[med-svn] r11380 - trunk/packages/strap-base/trunk/debian
Author: christophgil-guest Date: 2012-06-19 05:38:25 + (Tue, 19 Jun 2012) New Revision: 11380 Modified: trunk/packages/strap-base/trunk/debian/control Log: Improved description Modified: trunk/packages/strap-base/trunk/debian/control === --- trunk/packages/strap-base/trunk/debian/control 2012-06-19 05:37:48 UTC (rev 11379) +++ trunk/packages/strap-base/trunk/debian/control 2012-06-19 05:38:25 UTC (rev 11380) @@ -16,12 +16,12 @@ Suggests: strap Enhances: Description: Minimal environment for the bioinformatics tool Strap for - aligning proteins by sequence and/or 3D-structure. This package is - sufficient to run /usr/bin/strap-protein-alignment. But required - debian packages for 3D-visualization, automated sequence alignment - and 3D-superposition are not installed automatically. End users - should therefore install the debian package strap which links these - required packages. The strap-base package may be a dependency of - another debian package if used as a viewer for proteins, alignments - and 3D-superpositions. + viewing and editing protein sequence alignments and 3D-structure + superpositions. The package strap-base may be loaded by other debian packages + which use strap as an interactive view for sequence alignments and + 3D-superpositions. End users should rather install the debian + package strap which also installs all required software for + 3D-visualization, automated sequence alignment, 3D-superposition and + PDF-output. + ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r11379 - in trunk/packages/strap/trunk/debian: . bin man
Author: christophgil-guest Date: 2012-06-19 05:37:48 + (Tue, 19 Jun 2012) New Revision: 11379 Modified: trunk/packages/strap/trunk/debian/bin/strap_util_toClustal trunk/packages/strap/trunk/debian/bin/strap_util_toFasta trunk/packages/strap/trunk/debian/bin/strap_util_toMultipleFasta trunk/packages/strap/trunk/debian/bin/toXXX.sh trunk/packages/strap/trunk/debian/control trunk/packages/strap/trunk/debian/man/strap_util_toClustal.1 trunk/packages/strap/trunk/debian/man/strap_util_toFasta.1 trunk/packages/strap/trunk/debian/man/strap_util_toMultipleFasta.1 Log: Fixed shell scripts Modified: trunk/packages/strap/trunk/debian/bin/strap_util_toClustal === --- trunk/packages/strap/trunk/debian/bin/strap_util_toClustal 2012-06-19 03:55:02 UTC (rev 11378) +++ trunk/packages/strap/trunk/debian/bin/strap_util_toClustal 2012-06-19 05:37:48 UTC (rev 11379) @@ -18,6 +18,6 @@ # which would set heap size to 500 Megabytes. -$JAVA_HOME/bin/java $xmx -cp /usr/lib/strap-base/strap-protein-alignment-1.jar charite.christo.strap.Strap -toClustal +$JAVA_HOME/bin/java $xmx -cp /usr/lib/strap-base/strap-protein-alignment-1.jar charite.christo.strap.Strap -toClustal $* Modified: trunk/packages/strap/trunk/debian/bin/strap_util_toFasta === --- trunk/packages/strap/trunk/debian/bin/strap_util_toFasta2012-06-19 03:55:02 UTC (rev 11378) +++ trunk/packages/strap/trunk/debian/bin/strap_util_toFasta2012-06-19 05:37:48 UTC (rev 11379) @@ -18,6 +18,6 @@ # which would set heap size to 500 Megabytes. -$JAVA_HOME/bin/java $xmx -cp /usr/lib/strap-base/strap-protein-alignment-1.jar charite.christo.strap.Strap -toFasta +$JAVA_HOME/bin/java $xmx -cp /usr/lib/strap-base/strap-protein-alignment-1.jar charite.christo.strap.Strap -toFasta $* Modified: trunk/packages/strap/trunk/debian/bin/strap_util_toMultipleFasta === --- trunk/packages/strap/trunk/debian/bin/strap_util_toMultipleFasta 2012-06-19 03:55:02 UTC (rev 11378) +++ trunk/packages/strap/trunk/debian/bin/strap_util_toMultipleFasta 2012-06-19 05:37:48 UTC (rev 11379) @@ -18,6 +18,6 @@ # which would set heap size to 500 Megabytes. -$JAVA_HOME/bin/java $xmx -cp /usr/lib/strap-base/strap-protein-alignment-1.jar charite.christo.strap.Strap -toMultipleFasta +$JAVA_HOME/bin/java $xmx -cp /usr/lib/strap-base/strap-protein-alignment-1.jar charite.christo.strap.Strap -toMultipleFasta $* Modified: trunk/packages/strap/trunk/debian/bin/toXXX.sh === --- trunk/packages/strap/trunk/debian/bin/toXXX.sh 2012-06-19 03:55:02 UTC (rev 11378) +++ trunk/packages/strap/trunk/debian/bin/toXXX.sh 2012-06-19 05:37:48 UTC (rev 11379) @@ -18,6 +18,6 @@ # which would set heap size to 500 Megabytes. -$JAVA_HOME/bin/java $xmx -cp /usr/lib/strap-base/strap-protein-alignment-1.jar charite.christo.strap.Strap -toXXX +$JAVA_HOME/bin/java $xmx -cp /usr/lib/strap-base/strap-protein-alignment-1.jar charite.christo.strap.Strap -toXXX $* Modified: trunk/packages/strap/trunk/debian/control === --- trunk/packages/strap/trunk/debian/control 2012-06-19 03:55:02 UTC (rev 11378) +++ trunk/packages/strap/trunk/debian/control 2012-06-19 05:37:48 UTC (rev 11379) @@ -23,11 +23,12 @@ graphical user interface which follows the paradigms of modern user interfaces such as drag'n drop. The sequence alignment view and the Pymol 3D-visualization are tightly linked. Information can be - attached to residue selections such as free text notes as well as 3D - and 1D display styles. Figures can be created in publication - quality. The alignment can be exported in several formats: PDF, - MS-Word, HTML, Jalview, Multiple-Fasta, ClustalW, MSF, HSSP - see - http://3d-alignment.eu/ for details. Interactive alignments can be - published in Web-pages. For this purpose, HTML code is generated - automatically. Strap is scriptable and can be used by programs and - web-services to display sequence alignments and 3D-superpositions. + attached to residue selections such as free text notes, + cross-references as well as 3D and 1D display style commands. + Figures can be created in publication quality. The alignment can be + exported in several formats: PDF, MS-Word, HTML, Jalview, + Multiple-Fasta, ClustalW, MSF, HSSP - see http://3d-alignment.eu/ for + details. Interactive alignments can be published in Web-pages. For + this purpose, HTML code is generated automatically. Strap is + scriptable and can be used by programs and web-services to display + sequence alignments and 3D-superpositions. Modified: trunk/packages/strap/trunk/debian/man/strap_util_toClustal.1
[med-svn] r11378 - trunk/packages/fis-gtm/fis-gtm/trunk/debian
Author: yoh Date: 2012-06-19 03:55:02 + (Tue, 19 Jun 2012) New Revision: 11378 Modified: trunk/packages/fis-gtm/fis-gtm/trunk/debian/rules Log: BF: assure that installed files are writable -- there remain links to be adjusted, things might need to be cleaned etc Modified: trunk/packages/fis-gtm/fis-gtm/trunk/debian/rules === --- trunk/packages/fis-gtm/fis-gtm/trunk/debian/rules 2012-06-19 03:54:59 UTC (rev 11377) +++ trunk/packages/fis-gtm/fis-gtm/trunk/debian/rules 2012-06-19 03:55:02 UTC (rev 11378) @@ -25,7 +25,13 @@ cd debian/$(BINPKG)-stage1/usr/$(GTM_INSTALL_DIR) && \ gtm_destdir=$(CURDIR)/debian/$(BINPKG) \ ./gtminstall --utf8 default --installdir $(CURDIR)/debian/$(BINPKG)/usr/$(GTM_INSTALL_DIR) + @echo "I: Fixing up permissions for removed write rights -- we aren't done yet!" + chmod +w -R $(CURDIR)/debian/$(BINPKG)/usr/$(GTM_INSTALL_DIR) +# yoh: although it might sound to remove write permissions for the +# deployed materials, as far as I see it, it is useless, since the +# user (root) would always be able to revert them to become writable. + override_dh_link: echo '/usr/lib/fis-gtm/$(UVERDIR) /usr/lib/fis-gtm/current' > debian/fis-gtm.links dh_link ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r11377 - trunk/packages/fis-gtm/fis-gtm/trunk/debian
Author: yoh
Date: 2012-06-19 03:54:59 + (Tue, 19 Jun 2012)
New Revision: 11377
Modified:
trunk/packages/fis-gtm/fis-gtm/trunk/debian/rules
Log:
ENH: relying on Brad's patch (to be committed) provide 2nd stage
build/installation
Modified: trunk/packages/fis-gtm/fis-gtm/trunk/debian/rules
===
--- trunk/packages/fis-gtm/fis-gtm/trunk/debian/rules 2012-06-19 03:54:56 UTC
(rev 11376)
+++ trunk/packages/fis-gtm/fis-gtm/trunk/debian/rules 2012-06-19 03:54:59 UTC
(rev 11377)
@@ -12,20 +12,19 @@
UVERDIR := V$(UVER)_$(ARCH)
SRCPKG := $(shell dpkg-parsechangelog | sed -n 's/^Source: //p')
BINPKG := $(shell awk '/Package:.*[0-9]/{print $$2;}' debian/control)
+GTM_INSTALL_DIR := lib/fis-gtm/$(UVERDIR)
%:
dh $@
override_dh_auto_configure:
- dh_auto_configure -- -DCMAKE_INSTALL_PREFIX:PATH=/usr
-DGTM_INSTALL_DIR=lib/fis-gtm/$(UVERDIR)
+ dh_auto_configure -- -DCMAKE_INSTALL_PREFIX:PATH=/usr
-DGTM_INSTALL_DIR=$(GTM_INSTALL_DIR)
-# At some point in the future, GT.M developers will support DESTDIR
-# and then it will look like:
-#override_dh_auto_install:
-# ./pro/gtminstall --utf8 default --installdir /usr/lib/fis-gtm/VERSION
DESTDIR=$(CURDIR)/debian/$(BINPKG)
-
override_dh_auto_install:
- dh_auto_install --destdir=debian/$(BINPKG) $@
+ dh_auto_install --destdir=debian/$(BINPKG)-stage1 $@
+ cd debian/$(BINPKG)-stage1/usr/$(GTM_INSTALL_DIR) && \
+ gtm_destdir=$(CURDIR)/debian/$(BINPKG) \
+ ./gtminstall --utf8 default --installdir
$(CURDIR)/debian/$(BINPKG)/usr/$(GTM_INSTALL_DIR)
override_dh_link:
echo '/usr/lib/fis-gtm/$(UVERDIR) /usr/lib/fis-gtm/current' >
debian/fis-gtm.links
@@ -43,8 +42,7 @@
override_dh_auto_clean:
dh_auto_clean
- #for f in ./$(SRC_EXTRAS_DIR)/*; do \
- # rm -rf $$(basename $$f); done
+ rm -rf debian/$(BINPKG)-stage1
rm -f debian/fis-gtm.links
override_dh_installchangelogs:
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[med-svn] r11376 - trunk/packages/fis-gtm/fis-gtm/trunk/debian
Author: yoh Date: 2012-06-19 03:54:56 + (Tue, 19 Jun 2012) New Revision: 11376 Modified: trunk/packages/fis-gtm/fis-gtm/trunk/debian/changelog Log: Adjusted the changelog to reflect that we are packaging some GIT snapshot Modified: trunk/packages/fis-gtm/fis-gtm/trunk/debian/changelog === --- trunk/packages/fis-gtm/fis-gtm/trunk/debian/changelog 2012-06-18 18:02:25 UTC (rev 11375) +++ trunk/packages/fis-gtm/fis-gtm/trunk/debian/changelog 2012-06-19 03:54:56 UTC (rev 11376) @@ -1,7 +1,8 @@ -fis-gtm (5.5-000-1) UNRELEASED; urgency=low +fis-gtm (5.5-000+git80-g211bd16-1) UNRELEASED; urgency=low [ Luis Ibanez ] - * Initial release (Closes: #541239) + * Initial release (Closes: #541239) based on not yet released work of +FIS+Kitware teams on building using cmake * New upstream version 5.5 * Adding cmake configuration to facilitate builds in multiple platforms. * debian/rules: ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [SCM] emboss branch, master, updated. debian/6.3.1-6-27-gccd037b
The following commit has been merged in the master branch: commit ccd037b629bc3f7e58c4606da760e4ed3eea87e5 Author: Andreas Tille Date: Mon Jun 18 20:54:34 2012 +0200 Fix lintian errors about missing changelog files diff --git a/debian/changelog b/debian/changelog index 156e251..7d7f636 100644 --- a/debian/changelog +++ b/debian/changelog @@ -7,6 +7,7 @@ emboss (6.4.0-1) UNRELEASED; urgency=low [ Andreas Tille ] * debian/upstream: separate reference section + * debian/rules: Make sure every binary package has a changelog file -- Charles Plessy Wed, 20 Jul 2011 13:22:15 +0900 diff --git a/debian/rules b/debian/rules index a94e909..6b774ae 100755 --- a/debian/rules +++ b/debian/rules @@ -87,7 +87,7 @@ override_dh_auto_test: cd test/qa && LS_COLORS='' EMBOSSRC=$(CURDIR)/test PATH=$(CURDIR)/emboss:$$PATH EMBOSS_ROOT=../../../ ./qatest.csh override_dh_installchangelogs: - dh_installchangelogs -a ChangeLog + dh_installchangelogs -k ChangeLog override_dh_installman: dh_installman -a -p emboss -- The European Molecular Biology Open Software Suite. ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r11375 - in trunk/packages/meme/trunk: . debian
Author: alteholz
Date: 2012-06-18 18:02:25 + (Mon, 18 Jun 2012)
New Revision: 11375
Removed:
trunk/packages/meme/trunk/README.status
Modified:
trunk/packages/meme/trunk/debian/control
trunk/packages/meme/trunk/debian/meme-examples.install
trunk/packages/meme/trunk/debian/rules
Log:
more progress, less lintian complaints
Deleted: trunk/packages/meme/trunk/README.status
===
--- trunk/packages/meme/trunk/README.status 2012-06-18 09:09:29 UTC (rev
11374)
+++ trunk/packages/meme/trunk/README.status 2012-06-18 18:02:25 UTC (rev
11375)
@@ -1,7 +0,0 @@
-Format: 1
-Status: draft
-Comment: >
- Work on this project was started by Steffen Möller but has stalled.
- It is continued by H. Soon Gweon and
- Andreas Tille
Modified: trunk/packages/meme/trunk/debian/control
===
--- trunk/packages/meme/trunk/debian/control2012-06-18 09:09:29 UTC (rev
11374)
+++ trunk/packages/meme/trunk/debian/control2012-06-18 18:02:25 UTC (rev
11375)
@@ -6,7 +6,10 @@
Uploaders: Andreas Tille ,
H. Soon Gweon ,
Thorsten Alteholz
-Build-Depends: debhelper (>= 9), dh-autoreconf, libxslt1-dev
+Build-Depends: debhelper (>= 9),
+ dh-autoreconf,
+ libxslt1-dev,
+ python-all (>= 2.6.6-3~)
Standards-Version: 3.9.3
Homepage: http://meme.nbcr.net/meme/
Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/meme/trunk/
@@ -35,11 +38,13 @@
Recommends: meme
Depends: ${misc:Depends}
Description: Example files for the MEME motif searcher
- This package includes the example files that come with MEME
+ This package includes the example files that come with MEME. They can be used
+ to either check the functionality of the software or play around with the
+ possibilities.
Package: glam2
Architecture: any
-Depends: ${shlibs:Depends}, ${misc:Depends}
+Depends: ${shlibs:Depends}, ${misc:Depends}, ${python:Depends}
Description: gapped protein motifs from unaligned sequences
GLAM2 is a software package for finding motifs in sequences, typically
amino-acid or nucleotide sequences. A motif is a re-occurring sequence
Modified: trunk/packages/meme/trunk/debian/meme-examples.install
===
--- trunk/packages/meme/trunk/debian/meme-examples.install 2012-06-18
09:09:29 UTC (rev 11374)
+++ trunk/packages/meme/trunk/debian/meme-examples.install 2012-06-18
18:02:25 UTC (rev 11375)
@@ -1 +1 @@
-/examples /usr/share/doc/meme/examples
+/examples /usr/share/doc/meme
Modified: trunk/packages/meme/trunk/debian/rules
===
--- trunk/packages/meme/trunk/debian/rules 2012-06-18 09:09:29 UTC (rev
11374)
+++ trunk/packages/meme/trunk/debian/rules 2012-06-18 18:02:25 UTC (rev
11375)
@@ -1,13 +1,14 @@
#!/usr/bin/make -f
# debian/rules file for meme
# Andreas Tille
+# Thorsten Alteholz
# GPL
DBPATH=/var/lib/meme
LOGPATH=/var/log/meme
%:
- dh $@ --with autoreconf
+ dh $@ --with autoreconf,python2
override_dh_auto_configure:
./configure --prefix=/usr --mandir=\$${prefix}/share/man
--infodir=\$${prefix}/share/info --host=$(DEB_HOST_GNU_TYPE)
--build=$(DEB_BUILD_GNU_TYPE) --sysconfdir=/etc/meme \
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[med-svn] r11374 - trunk/packages/mosaik-aligner/trunk/debian
Author: tille
Date: 2012-06-18 09:09:29 + (Mon, 18 Jun 2012)
New Revision: 11374
Modified:
trunk/packages/mosaik-aligner/trunk/debian/control
Log:
Take over description from tasks file
Modified: trunk/packages/mosaik-aligner/trunk/debian/control
===
--- trunk/packages/mosaik-aligner/trunk/debian/control 2012-06-18 09:08:06 UTC
(rev 11373)
+++ trunk/packages/mosaik-aligner/trunk/debian/control 2012-06-18 09:09:29 UTC
(rev 11374)
@@ -13,9 +13,14 @@
Package: mosaik-aligner
Architecture: any
Depends: ${shlibs:Depends}, ${misc:Depends}
-Description: reference-guided aligner for next-generation sequencing
technologies
+Description: reference-guided aligner for next-generation sequencing
MosaikBuild converts various sequence formats into Mosaik’s native read
format. MosaikAligner pairwise aligns each read to a specified series of
reference sequences. MosaikSort resolves paired-end reads and sorts the
alignments by the reference sequence coordinates. Finally, MosaikText
converts alignments to different text-based formats.
+ .
+ At this time, the workflow consists of supplying sequences in FASTA,
+ FASTQ, Illumina Bustard & Gerald, or SRF file formats and producing
+ results in the BLAT axt, the BAM/SAM, the UCSC Genome Browser bed, or
+ the Illumina ELAND formats.
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[med-svn] r11373 - trunk/packages/mosaik-aligner/trunk/debian
Author: tille Date: 2012-06-18 09:08:06 + (Mon, 18 Jun 2012) New Revision: 11373 Modified: trunk/packages/mosaik-aligner/trunk/debian/copyright Log: Make copyright really machine readable Modified: trunk/packages/mosaik-aligner/trunk/debian/copyright === --- trunk/packages/mosaik-aligner/trunk/debian/copyright2012-06-18 07:58:37 UTC (rev 11372) +++ trunk/packages/mosaik-aligner/trunk/debian/copyright2012-06-18 09:08:06 UTC (rev 11373) @@ -1,4 +1,4 @@ -Format: http://dep.debian.net/deps/dep5/ +Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: Mosaik Upstream-Contact: Wan-Ping Source: http://code.google.com/p/mosaik-aligner/ @@ -6,16 +6,22 @@ Files: * Copyright: © 2009-2010 Michael Stromberg & Wan-Ping Lee License: MIT + +Files: debian/* +Copyright: © 2011 Andreas Tille +License: MIT + +License: MIT Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: - + . The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. - + . THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE @@ -24,14 +30,3 @@ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. -Files: src/CommonSource/Utilities/sqlite3.* -Upstream Author: D. Richard Hipp -Copyright: The author disclaims all copyright. -License: Public Domain -Remark: This code was stripped from original tarball and the Debian packaged - sqlite is used - -Files: debian/* -Copyright: © 2011 Andreas Tille -License: PD - The packaging work is in the public domain unless stated otherwise. ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r11372 - trunk/packages/gnumed-client/trunk/debian
Author: tille Date: 2012-06-18 07:58:37 + (Mon, 18 Jun 2012) New Revision: 11372 Modified: trunk/packages/gnumed-client/trunk/debian/control Log: Adjust long description according to hint from upstream Modified: trunk/packages/gnumed-client/trunk/debian/control === --- trunk/packages/gnumed-client/trunk/debian/control 2012-06-17 21:15:55 UTC (rev 11371) +++ trunk/packages/gnumed-client/trunk/debian/control 2012-06-18 07:58:37 UTC (rev 11372) @@ -31,8 +31,8 @@ This is the GNUmed Electronic Medical Record. Its purpose is to enable doctors to keep a medically sound record on their patients' health. It does not currently provide functionality - for billing and stock keeping. Clinical features are well-tested - by real doctors in the field. + for stock keeping. Clinical features are well-tested by real + doctors in the field. . While the GNUmed team has taken the utmost care to make sure the medical records are safe at all times you still need to ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
