diff --git a/README.md b/README.md
index 0ba0bdab3d4d219cb42e0a5b8f7b4225740e575c..16b463f592ebf2b0dd66917c8bc44e00fa126c92 100644
--- a/README.md
+++ b/README.md
@@ -69,6 +69,21 @@ Hub-CDB and Institut Pasteur
Use the gitlab tag of the docker image (e.g., gitlab_v5.0) to get the description of the modifications below
+### v8.1
+
+Dockerfiles modified: <br />
+ubuntu\v16.04\alien_trimmer\v0.4.0 at date 20220114: locales added
+
+
+### v8.0
+
+Dockerfiles added: <br />
+ubuntu\v16.04\bedtools\v1.14 at date 20220114
+Dockerfiles modified: <br />
+ubuntu\v16.04\bash-extended\v4.0 at date 20220114: locales added
+ubuntu\v16.04\samtools\v1.14 at date 20220114: locales added
+ubuntu\v16.04\bowtie2-extended\v2.0 at date 20220114: locales added
+
### v7.0
diff --git a/ubuntu/v16.04/alien_trimmer/v0.4.0/Dockerfile b/ubuntu/v16.04/alien_trimmer/v0.4.0/Dockerfile
index c62ba14d5fcab94b54aac11f7e6b038807e2b1d0..797dc909b50a41769712f580883017af32c6a7f2 100644
--- a/ubuntu/v16.04/alien_trimmer/v0.4.0/Dockerfile
+++ b/ubuntu/v16.04/alien_trimmer/v0.4.0/Dockerfile
@@ -1,9 +1,36 @@
+#########################################################################
+## ##
+## Dockerfile ##
+## Alien Trimmer ##
+## ##
+## 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>
+
# Alien Trimmer
# ftp://ftp.pasteur.fr/pub/gensoft/projects/AlienTrimmer/
# v0.4.0
+
+
# base image: ubuntu:16.04 + coreutils v8.30 + gawk v5.1.0 + bc v1.07 + git v2.33.1
-FROM gmillot/bash-extended_v3.0:gitlab_v4.0
+FROM gmillot/bash-extended_v4.0:gitlab_v8.0
# Warning: the name must be exactly what is written in the docker images interface, or sudo docker image ls
LABEL Gael.Millot=gael.millot@pasteur.fr
@@ -11,28 +38,38 @@ LABEL gitlab.dockerfiles="https://gitlab.pasteur.fr/gmillot/dockerfiles"
COPY AlienTrimmer.sh /usr/local/bin/AlienTrimmer
-RUN apt-get update --fix-missing \
-# update apt-get
-&& apt-get upgrade \
-# end update apt-get
-# install the required dependencies
-&& apt-get install -y wget openjdk-8-jre openjdk-8-jdk \
-# end install the required dependencies
-
-# alientrimmer install
-&& cd /usr/local/ \
-&& wget ftp://ftp.pasteur.fr/pub/gensoft/projects/AlienTrimmer/AlienTrimmer_0.4.0.tar.gz \
-&& tar -xzvf AlienTrimmer_0.4.0.tar.gz \
-&& rm -rf AlienTrimmer_0.4.0.tar.gz \
-&& cd AlienTrimmer_0.4.0/src \
-&& javac AlienTrimmer.java \
-&& chmod +x /usr/local/bin/AlienTrimmer \
-# end alientrimmer install
-
-# important to remove the dependencies after installation to save space in the image that will be built
-&& apt-get remove -y wget openjdk-8-jdk \
-&& apt-get autoremove -y \
-&& apt-get clean \
-&& rm -rf /var/lib/apt/lists/*
+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 \
+ # alientrimmer install
+ && echo "\n\n\n\n================\n\napt-get install\n\n================\n\n\n\n" >> /building.log \
+ && apt-get install -y \
+ wget \
+ openjdk-8-jre \
+ openjdk-8-jdk \
+ | tee -a /building.log \
+ && echo "\n\n\n\n================\n\nAlienTrimmer installation\n\n================\n\n\n\n" >> /building.log \
+ && cd /usr/local/ \
+ && wget ftp://ftp.pasteur.fr/pub/gensoft/projects/AlienTrimmer/AlienTrimmer_0.4.0.tar.gz \
+ && tar -xzvf AlienTrimmer_0.4.0.tar.gz \
+ && rm -rf AlienTrimmer_0.4.0.tar.gz \
+ && cd AlienTrimmer_0.4.0/src \
+ && javac AlienTrimmer.java \
+ && chmod +x /usr/local/bin/AlienTrimmer \
+ && apt-get remove -y \
+ wget \
+ openjdk-8-jdk \
+ # end alientrimmer 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\nNone\n\n" >> /building.log # \
+ # && apt-cache policy \
+ # >> /building.log
ENTRYPOINT ["/usr/local/bin/AlienTrimmer"]
\ No newline at end of file
diff --git a/ubuntu/v16.04/alien_trimmer/v0.4.0/building.log b/ubuntu/v16.04/alien_trimmer/v0.4.0/building.log
new file mode 100644
index 0000000000000000000000000000000000000000..be7b106c34513aa662994d63514d08e79d34c33a
--- /dev/null
+++ b/ubuntu/v16.04/alien_trimmer/v0.4.0/building.log
@@ -0,0 +1,1007 @@
+
+
+
+
+================
+
+apt-get update
+
+================
+
+
+
+
+Get:1 http://security.ubuntu.com/ubuntu xenial-security InRelease [109 kB]
+Get:2 http://archive.ubuntu.com/ubuntu xenial InRelease [247 kB]
+Get:3 http://security.ubuntu.com/ubuntu xenial-security/main amd64 Packages [2,051 kB]
+Get:4 http://archive.ubuntu.com/ubuntu xenial-updates InRelease [109 kB]
+Get:5 http://archive.ubuntu.com/ubuntu xenial-backports InRelease [107 kB]
+Get:6 http://archive.ubuntu.com/ubuntu xenial/main amd64 Packages [1,558 kB]
+Get:7 http://archive.ubuntu.com/ubuntu xenial/restricted amd64 Packages [14.1 kB]
+Get:8 http://archive.ubuntu.com/ubuntu xenial/universe amd64 Packages [9,827 kB]
+Get:9 http://security.ubuntu.com/ubuntu xenial-security/restricted amd64 Packages [15.9 kB]
+Get:10 http://security.ubuntu.com/ubuntu xenial-security/universe amd64 Packages [984 kB]
+Get:11 http://security.ubuntu.com/ubuntu xenial-security/multiverse amd64 Packages [8,820 B]
+Get:12 http://archive.ubuntu.com/ubuntu xenial/multiverse amd64 Packages [176 kB]
+Get:13 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 Packages [2,560 kB]
+Get:14 http://archive.ubuntu.com/ubuntu xenial-updates/restricted amd64 Packages [16.4 kB]
+Get:15 http://archive.ubuntu.com/ubuntu xenial-updates/universe amd64 Packages [1,544 kB]
+Get:16 http://archive.ubuntu.com/ubuntu xenial-updates/multiverse amd64 Packages [26.2 kB]
+Get:17 http://archive.ubuntu.com/ubuntu xenial-backports/main amd64 Packages [10.9 kB]
+Get:18 http://archive.ubuntu.com/ubuntu xenial-backports/universe amd64 Packages [12.7 kB]
+Fetched 19.4 MB in 18s (1,044 kB/s)
+Reading package lists...
+
+
+
+
+================
+
+apt-get install
+
+================
+
+
+
+
+Reading package lists...
+Building dependency tree...
+Reading state information...
+The following additional packages will be installed:
+ ca-certificates-java dbus fontconfig fontconfig-config fonts-dejavu-core
+ fonts-dejavu-extra hicolor-icon-theme java-common libasound2 libasound2-data
+ libasyncns0 libatk1.0-0 libatk1.0-data libavahi-client3 libavahi-common-data
+ libavahi-common3 libcairo2 libcap-ng0 libcups2 libdatrie1 libdbus-1-3
+ libdrm-amdgpu1 libdrm-common libdrm-intel1 libdrm-nouveau2 libdrm-radeon1
+ libdrm2 libelf1 libflac8 libfontconfig1 libfreetype6 libgdk-pixbuf2.0-0
+ libgdk-pixbuf2.0-common libgif7 libgl1-mesa-dri libgl1-mesa-glx
+ libglapi-mesa libglib2.0-0 libglib2.0-data libgraphite2-3 libgtk2.0-0
+ libgtk2.0-bin libgtk2.0-common libharfbuzz0b libice-dev libice6 libicu55
+ libjbig0 libjpeg-turbo8 libjpeg8 liblcms2-2 libllvm6.0 libnspr4 libnss3
+ libnss3-nssdb libogg0 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0
+ libpciaccess0 libpcsclite1 libpixman-1-0 libpng12-0 libpthread-stubs0-dev
+ libpulse0 libsensors4 libsm-dev libsm6 libsndfile1 libthai-data libthai0
+ libtiff5 libtxc-dxtn-s2tc0 libvorbis0a libvorbisenc2 libwrap0 libx11-dev
+ libx11-doc libx11-xcb1 libxau-dev libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0
+ libxcb-present0 libxcb-render0 libxcb-shm0 libxcb-sync1 libxcb1-dev
+ libxcomposite1 libxcursor1 libxdamage1 libxdmcp-dev libxfixes3 libxi6
+ libxinerama1 libxml2 libxrandr2 libxrender1 libxshmfence1 libxt-dev libxt6
+ libxtst6 libxxf86vm1 openjdk-8-jdk-headless openjdk-8-jre-headless sgml-base
+ shared-mime-info tcpd ucf x11-common x11proto-core-dev x11proto-input-dev
+ x11proto-kb-dev xdg-user-dirs xml-core xorg-sgml-doctools xtrans-dev
+Suggested packages:
+ dbus-user-session | dbus-x11 default-jre libasound2-plugins alsa-utils
+ cups-common librsvg2-common gvfs libice-doc liblcms2-utils pciutils pcscd
+ pulseaudio lm-sensors libsm-doc libxcb-doc libxt-doc openjdk-8-demo
+ openjdk-8-source visualvm icedtea-8-plugin libnss-mdns fonts-ipafont-gothic
+ fonts-ipafont-mincho fonts-wqy-microhei fonts-wqy-zenhei fonts-indic
+ sgml-base-doc debhelper
+The following NEW packages will be installed:
+ ca-certificates-java dbus fontconfig fontconfig-config fonts-dejavu-core
+ fonts-dejavu-extra hicolor-icon-theme java-common libasound2 libasound2-data
+ libasyncns0 libatk1.0-0 libatk1.0-data libavahi-client3 libavahi-common-data
+ libavahi-common3 libcairo2 libcap-ng0 libcups2 libdatrie1 libdbus-1-3
+ libdrm-amdgpu1 libdrm-common libdrm-intel1 libdrm-nouveau2 libdrm-radeon1
+ libdrm2 libelf1 libflac8 libfontconfig1 libfreetype6 libgdk-pixbuf2.0-0
+ libgdk-pixbuf2.0-common libgif7 libgl1-mesa-dri libgl1-mesa-glx
+ libglapi-mesa libglib2.0-0 libglib2.0-data libgraphite2-3 libgtk2.0-0
+ libgtk2.0-bin libgtk2.0-common libharfbuzz0b libice-dev libice6 libicu55
+ libjbig0 libjpeg-turbo8 libjpeg8 liblcms2-2 libllvm6.0 libnspr4 libnss3
+ libnss3-nssdb libogg0 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0
+ libpciaccess0 libpcsclite1 libpixman-1-0 libpng12-0 libpthread-stubs0-dev
+ libpulse0 libsensors4 libsm-dev libsm6 libsndfile1 libthai-data libthai0
+ libtiff5 libtxc-dxtn-s2tc0 libvorbis0a libvorbisenc2 libwrap0 libx11-dev
+ libx11-doc libx11-xcb1 libxau-dev libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0
+ libxcb-present0 libxcb-render0 libxcb-shm0 libxcb-sync1 libxcb1-dev
+ libxcomposite1 libxcursor1 libxdamage1 libxdmcp-dev libxfixes3 libxi6
+ libxinerama1 libxml2 libxrandr2 libxrender1 libxshmfence1 libxt-dev libxt6
+ libxtst6 libxxf86vm1 openjdk-8-jdk openjdk-8-jdk-headless openjdk-8-jre
+ openjdk-8-jre-headless sgml-base shared-mime-info tcpd ucf wget x11-common
+ x11proto-core-dev x11proto-input-dev x11proto-kb-dev xdg-user-dirs xml-core
+ xorg-sgml-doctools xtrans-dev
+0 upgraded, 120 newly installed, 0 to remove and 0 not upgraded.
+Need to get 83.4 MB of archives.
+After this operation, 449 MB of additional disk space will be used.
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+Get:3 http://archive.ubuntu.com/ubuntu xenial/main amd64 fonts-dejavu-core all 2.35-1 [1,039 kB]
+Get:4 http://archive.ubuntu.com/ubuntu xenial/main amd64 ucf all 3.0036 [52.9 kB]
+Get:5 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 fontconfig-config all 2.11.94-0ubuntu1.1 [49.9 kB]
+Get:6 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libpng12-0 amd64 1.2.54-1ubuntu1.1 [116 kB]
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(Reading database ... 16015 files and directories currently installed.)
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+Unpacking libgif7:amd64 (5.1.4-0.3~16.04.1) ...
+Selecting previously unselected package libglapi-mesa:amd64.
+Preparing to unpack .../libglapi-mesa_18.0.5-0ubuntu0~16.04.1_amd64.deb ...
+Unpacking libglapi-mesa:amd64 (18.0.5-0ubuntu0~16.04.1) ...
+Selecting previously unselected package libllvm6.0:amd64.
+Preparing to unpack .../libllvm6.0_1%3a6.0-1ubuntu2~16.04.1_amd64.deb ...
+Unpacking libllvm6.0:amd64 (1:6.0-1ubuntu2~16.04.1) ...
+Selecting previously unselected package libsensors4:amd64.
+Preparing to unpack .../libsensors4_1%3a3.4.0-2_amd64.deb ...
+Unpacking libsensors4:amd64 (1:3.4.0-2) ...
+Selecting previously unselected package libgl1-mesa-dri:amd64.
+Preparing to unpack .../libgl1-mesa-dri_18.0.5-0ubuntu0~16.04.1_amd64.deb ...
+Unpacking libgl1-mesa-dri:amd64 (18.0.5-0ubuntu0~16.04.1) ...
+Selecting previously unselected package libx11-xcb1:amd64.
+Preparing to unpack .../libx11-xcb1_2%3a1.6.3-1ubuntu2.2_amd64.deb ...
+Unpacking libx11-xcb1:amd64 (2:1.6.3-1ubuntu2.2) ...
+Selecting previously unselected package libxcb-dri2-0:amd64.
+Preparing to unpack .../libxcb-dri2-0_1.11.1-1ubuntu1_amd64.deb ...
+Unpacking libxcb-dri2-0:amd64 (1.11.1-1ubuntu1) ...
+Selecting previously unselected package libxcb-dri3-0:amd64.
+Preparing to unpack .../libxcb-dri3-0_1.11.1-1ubuntu1_amd64.deb ...
+Unpacking libxcb-dri3-0:amd64 (1.11.1-1ubuntu1) ...
+Selecting previously unselected package libxcb-glx0:amd64.
+Preparing to unpack .../libxcb-glx0_1.11.1-1ubuntu1_amd64.deb ...
+Unpacking libxcb-glx0:amd64 (1.11.1-1ubuntu1) ...
+Selecting previously unselected package libxcb-present0:amd64.
+Preparing to unpack .../libxcb-present0_1.11.1-1ubuntu1_amd64.deb ...
+Unpacking libxcb-present0:amd64 (1.11.1-1ubuntu1) ...
+Selecting previously unselected package libxcb-sync1:amd64.
+Preparing to unpack .../libxcb-sync1_1.11.1-1ubuntu1_amd64.deb ...
+Unpacking libxcb-sync1:amd64 (1.11.1-1ubuntu1) ...
+Selecting previously unselected package libgl1-mesa-glx:amd64.
+Preparing to unpack .../libgl1-mesa-glx_18.0.5-0ubuntu0~16.04.1_amd64.deb ...
+Unpacking libgl1-mesa-glx:amd64 (18.0.5-0ubuntu0~16.04.1) ...
+Selecting previously unselected package libgraphite2-3:amd64.
+Preparing to unpack .../libgraphite2-3_1.3.10-0ubuntu0.16.04.1_amd64.deb ...
+Unpacking libgraphite2-3:amd64 (1.3.10-0ubuntu0.16.04.1) ...
+Selecting previously unselected package libgtk2.0-common.
+Preparing to unpack .../libgtk2.0-common_2.24.30-1ubuntu1.16.04.2_all.deb ...
+Unpacking libgtk2.0-common (2.24.30-1ubuntu1.16.04.2) ...
+Selecting previously unselected package libthai-data.
+Preparing to unpack .../libthai-data_0.1.24-2_all.deb ...
+Unpacking libthai-data (0.1.24-2) ...
+Selecting previously unselected package libthai0:amd64.
+Preparing to unpack .../libthai0_0.1.24-2_amd64.deb ...
+Unpacking libthai0:amd64 (0.1.24-2) ...
+Selecting previously unselected package libpango-1.0-0:amd64.
+Preparing to unpack .../libpango-1.0-0_1.38.1-1_amd64.deb ...
+Unpacking libpango-1.0-0:amd64 (1.38.1-1) ...
+Selecting previously unselected package libharfbuzz0b:amd64.
+Preparing to unpack .../libharfbuzz0b_1.0.1-1ubuntu0.1_amd64.deb ...
+Unpacking libharfbuzz0b:amd64 (1.0.1-1ubuntu0.1) ...
+Selecting previously unselected package libpangoft2-1.0-0:amd64.
+Preparing to unpack .../libpangoft2-1.0-0_1.38.1-1_amd64.deb ...
+Unpacking libpangoft2-1.0-0:amd64 (1.38.1-1) ...
+Selecting previously unselected package libpangocairo-1.0-0:amd64.
+Preparing to unpack .../libpangocairo-1.0-0_1.38.1-1_amd64.deb ...
+Unpacking libpangocairo-1.0-0:amd64 (1.38.1-1) ...
+Selecting previously unselected package libxcursor1:amd64.
+Preparing to unpack .../libxcursor1_1%3a1.1.14-1ubuntu0.16.04.2_amd64.deb ...
+Unpacking libxcursor1:amd64 (1:1.1.14-1ubuntu0.16.04.2) ...
+Selecting previously unselected package libxrandr2:amd64.
+Preparing to unpack .../libxrandr2_2%3a1.5.0-1_amd64.deb ...
+Unpacking libxrandr2:amd64 (2:1.5.0-1) ...
+Selecting previously unselected package libgtk2.0-0:amd64.
+Preparing to unpack .../libgtk2.0-0_2.24.30-1ubuntu1.16.04.2_amd64.deb ...
+Unpacking libgtk2.0-0:amd64 (2.24.30-1ubuntu1.16.04.2) ...
+Selecting previously unselected package libgtk2.0-bin.
+Preparing to unpack .../libgtk2.0-bin_2.24.30-1ubuntu1.16.04.2_amd64.deb ...
+Unpacking libgtk2.0-bin (2.24.30-1ubuntu1.16.04.2) ...
+Selecting previously unselected package xorg-sgml-doctools.
+Preparing to unpack .../xorg-sgml-doctools_1%3a1.11-1_all.deb ...
+Unpacking xorg-sgml-doctools (1:1.11-1) ...
+Selecting previously unselected package x11proto-core-dev.
+Preparing to unpack .../x11proto-core-dev_7.0.31-1~ubuntu16.04.2_all.deb ...
+Unpacking x11proto-core-dev (7.0.31-1~ubuntu16.04.2) ...
+Selecting previously unselected package libice-dev:amd64.
+Preparing to unpack .../libice-dev_2%3a1.0.9-1_amd64.deb ...
+Unpacking libice-dev:amd64 (2:1.0.9-1) ...
+Selecting previously unselected package libpthread-stubs0-dev:amd64.
+Preparing to unpack .../libpthread-stubs0-dev_0.3-4_amd64.deb ...
+Unpacking libpthread-stubs0-dev:amd64 (0.3-4) ...
+Selecting previously unselected package libvorbis0a:amd64.
+Preparing to unpack .../libvorbis0a_1.3.5-3ubuntu0.2_amd64.deb ...
+Unpacking libvorbis0a:amd64 (1.3.5-3ubuntu0.2) ...
+Selecting previously unselected package libvorbisenc2:amd64.
+Preparing to unpack .../libvorbisenc2_1.3.5-3ubuntu0.2_amd64.deb ...
+Unpacking libvorbisenc2:amd64 (1.3.5-3ubuntu0.2) ...
+Selecting previously unselected package libsndfile1:amd64.
+Preparing to unpack .../libsndfile1_1.0.25-10ubuntu0.16.04.3_amd64.deb ...
+Unpacking libsndfile1:amd64 (1.0.25-10ubuntu0.16.04.3) ...
+Selecting previously unselected package libpulse0:amd64.
+Preparing to unpack .../libpulse0_1%3a8.0-0ubuntu3.15_amd64.deb ...
+Unpacking libpulse0:amd64 (1:8.0-0ubuntu3.15) ...
+Selecting previously unselected package libsm-dev:amd64.
+Preparing to unpack .../libsm-dev_2%3a1.2.2-1_amd64.deb ...
+Unpacking libsm-dev:amd64 (2:1.2.2-1) ...
+Selecting previously unselected package libxau-dev:amd64.
+Preparing to unpack .../libxau-dev_1%3a1.0.8-1_amd64.deb ...
+Unpacking libxau-dev:amd64 (1:1.0.8-1) ...
+Selecting previously unselected package libxdmcp-dev:amd64.
+Preparing to unpack .../libxdmcp-dev_1%3a1.1.2-1.1_amd64.deb ...
+Unpacking libxdmcp-dev:amd64 (1:1.1.2-1.1) ...
+Selecting previously unselected package x11proto-input-dev.
+Preparing to unpack .../x11proto-input-dev_2.3.1-1_all.deb ...
+Unpacking x11proto-input-dev (2.3.1-1) ...
+Selecting previously unselected package x11proto-kb-dev.
+Preparing to unpack .../x11proto-kb-dev_1.0.7-0ubuntu1_all.deb ...
+Unpacking x11proto-kb-dev (1.0.7-0ubuntu1) ...
+Selecting previously unselected package xtrans-dev.
+Preparing to unpack .../xtrans-dev_1.3.5-1_all.deb ...
+Unpacking xtrans-dev (1.3.5-1) ...
+Selecting previously unselected package libxcb1-dev:amd64.
+Preparing to unpack .../libxcb1-dev_1.11.1-1ubuntu1_amd64.deb ...
+Unpacking libxcb1-dev:amd64 (1.11.1-1ubuntu1) ...
+Selecting previously unselected package libx11-dev:amd64.
+Preparing to unpack .../libx11-dev_2%3a1.6.3-1ubuntu2.2_amd64.deb ...
+Unpacking libx11-dev:amd64 (2:1.6.3-1ubuntu2.2) ...
+Selecting previously unselected package libx11-doc.
+Preparing to unpack .../libx11-doc_2%3a1.6.3-1ubuntu2.2_all.deb ...
+Unpacking libx11-doc (2:1.6.3-1ubuntu2.2) ...
+Selecting previously unselected package libxt6:amd64.
+Preparing to unpack .../libxt6_1%3a1.1.5-0ubuntu1_amd64.deb ...
+Unpacking libxt6:amd64 (1:1.1.5-0ubuntu1) ...
+Selecting previously unselected package libxt-dev:amd64.
+Preparing to unpack .../libxt-dev_1%3a1.1.5-0ubuntu1_amd64.deb ...
+Unpacking libxt-dev:amd64 (1:1.1.5-0ubuntu1) ...
+Selecting previously unselected package openjdk-8-jre:amd64.
+Preparing to unpack .../openjdk-8-jre_8u292-b10-0ubuntu1~16.04.1_amd64.deb ...
+Unpacking openjdk-8-jre:amd64 (8u292-b10-0ubuntu1~16.04.1) ...
+Selecting previously unselected package openjdk-8-jdk-headless:amd64.
+Preparing to unpack .../openjdk-8-jdk-headless_8u292-b10-0ubuntu1~16.04.1_amd64.deb ...
+Unpacking openjdk-8-jdk-headless:amd64 (8u292-b10-0ubuntu1~16.04.1) ...
+Selecting previously unselected package openjdk-8-jdk:amd64.
+Preparing to unpack .../openjdk-8-jdk_8u292-b10-0ubuntu1~16.04.1_amd64.deb ...
+Unpacking openjdk-8-jdk:amd64 (8u292-b10-0ubuntu1~16.04.1) ...
+Selecting previously unselected package tcpd.
+Preparing to unpack .../tcpd_7.6.q-25_amd64.deb ...
+Unpacking tcpd (7.6.q-25) ...
+Processing triggers for libc-bin (2.23-0ubuntu11.3) ...
+Processing triggers for systemd (229-4ubuntu21.31) ...
+Processing triggers for ca-certificates (20210119~16.04.1) ...
+Updating certificates in /etc/ssl/certs...
+0 added, 0 removed; done.
+Running hooks in /etc/ca-certificates/update.d...
+done.
+Setting up libglib2.0-0:amd64 (2.48.2-0ubuntu4.8) ...
+No schema files found: doing nothing.
+Setting up sgml-base (1.26+nmu4ubuntu1) ...
+Setting up fonts-dejavu-core (2.35-1) ...
+Setting up ucf (3.0036) ...
+debconf: unable to initialize frontend: Dialog
+debconf: (TERM is not set, so the dialog frontend is not usable.)
+debconf: falling back to frontend: Readline
+Setting up fontconfig-config (2.11.94-0ubuntu1.1) ...
+Setting up libpng12-0:amd64 (1.2.54-1ubuntu1.1) ...
+Setting up libfreetype6:amd64 (2.6.1-0.1ubuntu2.5) ...
+Setting up libfontconfig1:amd64 (2.11.94-0ubuntu1.1) ...
+Setting up fontconfig (2.11.94-0ubuntu1.1) ...
+Regenerating fonts cache... done.
+Setting up libasyncns0:amd64 (0.8-5build1) ...
+Setting up x11-common (1:7.7+13ubuntu3.1) ...
+debconf: unable to initialize frontend: Dialog
+debconf: (TERM is not set, so the dialog frontend is not usable.)
+debconf: falling back to frontend: Readline
+update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults
+invoke-rc.d: could not determine current runlevel
+invoke-rc.d: policy-rc.d denied execution of start.
+Setting up libice6:amd64 (2:1.0.9-1) ...
+Setting up libjpeg-turbo8:amd64 (1.4.2-0ubuntu3.4) ...
+Setting up libogg0:amd64 (1.3.2-1) ...
+Setting up libsm6:amd64 (2:1.2.2-1) ...
+Setting up libwrap0:amd64 (7.6.q-25) ...
+Setting up libxcomposite1:amd64 (1:0.4.4-1) ...
+Setting up libxdamage1:amd64 (1:1.1.4-2) ...
+Setting up libxfixes3:amd64 (1:5.0.1-2) ...
+Setting up libxinerama1:amd64 (2:1.1.3-1) ...
+Setting up libxshmfence1:amd64 (1.2-1) ...
+Setting up libxtst6:amd64 (2:1.2.2-1) ...
+Setting up libxxf86vm1:amd64 (1:1.1.4-1) ...
+Setting up libjbig0:amd64 (2.1-3.1) ...
+Setting up libtxc-dxtn-s2tc0:amd64 (0~git20131104-1.1) ...
+update-alternatives: using /usr/lib/x86_64-linux-gnu/libtxc_dxtn_s2tc.so.0 to provide /usr/lib/x86_64-linux-gnu/libtxc_dxtn.so (libtxc-dxtn-x86_64-linux-gnu) in auto mode
+Setting up libcap-ng0:amd64 (0.7.7-1) ...
+Setting up libdbus-1-3:amd64 (1.10.6-1ubuntu3.6) ...
+Setting up dbus (1.10.6-1ubuntu3.6) ...
+Setting up libdrm-common (2.4.91-2~16.04.1) ...
+Setting up libdrm2:amd64 (2.4.91-2~16.04.1) ...
+Setting up libelf1:amd64 (0.165-3ubuntu1.2) ...
+Setting up libglib2.0-data (2.48.2-0ubuntu4.8) ...
+Setting up libicu55:amd64 (55.1-7ubuntu0.5) ...
+Setting up libxml2:amd64 (2.9.3+dfsg1-1ubuntu0.7) ...
+Setting up shared-mime-info (1.5-2ubuntu0.2) ...
+Setting up wget (1.17.1-1ubuntu1.5) ...
+Setting up xdg-user-dirs (0.15-2ubuntu6.16.04.1) ...
+Setting up xml-core (0.13+nmu2) ...
+Setting up java-common (0.56ubuntu2) ...
+Setting up libavahi-common-data:amd64 (0.6.32~rc+dfsg-1ubuntu2.3) ...
+Setting up libavahi-common3:amd64 (0.6.32~rc+dfsg-1ubuntu2.3) ...
+Setting up libavahi-client3:amd64 (0.6.32~rc+dfsg-1ubuntu2.3) ...
+Setting up libcups2:amd64 (2.1.3-4ubuntu0.11) ...
+Setting up liblcms2-2:amd64 (2.6-3ubuntu2.1) ...
+Setting up libjpeg8:amd64 (8c-2ubuntu8) ...
+Setting up libnspr4:amd64 (2:4.13.1-0ubuntu0.16.04.1) ...
+Setting up libpcsclite1:amd64 (1.8.14-1ubuntu1.16.04.1) ...
+Setting up libxi6:amd64 (2:1.7.6-1) ...
+Setting up libxrender1:amd64 (1:0.9.9-0ubuntu1) ...
+Setting up fonts-dejavu-extra (2.35-1) ...
+Setting up hicolor-icon-theme (0.15-0ubuntu1.1) ...
+Setting up libasound2-data (1.1.0-0ubuntu1) ...
+Setting up libasound2:amd64 (1.1.0-0ubuntu1) ...
+Setting up libatk1.0-data (2.18.0-1) ...
+Setting up libatk1.0-0:amd64 (2.18.0-1) ...
+Setting up libpixman-1-0:amd64 (0.33.6-1) ...
+Setting up libxcb-render0:amd64 (1.11.1-1ubuntu1) ...
+Setting up libxcb-shm0:amd64 (1.11.1-1ubuntu1) ...
+Setting up libcairo2:amd64 (1.14.6-1) ...
+Setting up libdatrie1:amd64 (0.2.10-2) ...
+Setting up libdrm-amdgpu1:amd64 (2.4.91-2~16.04.1) ...
+Setting up libpciaccess0:amd64 (0.13.4-1) ...
+Setting up libdrm-intel1:amd64 (2.4.91-2~16.04.1) ...
+Setting up libdrm-nouveau2:amd64 (2.4.91-2~16.04.1) ...
+Setting up libdrm-radeon1:amd64 (2.4.91-2~16.04.1) ...
+Setting up libflac8:amd64 (1.3.1-4) ...
+Setting up libtiff5:amd64 (4.0.6-1ubuntu0.8) ...
+Setting up libgdk-pixbuf2.0-common (2.32.2-1ubuntu1.6) ...
+Setting up libgdk-pixbuf2.0-0:amd64 (2.32.2-1ubuntu1.6) ...
+Setting up libgif7:amd64 (5.1.4-0.3~16.04.1) ...
+Setting up libglapi-mesa:amd64 (18.0.5-0ubuntu0~16.04.1) ...
+Setting up libllvm6.0:amd64 (1:6.0-1ubuntu2~16.04.1) ...
+Setting up libsensors4:amd64 (1:3.4.0-2) ...
+Setting up libgl1-mesa-dri:amd64 (18.0.5-0ubuntu0~16.04.1) ...
+Setting up libx11-xcb1:amd64 (2:1.6.3-1ubuntu2.2) ...
+Setting up libxcb-dri2-0:amd64 (1.11.1-1ubuntu1) ...
+Setting up libxcb-dri3-0:amd64 (1.11.1-1ubuntu1) ...
+Setting up libxcb-glx0:amd64 (1.11.1-1ubuntu1) ...
+Setting up libxcb-present0:amd64 (1.11.1-1ubuntu1) ...
+Setting up libxcb-sync1:amd64 (1.11.1-1ubuntu1) ...
+Setting up libgl1-mesa-glx:amd64 (18.0.5-0ubuntu0~16.04.1) ...
+update-alternatives: using /usr/lib/x86_64-linux-gnu/mesa/ld.so.conf to provide /etc/ld.so.conf.d/x86_64-linux-gnu_GL.conf (x86_64-linux-gnu_gl_conf) in auto mode
+Setting up libgraphite2-3:amd64 (1.3.10-0ubuntu0.16.04.1) ...
+Setting up libgtk2.0-common (2.24.30-1ubuntu1.16.04.2) ...
+Setting up libthai-data (0.1.24-2) ...
+Setting up libthai0:amd64 (0.1.24-2) ...
+Setting up libpango-1.0-0:amd64 (1.38.1-1) ...
+Setting up libharfbuzz0b:amd64 (1.0.1-1ubuntu0.1) ...
+Setting up libpangoft2-1.0-0:amd64 (1.38.1-1) ...
+Setting up libpangocairo-1.0-0:amd64 (1.38.1-1) ...
+Setting up libxcursor1:amd64 (1:1.1.14-1ubuntu0.16.04.2) ...
+Setting up libxrandr2:amd64 (2:1.5.0-1) ...
+Setting up libgtk2.0-0:amd64 (2.24.30-1ubuntu1.16.04.2) ...
+Setting up libgtk2.0-bin (2.24.30-1ubuntu1.16.04.2) ...
+Setting up xorg-sgml-doctools (1:1.11-1) ...
+Setting up x11proto-core-dev (7.0.31-1~ubuntu16.04.2) ...
+Setting up libice-dev:amd64 (2:1.0.9-1) ...
+Setting up libpthread-stubs0-dev:amd64 (0.3-4) ...
+Setting up libvorbis0a:amd64 (1.3.5-3ubuntu0.2) ...
+Setting up libvorbisenc2:amd64 (1.3.5-3ubuntu0.2) ...
+Setting up libsndfile1:amd64 (1.0.25-10ubuntu0.16.04.3) ...
+Setting up libpulse0:amd64 (1:8.0-0ubuntu3.15) ...
+Setting up libsm-dev:amd64 (2:1.2.2-1) ...
+Setting up libxau-dev:amd64 (1:1.0.8-1) ...
+Setting up libxdmcp-dev:amd64 (1:1.1.2-1.1) ...
+Setting up x11proto-input-dev (2.3.1-1) ...
+Setting up x11proto-kb-dev (1.0.7-0ubuntu1) ...
+Setting up xtrans-dev (1.3.5-1) ...
+Setting up libxcb1-dev:amd64 (1.11.1-1ubuntu1) ...
+Setting up libx11-dev:amd64 (2:1.6.3-1ubuntu2.2) ...
+Setting up libx11-doc (2:1.6.3-1ubuntu2.2) ...
+Setting up libxt6:amd64 (1:1.1.5-0ubuntu1) ...
+Setting up libxt-dev:amd64 (1:1.1.5-0ubuntu1) ...
+Setting up tcpd (7.6.q-25) ...
+Setting up libnss3-nssdb (2:3.28.4-0ubuntu0.16.04.14) ...
+Setting up libnss3:amd64 (2:3.28.4-0ubuntu0.16.04.14) ...
+Setting up openjdk-8-jre-headless:amd64 (8u292-b10-0ubuntu1~16.04.1) ...
+update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/jre/bin/rmid to provide /usr/bin/rmid (rmid) in auto mode
+update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/jre/bin/java to provide /usr/bin/java (java) in auto mode
+update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/jre/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode
+update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/jre/bin/jjs to provide /usr/bin/jjs (jjs) in auto mode
+update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/jre/bin/pack200 to provide /usr/bin/pack200 (pack200) in auto mode
+update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/jre/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode
+update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/jre/bin/unpack200 to provide /usr/bin/unpack200 (unpack200) in auto mode
+update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/jre/bin/orbd to provide /usr/bin/orbd (orbd) in auto mode
+update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/jre/bin/servertool to provide /usr/bin/servertool (servertool) in auto mode
+update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/jre/bin/tnameserv to provide /usr/bin/tnameserv (tnameserv) in auto mode
+update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/jre/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode
+Setting up ca-certificates-java (20160321ubuntu1) ...
+Adding debian:Buypass_Class_2_Root_CA.pem
+Adding debian:Microsec_e-Szigno_Root_CA_2009.pem
+Adding debian:XRamp_Global_CA_Root.pem
+Adding debian:Certigna_Root_CA.pem
+Adding debian:TrustCor_RootCert_CA-2.pem
+Adding debian:Network_Solutions_Certificate_Authority.pem
+Adding debian:VeriSign_Universal_Root_Certification_Authority.pem
+Adding debian:Staat_der_Nederlanden_Root_CA_-_G3.pem
+Adding debian:Entrust_Root_Certification_Authority_-_G4.pem
+Adding debian:T-TeleSec_GlobalRoot_Class_3.pem
+Adding debian:QuoVadis_Root_CA_1_G3.pem
+Adding debian:Global_Chambersign_Root_-_2008.pem
+Adding debian:Cybertrust_Global_Root.pem
+Adding debian:AC_RAIZ_FNMT-RCM.pem
+Adding debian:USERTrust_RSA_Certification_Authority.pem
+Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem
+Adding debian:CFCA_EV_ROOT.pem
+Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem
+Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem
+Adding debian:DigiCert_Assured_ID_Root_CA.pem
+Adding debian:GTS_Root_R4.pem
+Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem
+Adding debian:Actalis_Authentication_Root_CA.pem
+Adding debian:Hongkong_Post_Root_CA_3.pem
+Adding debian:GlobalSign_Root_CA_-_R3.pem
+Adding debian:Security_Communication_Root_CA.pem
+Adding debian:GTS_Root_R3.pem
+Adding debian:TrustCor_ECA-1.pem
+Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem
+Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem
+Adding debian:Amazon_Root_CA_2.pem
+Adding debian:Certigna.pem
+Adding debian:GlobalSign_Root_CA.pem
+Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem
+Adding debian:COMODO_RSA_Certification_Authority.pem
+Adding debian:DigiCert_Global_Root_G2.pem
+Adding debian:SecureSign_RootCA11.pem
+Adding debian:SZAFIR_ROOT_CA2.pem
+Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem
+Adding debian:GTS_Root_R2.pem
+Adding debian:AffirmTrust_Premium_ECC.pem
+Adding debian:Trustwave_Global_Certification_Authority.pem
+Adding debian:SSL.com_Root_Certification_Authority_ECC.pem
+Adding debian:DigiCert_Trusted_Root_G4.pem
+Adding debian:NAVER_Global_Root_Certification_Authority.pem
+Adding debian:Baltimore_CyberTrust_Root.pem
+Adding debian:E-Tugra_Certification_Authority.pem
+Adding debian:T-TeleSec_GlobalRoot_Class_2.pem
+Adding debian:Certum_Trusted_Network_CA.pem
+Adding debian:SwissSign_Gold_CA_-_G2.pem
+Adding debian:Hongkong_Post_Root_CA_1.pem
+Adding debian:Entrust_Root_Certification_Authority.pem
+Adding debian:USERTrust_ECC_Certification_Authority.pem
+Adding debian:emSign_ECC_Root_CA_-_G3.pem
+Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem
+Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem
+Adding debian:DigiCert_Global_Root_G3.pem
+Adding debian:ISRG_Root_X1.pem
+Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem
+Adding debian:GDCA_TrustAUTH_R5_ROOT.pem
+Adding debian:Go_Daddy_Class_2_CA.pem
+Adding debian:GTS_Root_R1.pem
+Adding debian:COMODO_ECC_Certification_Authority.pem
+Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem
+Adding debian:emSign_Root_CA_-_G1.pem
+Adding debian:UCA_Global_G2_Root.pem
+Adding debian:QuoVadis_Root_CA_2_G3.pem
+Adding debian:Certum_Trusted_Network_CA_2.pem
+Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem
+Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem
+Adding debian:QuoVadis_Root_CA_2.pem
+Adding debian:ACCVRAIZ1.pem
+Adding debian:TeliaSonera_Root_CA_v1.pem
+Adding debian:SecureTrust_CA.pem
+Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem
+Adding debian:ePKI_Root_Certification_Authority.pem
+Adding debian:AffirmTrust_Networking.pem
+Adding debian:TWCA_Global_Root_CA.pem
+Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem
+Adding debian:Staat_der_Nederlanden_EV_Root_CA.pem
+Adding debian:QuoVadis_Root_CA_3_G3.pem
+Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem
+Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem
+Adding debian:Chambers_of_Commerce_Root_-_2008.pem
+Adding debian:certSIGN_ROOT_CA.pem
+Adding debian:emSign_Root_CA_-_C1.pem
+Adding debian:QuoVadis_Root_CA.pem
+Adding debian:GlobalSign_Root_CA_-_R6.pem
+Adding debian:Amazon_Root_CA_1.pem
+Adding debian:Trustis_FPS_Root_CA.pem
+Adding debian:DST_Root_CA_X3.pem
+Adding debian:TWCA_Root_Certification_Authority.pem
+Adding debian:IdenTrust_Commercial_Root_CA_1.pem
+Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem
+Adding debian:SwissSign_Silver_CA_-_G2.pem
+Adding debian:certSIGN_Root_CA_G2.pem
+Adding debian:e-Szigno_Root_CA_2017.pem
+Adding debian:DigiCert_Assured_ID_Root_G3.pem
+Adding debian:COMODO_Certification_Authority.pem
+Adding debian:Buypass_Class_3_Root_CA.pem
+Adding debian:AffirmTrust_Premium.pem
+Adding debian:CA_Disig_Root_R2.pem
+Adding debian:QuoVadis_Root_CA_3.pem
+Adding debian:UCA_Extended_Validation_Root.pem
+Adding debian:Amazon_Root_CA_3.pem
+Adding debian:emSign_ECC_Root_CA_-_C3.pem
+Adding debian:GeoTrust_Primary_Certification_Authority_-_G2.pem
+Adding debian:Secure_Global_CA.pem
+Adding debian:Amazon_Root_CA_4.pem
+Adding debian:Comodo_AAA_Services_root.pem
+Adding debian:DigiCert_Assured_ID_Root_G2.pem
+Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem
+Adding debian:AffirmTrust_Commercial.pem
+Adding debian:Starfield_Class_2_CA.pem
+Adding debian:Sonera_Class_2_Root_CA.pem
+Adding debian:EC-ACC.pem
+Adding debian:TrustCor_RootCert_CA-1.pem
+Adding debian:Security_Communication_RootCA2.pem
+Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem
+Adding debian:DigiCert_Global_Root_CA.pem
+Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2011.pem
+Adding debian:GlobalSign_Root_CA_-_R2.pem
+Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem
+Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem
+Adding debian:SSL.com_Root_Certification_Authority_RSA.pem
+Adding debian:Izenpe.com.pem
+Adding debian:Entrust_Root_Certification_Authority_-_G2.pem
+Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem
+Adding debian:Atos_TrustedRoot_2011.pem
+done.
+Setting up openjdk-8-jre:amd64 (8u292-b10-0ubuntu1~16.04.1) ...
+update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/jre/bin/policytool to provide /usr/bin/policytool (policytool) in auto mode
+Setting up openjdk-8-jdk-headless:amd64 (8u292-b10-0ubuntu1~16.04.1) ...
+update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/idlj to provide /usr/bin/idlj (idlj) in auto mode
+update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/jdeps to provide /usr/bin/jdeps (jdeps) in auto mode
+update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/wsimport to provide /usr/bin/wsimport (wsimport) in auto mode
+update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/rmic to provide /usr/bin/rmic (rmic) in auto mode
+update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/jinfo to provide /usr/bin/jinfo (jinfo) in auto mode
+update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/jsadebugd to provide /usr/bin/jsadebugd (jsadebugd) in auto mode
+update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/native2ascii to provide /usr/bin/native2ascii (native2ascii) in auto mode
+update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/jstat to provide /usr/bin/jstat (jstat) in auto mode
+update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/javac to provide /usr/bin/javac (javac) in auto mode
+update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/javah to provide /usr/bin/javah (javah) in auto mode
+update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/hsdb to provide /usr/bin/hsdb (hsdb) in auto mode
+update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/clhsdb to provide /usr/bin/clhsdb (clhsdb) in auto mode
+update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/jps to provide /usr/bin/jps (jps) in auto mode
+update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/jstack to provide /usr/bin/jstack (jstack) in auto mode
+update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/jrunscript to provide /usr/bin/jrunscript (jrunscript) in auto mode
+update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/javadoc to provide /usr/bin/javadoc (javadoc) in auto mode
+update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/javap to provide /usr/bin/javap (javap) in auto mode
+update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/jar to provide /usr/bin/jar (jar) in auto mode
+update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/extcheck to provide /usr/bin/extcheck (extcheck) in auto mode
+update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/schemagen to provide /usr/bin/schemagen (schemagen) in auto mode
+update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/xjc to provide /usr/bin/xjc (xjc) in auto mode
+update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/jmap to provide /usr/bin/jmap (jmap) in auto mode
+update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/jstatd to provide /usr/bin/jstatd (jstatd) in auto mode
+update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/jhat to provide /usr/bin/jhat (jhat) in auto mode
+update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/jdb to provide /usr/bin/jdb (jdb) in auto mode
+update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/serialver to provide /usr/bin/serialver (serialver) in auto mode
+update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/jfr to provide /usr/bin/jfr (jfr) in auto mode
+update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/wsgen to provide /usr/bin/wsgen (wsgen) in auto mode
+update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/jcmd to provide /usr/bin/jcmd (jcmd) in auto mode
+update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/jarsigner to provide /usr/bin/jarsigner (jarsigner) in auto mode
+Setting up openjdk-8-jdk:amd64 (8u292-b10-0ubuntu1~16.04.1) ...
+update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/appletviewer to provide /usr/bin/appletviewer (appletviewer) in auto mode
+update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/jconsole to provide /usr/bin/jconsole (jconsole) in auto mode
+Processing triggers for libc-bin (2.23-0ubuntu11.3) ...
+Processing triggers for systemd (229-4ubuntu21.31) ...
+Processing triggers for sgml-base (1.26+nmu4ubuntu1) ...
+Processing triggers for ca-certificates (20210119~16.04.1) ...
+Updating certificates in /etc/ssl/certs...
+0 added, 0 removed; done.
+Running hooks in /etc/ca-certificates/update.d...
+
+done.
+done.
+
+
+
+
+================
+
+AlienTrimmer installation
+
+================
+
+
+
+
+
+
+
+
+================
+
+apt-get autoremove
+
+================
+
+
+
+
+Reading package lists...
+Building dependency tree...
+Reading state information...
+The following packages will be REMOVED:
+ libice-dev libice6 libpthread-stubs0-dev libsm-dev libsm6 libx11-dev
+ libx11-doc libxau-dev libxcb1-dev libxdmcp-dev libxt-dev libxt6
+ openjdk-8-jdk-headless x11proto-core-dev x11proto-input-dev x11proto-kb-dev
+ xorg-sgml-doctools xtrans-dev
+0 upgraded, 0 newly installed, 18 to remove and 0 not upgraded.
+After this operation, 58.6 MB disk space will be freed.
+(Reading database ...
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 19657 files and directories currently installed.)
+Removing libxt-dev:amd64 (1:1.1.5-0ubuntu1) ...
+Removing libsm-dev:amd64 (2:1.2.2-1) ...
+Removing libice-dev:amd64 (2:1.0.9-1) ...
+Removing libxt6:amd64 (1:1.1.5-0ubuntu1) ...
+Removing libsm6:amd64 (2:1.2.2-1) ...
+Removing libice6:amd64 (2:1.0.9-1) ...
+Removing libx11-dev:amd64 (2:1.6.3-1ubuntu2.2) ...
+Removing libxcb1-dev:amd64 (1.11.1-1ubuntu1) ...
+Removing libpthread-stubs0-dev:amd64 (0.3-4) ...
+Removing libx11-doc (2:1.6.3-1ubuntu2.2) ...
+Removing libxau-dev:amd64 (1:1.0.8-1) ...
+Removing libxdmcp-dev:amd64 (1:1.1.2-1.1) ...
+Removing openjdk-8-jdk-headless:amd64 (8u292-b10-0ubuntu1~16.04.1) ...
+Removing x11proto-input-dev (2.3.1-1) ...
+Removing x11proto-core-dev (7.0.31-1~ubuntu16.04.2) ...
+Removing x11proto-kb-dev (1.0.7-0ubuntu1) ...
+Removing xorg-sgml-doctools (1:1.11-1) ...
+Removing xtrans-dev (1.3.5-1) ...
+Processing triggers for libc-bin (2.23-0ubuntu11.3) ...
+
+
+
+
+================
+
+apt-get clean
+
+================
+
+
+
+
+
+
+
+
+================
+
+rm
+
+================
+
+
+
+
+
+
+
+
+================
+
+installed packages
+
+================
+
+None
+
+
diff --git a/ubuntu/v16.04/bash-extended/v4.0/Dockerfile b/ubuntu/v16.04/bash-extended/v4.0/Dockerfile
new file mode 100644
index 0000000000000000000000000000000000000000..44093ed60819f802fbf7c678a788271bbb23e23f
--- /dev/null
+++ b/ubuntu/v16.04/bash-extended/v4.0/Dockerfile
@@ -0,0 +1,91 @@
+#########################################################################
+## ##
+## Dockerfile ##
+## Bash extended ##
+## ##
+## 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>
+
+# Coreutils - GNU core utilities
+# https://www.gnu.org/software/coreutils/
+# v8.25
+
+# gawk - GNU core utilities
+# https://www.gnu.org/software/gawk/
+# v4.1.3
+
+# bc - GNU core utilities
+# https://www.gnu.org/software/bc/
+# v1.06.95
+
+# git - github
+# https://github.com/git/git/archive/refs/tags/
+# v2.7.4
+
+# base image: ubuntu:16.04
+FROM ubuntu:16.04
+# 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"
+
+# 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 \
+ # install US locales
+ && echo "\n\n\n\n================\n\napt-get install\n\n================\n\n\n\n" >> /building.log \
+ && apt-get install -y \
+ locales \
+ locales-all \
+ | tee -a /building.log \
+ # end install US locales
+ # install the packages
+ && apt-get install -y \
+ coreutils=8.25-2ubuntu3~16.04 \
+ gawk=1:4.1.3+dfsg-0.1 \
+ bc=1.06.95-9build1 \
+ git=1:2.7.4-0ubuntu1.10 \
+ | tee -a /building.log \
+ # end install the packages
+ # 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 \
+ locales \
+ locales-all \
+ >> /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 ["/bin/bash"]
\ No newline at end of file
diff --git a/ubuntu/v16.04/bcftools/v1.14/Dockerfile b/ubuntu/v16.04/bcftools/v1.14/Dockerfile
index cca752d764d0d2a4219313f19e23f18066e0b11b..15ed833177d00da06668625c8fd654ab5d7dc426 100644
--- a/ubuntu/v16.04/bcftools/v1.14/Dockerfile
+++ b/ubuntu/v16.04/bcftools/v1.14/Dockerfile
@@ -1,10 +1,36 @@
+#########################################################################
+## ##
+## Dockerfile ##
+## bcftools ##
+## ##
+## 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>
+
+
# bcftools
# https://github.com/samtools/bcftools/releases/tag/1.14
-
+# http://www.htslib.org/download/
# v1.14
# base image: ubuntu:16.04 + coreutils v8.30 + gawk v5.1.0 + bc v1.07 + git v2.33.1
-FROM gmillot/bash-extended_v3.0:gitlab_v4.0
+FROM gmillot/bash-extended_v4.0:gitlab_v8.0
# Warning: the name must be exactly what is written in the docker images interface, or sudo docker image ls
@@ -15,30 +41,76 @@ ENV HTS_VERSION=1.14
ENV BCFTOOLS_VERSION=1.14
# bcftools install
-RUN apt-get update --fix-missing \
-&& apt-get install -y wget gcc make git libbz2-dev zlib1g zlib1g-dev liblzma5 liblzma-dev libncurses5 libncurses5-dev bzip2 libcurl4-openssl-dev libssl-dev libgetopt-complete-perl \
-&& cd /usr/local/ \
-&& git clone https://github.com/samtools/htslib.git \
-&& cd htslib \
-&& git checkout ${HTS_VERSION} \
-&& git submodule update --init --recursive \
-&& make \
-&& cd .. \
-&& git clone https://github.com/samtools/bcftools.git \
-&& cd bcftools \
-&& git checkout ${BCFTOOLS_VERSION} \
-&& make \
-&& make install \
-&& cd /usr/local/ \
-&& rm -rf /usr/local/htslib \
-&& rm -rf /usr/local/bcftools \
-# end bcftools install
-
-# && apt-get remove -y wget tar xz-utils make gcc \ # inactivated because generate errors of pkg dependency
-# important to remove the dependencies after installation to save space in the image that will be built
-&& apt-get autoremove -y \
-&& apt-get clean \
-&& rm -rf /var/lib/apt/lists/*
+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 \
+ # samtools install
+ && echo "\n\n\n\n================\n\napt-get install\n\n================\n\n\n\n" >> /building.log \
+ && apt-get install -y \
+ wget \
+ gcc \
+ make \
+ git \
+ libbz2-dev \
+ zlib1g \
+ zlib1g-dev \
+ liblzma5 \
+ liblzma-dev \
+ libncurses5 \
+ libncurses5-dev \
+ bzip2 \
+ libcurl4-openssl-dev \
+ libssl-dev \
+ libgetopt-complete-perl \
+ | tee -a /building.log \
+ && echo "\n\n\n\n================\n\nsamtools installation\n\n================\n\n\n\n" >> /building.log \
+ && cd /usr/local/ \
+ && git clone https://github.com/samtools/htslib.git \
+ && cd htslib \
+ && git checkout ${HTS_VERSION} \
+ && git submodule update --init --recursive \
+ && make \
+ && cd .. \
+ && git clone https://github.com/samtools/bcftools.git \
+ && cd bcftools \
+ && git checkout ${BCFTOOLS_VERSION} \
+ && make \
+ && make install \
+ && cd /usr/local/ \
+ && rm -rf /usr/local/htslib \
+ && rm -rf /usr/local/bcftools \
+ # end bcftools install
+ && apt-get remove -y \
+ wget \
+ gcc \
+ make \
+ git \
+ # important to remove the dependencies after installation to save space in the image that will be built
+ && 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 \
+ wget \
+ gcc \
+ make \
+ git \
+ libbz2-dev \
+ zlib1g \
+ zlib1g-dev \
+ liblzma5 \
+ liblzma-dev \
+ libncurses5 \
+ libncurses5-dev \
+ bzip2 \
+ libcurl4-openssl-dev \
+ libssl-dev \
+ libgetopt-complete-perl \
+ >> /building.log
ENTRYPOINT ["/usr/local/bin/bcftools"]
diff --git a/ubuntu/v16.04/bedtools/2.30.0/Dockerfile b/ubuntu/v16.04/bedtools/2.30.0/Dockerfile
new file mode 100644
index 0000000000000000000000000000000000000000..3da7178857f3eb82168f8d18a7f3f7a75468933a
--- /dev/null
+++ b/ubuntu/v16.04/bedtools/2.30.0/Dockerfile
@@ -0,0 +1,92 @@
+#########################################################################
+## ##
+## Dockerfile ##
+## Bedtools ##
+## ##
+## 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 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>
+
+# bedtools
+# https://bedtools.readthedocs.io/en/latest/content/installation.html
+# v2.30.0
+
+
+# base image: ubuntu:16.04
+FROM gmillot/bash-extended_v4.0:gitlab_v8.0
+# Warning: the name must be exactly what is written in the docker images interface, or sudo docker image ls
+
+LABEL Gael.Millot=gael.millot@pasteur.fr
+LABEL gitlab.dockerfiles="https://gitlab.pasteur.fr/gmillot/dockerfiles"
+
+
+ENV VERSION="2.30.0"
+
+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 \
+ # samtools install
+ && echo "\n\n\n\n================\n\napt-get install\n\n================\n\n\n\n" >> /building.log \
+ && apt-get install -y \
+ wget \
+ gcc \
+ g++ \
+ make \
+ zlib1g \
+ zlib1g-dev \
+ libbz2-dev \
+ liblzma5 \
+ liblzma-dev \
+ python \
+ | tee -a /building.log \
+ && echo "\n\n\n\n================\n\nsamtools installation\n\n================\n\n\n\n" >> /building.log \
+ && cd /usr/local/ \
+ && wget -O bedtools.tar.gz https://github.com/arq5x/bedtools2/releases/download/v${VERSION}/bedtools-${VERSION}.tar.gz \
+ && tar -xzvf bedtools.tar.gz \
+ && rm -rf bedtools.tar.gz \
+ && cd bedtools2 \
+ && make \
+ && mv bin/* /usr/local/bin \
+ && cd /usr/local \
+ && rm -rf /usr/local/bedtools2 \
+ && apt-get remove -y \
+ wget \
+ gcc \
+ g++ \
+ make \
+ # end samtools 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 \
+ zlib1g \
+ zlib1g-dev \
+ libbz2-dev \
+ liblzma5 \
+ liblzma-dev \
+ python \
+ >> /building.log
+
+ENTRYPOINT ["/bin/bash"]
+# ENTRYPOINT ["/usr/local/bin/samtools"]
\ No newline at end of file
diff --git a/ubuntu/v16.04/bowtie2-extended/v2.0/Dockerfile b/ubuntu/v16.04/bowtie2-extended/v2.0/Dockerfile
new file mode 100644
index 0000000000000000000000000000000000000000..ead3c12a8740f5d73210a4f9678fe36bf243308d
--- /dev/null
+++ b/ubuntu/v16.04/bowtie2-extended/v2.0/Dockerfile
@@ -0,0 +1,129 @@
+#########################################################################
+## ##
+## Dockerfile ##
+## Bowtie2 extended ##
+## ##
+## 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>
+
+# samtools
+# http://www.htslib.org/
+# https://github.com/samtools/samtools/tags
+# v1.14
+
+# bowtie2
+# http://bowtie-bio.sf.net/bowtie2
+# v2.3.4.3
+
+
+
+# base image: ubuntu:16.04
+FROM gmillot/bash-extended_v4.0:gitlab_v8.0
+# Warning: the name must be exactly what is written in the docker images interface, or sudo docker image ls
+
+LABEL Gael.Millot=gael.millot@pasteur.fr
+LABEL gitlab.dockerfiles="https://gitlab.pasteur.fr/gmillot/dockerfiles"
+
+
+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 \
+ # samtools install
+ && echo "\n\n\n\n================\n\napt-get install\n\n================\n\n\n\n" >> /building.log \
+ && apt-get install -y \
+ wget \
+ gcc \
+ make \
+ libbz2-dev \
+ zlib1g \
+ zlib1g-dev \
+ liblzma5 \
+ liblzma-dev \
+ libncurses5 \
+ libncurses5-dev \
+ bzip2 \
+ | tee -a /building.log \
+ && echo "\n\n\n\n================\n\nsamtools installation\n\n================\n\n\n\n" >> /building.log \
+ && cd /usr/local/ \
+ && wget -O samtools.tar.bz2 https://github.com/samtools/samtools/releases/download/1.14/samtools-1.14.tar.bz2 \
+ && tar -xjvf samtools.tar.bz2 \
+ && rm -rf samtools.tar.bz2 \
+ && cd samtools-1.14 \
+ && ./configure \
+ && make \
+ && make install \
+ && cd /usr/local \
+ && rm -rf /usr/local/samtools-1.14 \
+ && apt-get remove -y \
+ wget \
+ gcc \
+ make \
+ libbz2-dev \
+ zlib1g-dev \
+ liblzma-dev \
+ libncurses5-dev \
+ bzip2 \
+ # end samtools install
+ # bowtie2 install
+ && echo "\n\n\n\n================\n\napt-get install\n\n================\n\n\n\n" >> /building.log \
+ && apt-get install -y \
+ wget \
+ gcc \
+ g++ \
+ make \
+ libtbb2 \
+ libtbb-dev \
+ zlib1g \
+ zlib1g-dev \
+ perl \
+ python \
+ && echo "\n\n\n\n================\n\nbowtie2 installation\n\n================\n\n\n\n" >> /building.log \
+ && cd /usr/local/ \
+ && wget -O bowtie.tar.gz https://github.com/BenLangmead/bowtie2/archive/v2.3.4.3.tar.gz \
+ && tar -xzvf bowtie.tar.gz \
+ && rm -rf bowtie.tar.gz \
+ && cd bowtie2-2.3.4.3 \
+ && make \
+ && mv bowtie2 bowtie2-align-s bowtie2-align-l bowtie2-build \
+ bowtie2-build-s bowtie2-build-l bowtie2-inspect \
+ bowtie2-inspect-s bowtie2-inspect-l /usr/local/bin/ \
+ && cd /usr/local \
+ && rm -rf /usr/local/bowtie2-2.3.4.3 \
+ && apt-get remove -y \
+ wget \
+ gcc \
+ g++ \
+ make \
+ libtbb-dev \
+ zlib1g-dev \
+ # end bowtie2 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 zlib1g liblzma5 libncurses5 libtbb2 perl python >> /building.log
+
+ENTRYPOINT ["/bin/bash"]
+# ENTRYPOINT ["/usr/local/bin/samtools"]
\ No newline at end of file
diff --git a/ubuntu/v16.04/samtools/v1.14/Dockerfile b/ubuntu/v16.04/samtools/v1.14/Dockerfile
index 96dc08671d726137066530b0d0870b2635e6cf86..81091956a94645d4fffd5e1de27e55826f3c1ff7 100644
--- a/ubuntu/v16.04/samtools/v1.14/Dockerfile
+++ b/ubuntu/v16.04/samtools/v1.14/Dockerfile
@@ -12,15 +12,14 @@
-# to get the log of the building:
+# to see the log of the building:
# sudo docker run -ti --entrypoint bash <IMAGE_NAME>
# cat building.log
-# to get all the ubuntu packages:
+# to export the log file of the image building from the container:
+# sudo docker images
# sudo docker run -ti --entrypoint bash <IMAGE_NAME>
-# apt-get update ; apt-cache policy zlib1g liblzma5 libncurses5
-
-# to export a file from the container:
+# exit
# sudo docker container ls -a # to get all the active containers
# sudo docker cp <containerNAMES>:/building.log </host/path/target>
@@ -31,7 +30,7 @@
# base image: ubuntu:16.04
-FROM gmillot/bash-extended_v3.0:gitlab_v4.0
+FROM gmillot/bash-extended_v4.0:gitlab_v8.0
# Warning: the name must be exactly what is written in the docker images interface, or sudo docker image ls
LABEL Gael.Millot=gael.millot@pasteur.fr
@@ -86,7 +85,11 @@ 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 zlib1g liblzma5 libncurses5 >> /building.log
+ && apt-cache policy \
+ zlib1g \
+ liblzma5 \
+ libncurses5 \
+ >> /building.log
ENTRYPOINT ["/bin/bash"]
# ENTRYPOINT ["/usr/local/bin/samtools"]
\ No newline at end of file