diff --git a/README.md b/README.md
index 8bbd0392290a2df500bb3a168cd9fffa14fa62f4..03f448a9ff7de7e351b5a96b19fe573b6dec1f92 100644
--- a/README.md
+++ b/README.md
@@ -75,8 +75,10 @@ Use the gitlab tag of the docker image (e.g., gitlab_v5.0) to get the descriptio
### 9.1
Dockerfiles added: <br />
-ubuntu/v20.04/slivar/v1.0 at date 20221002: from ubuntu:20.04 with samtools and slivar added
+ubuntu/v20.04/extended/v1.0 at date 20221002: from ubuntu:20.04 with git bc gawk coreutils added
+ubuntu/v20.04/slivar/v2.0 at date 20221002: from ubuntu:20.04 with samtools and slivar added
ubuntu/v20.04/samtools/v1.0 at date 20221002: from ubuntu:20.04 with samtools added
+ubuntu/v20.04/htslib/v1.0 at date 20221002: from ubuntu:20.04 with samtools added
### 9.0
diff --git a/ubuntu/v20.04/htslib/v1.0/Dockerfile b/ubuntu/v20.04/htslib/v1.0/Dockerfile
new file mode 100644
index 0000000000000000000000000000000000000000..4613f61f430092979d9eaf89b2886eb0b696fe00
--- /dev/null
+++ b/ubuntu/v20.04/htslib/v1.0/Dockerfile
@@ -0,0 +1,103 @@
+#########################################################################
+## ##
+## Dockerfile ##
+## htslib ##
+## ##
+## Gael A. Millot ##
+## Bioinformatics and Biostatistics Hub ##
+## Computational Biology Department ##
+## Institut Pasteur Paris ##
+## ##
+#########################################################################
+
+
+
+# to see the log of the building:
+# sudo docker run -ti --entrypoint bash <IMAGE_NAME>
+# cat building.log
+
+# to export the log file of the image building from the container:
+# sudo docker images
+# sudo docker run -ti --entrypoint bash <IMAGE_NAME>
+# exit
+# sudo docker container ls -a # to get all the active containers
+# sudo docker cp <containerNAMES>:/building.log </host/path/target>
+
+# base image: ubuntu:16.04
+FROM gmillot/ubuntu-extended_v1.0:gitlab_v9.1
+# Warning: the name must be exactly what is written in the docker images interface, or sudo docker image ls. But here, since the image is not present locally, docker will search it on docker hub. Thus, gmillot/ubuntu:16.04 iw not correct
+
+LABEL Gael.Millot=gael.millot@pasteur.fr
+LABEL gitlab.dockerfiles="https://gitlab.pasteur.fr/gmillot/dockerfiles"
+
+
+ENV APT_GET_LINUX_LIB="\
+ zlib1g \
+ liblzma5 \
+ libncurses5 \
+"
+ENV APT_GET_LINUX_LIB_RM="\
+ wget \
+ gcc \
+ make \
+ libbz2-dev \
+ zlib1g-dev \
+ liblzma-dev \
+ libncurses5-dev \
+ bzip2 \
+"
+
+ENV APT_LINUX_LIB=""
+
+ENV HTSLIB_VERSION="1.16"
+
+
+# update apt-get
+RUN echo "\n\n\n\n================\n\napt-get update\n\n================\n\n\n\n" > /building.log \
+ && apt-get update --fix-missing \
+ | tee -a building.log ; echo "\n\n\n\n================\n\napt-get install\n\n================\n\n\n\n" >> building.log \
+ && apt-get install -y $APT_GET_LINUX_LIB $APT_GET_LINUX_LIB_RM \
+ | tee -a building.log ; echo "\n\n\n\n================\n\napt install\n\n================\n\n\n\n" >> building.log \
+ && apt -y install $APT_LINUX_LIB \
+ | tee -a building.log \
+ # end install the packages
+ # htslib install
+ && echo "\n\n\n\n================\n\htslib installation\n\n================\n\n\n\n" >> /building.log \
+ && cd /usr/local/ \
+ && wget -O htslib.tar.bz2 https://github.com/samtools/htslib/releases/download/$HTSLIB_VERSION/htslib-$HTSLIB_VERSION.tar.bz2 \
+ && tar -xjvf htslib.tar.bz2 \
+ && rm -rf htslib.tar.bz2 \
+ && cd htslib-$HTSLIB_VERSION \
+ && ./configure \
+ && make \
+ && make install \
+
+ && cd /usr/local \
+ && rm -rf /usr/local/htslib-$HTSLIB_VERSION \
+ && apt-get remove -y $APT_GET_LINUX_LIB_RM\
+ # end htslib install
+ # cleaning
+ && echo "\n\n\n\n================\n\napt-get autoremove\n\n================\n\n\n\n" >> /building.log \
+ && apt-get autoremove -y \
+ | tee -a /building.log ; echo "\n\n\n\n================\n\napt-get clean\n\n================\n\n\n\n" >> /building.log \
+ && apt-get clean \
+ | tee -a /building.log ; echo "\n\n\n\n================\n\nrm\n\n================\n\n\n\n" >> /building.log \
+ && rm -rf /var/lib/apt/lists/* \
+ | tee -a /building.log \
+ && echo "\n\n\n\n================\n\ninstalled packages\n\n================\n\n\n\n" >> /building.log \
+ && apt-cache policy $APT_GET_LINUX_LIB $APT_LINUX_LIB \
+ >> /building.log \
+ && echo "htslib version $HTSLIB_VERSION" >> /building.log
+
+# https://askubuntu.com/questions/179955/var-lib-apt-lists-is-huge
+# folder filled after running sudo apt-get update (or use the Refresh button in a package manager), a list of packages will get downloaded from the Ubuntu servers. These files are then stored in /var/lib/apt/lists/. You can safely remove the contents of that directory as it is recreated when you refresh the package lists. If you remove the files, but do not run apt-get update to fetch the lists, commands like apt-cache will fail to provide information (since the cache is empty)
+# apt-cache policy print all the indicated package info
+# end cleaning
+
+ENV LC_ALL en_US.UTF-8
+ENV LANG en_US.UTF-8
+ENV LANGUAGE en_US.UTF-8
+ENV LC_NUMERIC en_US.UTF-8
+
+ENTRYPOINT ["/usr/bin/bash" , "-l"]
+# The -l option (according to the man page) makes "bash act as if it had been invoked as a login shell". Login shells read certain initialization files from your home directory, such as .bash_profile. Variables set in .bash_profile override when bash launches.
\ No newline at end of file
diff --git a/ubuntu/v20.04/htslib/v1.0/building.log b/ubuntu/v20.04/htslib/v1.0/building.log
new file mode 100644
index 0000000000000000000000000000000000000000..1998027b14704c59b535c9626bc792509b5ea37d
--- /dev/null
+++ b/ubuntu/v20.04/htslib/v1.0/building.log
@@ -0,0 +1,435 @@
+
+
+
+
+================
+
+apt-get update
+
+================
+
+
+
+
+Get:1 http://archive.ubuntu.com/ubuntu focal InRelease [265 kB]
+Get:2 http://archive.ubuntu.com/ubuntu focal-updates InRelease [114 kB]
+Get:3 http://archive.ubuntu.com/ubuntu focal-backports InRelease [108 kB]
+Get:4 http://security.ubuntu.com/ubuntu focal-security InRelease [114 kB]
+Get:5 http://archive.ubuntu.com/ubuntu focal/universe amd64 Packages [11.3 MB]
+Get:6 http://security.ubuntu.com/ubuntu focal-security/restricted amd64 Packages [1,552 kB]
+Get:7 http://archive.ubuntu.com/ubuntu focal/main amd64 Packages [1,275 kB]
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+Get:10 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 Packages [2,644 kB]
+Get:11 http://archive.ubuntu.com/ubuntu focal-updates/restricted amd64 Packages [1,667 kB]
+Get:12 http://archive.ubuntu.com/ubuntu focal-updates/universe amd64 Packages [1,212 kB]
+Get:13 http://archive.ubuntu.com/ubuntu focal-updates/multiverse amd64 Packages [30.2 kB]
+Get:14 http://archive.ubuntu.com/ubuntu focal-backports/main amd64 Packages [55.2 kB]
+Get:15 http://archive.ubuntu.com/ubuntu focal-backports/universe amd64 Packages [27.4 kB]
+Get:16 http://security.ubuntu.com/ubuntu focal-security/universe amd64 Packages [910 kB]
+Get:17 http://security.ubuntu.com/ubuntu focal-security/multiverse amd64 Packages [27.5 kB]
+Get:18 http://security.ubuntu.com/ubuntu focal-security/main amd64 Packages [2,178 kB]
+Fetched 23.7 MB in 7s (3,479 kB/s)
+Reading package lists...
+
+
+
+
+================
+
+apt-get install
+
+================
+
+
+
+
+Reading package lists...
+Building dependency tree...
+Reading state information...
+bzip2 is already the newest version (1.0.8-2).
+zlib1g is already the newest version (1:1.2.11.dfsg-2ubuntu1.3).
+The following additional packages will be installed:
+ binutils binutils-common binutils-x86-64-linux-gnu bzip2-doc cpp cpp-9 gcc-9
+ gcc-9-base libasan5 libatomic1 libbinutils libc-dev-bin libc6 libc6-dev
+ libcc1-0 libcrypt-dev libctf-nobfd0 libctf0 libgcc-9-dev libgomp1 libgpm2
+ libisl22 libitm1 liblsan0 libmpc3 libncurses-dev libquadmath0 libtinfo5
+ libtsan0 libubsan1 linux-libc-dev manpages manpages-dev
+Suggested packages:
+ binutils-doc cpp-doc gcc-9-locales gcc-multilib autoconf automake libtool
+ flex bison gdb gcc-doc gcc-9-multilib gcc-9-doc glibc-doc gpm liblzma-doc
+ ncurses-doc make-doc man-browser
+The following NEW packages will be installed:
+ binutils binutils-common binutils-x86-64-linux-gnu bzip2-doc cpp cpp-9 gcc
+ gcc-9 gcc-9-base libasan5 libatomic1 libbinutils libbz2-dev libc-dev-bin
+ libc6-dev libcc1-0 libcrypt-dev libctf-nobfd0 libctf0 libgcc-9-dev libgomp1
+ libgpm2 libisl22 libitm1 liblsan0 liblzma-dev libmpc3 libncurses-dev
+ libncurses5 libncurses5-dev libquadmath0 libtinfo5 libtsan0 libubsan1
+ linux-libc-dev make manpages manpages-dev wget zlib1g-dev
+The following packages will be upgraded:
+ libc6 liblzma5
+2 upgraded, 40 newly installed, 0 to remove and 21 not upgraded.
+Need to get 40.0 MB of archives.
+After this operation, 158 MB of additional disk space will be used.
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+Fetched 40.0 MB in 8s (5,108 kB/s)
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+debconf: falling back to frontend: Readline
+Unpacking libc6:amd64 (2.31-0ubuntu9.9) over (2.31-0ubuntu9.7) ...
+Setting up libc6:amd64 (2.31-0ubuntu9.9) ...
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+Unpacking gcc-9 (9.4.0-1ubuntu1~20.04.1) ...
+Selecting previously unselected package gcc.
+Preparing to unpack .../25-gcc_4%3a9.3.0-1ubuntu2_amd64.deb ...
+Unpacking gcc (4:9.3.0-1ubuntu2) ...
+Selecting previously unselected package libc-dev-bin.
+Preparing to unpack .../26-libc-dev-bin_2.31-0ubuntu9.9_amd64.deb ...
+Unpacking libc-dev-bin (2.31-0ubuntu9.9) ...
+Selecting previously unselected package linux-libc-dev:amd64.
+Preparing to unpack .../27-linux-libc-dev_5.4.0-126.142_amd64.deb ...
+Unpacking linux-libc-dev:amd64 (5.4.0-126.142) ...
+Selecting previously unselected package libcrypt-dev:amd64.
+Preparing to unpack .../28-libcrypt-dev_1%3a4.4.10-10ubuntu4_amd64.deb ...
+Unpacking libcrypt-dev:amd64 (1:4.4.10-10ubuntu4) ...
+Selecting previously unselected package libc6-dev:amd64.
+Preparing to unpack .../29-libc6-dev_2.31-0ubuntu9.9_amd64.deb ...
+Unpacking libc6-dev:amd64 (2.31-0ubuntu9.9) ...
+Selecting previously unselected package libbz2-dev:amd64.
+Preparing to unpack .../30-libbz2-dev_1.0.8-2_amd64.deb ...
+Unpacking libbz2-dev:amd64 (1.0.8-2) ...
+Selecting previously unselected package libgpm2:amd64.
+Preparing to unpack .../31-libgpm2_1.20.7-5_amd64.deb ...
+Unpacking libgpm2:amd64 (1.20.7-5) ...
+Selecting previously unselected package libncurses-dev:amd64.
+Preparing to unpack .../32-libncurses-dev_6.2-0ubuntu2_amd64.deb ...
+Unpacking libncurses-dev:amd64 (6.2-0ubuntu2) ...
+Selecting previously unselected package libtinfo5:amd64.
+Preparing to unpack .../33-libtinfo5_6.2-0ubuntu2_amd64.deb ...
+Unpacking libtinfo5:amd64 (6.2-0ubuntu2) ...
+Selecting previously unselected package libncurses5:amd64.
+Preparing to unpack .../34-libncurses5_6.2-0ubuntu2_amd64.deb ...
+Unpacking libncurses5:amd64 (6.2-0ubuntu2) ...
+Selecting previously unselected package libncurses5-dev:amd64.
+Preparing to unpack .../35-libncurses5-dev_6.2-0ubuntu2_amd64.deb ...
+Unpacking libncurses5-dev:amd64 (6.2-0ubuntu2) ...
+Selecting previously unselected package make.
+Preparing to unpack .../36-make_4.2.1-1.2_amd64.deb ...
+Unpacking make (4.2.1-1.2) ...
+Selecting previously unselected package manpages-dev.
+Preparing to unpack .../37-manpages-dev_5.05-1_all.deb ...
+Unpacking manpages-dev (5.05-1) ...
+Selecting previously unselected package zlib1g-dev:amd64.
+Preparing to unpack .../38-zlib1g-dev_1%3a1.2.11.dfsg-2ubuntu1.3_amd64.deb ...
+Unpacking zlib1g-dev:amd64 (1:1.2.11.dfsg-2ubuntu1.3) ...
+Selecting previously unselected package liblzma-dev:amd64.
+Preparing to unpack .../39-liblzma-dev_5.2.4-1ubuntu1.1_amd64.deb ...
+Unpacking liblzma-dev:amd64 (5.2.4-1ubuntu1.1) ...
+Setting up bzip2-doc (1.0.8-2) ...
+Setting up libgpm2:amd64 (1.20.7-5) ...
+Setting up wget (1.20.3-1ubuntu2) ...
+Setting up manpages (5.05-1) ...
+Setting up binutils-common:amd64 (2.34-6ubuntu1.3) ...
+Setting up linux-libc-dev:amd64 (5.4.0-126.142) ...
+Setting up libctf-nobfd0:amd64 (2.34-6ubuntu1.3) ...
+Setting up libgomp1:amd64 (10.3.0-1ubuntu1~20.04) ...
+Setting up make (4.2.1-1.2) ...
+Setting up libquadmath0:amd64 (10.3.0-1ubuntu1~20.04) ...
+Setting up libmpc3:amd64 (1.1.0-1) ...
+Setting up libatomic1:amd64 (10.3.0-1ubuntu1~20.04) ...
+Setting up liblzma-dev:amd64 (5.2.4-1ubuntu1.1) ...
+Setting up libubsan1:amd64 (10.3.0-1ubuntu1~20.04) ...
+Setting up libcrypt-dev:amd64 (1:4.4.10-10ubuntu4) ...
+Setting up libisl22:amd64 (0.22.1-1) ...
+Setting up libbinutils:amd64 (2.34-6ubuntu1.3) ...
+Setting up libc-dev-bin (2.31-0ubuntu9.9) ...
+Setting up libtinfo5:amd64 (6.2-0ubuntu2) ...
+Setting up libcc1-0:amd64 (10.3.0-1ubuntu1~20.04) ...
+Setting up liblsan0:amd64 (10.3.0-1ubuntu1~20.04) ...
+Setting up libitm1:amd64 (10.3.0-1ubuntu1~20.04) ...
+Setting up gcc-9-base:amd64 (9.4.0-1ubuntu1~20.04.1) ...
+Setting up libtsan0:amd64 (10.3.0-1ubuntu1~20.04) ...
+Setting up libctf0:amd64 (2.34-6ubuntu1.3) ...
+Setting up manpages-dev (5.05-1) ...
+Setting up libncurses5:amd64 (6.2-0ubuntu2) ...
+Setting up libasan5:amd64 (9.4.0-1ubuntu1~20.04.1) ...
+Setting up cpp-9 (9.4.0-1ubuntu1~20.04.1) ...
+Setting up libc6-dev:amd64 (2.31-0ubuntu9.9) ...
+Setting up binutils-x86-64-linux-gnu (2.34-6ubuntu1.3) ...
+Setting up libbz2-dev:amd64 (1.0.8-2) ...
+Setting up libncurses-dev:amd64 (6.2-0ubuntu2) ...
+Setting up binutils (2.34-6ubuntu1.3) ...
+Setting up libgcc-9-dev:amd64 (9.4.0-1ubuntu1~20.04.1) ...
+Setting up zlib1g-dev:amd64 (1:1.2.11.dfsg-2ubuntu1.3) ...
+Setting up cpp (4:9.3.0-1ubuntu2) ...
+Setting up libncurses5-dev:amd64 (6.2-0ubuntu2) ...
+Setting up gcc-9 (9.4.0-1ubuntu1~20.04.1) ...
+Setting up gcc (4:9.3.0-1ubuntu2) ...
+Processing triggers for libc-bin (2.31-0ubuntu9.7) ...
+
+
+
+
+================
+
+apt install
+
+================
+
+
+
+
+Reading package lists...
+Building dependency tree...
+Reading state information...
+0 upgraded, 0 newly installed, 0 to remove and 21 not upgraded.
+
+
+
+
+================
+\htslib installation
+
+================
+
+
+
+
+
+
+
+
+================
+
+apt-get autoremove
+
+================
+
+
+
+
+Reading package lists...
+Building dependency tree...
+Reading state information...
+The following packages will be REMOVED:
+ binutils binutils-common binutils-x86-64-linux-gnu bzip2-doc cpp cpp-9 gcc-9
+ gcc-9-base libasan5 libatomic1 libbinutils libc-dev-bin libc6-dev libcc1-0
+ libcrypt-dev libctf-nobfd0 libctf0 libgcc-9-dev libgomp1 libisl22 libitm1
+ liblsan0 libmpc3 libncurses-dev libquadmath0 libtsan0 libubsan1
+ linux-libc-dev manpages manpages-dev
+0 upgraded, 0 newly installed, 30 to remove and 21 not upgraded.
+After this operation, 155 MB disk space will be freed.
+(Reading database ...
(Reading database ... 5%
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(Reading database ... 95%
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(Reading database ... 20376 files and directories currently installed.)
+Removing gcc-9 (9.4.0-1ubuntu1~20.04.1) ...
+Removing binutils (2.34-6ubuntu1.3) ...
+Removing binutils-x86-64-linux-gnu (2.34-6ubuntu1.3) ...
+Removing libctf0:amd64 (2.34-6ubuntu1.3) ...
+Removing libbinutils:amd64 (2.34-6ubuntu1.3) ...
+Removing binutils-common:amd64 (2.34-6ubuntu1.3) ...
+Removing bzip2-doc (1.0.8-2) ...
+Removing cpp (4:9.3.0-1ubuntu2) ...
+Removing cpp-9 (9.4.0-1ubuntu1~20.04.1) ...
+Removing libgcc-9-dev:amd64 (9.4.0-1ubuntu1~20.04.1) ...
+Removing libasan5:amd64 (9.4.0-1ubuntu1~20.04.1) ...
+Removing gcc-9-base:amd64 (9.4.0-1ubuntu1~20.04.1) ...
+Removing libatomic1:amd64 (10.3.0-1ubuntu1~20.04) ...
+Removing libncurses-dev:amd64 (6.2-0ubuntu2) ...
+Removing libc6-dev:amd64 (2.31-0ubuntu9.9) ...
+Removing libc-dev-bin (2.31-0ubuntu9.9) ...
+Removing libcc1-0:amd64 (10.3.0-1ubuntu1~20.04) ...
+Removing libcrypt-dev:amd64 (1:4.4.10-10ubuntu4) ...
+Removing libctf-nobfd0:amd64 (2.34-6ubuntu1.3) ...
+Removing libgomp1:amd64 (10.3.0-1ubuntu1~20.04) ...
+Removing libisl22:amd64 (0.22.1-1) ...
+Removing libitm1:amd64 (10.3.0-1ubuntu1~20.04) ...
+Removing liblsan0:amd64 (10.3.0-1ubuntu1~20.04) ...
+Removing libmpc3:amd64 (1.1.0-1) ...
+Removing libquadmath0:amd64 (10.3.0-1ubuntu1~20.04) ...
+Removing libtsan0:amd64 (10.3.0-1ubuntu1~20.04) ...
+Removing libubsan1:amd64 (10.3.0-1ubuntu1~20.04) ...
+Removing linux-libc-dev:amd64 (5.4.0-126.142) ...
+Removing manpages-dev (5.05-1) ...
+Removing manpages (5.05-1) ...
+Processing triggers for libc-bin (2.31-0ubuntu9.7) ...
+
+
+
+
+================
+
+apt-get clean
+
+================
+
+
+
+
+
+
+
+
+================
+
+rm
+
+================
+
+
+
+
+
+
+
+
+================
+
+installed packages
+
+================
+
+
+
+
+zlib1g:
+ Installed: 1:1.2.11.dfsg-2ubuntu1.3
+ Candidate: 1:1.2.11.dfsg-2ubuntu1.3
+ Version table:
+ *** 1:1.2.11.dfsg-2ubuntu1.3 100
+ 100 /var/lib/dpkg/status
+liblzma5:
+ Installed: 5.2.4-1ubuntu1.1
+ Candidate: 5.2.4-1ubuntu1.1
+ Version table:
+ *** 5.2.4-1ubuntu1.1 100
+ 100 /var/lib/dpkg/status
+libncurses5:
+ Installed: 6.2-0ubuntu2
+ Candidate: 6.2-0ubuntu2
+ Version table:
+ *** 6.2-0ubuntu2 100
+ 100 /var/lib/dpkg/status
+htslib version 1.16
diff --git a/ubuntu/v20.04/samtools/v1.0/Dockerfile b/ubuntu/v20.04/samtools/v1.0/Dockerfile
index c3521ad880b256047d69f2d8cd07c103fa48012c..f127b54c314d4335b1754ff91b7dc93098da14d6 100644
--- a/ubuntu/v20.04/samtools/v1.0/Dockerfile
+++ b/ubuntu/v20.04/samtools/v1.0/Dockerfile
@@ -84,7 +84,7 @@ RUN echo "\n\n\n\n================\n\napt-get update\n\n================\n\n\n\n
&& rm -rf /var/lib/apt/lists/* \
| tee -a /building.log \
&& echo "\n\n\n\n================\n\ninstalled packages\n\n================\n\n\n\n" >> /building.log \
- && apt-cache policy $APT_GET_LINUX_LIB $APT_LINUX_LIB samtools \
+ && apt-cache policy $APT_GET_LINUX_LIB $APT_LINUX_LIB \
>> /building.log \
&& samtools --version >> /building.log
# https://askubuntu.com/questions/179955/var-lib-apt-lists-is-huge
diff --git a/ubuntu/v20.04/slivar/v2.0/Dockerfile b/ubuntu/v20.04/slivar/v2.0/Dockerfile
index 2a55cd398271d8a50a1764d48c76c25615ce26a5..da20e82c6da0cc2a821079fcbf6f11477dac37de 100644
--- a/ubuntu/v20.04/slivar/v2.0/Dockerfile
+++ b/ubuntu/v20.04/slivar/v2.0/Dockerfile
@@ -25,7 +25,7 @@
# base image: ubuntu:20.04
-FROM gmillot/samtools_v1.0:gitlab_v9.1
+FROM gmillot/htslib_v1.0:gitlab_v9.1
# Warning: the name must be exactly what is written in the docker images interface, or sudo docker image ls. But here, since the image is not present locally, docker will search it on docker hub. Thus, gmillot/ubuntu:16.04 iw not correct
LABEL Gael.Millot=gael.millot@pasteur.fr
@@ -39,7 +39,7 @@ ENV APT_GET_LINUX_LIB_RM=""
ENV APT_LINUX_LIB=""
-
+ENV SLIVAR_VERSION="v0.2.7"
# add gensoft deb repo pgp public key to apt trusted ones
# and install modules
@@ -58,7 +58,7 @@ RUN echo "\n\n\n\n================\n\napt-get update\n\n================\n\n\n\n
RUN echo "\n\n\n\n================\n\slivar install\n\n================\n\n\n\n" >> /building.log \
- && wget https://github.com/brentp/slivar/releases/download/v0.2.7/slivar \
+ && wget https://github.com/brentp/slivar/releases/download/${SLIVAR_VERSION}/slivar \
&& chmod 755 slivar \
| tee -a /building.log \
@@ -76,8 +76,7 @@ RUN echo "\n\n\n\n================\n\napt-get autoremove\n\n================\n\n
locales-all \
$APT_GET_LINUX_LIB \
>> /building.log \
- && samtools --version >> /building.log \
- && echo "slivar version v0.2.7" >> /building.log
+ && echo "slivar version ${SLIVAR_VERSION}" >> /building.log
ENV LC_ALL en_US.UTF-8
ENV LANG en_US.UTF-8
diff --git a/ubuntu/v20.04/slivar/v2.0/building.log b/ubuntu/v20.04/slivar/v2.0/building.log
index 315a6080ff0b79eedfccdcf095f83ee1d97fae5d..84a42b68e6877e2d193951013fb070fd18102a81 100644
--- a/ubuntu/v20.04/slivar/v2.0/building.log
+++ b/ubuntu/v20.04/slivar/v2.0/building.log
@@ -11,25 +11,25 @@ apt-get update
-Get:1 http://security.ubuntu.com/ubuntu focal-security InRelease [114 kB]
-Get:2 http://archive.ubuntu.com/ubuntu focal InRelease [265 kB]
-Get:3 http://security.ubuntu.com/ubuntu focal-security/universe amd64 Packages [910 kB]
-Get:4 http://security.ubuntu.com/ubuntu focal-security/multiverse amd64 Packages [27.5 kB]
-Get:5 http://security.ubuntu.com/ubuntu focal-security/restricted amd64 Packages [1,552 kB]
-Get:6 http://archive.ubuntu.com/ubuntu focal-updates InRelease [114 kB]
-Get:7 http://archive.ubuntu.com/ubuntu focal-backports InRelease [108 kB]
-Get:8 http://archive.ubuntu.com/ubuntu focal/multiverse amd64 Packages [177 kB]
-Get:9 http://archive.ubuntu.com/ubuntu focal/universe amd64 Packages [11.3 MB]
-Get:10 http://security.ubuntu.com/ubuntu focal-security/main amd64 Packages [2,178 kB]
-Get:11 http://archive.ubuntu.com/ubuntu focal/restricted amd64 Packages [33.4 kB]
-Get:12 http://archive.ubuntu.com/ubuntu focal/main amd64 Packages [1,275 kB]
-Get:13 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 Packages [2,644 kB]
+Get:1 http://archive.ubuntu.com/ubuntu focal InRelease [265 kB]
+Get:2 http://security.ubuntu.com/ubuntu focal-security InRelease [114 kB]
+Get:3 http://archive.ubuntu.com/ubuntu focal-updates InRelease [114 kB]
+Get:4 http://archive.ubuntu.com/ubuntu focal-backports InRelease [108 kB]
+Get:5 http://archive.ubuntu.com/ubuntu focal/main amd64 Packages [1,275 kB]
+Get:6 http://security.ubuntu.com/ubuntu focal-security/restricted amd64 Packages [1,552 kB]
+Get:7 http://archive.ubuntu.com/ubuntu focal/universe amd64 Packages [11.3 MB]
+Get:8 http://security.ubuntu.com/ubuntu focal-security/multiverse amd64 Packages [27.5 kB]
+Get:9 http://security.ubuntu.com/ubuntu focal-security/universe amd64 Packages [910 kB]
+Get:10 http://archive.ubuntu.com/ubuntu focal/restricted amd64 Packages [33.4 kB]
+Get:11 http://archive.ubuntu.com/ubuntu focal/multiverse amd64 Packages [177 kB]
+Get:12 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 Packages [2,644 kB]
+Get:13 http://security.ubuntu.com/ubuntu focal-security/main amd64 Packages [2,178 kB]
Get:14 http://archive.ubuntu.com/ubuntu focal-updates/restricted amd64 Packages [1,667 kB]
-Get:15 http://archive.ubuntu.com/ubuntu focal-updates/universe amd64 Packages [1,206 kB]
+Get:15 http://archive.ubuntu.com/ubuntu focal-updates/universe amd64 Packages [1,212 kB]
Get:16 http://archive.ubuntu.com/ubuntu focal-updates/multiverse amd64 Packages [30.2 kB]
-Get:17 http://archive.ubuntu.com/ubuntu focal-backports/main amd64 Packages [55.2 kB]
-Get:18 http://archive.ubuntu.com/ubuntu focal-backports/universe amd64 Packages [27.4 kB]
-Fetched 23.7 MB in 32s (731 kB/s)
+Get:17 http://archive.ubuntu.com/ubuntu focal-backports/universe amd64 Packages [27.4 kB]
+Get:18 http://archive.ubuntu.com/ubuntu focal-backports/main amd64 Packages [55.2 kB]
+Fetched 23.7 MB in 8s (2,980 kB/s)
Reading package lists...
@@ -141,7 +141,7 @@ Get:58 http://archive.ubuntu.com/ubuntu focal/main amd64 libalgorithm-diff-xs-pe
Get:59 http://archive.ubuntu.com/ubuntu focal/main amd64 libalgorithm-merge-perl all 0.08-3 [12.0 kB]
Get:60 http://archive.ubuntu.com/ubuntu focal/main amd64 libfile-fcntllock-perl amd64 0.22-3build4 [33.1 kB]
Get:61 http://archive.ubuntu.com/ubuntu focal/main amd64 manpages-dev all 5.05-1 [2,266 kB]
-Fetched 49.9 MB in 19s (2,595 kB/s)
+Fetched 49.9 MB in 16s (3,168 kB/s)
Selecting previously unselected package liblocale-gettext-perl.
(Reading database ...
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(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 15774 files and directories currently installed.)
Preparing to unpack .../liblocale-gettext-perl_1.07-4_amd64.deb ...
@@ -489,29 +489,4 @@ build-essential:
Version table:
*** 12.8ubuntu1.1 100
100 /var/lib/dpkg/status
-samtools 1.14
-Using htslib 1.14
-Copyright (C) 2021 Genome Research Ltd.
-
-Samtools compilation details:
- Features: build=configure curses=yes
- CC: gcc
- CPPFLAGS:
- CFLAGS: -Wall -g -O2
- LDFLAGS:
- HTSDIR: htslib-1.14
- LIBS:
- CURSES_LIB: -lncursesw
-
-HTSlib compilation details:
- Features: build=configure plugins=no libcurl=no S3=no GCS=no libdeflate=no lzma=yes bzip2=yes htscodecs=1.1.1-1-ged325d7
- CC: gcc
- CPPFLAGS:
- CFLAGS: -Wall -g -O2 -fvisibility=hidden
- LDFLAGS: -fvisibility=hidden
-
-HTSlib URL scheme handlers present:
- built-in: preload, data, file
- crypt4gh-needed: crypt4gh
- mem: mem
slivar version v0.2.7