mode 100644
index 0000000..49f4a16
--- /dev/null
+++ b/docs/cms/zope-zms.txt
@@ -0,0 +1,24 @@
+zope-zms: Content management for science, technology and medicine
+
+Some information about Zope ZMS from the Debian-Med project.
+
+ ZMS (Zope based Content Management for Science, Technology and Medicine)
+ is a ready to use solution for efficient electronic publishing. An easy
+ to handle graphical user interface for editors and flexible modelling
+ features (multiple languages, Metadata, content objects, XML
+ import/export, workflow etc.) allow an optimum of productivity: A
+ basic configuration to start with can be created with a few mouse clicks.
+
+ ZMS is perfectly suitable for hospitals, research institutions, NGOs
+ and small to medium-size international companies.
+
+ The ZMS concept is based on a consulting approach for the rational
+ publishing on the internet: the professional user is able to pursue
+ a consequently efficiency oriented producing base with the ZMS software
+ and can hereby also achieve important economic results in the so-called
+ low budget area. The modulation possibilities of the ZMS components and
+ the experienced producing steps makes out of ZMS an incomparable fast tool.
+
+ Homepage: http://www.zms-publishing.com/
+
+ Read /usr/share/doc/zope-zms/README.Debian for the first steps.
diff --git a/menu/bio b/menu/bio
index 07b83d6..ff200e9 100644
--- a/menu/bio
+++ b/menu/bio
@@ -1,15 +1,19 @@
+?package(med-bio):needs="text" section="Med/Microbiology"\
+ title="Boxshade" command="/usr/bin/boxshade"
+?package(med-bio):needs="X11" section="Med/Microbiology"\
+ title="Bugsx" command="/usr/bin/bugsx -g +0+0" hints="Evolve Biomorphs"
?package(med-bio):needs="X11" section="Med/Microbiology"\
title="Garlic" command="/usr/bin/garlic" hints="Molecular Visualization"
?package(med-bio):needs="X11" section="Med/Microbiology"\
- title="Bugsx" command="/usr/bin/bugsx -g +0+0" hints="Evolve Biomorphs"
+ title="ghemical" command="/usr/bin/ghemical"
?package(med-bio):needs="X11" section="Med/Microbiology"\
title="NjPlot" command="/usr/bin/njplot" hints="Tree Drawing"
-?package(med-bio):needs="text" section="Med/Microbiology"\
- title="Tree-Puzzle" command="/usr/bin/tree-puzzle"\
- hints="Reconstruction of Phylogenetic Trees"
?package(med-bio):needs="x11" section="Med/Microbiology" \
title="PyMOL" command="/usr/bin/pymol" \
hints="PyMOL Molecular Graphics System"
?package(med-bio):needs="x11" section="Med/Microbiology" \
title="rasmol" command="/usr/bin/rasmol" \
hints="Molecule visualization and rendering"
+?package(med-bio):needs="text" section="Med/Microbiology"\
+ title="Tree-Puzzle" command="/usr/bin/tree-puzzle"\
+ hints="Reconstruction of Phylogenetic Trees"
diff --git a/menu/bio-dev b/menu/bio-dev
new file mode 100644
index 0000000..72f2f92
--- /dev/null
+++ b/menu/bio-dev
@@ -0,0 +1,4 @@
+?package(med-bio-dev):command="/usr/bin/vibrate /usr/bin/asntool" needs="X11" \
+ section="Med/Microbiology Development" title="asntool" hints="Biology" icon="/usr/share/pixmaps/asntool.xpm"
+?package(med-bio-dev):command="/usr/bin/vibrate /usr/bin/errhdr" needs="X11" \
+ section="Med/Microbiology Development" title="errhdr" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm"
diff --git a/menu/pharmacy b/menu/pharmacy
new file mode 100644
index 0000000..3968454
--- /dev/null
+++ b/menu/pharmacy
@@ -0,0 +1,3 @@
+?package(med-pharmacy):needs="X11" section="Med/Pharmacy" \
+ title="chemtool" icon="/usr/share/pixmaps/chemtool.xpm" \
+ hints="Chemical Structure Editor" command="/usr/bin/chemtool"
diff --git a/menu/physics b/menu/physics
new file mode 100644
index 0000000..1497c48
--- /dev/null
+++ b/menu/physics
@@ -0,0 +1,12 @@
+?package(med-physics):needs="x11" \
+ section="Med/Physics" \
+ title="Paw" \
+ command="paw++.dynamic"
+?package(med-physics):needs="text" \
+ section="Med/Physics" \
+ title="GNU R" \
+ command="/usr/bin/R"
+?package(med-physics):needs="text" \
+ section="Med/Physics" \
+ title="Octave (2.1)" \
+ command="/usr/bin/octave2.1"
diff --git a/tasks/bio b/tasks/bio
index e56bc5e..277b9dd 100644
--- a/tasks/bio
+++ b/tasks/bio
@@ -3,13 +3,15 @@ Description: Debian-Med micro-biology packages
This meta package will install micro-biology related Debian packages
for use in medical research.
-Depends: bioperl, blast2, bugsx, fastdnaml, fastlink, garlic, hmmer, \
+Depends: blast2, bugsx, fastdnaml, fastlink, garlic, hmmer, \
loki, ncbi-epcr, ncbi-tools-bin, ncbi-tools-x11, njplot, pymol, \
r-cran-qtl, rasmol, readseq, tigr-glimmer, tree-puzzle
-Suggests: biomode, r-base-core
Depends: boxshade
Depends: ghemical
Why: Molecular modelling of ligands of receptors
Responsible: Steffen Möller
+
+Suggests: clustalw | clustalw-mpi, clustalx, molphy, phylip, seaview, treetool
+Why: Non-free, thus only suggested.
diff --git a/tasks/bio-dev b/tasks/bio-dev
new file mode 100644
index 0000000..51edcd8
--- /dev/null
+++ b/tasks/bio-dev
@@ -0,0 +1,7 @@
+Architecture: all
+Description: Debian-Med packages for development of micro-biology applications
+ This meta package will install Debian packages which might be helpful
+ for development of applications for micro-biological research.
+
+Depends: bioperl, libncbi6-dev, libvibrant6-dev, mcl
+Suggests: biomode, r-base-core
diff --git a/tasks/pharmacy b/tasks/pharmacy
new file mode 100644
index 0000000..32209d3
--- /dev/null
+++ b/tasks/pharmacy
@@ -0,0 +1,7 @@
+Architecture: all
+Description: Debian-Med packages for pharmaceutical research
+ This meta package contains dependencies for a
+ collection of software and documentation which is useful for
+ pharmaceutical research.
+
+Depends: chemtool
diff --git a/tasks/physics b/tasks/physics
new file mode 100644
index 0000000..80e42c8
--- /dev/null
+++ b/tasks/physics
@@ -0,0 +1,15 @@
+Architecture: all
+Description: Debian-Med packages for medical physicists
+ This meta package contains dependencies for a
+ collection of software and documentation which is useful for
+ medical physicists in radiation oncology, diagnostics imaging
+ and related fields.
+
+Depends: paw++
+Why: Just depend from the user friendly version because it is easier to \
+ povide a menu item
+Recommends: paw
+Why: This is for the purists with exactly the same functionality as paw++
+Suggests: paw-demos
+
+Depends: r-base, octave
--
Debian Med metapackages
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