The following commit has been merged in the historic branch: commit b0a51476449d07638c4fd4f3beca147e9902a985 Author: Andreas Tille <ti...@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 <ti...@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 <ti...@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 (>= ${binary:Version}) Description: Debian-Med several tools This meta package will install tools for several purposes in health care. Currently it just depends from mencal. diff --git a/debian/control.stub b/debian/control.stub index 0af5a18..a6c819f 100644 --- a/debian/control.stub +++ b/debian/control.stub @@ -2,7 +2,7 @@ Source: debian-med Section: misc Priority: extra Maintainer: Andreas Tille <ti...@debian.org> -Build-Depends-Indep: debhelper (>= 4), cdd-dev (>= 0.3) +Build-Depends-Indep: debhelper (>= 4), cdd-dev (>= 0.3.2) Standards-Version: 3.6.1 Package: med diff --git a/debian/rules b/debian/rules index 47f7aef..f6cd24d 100755 --- a/debian/rules +++ b/debian/rules @@ -5,7 +5,8 @@ # Uncomment this to turn on verbose mode. #export DH_VERBOSE=1 -pkgsrc=debian-med +cdd=med +pkgsrc=debian-$(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 M�ller + +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
_______________________________________________ Blends-commit mailing list Blends-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/blends-commit