[med-svn] [Git][med-team/discosnp][master] 15 commits: Drop again unneeded override
Andreas Tille
gitlab at salsa.debian.org
Wed Jan 23 11:40:43 GMT 2019
Andreas Tille pushed to branch master at Debian Med / discosnp
Commits:
243fa2e1 by Andreas Tille at 2019-01-23T08:16:54Z
Drop again unneeded override
- - - - -
49d83821 by Andreas Tille at 2019-01-23T08:56:24Z
fix dh_install
- - - - -
02745be2 by Andreas Tille at 2019-01-23T09:06:03Z
Cleanup d/rules
- - - - -
2140f9ba by Andreas Tille at 2019-01-23T09:28:08Z
Do not install something directly into /usr
- - - - -
c76a4c59 by Andreas Tille at 2019-01-23T09:30:39Z
Fix interpreter path
- - - - -
212d4b33 by Andreas Tille at 2019-01-23T09:53:53Z
fix install pathes
- - - - -
9c747f4f by Andreas Tille at 2019-01-23T10:17:03Z
There is no point in delivering read_file_names in /usr/bin
- - - - -
1a8df365 by Andreas Tille at 2019-01-23T10:24:54Z
Fix path in scripts, add python3 Depends
- - - - -
3f8b3e0b by Andreas Tille at 2019-01-23T10:25:31Z
Add primitive autogenerated manpages
- - - - -
c61a3430 by Andreas Tille at 2019-01-23T10:31:08Z
Fix spelling
- - - - -
376439a1 by Andreas Tille at 2019-01-23T10:32:17Z
Fix copyright
- - - - -
d5825cbb by Andreas Tille at 2019-01-23T10:33:11Z
read_file_names is binary and needs to got to /usr/lib
- - - - -
7f863b9e by Andreas Tille at 2019-01-23T10:34:43Z
lintian override according to https://lists.debian.org/debian-med/2018/06/msg00043.html
- - - - -
863de48c by Andreas Tille at 2019-01-23T10:40:04Z
Fix path of quick_hierarchical_clustering
- - - - -
c63c2549 by Andreas Tille at 2019-01-23T11:39:53Z
Fix spelling in manpages by recreating these after spelling fixes were applied.
- - - - -
17 changed files:
- debian/changelog
- debian/control
- debian/copyright
- + debian/createmanpages
- − debian/discosnp.install
- − debian/discosnp.manpages
- debian/docs
- + debian/install
- + debian/kissnp2.1
- + debian/kissreads2.1
- + debian/lintian-overrides
- + debian/manpages
- + debian/patches/no_install_to_wrong_dir.patch
- + debian/patches/path_to_readme_file_names.patch
- debian/patches/series
- + debian/patches/spelling.patch
- debian/rules
Changes:
=====================================
debian/changelog
=====================================
@@ -9,6 +9,7 @@ discosnp (2.3.0-1) UNRELEASED; urgency=medium
* Remove trailing whitespace in debian/control
* Remove trailing whitespace in debian/copyright
* Build-Depends: libboost-dev, libgatbcore-dev, libhdf5-dev, zlib1g-dev
+ * Fix dh_install
-- Andreas Tille <tille at debian.org> Sat, 20 Oct 2018 10:56:58 +0200
=====================================
debian/control
=====================================
@@ -20,6 +20,8 @@ Architecture: any
Depends: ${misc:Depends},
${shlibs:Depends},
${python3:Depends}
+ python3
+Recommends: gatb-core
Description: discovering Single Nucleotide Polymorphism from raw set(s) of reads
Software discoSnp is designed for discovering Single Nucleotide
Polymorphism (SNP) from raw set(s) of reads obtained with Next Generation
=====================================
debian/copyright
=====================================
@@ -6,20 +6,11 @@ Files: *
Copyright: 2013 INRIA / IRISA
License: CeCILL
-Files: minia/*
-Copyright: 2012 Rayan Chiki <rayan.chikhi at ens-cachan.org>
- 2012 Guillaume Rizk
-License: CeCILL
-
-Files: kissreads/include/libchash.h
+Files: tools/kissreads2/src/libchash.h
Copyright: 1998-2005, Google Inc
1998-2005 Craig Silverstein
License: BSD-3-clause
-Files: minia/ttmath/*
-Copyright: Tomasz Sowa <t.sowa at ttmath.org>
-License: BSD-3-clause
-
Files: debian/*
Copyright: 2013 Olivier Sallou <osallou at debian.org>
License: GPLv-2
=====================================
debian/createmanpages
=====================================
@@ -0,0 +1,33 @@
+#!/bin/sh
+MANDIR=debian
+mkdir -p $MANDIR
+
+VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//' -e 's/[+~]dfsg$//'`
+NAME=`grep "^Description:" debian/control | sed 's/^Description: *//' | head -n1`
+PROGNAME=`grep "^Package:" debian/control | sed 's/^Package: *//' | head -n1`
+
+AUTHOR=".SH AUTHOR\nThis manpage was written by $DEBFULLNAME for the Debian distribution and
+can be used for any other usage of the program.
+"
+
+# If program name is different from package name or title should be
+# different from package short description change this here
+progname=kissnp2
+help2man --no-info --no-discard-stderr --help-option=" -help" \
+ --name="detects SNPs and indels from read sets" \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=kissreads2
+help2man --no-info --no-discard-stderr --help-option=" -help" \
+ --name="enhances the kissnp2 results by computing per read set" \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+echo "$MANDIR/*.1" > debian/manpages
+
+cat <<EOT
+Please enhance the help2man output.
+The following web page might be helpful in doing so:
+ http://liw.fi/manpages/
+EOT
=====================================
debian/discosnp.install deleted
=====================================
@@ -1,5 +0,0 @@
-output_analyses/discoSnp_to_csv usr/bin/
-output_analyses/discoSnp_to_genotypes usr/bin/
-kissnp2/kissnp2 usr/bin/
-kissreads/kissreads usr/bin/
-data_sample usr/share/doc/discosnp/examples/
=====================================
debian/discosnp.manpages deleted
=====================================
@@ -1,2 +0,0 @@
-kissnp2.1
-kissreads.1
=====================================
debian/docs
=====================================
@@ -1 +1,3 @@
-README.txt
+README*
+doc/*
+test
=====================================
debian/install
=====================================
@@ -0,0 +1,3 @@
+scripts usr/share/discosnp
+scripts_RAD usr/share/discosnp
+run_discoSnp*.sh usr/bin
=====================================
debian/kissnp2.1
=====================================
@@ -0,0 +1,69 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.8.
+.TH KISSNP2 "1" "January 2019" "kissnp2 2.3.0" "User Commands"
+.SH NAME
+kissnp2 \- detects SNPs and indels from read sets
+.SH DESCRIPTION
+[Kissnp2 options]
+.TP
+\fB\-x\fR
+(0 arg) : keep truncated bubbles, that have no successors on the 2 paths at the same position
+.TP
+\fB\-P\fR
+(1 arg) : maximal number of polymorphism per bubble [default '1']
+.TP
+\fB\-D\fR
+(1 arg) : maximal size of a predicted indel [default '0']
+.TP
+\fB\-dont_output_first_coverage\fR (0 arg) :
+Don't output the first coverage threshold. Use this option whent the reference file is used for finding the variants
+.TP
+\fB\-in\fR
+(1 arg) : input file (likely a hdf5 file)
+.TP
+\fB\-coverage_file\fR
+(1 arg) : File (.h5) generated by kissnp2, containing the coverage threshold per read set [default '_removemeplease']
+.TP
+\fB\-out\fR
+(1 arg) : output name
+.TP
+\fB\-T\fR
+(0 arg) : extend found and stop at large polymorphism (extension=contigs) SNPs. Uncompatible with \fB\-t\fR
+.TP
+\fB\-t\fR
+(0 arg) : extend found and stop at first polymorphism (strict extension=unitigs) SNPs. Uncompatible with \fB\-T\fR
+.TP
+\fB\-max_symmetrical_crossroads\fR (1 arg) :
+In b2 mode only: maximal number of symmetrical croasroads traversed while trying to close a bubble. Default: no limit [default '\-1']
+.TP
+\fB\-b\fR
+(1 arg) : branching mode
+.IP
+0: forbid SNPs for which any of the two paths is branching (high precision, low recall)
+1: forbid SNPs for which the two paths are branching (e.g. the two paths can be created either with a 'A' or a 'C' at the same position (default value)
+2: No limitation on branching (low precision, high recall) [default '1']
+.TP
+\fB\-max_ambigous_indel\fR
+(1 arg) : Maximal size of ambiguity of INDELs. INDELS whose ambiguity is higher than this value are not output [default '20']
+.TP
+\fB\-l\fR
+(0 arg) : conserve low complexity SNPs
+.TP
+\fB\-nb\-cores\fR
+(1 arg) : number of cores [default '0']
+.TP
+\fB\-verbose\fR
+(1 arg) : verbosity level [default '1']
+.TP
+\fB\-version\fR
+(0 arg) : version
+.TP
+\fB\-help\fR
+(0 arg) : help
+.TP
+\fB\-bfs\-max\-depth\fR
+(1 arg) : maximum depth for BFS [default '200']
+.TP
+\fB\-bfs\-max\-breadth\fR
+(1 arg) : maximum breadth for BFS [default '20']
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
=====================================
debian/kissreads2.1
=====================================
@@ -0,0 +1,56 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.8.
+.TH KISSREADS2 "1" "January 2019" "kissreads2 2.3.0" "User Commands"
+.SH NAME
+kissreads2 \- enhances the kissnp2 results by computing per read set
+.SH DESCRIPTION
+[Kissreads2 options]
+.TP
+\fB\-x\fR
+(0 arg) : radseq option, homogeneous read depth along the prediction
+.TP
+\fB\-predictions\fR
+(1 arg) : Input predictions
+.TP
+\fB\-reads\fR
+(1 arg) : Input reads
+.TP
+\fB\-unco\fR
+(1 arg) : Output uncoherent file name [default '/dev/null']
+.TP
+\fB\-co\fR
+(1 arg) : Output coherent file name
+.TP
+\fB\-hamming\fR
+(1 arg) : Maximal hamming distance authorized while maping [default '1']
+.TP
+\fB\-coverage_file\fR (1 arg) :
+File (.h5) generated by kissnp2, containing the coverage threshold per read set [default '_removemeplease']
+.TP
+\fB\-k\fR
+(1 arg) : Size of k, used as minial overlap and kmer spanning read coherence [default '31']
+.TP
+\fB\-index_stride\fR
+(1 arg) : Index Stride [default '2']
+.TP
+\fB\-size_seeds\fR
+(1 arg) : Size of the used seeds (distinct from the size of k) [default '25']
+.TP
+\fB\-output_fasta\fR
+(0 arg) : Output standard Fasta. By default the output is formatted especially for the discoSnp++ pipeline
+.TP
+\fB\-genotype\fR
+(0 arg) : Compute genotypes
+.TP
+\fB\-nb\-cores\fR
+(1 arg) : number of cores [default '0']
+.TP
+\fB\-verbose\fR
+(1 arg) : verbosity level [default '1']
+.TP
+\fB\-version\fR
+(0 arg) : version
+.TP
+\fB\-help\fR
+(0 arg) : help
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
=====================================
debian/lintian-overrides
=====================================
@@ -0,0 +1,3 @@
+# see https://lists.debian.org/debian-med/2018/06/msg00043.html
+discosnp: script-with-language-extension usr/bin/run_discoSnp++.sh
+discosnp: script-with-language-extension usr/bin/run_discoSnpRad.sh
=====================================
debian/manpages
=====================================
@@ -0,0 +1 @@
+debian/*.1
=====================================
debian/patches/no_install_to_wrong_dir.patch
=====================================
@@ -0,0 +1,25 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Mon, 21 Jan 2019 09:01:19 +0100
+Description: Failed to fix these install dirs, deactivate completely and use dh_install
+
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -81,12 +81,12 @@ SET (CPACK_SOURCE_IGNORE_FILES
+ )
+
+ # For creating the BINARY package we include the files we want
+-INSTALL (DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/doc DESTINATION .)
+-INSTALL (DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/test DESTINATION .)
+-INSTALL (DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/scripts DESTINATION . FILES_MATCHING REGEX ".*\\.(py|sh)$" PATTERN "jenkins" EXCLUDE)
+-INSTALL (FILES ${CMAKE_CURRENT_SOURCE_DIR}/run_discoSnp++.sh DESTINATION .)
+-INSTALL (FILES ${CMAKE_CURRENT_SOURCE_DIR}/README.md DESTINATION .)
+-INSTALL (FILES ${CMAKE_CURRENT_SOURCE_DIR}/LICENSE DESTINATION .)
++#INSTALL (DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/doc DESTINATION .)
++#INSTALL (DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/test DESTINATION .)
++#INSTALL (DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/scripts DESTINATION . FILES_MATCHING REGEX ".*\\.(py|sh)$" PATTERN "jenkins" EXCLUDE)
++#INSTALL (FILES ${CMAKE_CURRENT_SOURCE_DIR}/run_discoSnp++.sh DESTINATION .)
++#INSTALL (FILES ${CMAKE_CURRENT_SOURCE_DIR}/README.md DESTINATION .)
++#INSTALL (FILES ${CMAKE_CURRENT_SOURCE_DIR}/LICENSE DESTINATION .)
+
+ # We include the "bin" tag into binary archive file name
+ set (CPACK_PACKAGE_FILE_NAME ${PROJECT_NAME}-${CPACK_PACKAGE_VERSION}-bin-${CMAKE_SYSTEM_NAME})
=====================================
debian/patches/path_to_readme_file_names.patch
=====================================
@@ -0,0 +1,74 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Mon, 21 Jan 2019 09:01:19 +0100
+Description: There is no point in delivering read_file_names in /usr/bin
+ It is available in /usr/share/discosnp/bin/read_file_names - this patch adapts
+ the scripts using it.
+ .
+ Some other issues of these scripts are fixed as well.
+
+--- a/run_discoSnpRad.sh
++++ b/run_discoSnpRad.sh
+@@ -65,7 +65,7 @@ genotyping="-genotype"
+ remove=1
+ verbose=1
+ short_read_connector_path=""
+-EDIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )
++EDIR=/usr
+
+ if [ -d "$EDIR/build/" ] ; then # VERSION SOURCE COMPILED
+ read_file_names_bin=$EDIR/build/bin/read_file_names
+@@ -73,14 +73,14 @@ if [ -d "$EDIR/build/" ] ; then # VERSIO
+ kissnp2_bin=$EDIR/build/bin/kissnp2
+ kissreads2_bin=$EDIR/build/bin/kissreads2
+ else # VERSION BINARY
+- read_file_names_bin=$EDIR/bin/read_file_names
++ read_file_names_bin=/usr/lib/discosnp/bin/read_file_names
+ dbgh5_bin=$EDIR/bin/dbgh5
+ kissnp2_bin=$EDIR/bin/kissnp2
+ kissreads2_bin=$EDIR/bin/kissreads2
+ fi
+
+
+-chmod +x $EDIR/scripts/*.sh $EDIR/scripts_RAD/*.sh $EDIR/run_discoSnpRad.sh 2>/dev/null # Usefull for binary distributions
++# chmod +x $EDIR/scripts/*.sh $EDIR/scripts_RAD/*.sh $EDIR/run_discoSnpRad.sh 2>/dev/null # Usefull for binary distributions
+
+ useref=""
+ genome=""
+--- a/run_discoSnp++.sh
++++ b/run_discoSnp++.sh
+@@ -54,7 +54,7 @@ paired=""
+ remove=1
+ verbose=1
+ e=""
+-EDIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )
++EDIR=/usr
+
+ if [ -d "$EDIR/build/" ] ; then # VERSION SOURCE COMPILED
+ read_file_names_bin=$EDIR/build/bin/read_file_names
+@@ -62,13 +62,13 @@ if [ -d "$EDIR/build/" ] ; then # VERSIO
+ kissnp2_bin=$EDIR/build/bin/kissnp2
+ kissreads2_bin=$EDIR/build/bin/kissreads2
+ else # VERSION BINARY
+- read_file_names_bin=$EDIR/bin/read_file_names
++ read_file_names_bin=/usr/lib/discosnp/bin/read_file_names
+ dbgh5_bin=$EDIR/bin/dbgh5
+ kissnp2_bin=$EDIR/bin/kissnp2
+ kissreads2_bin=$EDIR/bin/kissreads2
+ fi
+
+-chmod +x $EDIR/scripts/*.sh $EDIR/run_discoSnpRad.sh 2>/dev/null # Usefull for binary distributions
++#chmod +x $EDIR/scripts/*.sh $EDIR/run_discoSnpRad.sh 2>/dev/null # Usefull for binary distributions
+
+ useref=""
+ genome=""
+--- a/scripts_RAD/discoRAD_finalization.sh
++++ b/scripts_RAD/discoRAD_finalization.sh
+@@ -61,7 +61,7 @@ cmd="${short_read_connector_directory}/s
+ echo -e "\t\t$cmd"
+ $cmd
+ # Compute the clustering
+-cmd="${EDIR}/../build/bin/quick_hierarchical_clustering ${discofile}.txt > ${discofile}.cluster"
++cmd="/usr/lib/discosnp/bin/quick_hierarchical_clustering ${discofile}.txt > ${discofile}.cluster"
+ echo -e "\t\t$cmd"
+ $cmd > ${discofile}.cluster
+ # Generate a .fa file with clustering information
=====================================
debian/patches/series
=====================================
@@ -1 +1,4 @@
use_debian_packaged_gatb-core.patch
+no_install_to_wrong_dir.patch
+path_to_readme_file_names.patch
+spelling.patch
=====================================
debian/patches/spelling.patch
=====================================
@@ -0,0 +1,37 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Mon, 21 Jan 2019 09:01:19 +0100
+Description: Fix spelling
+
+--- a/tools/kissnp2/src/Kissnp2.cpp
++++ b/tools/kissnp2/src/Kissnp2.cpp
+@@ -53,8 +53,8 @@ Kissnp2::Kissnp2 () : Tool ("Kissnp2")
+ getParser()->push_front (new OptionNoParam (STR_DISCOSNP_LOW_COMPLEXITY, "conserve low complexity SNPs", false));
+ getParser()->push_front (new OptionOneParam (STR_MAX_AMBIGOUS_INDELS, "Maximal size of ambiguity of INDELs. INDELS whose ambiguity is higher than this value are not output", false, "20"));
+ getParser()->push_front (new OptionOneParam (STR_DISCOSNP_AUTHORISED_BRANCHING, "branching mode\n"
+- "\t\t0: forbid SNPs for wich any of the two paths is branching (high precision, low recall)\n"
+- "\t\t1: forbid SNPs for wich the two paths are branching (e.g. the two paths can be created either with a 'A' or a 'C' at the same position (default value)\n"
++ "\t\t0: forbid SNPs for which any of the two paths is branching (high precision, low recall)\n"
++ "\t\t1: forbid SNPs for which the two paths are branching (e.g. the two paths can be created either with a 'A' or a 'C' at the same position (default value)\n"
+ "\t\t2: No limitation on branching (low precision, high recall)", false, "1"));
+ getParser()->push_front (new OptionOneParam (STR_MAX_SYMMETRICAL_CROSSROADS,"In b2 mode only: maximal number of symmetrical croasroads traversed while trying to close a bubble. Default: no limit", false, "-1"));
+
+@@ -63,7 +63,7 @@ Kissnp2::Kissnp2 () : Tool ("Kissnp2")
+ getParser()->push_front (new OptionOneParam (STR_URI_OUTPUT, "output name", true));
+ getParser()->push_front (new OptionOneParam (STR_KISSNP2_COVERAGE_FILE_NAME, "File (.h5) generated by kissnp2, containing the coverage threshold per read set", false, "_removemeplease"));
+ getParser()->push_front (new OptionOneParam (STR_URI_INPUT, "input file (likely a hdf5 file)", true));
+- getParser()->push_front (new OptionNoParam (STR_KISSNP2_DONT_OUTPUT_FIRST_COV, "Don't output the first coverage threshold. Use this option whent the refernece file is used for finding the variants", false));
++ getParser()->push_front (new OptionNoParam (STR_KISSNP2_DONT_OUTPUT_FIRST_COV, "Don't output the first coverage threshold. Use this option whent the reference file is used for finding the variants", false));
+
+
+ getParser()->push_front (new OptionOneParam (STR_MAX_INDEL_SIZE, "maximal size of a predicted indel", false, "0"));
+--- a/tools/kissreads2/src/Kissreads2.cpp
++++ b/tools/kissreads2/src/Kissreads2.cpp
+@@ -41,7 +41,7 @@ Kissreads2::Kissreads2 () : Tool ("Kissr
+ /** We add options known by kissnp2. */
+
+ getParser()->push_front (new OptionNoParam (STR_KISSREADS_GENOTYPE, "Compute genotypes", false));
+- getParser()->push_front (new OptionNoParam (STR_KISSREADS_OUTPUT_FASTA, "Output standart Fasta. By default the output is formatted especially for the discoSnp++ pipeline", false));
++ getParser()->push_front (new OptionNoParam (STR_KISSREADS_OUTPUT_FASTA, "Output standard Fasta. By default the output is formatted especially for the discoSnp++ pipeline", false));
+
+ getParser()->push_front (new OptionOneParam (STR_KISSREADS_SIZE_SEEDS, "Size of the used seeds (distinct from the size of k)", false, "25"));
+ getParser()->push_front (new OptionOneParam (STR_KISSREADS_INDEX_STRIDE, "Index Stride", false, "2"));
=====================================
debian/rules
=====================================
@@ -5,9 +5,15 @@
include /usr/share/dpkg/default.mk
+
%:
dh $@
- dh_clean
-override_dh_auto_configure:
- dh_auto_configure -- -DLINK_DIRECTORIES:STRING='/usr/$(DEB_HOST_MULTIARCH)/hdf5/serial' # --trace-expand
+override_dh_install:
+ dh_install
+ mkdir -p debian/$(DEB_SOURCE)/usr/lib/$(DEB_SOURCE)/bin
+ mv debian/$(DEB_SOURCE)/usr/bin/read_file_names debian/$(DEB_SOURCE)/usr/lib/$(DEB_SOURCE)/bin
+ mv debian/$(DEB_SOURCE)/usr/bin/quick_hierarchical_clustering debian/$(DEB_SOURCE)/usr/lib/$(DEB_SOURCE)/bin
+ for pl in `grep -Rl -e '#![[:space:]]*/bin/python' -e '#![[:space:]]*python' debian/*/usr/*` ; do \
+ sed -i '1s?^#!.*python?#!/usr/bin/python3?' $${pl} ; \
+ done
View it on GitLab: https://salsa.debian.org/med-team/discosnp/compare/0a25d26692064f403ea02242af8263f028c4bee9...c63c254996fc9d8b17ccad008e264cbc6c459cdc
--
View it on GitLab: https://salsa.debian.org/med-team/discosnp/compare/0a25d26692064f403ea02242af8263f028c4bee9...c63c254996fc9d8b17ccad008e264cbc6c459cdc
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