[med-svn] [Git][med-team/allelecount][upstream] New upstream version 4.2.1
Nilesh Patra
gitlab at salsa.debian.org
Sat Nov 21 12:06:56 GMT 2020
Nilesh Patra pushed to branch upstream at Debian Med / allelecount
Commits:
77e90fde by Nilesh Patra at 2020-11-21T17:29:52+05:30
New upstream version 4.2.1
- - - - -
19 changed files:
- CHANGES.md
- Dockerfile
- README.md
- build/opt-build.sh
- c/src/alleleCounter.c
- c/src/bam_access.c
- c/src/bam_access.h
- c/tests/bam_access_tests.c
- c/tests/minunit.h
- c/tests/runtests.sh
- perl/Makefile.PL
- perl/bin/alleleCounter.pl
- perl/lib/Sanger/CGP/AlleleCount.pm
- perl/lib/Sanger/CGP/AlleleCount/Genotype.pm
- perl/t/1_pm_compile.t
- perl/t/2_pl_compile.t
- perl/t/genotype.t
- prerelease.sh
- setup.sh
Changes:
=====================================
CHANGES.md
=====================================
@@ -1,5 +1,11 @@
# CHANGES
+## v4.2.1
+
+* Update so docker and native install use same install scripts behind the scenes
+* Docker now actually has htslib 1.11
+* htslib compiled with libdeflate for improved performance
+
## v4.2.0
* Updated to hstlib 1.11
=====================================
Dockerfile
=====================================
@@ -1,32 +1,33 @@
-FROM ubuntu:16.04 as builder
+FROM ubuntu:20.04 as builder
USER root
# ALL tool versions used by opt-build.sh
-ENV VER_HTSLIB="1.7"
+# need to keep in sync with setup.sh
+ENV VER_HTSLIB="1.11"
+ENV VER_LIBDEFLATE="v1.6"
RUN apt-get -yq update
-RUN apt-get install -yq --no-install-recommends \
-build-essential \
-apt-transport-https \
-curl \
-ca-certificates \
-make \
-bzip2 \
-gcc \
-locales \
-curl \
-wget \
-libtasn1-dev \
-libgnutls-dev \
-nettle-dev \
-libgmp-dev \
-libp11-kit-dev \
-zlib1g-dev \
-libbz2-dev \
-liblzma-dev \
-libcurl4-gnutls-dev \
-libncurses5-dev
+RUN apt-get install -yq --no-install-recommends
+RUN apt-get install -yq --no-install-recommends build-essential
+RUN apt-get install -yq --no-install-recommends apt-transport-https
+RUN apt-get install -yq --no-install-recommends curl
+RUN apt-get install -yq --no-install-recommends ca-certificates
+RUN apt-get install -yq --no-install-recommends make
+RUN apt-get install -yq --no-install-recommends bzip2
+RUN apt-get install -yq --no-install-recommends gcc
+RUN apt-get install -yq --no-install-recommends locales
+RUN apt-get install -yq --no-install-recommends curl
+RUN apt-get install -yq --no-install-recommends wget
+RUN apt-get install -yq --no-install-recommends libtasn1-dev
+RUN apt-get install -yq --no-install-recommends nettle-dev
+RUN apt-get install -yq --no-install-recommends libgmp-dev
+RUN apt-get install -yq --no-install-recommends libp11-kit-dev
+RUN apt-get install -yq --no-install-recommends zlib1g-dev
+RUN apt-get install -yq --no-install-recommends libbz2-dev
+RUN apt-get install -yq --no-install-recommends liblzma-dev
+RUN apt-get install -yq --no-install-recommends libcurl4-gnutls-dev
+RUN apt-get install -yq --no-install-recommends libncurses5-dev
RUN locale-gen en_US.UTF-8
RUN update-locale LANG=en_US.UTF-8
@@ -46,11 +47,10 @@ RUN bash build/opt-build.sh $OPT
COPY . .
RUN bash build/opt-build-local.sh $OPT
-FROM ubuntu:16.04
+FROM ubuntu:20.04
LABEL maintainer="cgphelp at sanger.ac.uk" \
uk.ac.sanger.cgp="Cancer, Ageing and Somatic Mutation, Wellcome Trust Sanger Institute" \
- version="v1.0.0" \
description="alleleCount docker"
RUN apt-get -yq update
=====================================
README.md
=====================================
@@ -125,7 +125,7 @@ The docker images are know to work correctly after import into a singularity ima
## LICENCE
```
-Copyright (c) 2014-2018 Genome Research Ltd.
+Copyright (c) 2014-2020 Genome Research Ltd.
Author: CASM/Cancer IT <cgphelp at sanger.ac.uk>
=====================================
build/opt-build.sh
=====================================
@@ -49,19 +49,33 @@ export MANPATH=`echo $INST_PATH/man:$INST_PATH/share/man:$MANPATH | perl -pe 's/
export PERL5LIB=`echo $INST_PATH/lib/perl5:$PERL5LIB | perl -pe 's/:\$//;'`
set -u
-## grab cpanm
-curl -L http://cpanmin.us | perl - App::cpanminus
-CPANM=`which cpanm`
+## INSTALL CPANMINUS
+curl -sSL https://cpanmin.us/ > $SETUP_DIR/cpanm
+perl $SETUP_DIR/cpanm --no-wget --no-interactive --notest --mirror http://cpan.metacpan.org -l $INST_PATH App::cpanminus
+rm -f $SETUP_DIR/cpanm
echo "Installing Perl base deps ..."
if [ ! -e $SETUP_DIR/basePerlDeps.success ]; then
perlmods=( "ExtUtils::CBuilder" "Module::Build~0.42" "Const::Fast" "File::Which" "LWP::UserAgent")
for i in "${perlmods[@]}" ; do
- $CPANM --no-interactive --notest --mirror http://cpan.metacpan.org -l $INST_PATH $i
+ cpanm --no-interactive --notest --mirror http://cpan.metacpan.org -l $INST_PATH $i
done
touch $SETUP_DIR/basePerlDeps.success
fi
+## libdeflate
+if [ ! -e $SETUP_DIR/libdeflate.success ]; then
+ rm -rf tmp_deflate
+ mkdir -p tmp_deflate
+ curl -sSL --retry 10 https://github.com/ebiggers/libdeflate/archive/${VER_LIBDEFLATE}.tar.gz > distro.tar.gz
+ tar --strip-components 1 -C tmp_deflate -zxf distro.tar.gz
+ cd tmp_deflate
+ PREFIX=$INST_PATH make -j$CPU CFLAGS="-fPIC -O3" install
+ cd ../
+ rm -rf distro.* tmp_deflate
+ touch $SETUP_DIR/libdeflate.success
+fi
+
SOURCE_HTSLIB="https://github.com/samtools/htslib/releases/download/${VER_HTSLIB}/htslib-${VER_HTSLIB}.tar.bz2"
cd $SETUP_DIR
@@ -78,7 +92,9 @@ if [ ! -e $SETUP_DIR/htslib.success ]; then
mkdir -p htslib
tar --strip-components 1 -C htslib -jxf htslib-${VER_HTSLIB}.tar.bz2
cd htslib
- ./configure --enable-plugins --enable-libcurl --prefix=$INST_PATH
+ ./configure --enable-plugins --enable-libcurl --with-libdeflate --prefix=$INST_PATH \
+ CPPFLAGS="-I$INST_PATH/include" \
+ LDFLAGS="-L${INST_PATH}/lib -Wl,-R${INST_PATH}/lib"
make -j$CPU
make install
cd $SETUP_DIR
=====================================
c/src/alleleCounter.c
=====================================
@@ -1,5 +1,5 @@
/** LICENSE
-* Copyright (c) 2014-2018 Genome Research Ltd.
+* Copyright (c) 2014-2020 Genome Research Ltd.
*
* Author: CASM/Cancer IT <cgphelp at sanger.ac.uk>
*
=====================================
c/src/bam_access.c
=====================================
@@ -1,5 +1,5 @@
/** LICENSE
-* Copyright (c) 2014-2018 Genome Research Ltd.
+* Copyright (c) 2014-2020 Genome Research Ltd.
*
* Author: CASM/Cancer IT <cgphelp at sanger.ac.uk>
*
=====================================
c/src/bam_access.h
=====================================
@@ -1,5 +1,5 @@
/** LICENSE
-* Copyright (c) 2014-2018 Genome Research Ltd.
+* Copyright (c) 2014-2020 Genome Research Ltd.
*
* Author: CASM/Cancer IT <cgphelp at sanger.ac.uk>
*
=====================================
c/tests/bam_access_tests.c
=====================================
@@ -1,5 +1,5 @@
/** LICENSE
-* Copyright (c) 2014-2018 Genome Research Ltd.
+* Copyright (c) 2014-2020 Genome Research Ltd.
*
* Author: CASM/Cancer IT <cgphelp at sanger.ac.uk>
*
=====================================
c/tests/minunit.h
=====================================
@@ -1,22 +1,22 @@
/** LICENSE
-* Copyright (c) 2014-2018 Genome Research Ltd.
-*
+* Copyright (c) 2014-2020 Genome Research Ltd.
+*
* Author: CASM/Cancer IT <cgphelp at sanger.ac.uk>
-*
-* This file is part of alleleCount.
-*
-* alleleCount is free software: you can redistribute it and/or modify it under
-* the terms of the GNU Affero General Public License as published by the Free
-* Software Foundation; either version 3 of the License, or (at your option) any
-* later version.
-*
-* This program is distributed in the hope that it will be useful, but WITHOUT
-* ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-* FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more
-* details.
-*
-* You should have received a copy of the GNU Affero General Public License
-* along with this program. If not, see <http://www.gnu.org/licenses/>.
+*
+* This file is part of alleleCount.
+*
+* alleleCount is free software: you can redistribute it and/or modify it under
+* the terms of the GNU Affero General Public License as published by the Free
+* Software Foundation; either version 3 of the License, or (at your option) any
+* later version.
+*
+* This program is distributed in the hope that it will be useful, but WITHOUT
+* ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+* FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more
+* details.
+*
+* You should have received a copy of the GNU Affero General Public License
+* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
#undef NDEBUG
=====================================
c/tests/runtests.sh
=====================================
@@ -1,22 +1,22 @@
########## LICENSE ##########
-# Copyright (c) 2014-2018 Genome Research Ltd.
-#
+# Copyright (c) 2014-2020 Genome Research Ltd.
+#
# Author: CASM/Cancer IT <cgphelp at sanger.ac.uk>
-#
-# This file is part of alleleCount.
-#
-# alleleCount is free software: you can redistribute it and/or modify it under
-# the terms of the GNU Affero General Public License as published by the Free
-# Software Foundation; either version 3 of the License, or (at your option) any
-# later version.
-#
-# This program is distributed in the hope that it will be useful, but WITHOUT
-# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-# FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more
-# details.
-#
-# You should have received a copy of the GNU Affero General Public License
-# along with this program. If not, see <http://www.gnu.org/licenses/>.
+#
+# This file is part of alleleCount.
+#
+# alleleCount is free software: you can redistribute it and/or modify it under
+# the terms of the GNU Affero General Public License as published by the Free
+# Software Foundation; either version 3 of the License, or (at your option) any
+# later version.
+#
+# This program is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+# FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Affero General Public License
+# along with this program. If not, see <http://www.gnu.org/licenses/>.
###########################
echo "Running unit tests:"
=====================================
perl/Makefile.PL
=====================================
@@ -1,7 +1,7 @@
#!/usr/bin/perl
##########LICENCE##########
-# Copyright (c) 2014-2018 Genome Research Ltd.
+# Copyright (c) 2014-2020 Genome Research Ltd.
#
# Author: CASM/Cancer IT <cgphelp at sanger.ac.uk>
#
=====================================
perl/bin/alleleCounter.pl
=====================================
@@ -1,7 +1,7 @@
#!/usr/bin/perl
##########LICENCE##########
-# Copyright (c) 2014-2018 Genome Research Ltd.
+# Copyright (c) 2014-2020 Genome Research Ltd.
#
# Author: CASM/Cancer IT <cgphelp at sanger.ac.uk>
#
=====================================
perl/lib/Sanger/CGP/AlleleCount.pm
=====================================
@@ -1,7 +1,7 @@
package Sanger::CGP::AlleleCount;
##########LICENCE##########
-# Copyright (c) 2014-2018 Genome Research Ltd.
+# Copyright (c) 2014-2020 Genome Research Ltd.
#
# Author: CASM/Cancer IT <cgphelp at sanger.ac.uk>
#
@@ -25,7 +25,7 @@ package Sanger::CGP::AlleleCount;
use strict;
use base 'Exporter';
-our $VERSION = '4.2.0';
+our $VERSION = '4.2.1';
our @EXPORT = qw($VERSION);
1;
=====================================
perl/lib/Sanger/CGP/AlleleCount/Genotype.pm
=====================================
@@ -1,7 +1,7 @@
package Sanger::CGP::AlleleCount::Genotype;
##########LICENCE##########
-# Copyright (c) 2014-2018 Genome Research Ltd.
+# Copyright (c) 2014-2020 Genome Research Ltd.
#
# Author: CASM/Cancer IT <cgphelp at sanger.ac.uk>
#
=====================================
perl/t/1_pm_compile.t
=====================================
@@ -1,21 +1,21 @@
##########LICENCE##########
-# Copyright (c) 2014-2018 Genome Research Ltd.
-#
+# Copyright (c) 2014-2020 Genome Research Ltd.
+#
# Author: CASM/Cancer IT <cgphelp at sanger.ac.uk>
-#
-# This file is part of alleleCount.
-#
-# alleleCount is free software: you can redistribute it and/or modify it under
-# the terms of the GNU Affero General Public License as published by the Free
-# Software Foundation; either version 3 of the License, or (at your option) any
-# later version.
-#
-# This program is distributed in the hope that it will be useful, but WITHOUT
-# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-# FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more
-# details.
-#
-# You should have received a copy of the GNU Affero General Public License
+#
+# This file is part of alleleCount.
+#
+# alleleCount is free software: you can redistribute it and/or modify it under
+# the terms of the GNU Affero General Public License as published by the Free
+# Software Foundation; either version 3 of the License, or (at your option) any
+# later version.
+#
+# This program is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+# FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Affero General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
##########LICENCE##########
=====================================
perl/t/2_pl_compile.t
=====================================
@@ -1,21 +1,21 @@
##########LICENCE##########
-# Copyright (c) 2014-2018 Genome Research Ltd.
-#
+# Copyright (c) 2014-2020 Genome Research Ltd.
+#
# Author: CASM/Cancer IT <cgphelp at sanger.ac.uk>
-#
-# This file is part of alleleCount.
-#
-# alleleCount is free software: you can redistribute it and/or modify it under
-# the terms of the GNU Affero General Public License as published by the Free
-# Software Foundation; either version 3 of the License, or (at your option) any
-# later version.
-#
-# This program is distributed in the hope that it will be useful, but WITHOUT
-# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-# FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more
-# details.
-#
-# You should have received a copy of the GNU Affero General Public License
+#
+# This file is part of alleleCount.
+#
+# alleleCount is free software: you can redistribute it and/or modify it under
+# the terms of the GNU Affero General Public License as published by the Free
+# Software Foundation; either version 3 of the License, or (at your option) any
+# later version.
+#
+# This program is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+# FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Affero General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
##########LICENCE##########
=====================================
perl/t/genotype.t
=====================================
@@ -1,5 +1,5 @@
##########LICENCE##########
-# Copyright (c) 2014-2018 Genome Research Ltd.
+# Copyright (c) 2014-2020 Genome Research Ltd.
#
# Author: CASM/Cancer IT <cgphelp at sanger.ac.uk>
#
=====================================
prerelease.sh
=====================================
@@ -1,7 +1,7 @@
#!/bin/bash
##########LICENCE##########
-# Copyright (c) 2014-2018 Genome Research Ltd.
+# Copyright (c) 2014-2020 Genome Research Ltd.
#
# Author: CASM/Cancer IT <cgphelp at sanger.ac.uk>
#
=====================================
setup.sh
=====================================
@@ -1,7 +1,7 @@
#!/bin/bash
##########LICENCE##########
-# Copyright (c) 2014-2018 Genome Research Ltd.
+# Copyright (c) 2014-2020 Genome Research Ltd.
#
# Author: CASM/Cancer IT <cgphelp at sanger.ac.uk>
#
@@ -21,52 +21,18 @@
# along with this program. If not, see <http://www.gnu.org/licenses/>.
##########LICENCE##########
-SOURCE_HTSLIB="https://github.com/samtools/htslib/releases/download/1.11/htslib-1.11.tar.bz2"
+# ALL tool versions used by opt-build.sh
+# need to keep in sync with Dockerfile
+export VER_HTSLIB="1.11"
+export VER_LIBDEFLATE="v1.6"
-EXP_SAMV="1.3.1"
-
-version_gt () {
- test $(printf '%s\n' $@ | sort -V | head -n 1) == "$1";
-}
-
-get_distro () {
- EXT=""
- DECOMP=""
- if [[ $2 == *.tar.bz2* ]] ; then
- EXT="tar.bz2"
- DECOMP="-j"
- elif [[ $2 == *.tar.gz* ]] ; then
- EXT="tar.gz"
- DECOMP="-z"
- else
- echo "I don't understand the file type for $1"
- exit 1
- fi
-
- if hash curl 2>/dev/null; then
- curl -sS -o $1.$EXT -L $2
- else
- wget -nv -O $1.$EXT $2
- fi
- mkdir -p $1
- tar --strip-components 1 -C $1 $DECOMP -xf $1.$EXT
-}
-
-get_file () {
-# output, source
- if hash curl 2>/dev/null; then
- curl -sS -o $1 -L $2
- else
- wget -nv -O $1 $2
- fi
-}
if [[ ($# -ne 1 && $# -ne 2) ]] ; then
echo "Please provide an installation path and optionally perl lib paths to allow, e.g."
echo " ./setup.sh /opt/myBundle"
echo "OR all elements versioned:"
- echo " ./setup.sh /opt/cgpVcf-X.X.X /opt/PCAP-X.X.X/lib/perl"
- exit 0
+ echo " ./setup.sh /opt/cgpPinel-X.X.X /opt/cgpVcf-X.X.X/lib/perl:/opt/PCAP-core-X.X.X/lib/perl"
+ exit 1
fi
INST_PATH=$1
@@ -75,17 +41,6 @@ if [[ $# -eq 2 ]] ; then
CGP_PERLLIBS=$2
fi
-
-CPU=`grep -c ^processor /proc/cpuinfo`
-if [ $? -eq 0 ]; then
- if [ "$CPU" -gt "6" ]; then
- CPU=6
- fi
-else
- CPU=1
-fi
-echo "Max compilation CPUs set to $CPU"
-
# get current directory
INIT_DIR=`pwd`
@@ -98,7 +53,6 @@ INST_PATH=`pwd`
cd $INIT_DIR
# make sure that build is self contained
-unset PERL5LIB
PERLROOT=$INST_PATH/lib/perl5
# allows user to knowingly specify other PERL5LIB areas.
@@ -108,91 +62,17 @@ else
export PERL5LIB="$PERLROOT:$CGP_PERLLIBS"
fi
-export PATH=$INST_PATH/bin:$PATH
-
-#create a location to build dependencies
-SETUP_DIR=$INIT_DIR/install_tmp
-mkdir -p $SETUP_DIR
-
-## grab cpanm and stick in workspace, then do a self upgrade into bin:
-get_file $SETUP_DIR/cpanm https://cpanmin.us/
-perl $SETUP_DIR/cpanm -l $INST_PATH App::cpanminus
-CPANM=`which cpanm`
-
-if [ -e $SETUP_DIR/basePerlDeps.success ]; then
- echo "Previously installed base perl deps..."
-else
- perlmods=( "ExtUtils::CBuilder" "Module::Build~0.42" "Const::Fast" "File::Which" "LWP::UserAgent")
- for i in "${perlmods[@]}" ; do
- $CPANM --no-interactive --notest --mirror http://cpan.metacpan.org -l $INST_PATH $i
- done
- touch $SETUP_DIR/basePerlDeps.success
-fi
-
-cd $SETUP_DIR
-
-if [ -e $SETUP_DIR/htslibGet.success ]; then
- echo " already staged ...";
-else
- echo
- cd $SETUP_DIR
- get_distro "htslib" $SOURCE_HTSLIB
- touch $SETUP_DIR/htslibGet.success
-fi
-
-echo -n "Building htslib ..."
-if [ -e $SETUP_DIR/htslib.success ]; then
- echo " previously installed ...";
-else
- echo
- mkdir -p htslib
- tar --strip-components 1 -C htslib -jxf htslib.tar.bz2
- cd htslib
- ./configure --enable-plugins --enable-libcurl --prefix=$INST_PATH
- make -j$CPU
- cd $SETUP_DIR
- touch $SETUP_DIR/htslib.success
-fi
-
-export HTSLIB="$SETUP_DIR/htslib"
-
-echo -n "Building alleleCounter ..."
-if [ -e "$SETUP_DIR/alleleCounter.success" ]; then
- echo " previously installed ...";
-else
- cd $INIT_DIR
- mkdir -p $INIT_DIR/c/bin
- make -C c clean
- make -C c -j$CPU
- cp $INIT_DIR/c/bin/alleleCounter $INST_PATH/bin/.
- touch $SETUP_DIR/alleleCounter.success
-fi
-
-cd $INIT_DIR/perl
-
-echo -n "Installing Perl prerequisites ..."
-if ! ( perl -MExtUtils::MakeMaker -e 1 >/dev/null 2>&1); then
- echo
- echo "WARNING: Your Perl installation does not seem to include a complete set of core modules. Attempting to cope with this, but if installation fails please make sure that at least ExtUtils::MakeMaker is installed. For most users, the best way to do this is to use your system's package manager: apt, yum, fink, homebrew, or similar."
-fi
-$CPANM --no-interactive --notest --mirror http://cpan.metacpan.org -l $INST_PATH/ --installdeps $INIT_DIR/perl/. < /dev/null
-
-echo -n "Installing alleleCount ..."
-cd $INIT_DIR/perl
-perl Makefile.PL INSTALL_BASE=$INST_PATH
-make
-make test
-make install
+export OPT=$INST_PATH
-# cleanup all junk
-rm -rf $SETUP_DIR
+bash build/opt-build.sh $INST_PATH
+bash build/opt-build-local.sh $INST_PATH
echo
echo
-echo "Please add the following to beginning of path:"
+echo "Please add the following to beginning of PATH:"
echo " $INST_PATH/bin"
-echo "Please add the following to beginning of PERL5LIB:"
-echo " $PERLROOT"
+echo "Please add the following to beginning of LD_LIBRARY_PATH:"
+echo " $INST_PATH/lib"
echo
exit 0
View it on GitLab: https://salsa.debian.org/med-team/allelecount/-/commit/77e90fde06749b7129ddaeb6853927d434708189
--
View it on GitLab: https://salsa.debian.org/med-team/allelecount/-/commit/77e90fde06749b7129ddaeb6853927d434708189
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