[Blends-commit] [SCM] med branch, historic, updated. 7fb9f5410d7eb48cf00689fadde5b6433746b1b6
Andreas Tille
tille at debian.org
Sun Aug 16 14:56:45 UTC 2015
The following commit has been merged in the historic branch:
commit 7fb9f5410d7eb48cf00689fadde5b6433746b1b6
Author: Andreas Tille <tille at debian.org>
Date: Sun Aug 16 16:51:45 2015 +0200
Commit what was uploaded as version 0.7
diff --git a/AUTHORS b/AUTHORS
new file mode 100644
index 0000000..e6be2a3
--- /dev/null
+++ b/AUTHORS
@@ -0,0 +1 @@
+Andreas Tille <tille at debian.org>
diff --git a/COPYING b/COPYING
new file mode 100644
index 0000000..d60c31a
--- /dev/null
+++ b/COPYING
@@ -0,0 +1,340 @@
+ GNU GENERAL PUBLIC LICENSE
+ Version 2, June 1991
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diff --git a/VERSION b/VERSION
new file mode 100644
index 0000000..eb49d7c
--- /dev/null
+++ b/VERSION
@@ -0,0 +1 @@
+0.7
diff --git a/common/common b/common/common
new file mode 100755
index 0000000..2c05a0a
--- /dev/null
+++ b/common/common
@@ -0,0 +1,6 @@
+#!/bin/sh
+## Prints some info about that package and lets auto-apt work
+dpkg --status `basename $0` | \
+ grep -v ^Priority | \
+ grep -v ^Section | \
+ grep -v ^Installed-Size
diff --git a/common/common.1 b/common/common.1
new file mode 100644
index 0000000..bc6086e
--- /dev/null
+++ b/common/common.1
@@ -0,0 +1,19 @@
+.TH med-common 1 "May 24, 2002" "Debian-Med"
+.SH NAME
+.B med-common
+.B med-<meta_package_name>
+\- package information and auto-apt helper
+
+.SH SYNOPSIS
+.B med-common
+.B med-<meta_package_name>
+
+.SH DESCRIPTION
+Print just a simple information page about every med-* package
+of the Debian-Med Custom Debian DIstribution. Each metapackage has a
+.I /usr/bin/med-<meta_package_name>
+file which should print some usefull informations and could be serve
+as auto-apt helper.
+
+.SH AUTHOR
+Andreas Tille <tille at debian.org>.
diff --git a/common/conf b/common/conf
new file mode 100644
index 0000000..a665e5a
--- /dev/null
+++ b/common/conf
@@ -0,0 +1,4 @@
+## 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
+
diff --git a/common/control b/common/control
new file mode 100644
index 0000000..717a050
--- /dev/null
+++ b/common/control
@@ -0,0 +1,11 @@
+Package: med-common
+Architecture: all
+Depends: adduser, debconf (>= 1.2), menu, cdd-common (>= 0.3)
+Description: Debian-Med Project common package
+ This package builds the basic infra structure of all med-* packages.
+ .
+ This package provides some files which are common to all med-* packages.
+ Moreover it introduces a method to handle system users in a group
+ med (easily adaptable to junior by setting view variables) using
+ debconf. This could be valuable for other internal projects.
+
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..757e07d
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,18 @@
+debian-med (0.7) unstable; urgency=low
+
+ * Switched to new version of cdd package (0.3) which has many
+ enhancements (no really important changes to the Debian-Med stuff
+ except that the packages have to be rebuilded with cdd-dev).
+ * New cdd-dev package cares for versioned dependency on med-common
+ Closes: #244903
+
+ -- Andreas Tille <tille at debian.org> Tue, 20 Apr 2004 11:21:16 +0200
+
+debian-med (0.6) unstable; urgency=medium
+
+ * Took over Debian-Edu method to build metapackages from one
+ common source.
+ The changelogs of the previous single meta package sources
+ can be found in the source package under debian/oldchangelogs.
+
+ -- Andreas Tille <tille at debian.org> Mon, 22 Mar 2004 19:21:55 +0100
diff --git a/med-imaging/debian/compat b/debian/compat
similarity index 100%
rename from med-imaging/debian/compat
rename to debian/compat
diff --git a/debian/control b/debian/control
new file mode 100644
index 0000000..f8d3d96
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,63 @@
+Source: debian-med
+Section: misc
+Priority: extra
+Maintainer: Andreas Tille <tille at debian.org>
+Build-Depends-Indep: debhelper (>= 4), cdd-dev (>= 0.3)
+Standards-Version: 3.6.1
+
+Package: med-common
+Architecture: all
+Depends: adduser, ${misc:Depends}, menu, cdd-common (>= 0.3)
+Description: Debian-Med Project common package
+ This package builds the basic infra structure of all med-* packages.
+ .
+ This package provides some files which are common to all med-* packages.
+ Moreover it introduces a method to handle system users in a group
+ med (easily adaptable to junior by setting view variables) using
+ debconf. This could be valuable for other internal projects.
+
+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
+Description: Debian-Med micro-biology packages
+ This meta package will install micro-biology related Debian packages
+ for use in medical research.
+
+Package: med-cms
+Architecture: all
+Depends: zope-zms, med-common (>= 0.8.3)
+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)
+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
+ OdontoLinux server which provides a system for managing a dental practice.
+
+Package: med-imaging
+Architecture: all
+Depends: ctn, ctsim, medcon, minc-tools, paul, xmedcon, med-common (>= 0.8.3)
+Suggests: imagemagick
+Description: Debian-Med imaging packages
+ This meta package will install Debian packages which might be useful in medical
+ image processing.
+
+Package: med-imaging-dev
+Architecture: all
+Depends: ctn-dev, libgtkimreg-dev, libmdc2-dev, libminc0-dev, med-common (>= 0.8.3)
+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-tools
+Architecture: all
+Depends: mencal, med-common (>= 0.8.3)
+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
new file mode 100644
index 0000000..0af5a18
--- /dev/null
+++ b/debian/control.stub
@@ -0,0 +1,9 @@
+Source: debian-med
+Section: misc
+Priority: extra
+Maintainer: Andreas Tille <tille at debian.org>
+Build-Depends-Indep: debhelper (>= 4), cdd-dev (>= 0.3)
+Standards-Version: 3.6.1
+
+Package: med
+Architecture: all
diff --git a/med-imaging/debian/copyright b/debian/copyright
similarity index 65%
rename from med-imaging/debian/copyright
rename to debian/copyright
index 1877356..864895f 100644
--- a/med-imaging/debian/copyright
+++ b/debian/copyright
@@ -1,4 +1,4 @@
-This package is Copyright 2002 by Andreas Tille <tille at debian.org>
+This package is Copyright 2004 by Andreas Tille <tille at debian.org>
This software is licensed under the GPL.
diff --git a/debian/med-templates b/debian/med-templates
new file mode 100644
index 0000000..b2bdb66
--- /dev/null
+++ b/debian/med-templates
@@ -0,0 +1,6 @@
+Template: med-common/group
+Type: multiselect
+_Choices: ${users}
+_Description: Please specify the Debian-Med users!
+ Here is a list of all normal users of the system. Now you can select
+ those users who should get a Debian-Med user menu.
diff --git a/debian/oldchangelogs/bio b/debian/oldchangelogs/bio
new file mode 100644
index 0000000..dcadccf
--- /dev/null
+++ b/debian/oldchangelogs/bio
@@ -0,0 +1,95 @@
+med-bio (0.5-6) unstable; urgency=low
+
+ * Added depends: ncbi-epcr, r-cran-qtl
+
+ -- Andreas Tille <tille at debian.org> Fri, 13 Feb 2004 12:11:37 +0100
+
+med-bio (0.5-5) unstable; urgency=low
+
+ * Added:
+ Depends: loki, tigr-glimmer
+ Suggests: r-base-core
+
+ -- Andreas Tille <tille at debian.org> Wed, 14 Jan 2004 08:31:37 +0100
+
+med-bio (0.5-4) unstable; urgency=low
+
+ * The "I'm against war" release
+ Mankind must put an end to war before war puts an end to mankind.
+ -- John F. Kennedy
+ * Depend from further packages:
+ blast2, ncbi-tools-bin, ncbi-tools-x11
+ * Standards-Version: 3.5.9
+ * debian/compat now stores debhelper compatibility version
+
+ -- Andreas Tille <tille at debian.org> Fri, 4 Apr 2003 08:21:01 +0200
+
+med-bio (0.5-2) unstable; urgency=low
+
+ * Depend from further packages:
+ bioperl, hmmer, rasmol
+ * Standards-Version: 3.5.8
+
+ -- Andreas Tille <tille at debian.org> Sun, 5 Jan 2003 21:37:07 +0100
+
+med-bio (0.5-1) unstable; urgency=low
+
+ * First attempt to use user menus unsing med-common package.
+ * Build-Depends-Indep med-common-dev to make building stuff more general
+
+ -- Andreas Tille <tille at debian.org> Mon, 24 Jun 2002 17:00:19 +0200
+
+med-bio (0.4-3) unstable; urgency=low
+
+ * Added list of dependend packages to package description.
+
+ -- Andreas Tille <tille at debian.org> Tue, 28 May 2002 21:53:41 +0200
+
+med-bio (0.4-2) unstable; urgency=low
+
+ * Added pymol to dependencies.
+ * Introduces /usr/bin/med-bio
+ to give auto-apt a chance to install the package
+ * Manpage for this script.
+ * Remark regarding to the menu entry which was introduced in the last
+ version:
+ The policy violation will be removed and we (Ben Amstrong - Debian-Jr
+ initiator and me) decided to find a better, i.e. user based, menu
+ system.
+
+ -- Andreas Tille <tille at debian.org> Tue, 28 May 2002 20:45:57 +0200
+
+med-bio (0.4-1) unstable; urgency=low
+
+ * Introduced Med/Microbiology menu
+ In the current form it forces a lintian error because it introduces
+ a new root menu section. I just want to show this as a suggestion in
+ some talks and afterwards will follow the consensus which might be
+ result in a policy change.
+
+ -- Andreas Tille <tille at debian.org> Sat, 18 May 2002 12:24:01 +0200
+
+med-bio (0.3-1) unstable; urgency=low
+
+ * Added garlic
+
+ -- Andreas Tille <tille at debian.org> Fri, 19 Apr 2002 15:06:27 +0200
+
+med-bio (0.2-1) unstable; urgency=low
+
+ * Added bugsx
+
+ -- Andreas Tille <tille at debian.org> Sun, 14 Apr 2002 18:44:55 +0200
+
+med-bio (0.1-2) unstable; urgency=low
+
+ * Added biomode, fastdnaml
+
+ -- Andreas Tille <tille at debian.org> Fri, 8 Feb 2002 08:29:38 +0100
+
+med-bio (0.1-1) unstable; urgency=low
+
+ * Initial release
+ closes: #132669
+
+ -- Andreas Tille <tille at debian.org> Wed, 6 Feb 2002 20:56:59 +0100
diff --git a/debian/oldchangelogs/cms b/debian/oldchangelogs/cms
new file mode 100644
index 0000000..5293a39
--- /dev/null
+++ b/debian/oldchangelogs/cms
@@ -0,0 +1,6 @@
+med-cms (0.1-1) unstable; urgency=low
+
+ * Initial release
+ closes: #226464
+
+ -- Andreas Tille <tille at debian.org> Tue, 6 Jan 2004 11:03:42 +0100
diff --git a/debian/oldchangelogs/dent b/debian/oldchangelogs/dent
new file mode 100644
index 0000000..eb3749e
--- /dev/null
+++ b/debian/oldchangelogs/dent
@@ -0,0 +1,60 @@
+med-dent (0.5-2) unstable; urgency=low
+
+ * Added French debconf translation
+ Closes: #236301
+ * Reenabled user menu via med_install_helper
+
+ -- Andreas Tille <tille at debian.org> Tue, 9 Mar 2004 09:17:33 +0100
+
+med-dent (0.5-1) unstable; urgency=low
+
+ * Switched to new debconf format (Thanks to
+ Martin Quinson <Martin.Quinson at tuxfamily.org>
+ for the patch.
+ Closes: Ã#234757
+ * Standards-Version: 3.6.1
+ * Depends: debianutils, mozilla-browser | www-browser
+ instead of galeon | www-browser
+ * med-dent script now uses sensible-browser
+ * used debian/install, debian/manpages, debian/compat
+
+ -- Andreas Tille <tille at debian.org> Thu, 26 Feb 2004 08:23:56 +0100
+
+med-dent (0.4-1) unstable; urgency=low
+
+ * Do not depend from Odontolinux! but ask user for the server name which
+ hosts the Odontolinux! server
+ Closes: #167585
+
+ -- Andreas Tille <tille at debian.org> Wed, 25 Dec 2002 11:07:15 +0100
+
+med-dent (0.3-1) unstable; urgency=low
+
+ * First attempt to use user menus unsing med-common package.
+ * Build-Depends-Indep med-common-dev to make building stuff more general
+
+ -- Andreas Tille <tille at debian.org> Tue, 25 Jun 2002 17:38:44 +0200
+
+med-dent (0.2-1) unstable; urgency=low
+
+ * Introduced Med/Dent menu
+ In the current form it forces a lintian error because it introduces
+ a new root menu section. I just want to show this as a suggestion in
+ some talks and afterwards will follow the consensus which might be
+ result in a policy change.
+ * Depends www-browser
+
+ -- Andreas Tille <tille at debian.org> Sat, 18 May 2002 17:53:56 +0200
+
+med-dent (0.1-2) unstable; urgency=low
+
+ * move to section misc instead of doc (where it stupidly landed)
+
+ -- Andreas Tille <tille at debian.org> Fri, 22 Feb 2002 12:14:35 +0100
+
+med-dent (0.1-1) unstable; urgency=low
+
+ * Initial release
+ closes: #132667
+
+ -- Andreas Tille <tille at debian.org> Wed, 6 Feb 2002 20:56:59 +0100
diff --git a/med-imaging/debian/changelog b/debian/oldchangelogs/imaging
similarity index 100%
rename from med-imaging/debian/changelog
rename to debian/oldchangelogs/imaging
diff --git a/debian/oldchangelogs/imaging-dev b/debian/oldchangelogs/imaging-dev
new file mode 100644
index 0000000..b265968
--- /dev/null
+++ b/debian/oldchangelogs/imaging-dev
@@ -0,0 +1,58 @@
+med-imaging-dev (0.3-4) unstable; urgency=low
+
+ * Removed librumba-dev from dependencies because it was removed from Debian
+ closes: #214230
+
+ -- Andreas Tille <tille at debian.org> Sun, 5 Oct 2003 20:45:59 +0200
+
+med-imaging-dev (0.3-3) unstable; urgency=low
+
+ * What difference does it make to the dead, the orphans and the homeless,
+ whether the mad destruction is wrought under the name of totalitarianism
+ or the holy name of liberty or democracy?
+ -- Mahatma Gandhi (1869 - 1948), "Non-Violence in Peace and War"
+ * Changed dependency from libmdc-dev to libmdc2-dev
+ closes: #190240
+
+ -- Andreas Tille <tille at debian.org> Wed, 23 Apr 2003 13:25:30 +0200
+
+med-imaging-dev (0.3-2) unstable; urgency=low
+
+ * The "I'm against war" release
+ Mankind must put an end to war before war puts an end to mankind.
+ -- John F. Kennedy
+ * Standards-Version: 3.5.9
+ * Added libmdc-dev, libminc0-dev
+ * debian/compat now stores debhelper compatibility version
+ * Build-Depends: debhelper (>= 4)
+
+ -- Andreas Tille <tille at debian.org> Mon, 14 Apr 2003 11:12:52 +0200
+
+med-imaging-dev (0.3-1) unstable; urgency=low
+
+ * First attempt to use user menus unsing med-common package.
+ * Build-Depends-Indep med-common-dev to make building stuff more general
+ * Added ctn-dev to to dependencies.
+ * "avoids" #150864
+ It does not close the bug because it is an enlightenment bug and so
+ it will be reassigned. But the bug will not show up any more with this
+ package because the menu section was renamed.
+
+ -- Andreas Tille <tille at debian.org> Wed, 26 Jun 2002 16:18:18 +0200
+
+med-imaging-dev (0.2-1) unstable; urgency=low
+
+ * Introduced Med/Microbiology menu
+ In the current form it forces a lintian error because it introduces
+ a new root menu section. I just want to show this as a suggestion in
+ some talks and afterwards will follow the consensus which might be
+ result in a policy change.
+
+ -- Andreas Tille <tille at debian.org> Sun, 19 May 2002 21:43:59 +0200
+
+med-imaging-dev (0.1-1) unstable; urgency=low
+
+ * Initial release
+ closes: #142459
+
+ -- Andreas Tille <tille at debian.org> Thu, 11 Apr 2002 17:45:50 +0200
diff --git a/debian/oldchangelogs/tools b/debian/oldchangelogs/tools
new file mode 100644
index 0000000..4d9fafc
--- /dev/null
+++ b/debian/oldchangelogs/tools
@@ -0,0 +1,42 @@
+med-tools (0.3-3) unstable; urgency=low
+
+ * Removed dependency on gnutrion
+ closes: #199107
+
+ -- Andreas Tille <tille at debian.org> Sun, 29 Jun 2003 07:45:53 +0200
+
+med-tools (0.3-2) unstable; urgency=low
+
+ * The "I'm against war" release
+ Mankind must put an end to war before war puts an end to mankind.
+ -- John F. Kennedy
+ * Standards-Version: 3.5.9
+ * Added gnutrition
+ * debian/compat now stores debhelper compatibility version
+ * Build-Depends: debhelper (>= 4)
+
+ -- Andreas Tille <tille at debian.org> Mon, 14 Apr 2003 09:40:43 +0200
+
+med-tools (0.3-1) unstable; urgency=low
+
+ * First attempt to use user menus unsing med-common package.
+ * Build-Depends-Indep med-common-dev to make building stuff more general
+
+ -- Andreas Tille <tille at debian.org> Tue, 25 Jun 2002 23:21:16 +0200
+
+med-tools (0.2-1) unstable; urgency=low
+
+ * Introduced Med/Microbiology menu
+ In the current form it forces a lintian error because it introduces
+ a new root menu section. I just want to show this as a suggestion in
+ some talks and afterwards will follow the consensus which might be
+ result in a policy change.
+
+ -- Andreas Tille <tille at debian.org> Sun, 19 May 2002 21:45:18 +0200
+
+med-tools (0.1-1) unstable; urgency=low
+
+ * Initial release
+ closes: #142901
+
+ -- Andreas Tille <tille at debian.org> Wed, 6 Feb 2002 20:56:59 +0100
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..47f7aef
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,90 @@
+#!/usr/bin/make -f
+# debian/rules for Debian-Med.
+# GNU copyright 2004 Andreas Tille, GPL.
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+pkgsrc=debian-med
+
+control: gen-control debian/control.stub tasks/* control-stamp
+control-stamp:
+ rm -f debian/control
+ cdd-gen-control -c -m -i
+
+ touch control-stamp
+
+build: control-stamp build-stamp
+build-stamp:
+ dh_testdir
+
+ #/usr/bin/docbook-to-man debian/meta-med.sgml > meta-med.1
+
+ touch build-stamp
+
+clean: debian/control
+ dh_testdir
+ dh_testroot
+ 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}
+ rm -rf debian/po
+
+ if [ -f debian/control ] ; then dh_clean ; fi
+ rm -f debian/control
+ ln -s control.stub debian/control
+
+
+install: control-stamp build
+ dh_testdir
+ dh_testroot
+ 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
+ dh_testdir
+ dh_testroot
+ dh_installdocs
+ dh_installexamples
+ dh_installmenu
+# dh_installlogrotate
+# dh_installemacsen
+# dh_installpam
+# dh_installmime
+# dh_installinit
+ dh_installcron
+ dh_installman
+ cdd-install-helper
+ dh_installdebconf
+# dh_installinfo
+ dh_installchangelogs
+ dh_link
+ dh_strip
+ dh_compress
+ dh_fixperms
+# dh_makeshlibs
+ dh_installdeb
+# dh_perl
+ dh_shlibdeps
+ dh_gencontrol
+ dh_md5sums
+ dh_builddeb
+
+dist:
+ distdir=$(pkgsrc)-`cat VERSION` ; \
+ rm -rf $${distdir} ; \
+ mkdir $${distdir} ; \
+ chmod 777 $${distdir} ; \
+ rsync -a --exclude $${distdir} --exclude CVS * $${distdir} ; \
+ GZIP=-9 tar -czf ../$(pkgsrc)_`cat VERSION`.tar.gz $${distdir} ; \
+ rm -rf $${distdir}
+
+binary: binary-indep binary-arch
+.PHONY: build clean binary-indep binary-arch binary install
diff --git a/debian/templates b/debian/templates
new file mode 100644
index 0000000..b2bdb66
--- /dev/null
+++ b/debian/templates
@@ -0,0 +1,6 @@
+Template: med-common/group
+Type: multiselect
+_Choices: ${users}
+_Description: Please specify the Debian-Med users!
+ Here is a list of all normal users of the system. Now you can select
+ those users who should get a Debian-Med user menu.
diff --git a/docs/bio/#biomode.txt b/docs/bio/#biomode.txt
new file mode 100644
index 0000000..b0dd5cd
--- /dev/null
+++ b/docs/bio/#biomode.txt
@@ -0,0 +1,11 @@
+BioMode: Emacs mode to edit genetic data
+
+Some information about Biomode from the Debian-Med project.
+
+ It provides you several interesting commands to take the antiparallel
+ of a region, convert it using readseq, runs blast on it, etc.
+
+This package is not really installed by the med-bio package but it is
+suggested. That means if you are comfortable with the powerful editor
+Emacs you might wish to install also the biomode package and make use
+of it by typing "M-x biomode".
diff --git a/docs/bio/bioperl.txt b/docs/bio/bioperl.txt
new file mode 100644
index 0000000..ecf4efb
--- /dev/null
+++ b/docs/bio/bioperl.txt
@@ -0,0 +1,13 @@
+Bioperl: Perl tools for computational molecular biology
+
+Some information about Bioperl from the Debian-Med project.
+
+ The Bioperl project is a coordinated effort to collect computational methods
+ routinely used in bioinformatics into a set of standard CPAN-style,
+ well-documented, and freely available Perl modules.
+
+The Homepage is http://bio.perl.org/
+
+You can get a good overview by the main manpage:
+
+ man bioperl
diff --git a/docs/bio/blast2.txt b/docs/bio/blast2.txt
new file mode 100644
index 0000000..4b2d43f
--- /dev/null
+++ b/docs/bio/blast2.txt
@@ -0,0 +1,19 @@
+Blast2: Basic Local Alignment Search Tool
+
+Some information about Blast2 from the Debian-Med project.
+
+ The famous sequence alignment program. This is "official" NCBI version, #2.
+ The blastall executable allows you to give a nucleotide or protein
+ sequence to the program. It is compared against databases and a summary of
+ matches is returned to the user.
+
+ The reference Web server is http://www.ncbi.nlm.nih.gov/BLAST/. There you
+ can obtain information about the databases to use which are not included
+ in Debian and how they can be retrieved manually.
+
+ More infromation about the blast2 tools can be obtained from the following
+ manpages:
+
+ copymat.1 formatdb.1 makemat.1 blast.1 blastclust.1 fastacmd.1 seedtop.1
+ impala.1 bl2seq.1 blastpgp.1 blastcl3.1 blastall.1 rpsblast.1 megablast.1
+
diff --git a/docs/bio/fastdnaml.txt b/docs/bio/fastdnaml.txt
new file mode 100644
index 0000000..76d1d1c
--- /dev/null
+++ b/docs/bio/fastdnaml.txt
@@ -0,0 +1,27 @@
+FastDNAml: Construction of Phylogenetic Trees
+
+Some information about fastDNAml from the Debian-Med project.
+
+ fastdnaml provides tools for construction of phylogenetic trees of DNA sequences
+
+ fastDNAml is a program derived from Joseph Felsenstein's version 3.3 DNAML
+ (part of his PHYLIP package). Users should consult the documentation for
+ DNAML before using this program.
+ fastDNAml is an attempt to solve the same problem as DNAML, but to do so
+ faster and using less memory, so that larger trees and/or more bootstrap
+ replicates become tractable. Much of fastDNAml is merely a recoding of the
+ PHYLIP 3.3 DNAML program from PASCAL to C.
+
+ For more detailed information see
+
+ man fastDNAml
+ man fastDNAml-util
+ view /usr/share/doc/fastdnaml/fastDNAml_doc_1.2.txt.gz
+
+ or test the examples under
+
+ /usr/share/doc/fastdnaml/examples
+
+ using the Makefile provided under
+
+ /usr/share/doc/fastdnaml/examples/tests
diff --git a/docs/bio/fastlink.txt b/docs/bio/fastlink.txt
new file mode 100644
index 0000000..cf5e87b
--- /dev/null
+++ b/docs/bio/fastlink.txt
@@ -0,0 +1,14 @@
+FastLink: Faster Pedigree
+
+Some information about fastlink from the Debian-Med project.
+
+ A faster version of pedigree programs of Linkage
+ Fastlink is much faster than the original Linkage but does not
+ implement all the programs.
+
+Unfortunately there is no manpage for the included tools which are
+ ilink, linkmap, lodscore, mlink
+
+Extensive documentation inclusive PostScript formatted papers are provided under
+
+ /usr/share/doc/fastlink
diff --git a/docs/bio/glimmer.txt b/docs/bio/glimmer.txt
new file mode 100644
index 0000000..3bc0073
--- /dev/null
+++ b/docs/bio/glimmer.txt
@@ -0,0 +1,32 @@
+Tigr Glimmer: Gene detection in archea and bacteria
+
+Some information about tigr-glimmer from the Debian-Med project.
+
+ Developed by the TIGR institute this software detects coding sequences in
+ bacteria and archea.
+
+ Glimmer is a system for finding genes in microbial DNA, especially the
+ genomes of bacteria and archaea. Glimmer (Gene Locator and Interpolated
+ Markov Modeler) uses interpolated Markov models (IMMs) to identify the
+ coding regions and distinguish them from noncoding DNA.
+
+ Homepage: http://www.tigr.org/software/glimmer/
+
+An overview about the various tools are given by the following manpages:
+
+ man glimmer2 (start with this)
+ man build-icm
+ man extract
+ man long-orfs
+
+More or less simple syntax help without detailed information is given by
+
+ man adjust
+ man anomaly
+ man check
+ man codon-usage
+ man compare-lists
+ man generate
+ man get-len
+ man run-glimmer2
+ man get-putative
diff --git a/docs/bio/hmmer.txt b/docs/bio/hmmer.txt
new file mode 100644
index 0000000..78cb4f9
--- /dev/null
+++ b/docs/bio/hmmer.txt
@@ -0,0 +1,17 @@
+Hmmer: Biological sequence analysis using profile hidden Markov models
+
+Some information about Hmmer from the Debian-Med project.
+
+ Hmmer is a suite of programs which use profile hidden Markov models
+ (profile HMMs) to model the primary structure consensus of a family of
+ protein or nucleic acid sequences.
+
+Homepage: http://hmmer.wustl.edu/
+
+You can get a good overview by the main manpage:
+
+ man hmmer
+
+The Hmmer users guide is available at
+
+ http://localhost/doc/hmmer/hmmer-html/index.html
diff --git a/docs/bio/loki.txt b/docs/bio/loki.txt
new file mode 100644
index 0000000..1d6aeea
--- /dev/null
+++ b/docs/bio/loki.txt
@@ -0,0 +1,17 @@
+Loki: MCMC linkage analysis on general pedigrees
+
+Some information about Loki from the Debian-Med project.
+
+ Performs Markov chain Monte Carlo multipoint linkage analysis on large,
+ complex pedigrees. The current package supports analyses on quantitative
+ traits only, although this restriction will be lifted in later versions.
+ Joint estimation of QTL number, position and effects uses Reversible Jump
+ MCMC. It is also possible to perform affected only IBD sharing analyses.
+
+ Homepage: http://loki.homeunix.net.
+
+You can get a good overview by the main manpage:
+
+ man loki
+
+It is suggested to install the loki-doc package.
diff --git a/docs/bio/ncbi-epcr.txt b/docs/bio/ncbi-epcr.txt
new file mode 100644
index 0000000..c2370d6
--- /dev/null
+++ b/docs/bio/ncbi-epcr.txt
@@ -0,0 +1,16 @@
+NCBI-EPCR: Tool to test a DNA sequence for the presence of sequence tagged sites
+
+Some information about NCBI-Tools-Bin from the Debian-Med project.
+
+ Electronic PCR feature to test a DNA sequence for the presence of
+ sequence tagged sites. e-PCR looks for STSs in DNA sequences by
+ searching for subsequences that closely match the PCR primers and have
+ the correct order, orientation, and spacing that they could plausibly
+ prime the amplification of a PCR product of the correct molecular weight
+ (Schuler, Genome Research 7:541-50, 1997).
+
+ Homepage: http://www.ncbi.nlm.nih.gov/genome/sts/epcr.cgi
+
+ For further information try:
+
+ man e-PCR
diff --git a/docs/bio/ncbi-tools-bin.txt b/docs/bio/ncbi-tools-bin.txt
new file mode 100644
index 0000000..425e6cf
--- /dev/null
+++ b/docs/bio/ncbi-tools-bin.txt
@@ -0,0 +1,13 @@
+NCBI-Tools-bin: NCBI libraries for biology applications (text-based utilities)
+
+Some information about NCBI-Tools-Bin from the Debian-Med project.
+
+ This package includes various utilities distributed with the NCBI C SDK.
+ None of the programs in this package require X; you can find the X-based
+ utilities in the ncbi-tools-x11 package. BLAST and related tools are
+ in a separate package (blast2).
+
+ The reference Web server is http://www.ncbi.nlm.nih.gov/BLAST/.
+
+ You can easily use the programs contained in the ncbi-tools-bin package
+ via the menu under Debian/Apps/Technical.
diff --git a/docs/bio/ncbi-tools-x11.txt b/docs/bio/ncbi-tools-x11.txt
new file mode 100644
index 0000000..4a0b70d
--- /dev/null
+++ b/docs/bio/ncbi-tools-x11.txt
@@ -0,0 +1,13 @@
+NCBI-Tools-X11: NCBI libraries for biology applications (X-based utilities)
+
+Some information about NCBI-Tools-X11 from the Debian-Med project.
+
+ This package includes some X-based utilities distributed with the
+ NCBI C SDK: Cn3D, Network Entrez, Sequin, ddv, and udv. These
+ programs are not part of ncbi-tools-bin because they depend on
+ several additional library packages.
+
+ The reference Web server is http://www.ncbi.nlm.nih.gov/BLAST/.
+
+ You can easily use the programs contained in the ncbi-tools-x11 package
+ via the menu under Debian/Apps/Technical.
diff --git a/docs/bio/readseq.txt b/docs/bio/readseq.txt
new file mode 100644
index 0000000..2a73b99
--- /dev/null
+++ b/docs/bio/readseq.txt
@@ -0,0 +1,17 @@
+ReadSeq: Conversion between sequence formats
+
+Some information about readseq from the Debian-Med project.
+
+ Reads and writes nucleic/protein sequences in various formats. Data
+ files may have multiple sequences. Readseq is particularly useful as it
+ automatically detects many sequence formats, and converts between them.
+
+Please read the manual for this program by
+
+ man readseq
+
+To test the program you could also test the examples under
+
+ /usr/share/doc/readseq/tests
+
+using the provided Makefile.
diff --git a/docs/imaging-dev/ctn-dev.txt b/docs/imaging-dev/ctn-dev.txt
new file mode 100644
index 0000000..45cbc61
--- /dev/null
+++ b/docs/imaging-dev/ctn-dev.txt
@@ -0,0 +1,15 @@
+CTN Development: CTN-Dicom support
+
+Some information about ctn from the Debian-Med project.
+
+The ctn package provides runtime files for Central Test Node,
+a DICOM implementation.
+DICOM is the standard for image storage, annotation, and networking.
+It is used widely for medical imaging.
+
+This is the development package.
+
+For further information have a look into the extensive documentation
+which is in the Debian package ctn-doc.
+
+The homepage is http://www.erl.wustl.edu/DICOM/ctn.html.
diff --git a/docs/imaging-dev/libgtkimreg-dev.txt b/docs/imaging-dev/libgtkimreg-dev.txt
new file mode 100644
index 0000000..b221ab4
--- /dev/null
+++ b/docs/imaging-dev/libgtkimreg-dev.txt
@@ -0,0 +1,12 @@
+Imreg Development: Image Sequences Development Support
+
+Some information about libgtkimreg-dev from the Debian-Med project.
+
+Please read
+
+ man gtkimreg
+ man gtkimmov
+
+for a detailed description for cutting and moving sets of images.
+A complex example of the usage of these libraries is the image viewer
+paul.
diff --git a/docs/imaging-dev/libmdc2-dev.txt b/docs/imaging-dev/libmdc2-dev.txt
new file mode 100644
index 0000000..ecec884
--- /dev/null
+++ b/docs/imaging-dev/libmdc2-dev.txt
@@ -0,0 +1,13 @@
+MedCon Development: Medical Image Conversion development
+
+Some information about libmdc-dev from the Debian-Med project.
+
+We are sorry that we can not present a more detailed description to this
+development package. We suggest further reading at the xmedcon homepage
+
+ http://xmedcon.sourceforge.net
+
+because it belongs to the XMedCon package.
+
+The following manpages might help you in getting started:
+ xmedcon-config medcon m-gif m-inw m-acr m-ecat m-anlz m-intf
diff --git a/docs/imaging-dev/libminc0-dev.txt b/docs/imaging-dev/libminc0-dev.txt
new file mode 100644
index 0000000..603cc49
--- /dev/null
+++ b/docs/imaging-dev/libminc0-dev.txt
@@ -0,0 +1,12 @@
+MINC Development: MNI medical image format development
+
+Some information about libminc0-dev from the Debian-Med project.
+
+The best way to get started with this development package is to read
+
+ http://localhost/doc/libminc0-dev/
+
+if you have a working webserver installed on your local machine or just
+browse
+
+ /usr/share/doc/libminc0-dev
diff --git a/med-imaging/ctn.txt b/docs/imaging/ctn.txt
similarity index 90%
rename from med-imaging/ctn.txt
rename to docs/imaging/ctn.txt
index 179b4ed..0a5627d 100644
--- a/med-imaging/ctn.txt
+++ b/docs/imaging/ctn.txt
@@ -1,3 +1,5 @@
+CTN: Runtime files for Central Test Node, a DICOM implementation
+
Some information about ctn from the Debian-Med project.
The ctn package provides runtime files for Central Test Node,
diff --git a/med-imaging/medcon.txt b/docs/imaging/medcon.txt
similarity index 83%
rename from med-imaging/medcon.txt
rename to docs/imaging/medcon.txt
index 6a77094..8fa8f8f 100644
--- a/med-imaging/medcon.txt
+++ b/docs/imaging/medcon.txt
@@ -1,6 +1,6 @@
-Some information about medcon from the Debian-Med project.
+MedCon: MEDical image (DICOM, ECAT, ...) CONversion tool
-Medcon is a MEDical image (DICOM, ECAT, ...) CONversion tool.
+Some information about medcon from the Debian-Med project.
The homepage is at
diff --git a/med-imaging/minc-tools.txt b/docs/imaging/minc-tools.txt
similarity index 96%
rename from med-imaging/minc-tools.txt
rename to docs/imaging/minc-tools.txt
index 48d431f..ff609fa 100644
--- a/med-imaging/minc-tools.txt
+++ b/docs/imaging/minc-tools.txt
@@ -1,3 +1,5 @@
+MINC Tools: MNI medical image format tools
+
Some information about minc-tools from the Debian-Med project.
The Minc file format is a highly flexible medical image file format
diff --git a/docs/tools/mencal.txt b/docs/tools/mencal.txt
new file mode 100644
index 0000000..f75cdc1
--- /dev/null
+++ b/docs/tools/mencal.txt
@@ -0,0 +1,10 @@
+MenCal: Menstruation Calendar
+
+Some information about mencal from the Debian-Med project.
+
+Please read
+
+ man mencal
+
+for a detailed description of options and the configuration file of the
+menstruation calendar. It is intended to be called from a text console.
diff --git a/med-imaging/debian/README.Debian b/med-imaging/debian/README.Debian
deleted file mode 100644
index 48d1f0b..0000000
--- a/med-imaging/debian/README.Debian
+++ /dev/null
@@ -1,9 +0,0 @@
-med-imaging is part of the Debian-Med project
----------------------------------------------
-
-This package is a metapackage; it depends on several other packages to make
-them be installed when it is installed. If you want to remove one of those
-packages, you have to remove this package as well. The other packages won't be
-touched.
-
-Andreas Tille <tille at debian.org> Thu, 11 Apr 2002 17:45:50 +0200
diff --git a/med-imaging/debian/control b/med-imaging/debian/control
deleted file mode 100644
index 7854e00..0000000
--- a/med-imaging/debian/control
+++ /dev/null
@@ -1,16 +0,0 @@
-Source: med-imaging
-Section: misc
-Priority: optional
-Maintainer: Andreas Tille <tille at debian.org>
-Build-Depends-Indep: debhelper (>= 4), med-common-dev
-Standards-Version: 3.5.9
-
-Package: med-imaging
-Architecture: all
-Depends: paul, ctsim, ctn, minc-tools, medcon, xmedcon, med-common
-Suggests: imagemagick
-Description: Debian Med imaging packages
- This meta package will install Debian packages which might be useful in medical
- image processing.
- .
- Currently it includes: ctsim, paul
diff --git a/med-imaging/debian/dirs b/med-imaging/debian/dirs
deleted file mode 100644
index 91f3a0c..0000000
--- a/med-imaging/debian/dirs
+++ /dev/null
@@ -1,2 +0,0 @@
-/usr/bin
-/etc/med/menu
diff --git a/med-imaging/debian/docs b/med-imaging/debian/docs
deleted file mode 100644
index 5ec78aa..0000000
--- a/med-imaging/debian/docs
+++ /dev/null
@@ -1 +0,0 @@
-ctn.txt
diff --git a/med-imaging/debian/menu b/med-imaging/debian/menu
deleted file mode 100644
index 4c6321e..0000000
--- a/med-imaging/debian/menu
+++ /dev/null
@@ -1,19 +0,0 @@
-?package(med-imaging):needs="text" section="Med/Imaging"\
- title="CTN" command="view /usr/share/doc/med-imaging/ctn.txt"\
- hints="RUMBA project brain imaging viewer"
-?package(med-imaging):needs="text" section="Med/Imaging"\
- title="MINC Tools" command="view /usr/share/doc/med-imaging/minc-tools.txt"\
- hints="MNI medical image format tools"
-?package(med-imaging):needs="text" section="Med/Imaging"\
- title="MedCon" command="view /usr/share/doc/med-imaging/medcon.txt"\
- hints="Medical Image (DICOM, ECAT, ...) conversion tool"
-?package(med-imaging):needs="X11" section="Med/Imaging"\
- title="Paul" icon="paul.xpm" command="/usr/bin/paul"\
- hints="Imageviewer designed for image sequences"
-?package(med-imaging):needs="X11" section="Med/Imaging"\
- title="CtSim" command="/usr/bin/ctsim"\
- hints="Computed Tomograpy Simulator"
-?package(med-imaging):needs=X11 section="Med/Imaging"\
- title="xmedcon" command="/usr/bin/xmedcon"\
- icon="/usr/X11R6/include/X11/pixmaps/xmedcon.xpm"\
- hints="Medical Image (DICOM, ECAT, ...) conversion tool"
diff --git a/med-imaging/debian/postinst b/med-imaging/debian/postinst
deleted file mode 100644
index 85d58ac..0000000
--- a/med-imaging/debian/postinst
+++ /dev/null
@@ -1,8 +0,0 @@
-#!/bin/sh -e
-
-PROJECT=med
-pkg=$(basename $0 | sed 's/\.postinst//')
-
-install-sub-menus ${PROJECT} ${pkg}
-
-#DEBHELPER#
diff --git a/med-imaging/debian/rules b/med-imaging/debian/rules
deleted file mode 100755
index 859aecd..0000000
--- a/med-imaging/debian/rules
+++ /dev/null
@@ -1,52 +0,0 @@
-#!/usr/bin/make -f
-# debian/rules for med-bio
-# This file is public domain software
-# Andreas Tille <tille at debian.org>
-#
-# Uncomment this to turn on verbose mode.
-#export DH_VERBOSE=1
-#
-# This is the debhelper compatibility version to use.
-export DH_COMPAT=3
-
-build: build-stamp
-build-stamp:
- dh_testdir
-
- touch build-stamp
-
-clean:
- dh_testdir
- dh_testroot
- rm -f build-stamp
-
- dh_clean
-
-install: build
- dh_testdir
- dh_testroot
- dh_clean -k
- dh_installdirs
-
-# Build architecture-independent files here.
-binary-indep: build install
- dh_testdir
- dh_testroot
- dh_installdocs
-# dh_installmenu
- med_install_helper
- dh_installchangelogs
- dh_link
- dh_compress
- dh_fixperms
- dh_installdeb
- dh_gencontrol
- dh_md5sums
- dh_builddeb
-
-# Build architecture-dependent files here.
-binary-arch: build install
-# We have nothing to do by default.
-
-binary: binary-indep binary-arch
-.PHONY: build clean binary-indep binary-arch binary install
diff --git a/menu/bio b/menu/bio
new file mode 100644
index 0000000..07b83d6
--- /dev/null
+++ b/menu/bio
@@ -0,0 +1,15 @@
+?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"
+?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"
diff --git a/menu/dent b/menu/dent
new file mode 100644
index 0000000..b34ef08
--- /dev/null
+++ b/menu/dent
@@ -0,0 +1,4 @@
+?package(med-dent):needs="X11" section="Med/Dent"\
+ title="OdontoLinux"\
+ command="/usr/bin/med-dent"\
+ hints="Web-Browser viewing OdontoLinux"
diff --git a/menu/imaging b/menu/imaging
new file mode 100644
index 0000000..5d7907f
--- /dev/null
+++ b/menu/imaging
@@ -0,0 +1,10 @@
+?package(med-imaging):needs="X11" section="Med/Imaging"\
+ title="Paul" icon="paul.xpm" command="/usr/bin/paul"\
+ hints="Imageviewer designed for image sequences"
+?package(med-imaging):needs="X11" section="Med/Imaging"\
+ title="CtSim" command="/usr/bin/ctsim"\
+ hints="Computed Tomograpy Simulator"
+?package(med-imaging):needs="X11" section="Med/Imaging"\
+ title="xmedcon" command="/usr/bin/xmedcon"\
+ icon="/usr/X11R6/include/X11/pixmaps/xmedcon.xpm"\
+ hints="Medical Image (DICOM, ECAT, ...) conversion tool"
diff --git a/menu/imaging-dev b/menu/imaging-dev
new file mode 100644
index 0000000..e69de29
diff --git a/menu/tools b/menu/tools
new file mode 100644
index 0000000..e6e7980
--- /dev/null
+++ b/menu/tools
@@ -0,0 +1,3 @@
+?package(med-tools):needs="text" section="Med/Tools"\
+ title="Nutrition analysis" command="/usr/bin/gnutrition"\
+ hints="/usr/share/pixmaps/gnutrition.xpm"
diff --git a/tasks/bio b/tasks/bio
new file mode 100644
index 0000000..e56bc5e
--- /dev/null
+++ b/tasks/bio
@@ -0,0 +1,15 @@
+Architecture: all
+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, \
+ 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
diff --git a/tasks/cms b/tasks/cms
new file mode 100644
index 0000000..a39f0fd
--- /dev/null
+++ b/tasks/cms
@@ -0,0 +1,6 @@
+Architecture: all
+Description: Debian-Med content management systems
+ This meta package will install packages which are useful to build a
+ content management system for medical care.
+
+Depends: zope-zms
diff --git a/tasks/dent b/tasks/dent
new file mode 100644
index 0000000..70bb264
--- /dev/null
+++ b/tasks/dent
@@ -0,0 +1,7 @@
+Architecture: all
+Description: Debian-Med package for dental practice client
+ This meta package will configure your system to act as client for the
+ OdontoLinux server which provides a system for managing a dental practice.
+
+Depends: debianutils (>= 2.6.2), mozilla-browser | www-browser, \
+ debconf (>= 1.2)
diff --git a/tasks/imaging b/tasks/imaging
new file mode 100644
index 0000000..6f908f6
--- /dev/null
+++ b/tasks/imaging
@@ -0,0 +1,7 @@
+Architecture: all
+Description: Debian-Med imaging packages
+ This meta package will install Debian packages which might be useful in medical
+ image processing.
+
+Depends: paul, ctsim, ctn, minc-tools, medcon, xmedcon
+Suggests: imagemagick
diff --git a/tasks/imaging-dev b/tasks/imaging-dev
new file mode 100644
index 0000000..fb958f5
--- /dev/null
+++ b/tasks/imaging-dev
@@ -0,0 +1,6 @@
+Architecture: all
+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.
+
+Depends: libgtkimreg-dev, ctn-dev, libminc0-dev, libmdc2-dev
diff --git a/tasks/tools b/tasks/tools
new file mode 100644
index 0000000..892882a
--- /dev/null
+++ b/tasks/tools
@@ -0,0 +1,6 @@
+Architecture: all
+Description: Debian-Med several tools
+ This meta package will install tools for several purposes in health care.
+ Currently it just depends from mencal.
+
+Depends: mencal
--
Debian Med metapackages
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