diff --git a/README.md b/README.md index 435e3b252641ce281161130f1a9d1f2c4d32d028..8bbd0392290a2df500bb3a168cd9fffa14fa62f4 100644 --- a/README.md +++ b/README.md @@ -72,6 +72,13 @@ Hub-CDB Institut Pasteur & DSI Institut Pasteur Use the gitlab tag of the docker image (e.g., gitlab_v5.0) to get the description of the modifications below +### 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/samtools/v1.0 at date 20221002: from ubuntu:20.04 with samtools added + + ### 9.0 Dockerfiles added: <br /> diff --git a/ubuntu/v20.04/extended/v1.0/Dockerfile b/ubuntu/v20.04/extended/v1.0/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..c2845296a9ed0beafc93df47c248d3a842a3c5c9 --- /dev/null +++ b/ubuntu/v20.04/extended/v1.0/Dockerfile @@ -0,0 +1,94 @@ +######################################################################### +## ## +## 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 gmillot/ubuntu-base_v20.04:gitlab_v8.5 +# 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="\ + locales \ + locales-all \ + coreutils \ + gawk \ + bc \ + git \ +" + +ENV APT_LINUX_LIB="" + + + +# 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 \ + | 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 + # 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 +# 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/extended/v1.0/building.log b/ubuntu/v20.04/extended/v1.0/building.log new file mode 100644 index 0000000000000000000000000000000000000000..4b51bfe6a1eac15ff3e24267e3e312fcf382ebff --- /dev/null +++ b/ubuntu/v20.04/extended/v1.0/building.log @@ -0,0 +1,537 @@ + + + + +================ + +apt-get update + +================ + + + + +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://security.ubuntu.com/ubuntu focal-security/main amd64 Packages [2178 kB] +Get:6 http://archive.ubuntu.com/ubuntu focal/universe amd64 Packages [11.3 MB] +Get:7 http://security.ubuntu.com/ubuntu focal-security/multiverse amd64 Packages [27.5 kB] +Get:8 http://security.ubuntu.com/ubuntu focal-security/restricted amd64 Packages [1552 kB] +Get:9 http://security.ubuntu.com/ubuntu focal-security/universe amd64 Packages [910 kB] +Get:10 http://archive.ubuntu.com/ubuntu focal/main amd64 Packages [1275 kB] +Get:11 http://archive.ubuntu.com/ubuntu focal/multiverse amd64 Packages [177 kB] +Get:12 http://archive.ubuntu.com/ubuntu focal/restricted amd64 Packages [33.4 kB] +Get:13 http://archive.ubuntu.com/ubuntu focal-updates/restricted amd64 Packages [1667 kB] +Get:14 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 Packages [2644 kB] +Get:15 http://archive.ubuntu.com/ubuntu focal-updates/universe amd64 Packages [1206 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/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 5s (4365 kB/s) +Reading package lists... + + + + +================ + +apt-get install + +================ + + + + +Reading package lists... +Building dependency tree... +Reading state information... +coreutils is already the newest version (8.30-3ubuntu2). +The following additional packages will be installed: + ca-certificates git-man krb5-locales less libasn1-8-heimdal libbrotli1 + libbsd0 libcbor0.6 libcurl3-gnutls libedit2 liberror-perl libexpat1 + libfido2-1 libgdbm-compat4 libgdbm6 libgssapi-krb5-2 libgssapi3-heimdal + libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal + libhx509-5-heimdal libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3 + libkrb5support0 libldap-2.4-2 libldap-common libmpfr6 libnghttp2-14 + libperl5.30 libpsl5 libreadline8 libroken18-heimdal librtmp1 libsasl2-2 + libsasl2-modules libsasl2-modules-db libsigsegv2 libsqlite3-0 libssh-4 + libssl1.1 libwind0-heimdal libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 + libxext6 libxmuu1 netbase openssh-client openssl patch perl + perl-modules-5.30 publicsuffix readline-common xauth +Suggested packages: + gawk-doc gettext-base git-daemon-run | git-daemon-sysvinit git-doc git-el + git-email git-gui gitk gitweb git-cvs git-mediawiki git-svn gdbm-l10n + krb5-doc krb5-user libsasl2-modules-gssapi-mit + | libsasl2-modules-gssapi-heimdal libsasl2-modules-ldap libsasl2-modules-otp + libsasl2-modules-sql keychain libpam-ssh monkeysphere ssh-askpass ed + diffutils-doc perl-doc libterm-readline-gnu-perl + | libterm-readline-perl-perl make libb-debug-perl liblocale-codes-perl + readline-doc +The following NEW packages will be installed: + bc ca-certificates gawk git git-man krb5-locales less libasn1-8-heimdal + libbrotli1 libbsd0 libcbor0.6 libcurl3-gnutls libedit2 liberror-perl + libexpat1 libfido2-1 libgdbm-compat4 libgdbm6 libgssapi-krb5-2 + libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal + libheimntlm0-heimdal libhx509-5-heimdal libk5crypto3 libkeyutils1 + libkrb5-26-heimdal libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common + libmpfr6 libnghttp2-14 libperl5.30 libpsl5 libreadline8 libroken18-heimdal + librtmp1 libsasl2-2 libsasl2-modules libsasl2-modules-db libsigsegv2 + libsqlite3-0 libssh-4 libssl1.1 libwind0-heimdal libx11-6 libx11-data + libxau6 libxcb1 libxdmcp6 libxext6 libxmuu1 locales locales-all netbase + openssh-client openssl patch perl perl-modules-5.30 publicsuffix + readline-common xauth +0 upgraded, 64 newly installed, 0 to remove and 23 not upgraded. +Need to get 35.0 MB of archives. +After this operation, 359 MB of additional disk space will be used. +Get:1 http://archive.ubuntu.com/ubuntu focal/main amd64 libmpfr6 amd64 4.0.2-1 [240 kB] +Get:2 http://archive.ubuntu.com/ubuntu focal/main amd64 readline-common all 8.0-4 [53.5 kB] +Get:3 http://archive.ubuntu.com/ubuntu focal/main amd64 libreadline8 amd64 8.0-4 [131 kB] +Get:4 http://archive.ubuntu.com/ubuntu focal/main amd64 libsigsegv2 amd64 2.12-2 [13.9 kB] +Get:5 http://archive.ubuntu.com/ubuntu focal/main amd64 gawk amd64 1:5.0.1+dfsg-1 [418 kB] +Get:6 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 perl-modules-5.30 all 5.30.0-9ubuntu0.2 [2738 kB] +Get:7 http://archive.ubuntu.com/ubuntu focal/main amd64 libgdbm6 amd64 1.18.1-5 [27.4 kB] +Get:8 http://archive.ubuntu.com/ubuntu focal/main amd64 libgdbm-compat4 amd64 1.18.1-5 [6244 B] +Get:9 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libperl5.30 amd64 5.30.0-9ubuntu0.2 [3952 kB] +Get:10 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 perl amd64 5.30.0-9ubuntu0.2 [224 kB] +Get:11 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libssl1.1 amd64 1.1.1f-1ubuntu2.16 [1321 kB] +Get:12 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 openssl amd64 1.1.1f-1ubuntu2.16 [621 kB] +Get:13 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 ca-certificates all 20211016~20.04.1 [144 kB] +Get:14 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 less amd64 551-1ubuntu0.1 [123 kB] +Get:15 http://archive.ubuntu.com/ubuntu focal/main amd64 libbsd0 amd64 0.10.0-1 [45.4 kB] +Get:16 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libexpat1 amd64 2.2.9-1ubuntu0.4 [74.4 kB] +Get:17 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libsqlite3-0 amd64 3.31.1-4ubuntu0.4 [549 kB] +Get:18 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 locales all 2.31-0ubuntu9.9 [3869 kB] +Get:19 http://archive.ubuntu.com/ubuntu focal/main amd64 netbase all 6.1 [13.1 kB] +Get:20 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 krb5-locales all 1.17-6ubuntu4.1 [11.4 kB] +Get:21 http://archive.ubuntu.com/ubuntu focal/main amd64 libcbor0.6 amd64 0.6.0-0ubuntu1 [21.1 kB] +Get:22 http://archive.ubuntu.com/ubuntu focal/main amd64 libedit2 amd64 3.1-20191231-1 [87.0 kB] +Get:23 http://archive.ubuntu.com/ubuntu focal/main amd64 libfido2-1 amd64 1.3.1-1ubuntu2 [47.9 kB] +Get:24 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libkrb5support0 amd64 1.17-6ubuntu4.1 [30.9 kB] +Get:25 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libk5crypto3 amd64 1.17-6ubuntu4.1 [79.9 kB] +Get:26 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libkeyutils1 amd64 1.6-6ubuntu1.1 [10.3 kB] +Get:27 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libkrb5-3 amd64 1.17-6ubuntu4.1 [330 kB] +Get:28 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libgssapi-krb5-2 amd64 1.17-6ubuntu4.1 [121 kB] +Get:29 http://archive.ubuntu.com/ubuntu focal/main amd64 libpsl5 amd64 0.21.0-1ubuntu1 [51.5 kB] +Get:30 http://archive.ubuntu.com/ubuntu focal/main amd64 libxau6 amd64 1:1.0.9-0ubuntu1 [7488 B] +Get:31 http://archive.ubuntu.com/ubuntu focal/main amd64 libxdmcp6 amd64 1:1.1.3-0ubuntu1 [10.6 kB] +Get:32 http://archive.ubuntu.com/ubuntu focal/main amd64 libxcb1 amd64 1.14-2 [44.7 kB] +Get:33 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libx11-data all 2:1.6.9-2ubuntu1.2 [113 kB] +Get:34 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libx11-6 amd64 2:1.6.9-2ubuntu1.2 [575 kB] +Get:35 http://archive.ubuntu.com/ubuntu focal/main amd64 libxext6 amd64 2:1.3.4-0ubuntu1 [29.1 kB] +Get:36 http://archive.ubuntu.com/ubuntu focal/main amd64 libxmuu1 amd64 2:1.1.3-0ubuntu1 [9728 B] +Get:37 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 openssh-client amd64 1:8.2p1-4ubuntu0.5 [671 kB] +Get:38 http://archive.ubuntu.com/ubuntu focal/main amd64 publicsuffix all 20200303.0012-1 [111 kB] +Get:39 http://archive.ubuntu.com/ubuntu focal/main amd64 xauth amd64 1:1.1-0ubuntu1 [25.0 kB] +Get:40 http://archive.ubuntu.com/ubuntu focal/main amd64 bc amd64 1.07.1-2build1 [86.3 kB] +Get:41 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libbrotli1 amd64 1.0.7-6ubuntu0.1 [267 kB] +Get:42 http://archive.ubuntu.com/ubuntu focal/main amd64 libroken18-heimdal amd64 7.7.0+dfsg-1ubuntu1 [41.8 kB] +Get:43 http://archive.ubuntu.com/ubuntu focal/main amd64 libasn1-8-heimdal amd64 7.7.0+dfsg-1ubuntu1 [181 kB] +Get:44 http://archive.ubuntu.com/ubuntu focal/main amd64 libheimbase1-heimdal amd64 7.7.0+dfsg-1ubuntu1 [29.7 kB] +Get:45 http://archive.ubuntu.com/ubuntu focal/main amd64 libhcrypto4-heimdal amd64 7.7.0+dfsg-1ubuntu1 [87.9 kB] +Get:46 http://archive.ubuntu.com/ubuntu focal/main amd64 libwind0-heimdal amd64 7.7.0+dfsg-1ubuntu1 [48.0 kB] +Get:47 http://archive.ubuntu.com/ubuntu focal/main amd64 libhx509-5-heimdal amd64 7.7.0+dfsg-1ubuntu1 [107 kB] +Get:48 http://archive.ubuntu.com/ubuntu focal/main amd64 libkrb5-26-heimdal amd64 7.7.0+dfsg-1ubuntu1 [208 kB] +Get:49 http://archive.ubuntu.com/ubuntu focal/main amd64 libheimntlm0-heimdal amd64 7.7.0+dfsg-1ubuntu1 [15.1 kB] +Get:50 http://archive.ubuntu.com/ubuntu focal/main amd64 libgssapi3-heimdal amd64 7.7.0+dfsg-1ubuntu1 [96.1 kB] +Get:51 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg-2ubuntu0.1 [14.7 kB] +Get:52 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libsasl2-2 amd64 2.1.27+dfsg-2ubuntu0.1 [49.3 kB] +Get:53 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libldap-common all 2.4.49+dfsg-2ubuntu1.9 [16.6 kB] +Get:54 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libldap-2.4-2 amd64 2.4.49+dfsg-2ubuntu1.9 [155 kB] +Get:55 http://archive.ubuntu.com/ubuntu focal/main amd64 libnghttp2-14 amd64 1.40.0-1build1 [78.7 kB] +Get:56 http://archive.ubuntu.com/ubuntu focal/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2build1 [54.9 kB] +Get:57 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libssh-4 amd64 0.9.3-2ubuntu2.2 [170 kB] +Get:58 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libcurl3-gnutls amd64 7.68.0-1ubuntu2.13 [233 kB] +Get:59 http://archive.ubuntu.com/ubuntu focal/main amd64 liberror-perl all 0.17029-1 [26.5 kB] +Get:60 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 git-man all 1:2.25.1-1ubuntu3.5 [886 kB] +Get:61 http://archive.ubuntu.com/ubuntu 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libk5crypto3:amd64. +Preparing to unpack .../20-libk5crypto3_1.17-6ubuntu4.1_amd64.deb ... +Unpacking libk5crypto3:amd64 (1.17-6ubuntu4.1) ... +Selecting previously unselected package libkeyutils1:amd64. +Preparing to unpack .../21-libkeyutils1_1.6-6ubuntu1.1_amd64.deb ... +Unpacking libkeyutils1:amd64 (1.6-6ubuntu1.1) ... +Selecting previously unselected package libkrb5-3:amd64. +Preparing to unpack .../22-libkrb5-3_1.17-6ubuntu4.1_amd64.deb ... +Unpacking libkrb5-3:amd64 (1.17-6ubuntu4.1) ... +Selecting previously unselected package libgssapi-krb5-2:amd64. +Preparing to unpack .../23-libgssapi-krb5-2_1.17-6ubuntu4.1_amd64.deb ... +Unpacking libgssapi-krb5-2:amd64 (1.17-6ubuntu4.1) ... +Selecting previously unselected package libpsl5:amd64. +Preparing to unpack .../24-libpsl5_0.21.0-1ubuntu1_amd64.deb ... +Unpacking libpsl5:amd64 (0.21.0-1ubuntu1) ... +Selecting previously unselected package libxau6:amd64. +Preparing to unpack .../25-libxau6_1%3a1.0.9-0ubuntu1_amd64.deb ... +Unpacking libxau6:amd64 (1:1.0.9-0ubuntu1) ... +Selecting previously unselected package libxdmcp6:amd64. +Preparing to unpack .../26-libxdmcp6_1%3a1.1.3-0ubuntu1_amd64.deb ... +Unpacking libxdmcp6:amd64 (1:1.1.3-0ubuntu1) ... +Selecting previously unselected package libxcb1:amd64. +Preparing to unpack .../27-libxcb1_1.14-2_amd64.deb ... +Unpacking libxcb1:amd64 (1.14-2) ... +Selecting previously unselected package libx11-data. +Preparing to unpack .../28-libx11-data_2%3a1.6.9-2ubuntu1.2_all.deb ... +Unpacking libx11-data (2:1.6.9-2ubuntu1.2) ... +Selecting previously unselected package libx11-6:amd64. +Preparing to unpack .../29-libx11-6_2%3a1.6.9-2ubuntu1.2_amd64.deb ... +Unpacking libx11-6:amd64 (2:1.6.9-2ubuntu1.2) ... +Selecting previously unselected package libxext6:amd64. +Preparing to unpack .../30-libxext6_2%3a1.3.4-0ubuntu1_amd64.deb ... +Unpacking libxext6:amd64 (2:1.3.4-0ubuntu1) ... +Selecting previously unselected package libxmuu1:amd64. +Preparing to unpack .../31-libxmuu1_2%3a1.1.3-0ubuntu1_amd64.deb ... +Unpacking libxmuu1:amd64 (2:1.1.3-0ubuntu1) ... +Selecting previously unselected package openssh-client. +Preparing to unpack .../32-openssh-client_1%3a8.2p1-4ubuntu0.5_amd64.deb ... +Unpacking openssh-client (1:8.2p1-4ubuntu0.5) ... +Selecting previously unselected package publicsuffix. +Preparing to unpack .../33-publicsuffix_20200303.0012-1_all.deb ... +Unpacking publicsuffix (20200303.0012-1) ... +Selecting previously unselected package xauth. +Preparing to unpack .../34-xauth_1%3a1.1-0ubuntu1_amd64.deb ... +Unpacking xauth (1:1.1-0ubuntu1) ... +Selecting previously unselected package bc. +Preparing to unpack .../35-bc_1.07.1-2build1_amd64.deb ... +Unpacking bc (1.07.1-2build1) ... +Selecting previously unselected package libbrotli1:amd64. +Preparing to unpack .../36-libbrotli1_1.0.7-6ubuntu0.1_amd64.deb ... +Unpacking libbrotli1:amd64 (1.0.7-6ubuntu0.1) ... +Selecting previously unselected package libroken18-heimdal:amd64. +Preparing to unpack .../37-libroken18-heimdal_7.7.0+dfsg-1ubuntu1_amd64.deb ... +Unpacking libroken18-heimdal:amd64 (7.7.0+dfsg-1ubuntu1) ... +Selecting previously unselected package libasn1-8-heimdal:amd64. +Preparing to unpack .../38-libasn1-8-heimdal_7.7.0+dfsg-1ubuntu1_amd64.deb ... +Unpacking libasn1-8-heimdal:amd64 (7.7.0+dfsg-1ubuntu1) ... +Selecting previously unselected package libheimbase1-heimdal:amd64. +Preparing to unpack .../39-libheimbase1-heimdal_7.7.0+dfsg-1ubuntu1_amd64.deb ... +Unpacking libheimbase1-heimdal:amd64 (7.7.0+dfsg-1ubuntu1) ... +Selecting previously unselected package libhcrypto4-heimdal:amd64. +Preparing to unpack .../40-libhcrypto4-heimdal_7.7.0+dfsg-1ubuntu1_amd64.deb ... +Unpacking libhcrypto4-heimdal:amd64 (7.7.0+dfsg-1ubuntu1) ... +Selecting previously unselected package libwind0-heimdal:amd64. +Preparing to unpack .../41-libwind0-heimdal_7.7.0+dfsg-1ubuntu1_amd64.deb ... +Unpacking libwind0-heimdal:amd64 (7.7.0+dfsg-1ubuntu1) ... +Selecting previously unselected package libhx509-5-heimdal:amd64. +Preparing to unpack .../42-libhx509-5-heimdal_7.7.0+dfsg-1ubuntu1_amd64.deb ... +Unpacking libhx509-5-heimdal:amd64 (7.7.0+dfsg-1ubuntu1) ... +Selecting previously unselected package libkrb5-26-heimdal:amd64. +Preparing to unpack .../43-libkrb5-26-heimdal_7.7.0+dfsg-1ubuntu1_amd64.deb ... +Unpacking libkrb5-26-heimdal:amd64 (7.7.0+dfsg-1ubuntu1) ... +Selecting previously unselected package libheimntlm0-heimdal:amd64. +Preparing to unpack .../44-libheimntlm0-heimdal_7.7.0+dfsg-1ubuntu1_amd64.deb ... +Unpacking libheimntlm0-heimdal:amd64 (7.7.0+dfsg-1ubuntu1) ... +Selecting previously unselected package libgssapi3-heimdal:amd64. +Preparing to unpack .../45-libgssapi3-heimdal_7.7.0+dfsg-1ubuntu1_amd64.deb ... +Unpacking libgssapi3-heimdal:amd64 (7.7.0+dfsg-1ubuntu1) ... +Selecting previously unselected package libsasl2-modules-db:amd64. +Preparing to unpack .../46-libsasl2-modules-db_2.1.27+dfsg-2ubuntu0.1_amd64.deb ... +Unpacking libsasl2-modules-db:amd64 (2.1.27+dfsg-2ubuntu0.1) ... +Selecting previously unselected package libsasl2-2:amd64. +Preparing to unpack .../47-libsasl2-2_2.1.27+dfsg-2ubuntu0.1_amd64.deb ... +Unpacking libsasl2-2:amd64 (2.1.27+dfsg-2ubuntu0.1) ... +Selecting previously unselected package libldap-common. +Preparing to unpack .../48-libldap-common_2.4.49+dfsg-2ubuntu1.9_all.deb ... +Unpacking libldap-common (2.4.49+dfsg-2ubuntu1.9) ... +Selecting previously unselected package libldap-2.4-2:amd64. +Preparing to unpack .../49-libldap-2.4-2_2.4.49+dfsg-2ubuntu1.9_amd64.deb ... +Unpacking libldap-2.4-2:amd64 (2.4.49+dfsg-2ubuntu1.9) ... +Selecting previously unselected package libnghttp2-14:amd64. +Preparing to unpack .../50-libnghttp2-14_1.40.0-1build1_amd64.deb ... +Unpacking libnghttp2-14:amd64 (1.40.0-1build1) ... +Selecting previously unselected package librtmp1:amd64. +Preparing to unpack .../51-librtmp1_2.4+20151223.gitfa8646d.1-2build1_amd64.deb ... +Unpacking librtmp1:amd64 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.../57-libsasl2-modules_2.1.27+dfsg-2ubuntu0.1_amd64.deb ... +Unpacking libsasl2-modules:amd64 (2.1.27+dfsg-2ubuntu0.1) ... +Selecting previously unselected package patch. +Preparing to unpack .../58-patch_2.7.6-6_amd64.deb ... +Unpacking patch (2.7.6-6) ... +Selecting previously unselected package locales-all. +Preparing to unpack .../59-locales-all_2.31-0ubuntu9.9_amd64.deb ... +Unpacking locales-all (2.31-0ubuntu9.9) ... +Setting up libexpat1:amd64 (2.2.9-1ubuntu0.4) ... +Setting up libxau6:amd64 (1:1.0.9-0ubuntu1) ... +Setting up libkeyutils1:amd64 (1.6-6ubuntu1.1) ... +Setting up libpsl5:amd64 (0.21.0-1ubuntu1) ... +Setting up perl-modules-5.30 (5.30.0-9ubuntu0.2) ... +Setting up gawk (1:5.0.1+dfsg-1) ... +Setting up libssl1.1:amd64 (1.1.1f-1ubuntu2.16) ... +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 libbrotli1:amd64 (1.0.7-6ubuntu0.1) ... +Setting up libsqlite3-0:amd64 (3.31.1-4ubuntu0.4) ... +Setting up libsasl2-modules:amd64 (2.1.27+dfsg-2ubuntu0.1) ... +Setting up libnghttp2-14:amd64 (1.40.0-1build1) ... +Setting up less (551-1ubuntu0.1) ... +Setting up bc (1.07.1-2build1) ... +Setting up krb5-locales (1.17-6ubuntu4.1) ... +Setting up libcbor0.6:amd64 (0.6.0-0ubuntu1) ... +Setting up locales (2.31-0ubuntu9.9) ... +debconf: unable to initialize frontend: Dialog +debconf: (TERM is not set, so the dialog frontend is not usable.) +debconf: falling back to frontend: Readline +locales-all installed, skipping locales generation +Setting up libldap-common (2.4.49+dfsg-2ubuntu1.9) ... +Setting up locales-all (2.31-0ubuntu9.9) ... +Setting up libkrb5support0:amd64 (1.17-6ubuntu4.1) ... +Setting up libsasl2-modules-db:amd64 (2.1.27+dfsg-2ubuntu0.1) ... +Setting up libx11-data (2:1.6.9-2ubuntu1.2) ... +Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2build1) ... +Setting up patch (2.7.6-6) ... +Setting up libk5crypto3:amd64 (1.17-6ubuntu4.1) ... +Setting up libsasl2-2:amd64 (2.1.27+dfsg-2ubuntu0.1) ... +Setting up libroken18-heimdal:amd64 (7.7.0+dfsg-1ubuntu1) ... +Setting up git-man (1:2.25.1-1ubuntu3.5) ... +Setting up netbase (6.1) ... +Setting up libkrb5-3:amd64 (1.17-6ubuntu4.1) ... +Setting up libfido2-1:amd64 (1.3.1-1ubuntu2) ... +Setting up openssl (1.1.1f-1ubuntu2.16) ... +Setting up libbsd0:amd64 (0.10.0-1) ... +Setting up publicsuffix (20200303.0012-1) ... +Setting up libheimbase1-heimdal:amd64 (7.7.0+dfsg-1ubuntu1) ... +Setting up libgdbm6:amd64 (1.18.1-5) ... +Setting up libxdmcp6:amd64 (1:1.1.3-0ubuntu1) ... +Setting up libxcb1:amd64 (1.14-2) ... +Setting up libasn1-8-heimdal:amd64 (7.7.0+dfsg-1ubuntu1) ... +Setting up libedit2:amd64 (3.1-20191231-1) ... +Setting up libhcrypto4-heimdal:amd64 (7.7.0+dfsg-1ubuntu1) ... +Setting up ca-certificates (20211016~20.04.1) ... +debconf: unable to initialize frontend: Dialog +debconf: (TERM is not set, so the dialog frontend is not usable.) +debconf: falling back to frontend: Readline +Updating certificates in /etc/ssl/certs... +127 added, 0 removed; done. +Setting up libwind0-heimdal:amd64 (7.7.0+dfsg-1ubuntu1) ... +Setting up libgssapi-krb5-2:amd64 (1.17-6ubuntu4.1) ... +Setting up libgdbm-compat4:amd64 (1.18.1-5) ... +Setting up libssh-4:amd64 (0.9.3-2ubuntu2.2) ... +Setting up libperl5.30:amd64 (5.30.0-9ubuntu0.2) ... +Setting up libx11-6:amd64 (2:1.6.9-2ubuntu1.2) ... +Setting up libxmuu1:amd64 (2:1.1.3-0ubuntu1) ... +Setting up openssh-client (1:8.2p1-4ubuntu0.5) ... +Setting up libhx509-5-heimdal:amd64 (7.7.0+dfsg-1ubuntu1) ... +Setting up libxext6:amd64 (2:1.3.4-0ubuntu1) ... +Setting up perl (5.30.0-9ubuntu0.2) ... +Setting up xauth (1:1.1-0ubuntu1) ... +Setting up libkrb5-26-heimdal:amd64 (7.7.0+dfsg-1ubuntu1) ... +Setting up libheimntlm0-heimdal:amd64 (7.7.0+dfsg-1ubuntu1) ... +Setting up liberror-perl (0.17029-1) ... +Setting up libgssapi3-heimdal:amd64 (7.7.0+dfsg-1ubuntu1) ... +Setting up libldap-2.4-2:amd64 (2.4.49+dfsg-2ubuntu1.9) ... +Setting up libcurl3-gnutls:amd64 (7.68.0-1ubuntu2.13) ... +Setting up git (1:2.25.1-1ubuntu3.5) ... +Processing triggers for libc-bin (2.31-0ubuntu9.7) ... +Processing triggers for ca-certificates (20211016~20.04.1) ... +Updating certificates in /etc/ssl/certs... +0 added, 0 removed; done. +Running hooks in /etc/ca-certificates/update.d... +done. + + + + +================ + +apt install + +================ + + + + +Reading package lists... +Building dependency tree... +Reading state information... +0 upgraded, 0 newly installed, 0 to remove and 23 not upgraded. + + + + +================ + +apt-get autoremove + +================ + + + + +Reading package lists... +Building dependency tree... +Reading state information... +0 upgraded, 0 newly installed, 0 to remove and 23 not upgraded. + + + + +================ + +apt-get clean + +================ + + + + + + + + +================ + +rm + +================ + + + + + + + + +================ + +installed packages + +================ + + + + +locales: + Installed: 2.31-0ubuntu9.9 + Candidate: 2.31-0ubuntu9.9 + Version table: + *** 2.31-0ubuntu9.9 100 + 100 /var/lib/dpkg/status +locales-all: + Installed: 2.31-0ubuntu9.9 + Candidate: 2.31-0ubuntu9.9 + Version table: + *** 2.31-0ubuntu9.9 100 + 100 /var/lib/dpkg/status +coreutils: + Installed: 8.30-3ubuntu2 + Candidate: 8.30-3ubuntu2 + Version table: + *** 8.30-3ubuntu2 100 + 100 /var/lib/dpkg/status +gawk: + Installed: 1:5.0.1+dfsg-1 + Candidate: 1:5.0.1+dfsg-1 + Version table: + *** 1:5.0.1+dfsg-1 100 + 100 /var/lib/dpkg/status +bc: + Installed: 1.07.1-2build1 + Candidate: 1.07.1-2build1 + Version table: + *** 1.07.1-2build1 100 + 100 /var/lib/dpkg/status +git: + Installed: 1:2.25.1-1ubuntu3.5 + Candidate: 1:2.25.1-1ubuntu3.5 + Version table: + *** 1:2.25.1-1ubuntu3.5 100 + 100 /var/lib/dpkg/status diff --git a/ubuntu/v20.04/samtools/v1.0/Dockerfile b/ubuntu/v20.04/samtools/v1.0/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..c3521ad880b256047d69f2d8cd07c103fa48012c --- /dev/null +++ b/ubuntu/v20.04/samtools/v1.0/Dockerfile @@ -0,0 +1,101 @@ +######################################################################### +## ## +## Dockerfile ## +## samtools ## +## ## +## 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="" + + + +# 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 + # samtools install + && 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 $APT_GET_LINUX_LIB_RM\ + # 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 $APT_GET_LINUX_LIB $APT_LINUX_LIB samtools \ + >> /building.log \ + && samtools --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/samtools/v1.0/building.log b/ubuntu/v20.04/samtools/v1.0/building.log new file mode 100644 index 0000000000000000000000000000000000000000..0fff0825d2c4952dc40331333e71e2a5e61f17ab --- /dev/null +++ b/ubuntu/v20.04/samtools/v1.0/building.log @@ -0,0 +1,460 @@ + + + + +================ + +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/restricted amd64 Packages [1,552 kB] +Get:4 http://archive.ubuntu.com/ubuntu focal-updates InRelease [114 kB] +Get:5 http://archive.ubuntu.com/ubuntu focal-backports InRelease [108 kB] +Get:6 http://archive.ubuntu.com/ubuntu focal/universe amd64 Packages [11.3 MB] +Get:7 http://archive.ubuntu.com/ubuntu focal/main amd64 Packages [1,275 kB] +Get:8 http://archive.ubuntu.com/ubuntu focal/multiverse amd64 Packages [177 kB] +Get:9 http://archive.ubuntu.com/ubuntu focal/restricted amd64 Packages [33.4 kB] +Get:10 http://archive.ubuntu.com/ubuntu focal-updates/multiverse amd64 Packages [30.2 kB] +Get:11 http://archive.ubuntu.com/ubuntu focal-updates/universe amd64 Packages [1,206 kB] +Get:12 http://archive.ubuntu.com/ubuntu focal-updates/restricted amd64 Packages [1,667 kB] +Get:13 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 Packages [2,644 kB] +Get:14 http://archive.ubuntu.com/ubuntu focal-backports/universe amd64 Packages [27.4 kB] +Get:15 http://archive.ubuntu.com/ubuntu focal-backports/main amd64 Packages [55.2 kB] +Get:16 http://security.ubuntu.com/ubuntu focal-security/main amd64 Packages [2,178 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/universe amd64 Packages [910 kB] +Fetched 23.7 MB in 17s (1,411 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. +Get:1 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libc6 amd64 2.31-0ubuntu9.9 [2,722 kB] +Get:2 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 liblzma5 amd64 5.2.4-1ubuntu1.1 [91.8 kB] +Get:3 http://archive.ubuntu.com/ubuntu focal/main amd64 manpages all 5.05-1 [1,314 kB] +Get:4 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 wget amd64 1.20.3-1ubuntu2 [348 kB] +Get:5 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 binutils-common amd64 2.34-6ubuntu1.3 [207 kB] +Get:6 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libbinutils amd64 2.34-6ubuntu1.3 [474 kB] +Get:7 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libctf-nobfd0 amd64 2.34-6ubuntu1.3 [47.4 kB] +Get:8 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libctf0 amd64 2.34-6ubuntu1.3 [46.6 kB] +Get:9 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 binutils-x86-64-linux-gnu amd64 2.34-6ubuntu1.3 [1,613 kB] +Get:10 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 binutils amd64 2.34-6ubuntu1.3 [3,380 B] +Get:11 http://archive.ubuntu.com/ubuntu focal/main amd64 bzip2-doc all 1.0.8-2 [501 kB] +Get:12 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 gcc-9-base amd64 9.4.0-1ubuntu1~20.04.1 [19.4 kB] +Get:13 http://archive.ubuntu.com/ubuntu focal/main amd64 libisl22 amd64 0.22.1-1 [592 kB] +Get:14 http://archive.ubuntu.com/ubuntu focal/main amd64 libmpc3 amd64 1.1.0-1 [40.8 kB] +Get:15 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 cpp-9 amd64 9.4.0-1ubuntu1~20.04.1 [7,500 kB] +Get:16 http://archive.ubuntu.com/ubuntu focal/main amd64 cpp amd64 4:9.3.0-1ubuntu2 [27.6 kB] +Get:17 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libcc1-0 amd64 10.3.0-1ubuntu1~20.04 [48.8 kB] +Get:18 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libgomp1 amd64 10.3.0-1ubuntu1~20.04 [102 kB] +Get:19 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libitm1 amd64 10.3.0-1ubuntu1~20.04 [26.2 kB] +Get:20 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libatomic1 amd64 10.3.0-1ubuntu1~20.04 [9,284 B] +Get:21 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libasan5 amd64 9.4.0-1ubuntu1~20.04.1 [2,751 kB] +Get:22 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 liblsan0 amd64 10.3.0-1ubuntu1~20.04 [835 kB] +Get:23 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libtsan0 amd64 10.3.0-1ubuntu1~20.04 [2,009 kB] +Get:24 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libubsan1 amd64 10.3.0-1ubuntu1~20.04 [784 kB] +Get:25 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libquadmath0 amd64 10.3.0-1ubuntu1~20.04 [146 kB] +Get:26 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libgcc-9-dev amd64 9.4.0-1ubuntu1~20.04.1 [2,359 kB] +Get:27 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 gcc-9 amd64 9.4.0-1ubuntu1~20.04.1 [8,274 kB] +Get:28 http://archive.ubuntu.com/ubuntu focal/main amd64 gcc amd64 4:9.3.0-1ubuntu2 [5,208 B] +Get:29 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libc-dev-bin amd64 2.31-0ubuntu9.9 [71.8 kB] +Get:30 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 linux-libc-dev amd64 5.4.0-126.142 [1,118 kB] +Get:31 http://archive.ubuntu.com/ubuntu focal/main amd64 libcrypt-dev amd64 1:4.4.10-10ubuntu4 [104 kB] +Get:32 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libc6-dev amd64 2.31-0ubuntu9.9 [2,519 kB] +Get:33 http://archive.ubuntu.com/ubuntu focal/main amd64 libbz2-dev amd64 1.0.8-2 [30.2 kB] +Get:34 http://archive.ubuntu.com/ubuntu focal/main amd64 libgpm2 amd64 1.20.7-5 [15.1 kB] +Get:35 http://archive.ubuntu.com/ubuntu focal/main amd64 libncurses-dev amd64 6.2-0ubuntu2 [339 kB] +Get:36 http://archive.ubuntu.com/ubuntu focal/universe amd64 libtinfo5 amd64 6.2-0ubuntu2 [83.0 kB] +Get:37 http://archive.ubuntu.com/ubuntu focal/universe amd64 libncurses5 amd64 6.2-0ubuntu2 [96.9 kB] +Get:38 http://archive.ubuntu.com/ubuntu focal/main amd64 libncurses5-dev amd64 6.2-0ubuntu2 [976 B] +Get:39 http://archive.ubuntu.com/ubuntu focal/main amd64 make amd64 4.2.1-1.2 [162 kB] +Get:40 http://archive.ubuntu.com/ubuntu focal/main amd64 manpages-dev all 5.05-1 [2,266 kB] +Get:41 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-2ubuntu1.3 [155 kB] +Get:42 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 liblzma-dev amd64 5.2.4-1ubuntu1.1 [147 kB] +Fetched 40.0 MB in 1min 12s (554 kB/s) +(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 ... 15780 files and directories currently installed.) +Preparing to unpack .../libc6_2.31-0ubuntu9.9_amd64.deb ... +debconf: unable to initialize frontend: Dialog +debconf: (TERM is not set, so the dialog frontend is not usable.) +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) ... +debconf: unable to initialize frontend: Dialog +debconf: (TERM is not set, so the dialog frontend is not usable.) +debconf: falling back to frontend: Readline +(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 ... 15780 files and directories currently installed.) +Preparing to unpack .../liblzma5_5.2.4-1ubuntu1.1_amd64.deb ... +Unpacking liblzma5:amd64 (5.2.4-1ubuntu1.1) over (5.2.4-1ubuntu1) ... +Setting up liblzma5:amd64 (5.2.4-1ubuntu1.1) ... +Selecting previously unselected package manpages. +(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 ... 15780 files and directories currently installed.) +Preparing to unpack .../00-manpages_5.05-1_all.deb ... +Unpacking manpages (5.05-1) ... +Selecting previously unselected package wget. +Preparing to unpack .../01-wget_1.20.3-1ubuntu2_amd64.deb ... +Unpacking wget (1.20.3-1ubuntu2) ... +Selecting previously unselected package binutils-common:amd64. +Preparing to unpack .../02-binutils-common_2.34-6ubuntu1.3_amd64.deb ... +Unpacking binutils-common:amd64 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.../14-libcc1-0_10.3.0-1ubuntu1~20.04_amd64.deb ... +Unpacking libcc1-0:amd64 (10.3.0-1ubuntu1~20.04) ... +Selecting previously unselected package libgomp1:amd64. +Preparing to unpack .../15-libgomp1_10.3.0-1ubuntu1~20.04_amd64.deb ... +Unpacking libgomp1:amd64 (10.3.0-1ubuntu1~20.04) ... +Selecting previously unselected package libitm1:amd64. +Preparing to unpack .../16-libitm1_10.3.0-1ubuntu1~20.04_amd64.deb ... +Unpacking libitm1:amd64 (10.3.0-1ubuntu1~20.04) ... +Selecting previously unselected package libatomic1:amd64. +Preparing to unpack .../17-libatomic1_10.3.0-1ubuntu1~20.04_amd64.deb ... +Unpacking libatomic1:amd64 (10.3.0-1ubuntu1~20.04) ... +Selecting previously unselected package libasan5:amd64. +Preparing to unpack .../18-libasan5_9.4.0-1ubuntu1~20.04.1_amd64.deb ... +Unpacking libasan5:amd64 (9.4.0-1ubuntu1~20.04.1) ... +Selecting previously unselected package liblsan0:amd64. +Preparing to unpack .../19-liblsan0_10.3.0-1ubuntu1~20.04_amd64.deb ... +Unpacking liblsan0:amd64 (10.3.0-1ubuntu1~20.04) ... +Selecting previously unselected package libtsan0:amd64. +Preparing to unpack .../20-libtsan0_10.3.0-1ubuntu1~20.04_amd64.deb ... +Unpacking libtsan0:amd64 (10.3.0-1ubuntu1~20.04) ... +Selecting previously unselected package libubsan1:amd64. +Preparing to unpack .../21-libubsan1_10.3.0-1ubuntu1~20.04_amd64.deb ... +Unpacking libubsan1:amd64 (10.3.0-1ubuntu1~20.04) ... +Selecting previously unselected package libquadmath0:amd64. +Preparing to unpack .../22-libquadmath0_10.3.0-1ubuntu1~20.04_amd64.deb ... +Unpacking libquadmath0:amd64 (10.3.0-1ubuntu1~20.04) ... +Selecting previously unselected package libgcc-9-dev:amd64. +Preparing to unpack .../23-libgcc-9-dev_9.4.0-1ubuntu1~20.04.1_amd64.deb ... +Unpacking libgcc-9-dev:amd64 (9.4.0-1ubuntu1~20.04.1) ... +Selecting previously unselected package gcc-9. +Preparing to unpack .../24-gcc-9_9.4.0-1ubuntu1~20.04.1_amd64.deb ... +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. + + + + +================ + +samtools 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% (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 ... 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 +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 diff --git a/ubuntu/v20.04/slivar/v2.0/Dockerfile b/ubuntu/v20.04/slivar/v2.0/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..2a55cd398271d8a50a1764d48c76c25615ce26a5 --- /dev/null +++ b/ubuntu/v20.04/slivar/v2.0/Dockerfile @@ -0,0 +1,88 @@ +######################################################################### +## ## +## Dockerfile ## +## Slivar ## +## ## +## 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:20.04 +FROM gmillot/samtools_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="\ + wget \ + build-essential \ +" +ENV APT_GET_LINUX_LIB_RM="" + +ENV APT_LINUX_LIB="" + + + +# add gensoft deb repo pgp public key to apt trusted ones +# and install modules +WORKDIR /usr/bin/ +# to avoid cd. All the following commands will occurs here. In addition, opening a container will be at this node. + + +# 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 the ubuntu packages + && echo "\n\n\n\n================\n\napt-get install\n\n================\n\n\n\n" >> /building.log \ + && DEBIAN_FRONTEND="noninteractive" apt-get install -y $APT_GET_LINUX_LIB \ + | tee -a /building.log + + +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 \ + && chmod 755 slivar \ + | tee -a /building.log \ + + # cleaning +RUN 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 \ + $APT_GET_LINUX_LIB \ + >> /building.log \ + && samtools --version >> /building.log \ + && echo "slivar version v0.2.7" >> /building.log + +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/slivar/v2.0/building.log b/ubuntu/v20.04/slivar/v2.0/building.log new file mode 100644 index 0000000000000000000000000000000000000000..315a6080ff0b79eedfccdcf095f83ee1d97fae5d --- /dev/null +++ b/ubuntu/v20.04/slivar/v2.0/building.log @@ -0,0 +1,517 @@ + + + + +================ + +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: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: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) +Reading package lists... + + + + +================ + +apt-get install + +================ + + + + +Reading package lists... +Building dependency tree... +Reading state information... +The following additional packages will be installed: + binutils binutils-common binutils-x86-64-linux-gnu bzip2 cpp cpp-9 dirmngr + dpkg-dev fakeroot g++ g++-9 gcc gcc-9 gcc-9-base gnupg gnupg-l10n + gnupg-utils gpg gpg-agent gpg-wks-client gpg-wks-server gpgconf gpgsm gpgv + libalgorithm-diff-perl libalgorithm-diff-xs-perl libalgorithm-merge-perl + libasan5 libassuan0 libatomic1 libbinutils libc-dev-bin libc6-dev libcc1-0 + libcrypt-dev libctf-nobfd0 libctf0 libdpkg-perl libfakeroot + libfile-fcntllock-perl libgcc-9-dev libgomp1 libisl22 libitm1 libksba8 + liblocale-gettext-perl liblsan0 libmpc3 libnpth0 libquadmath0 + libstdc++-9-dev libtsan0 libubsan1 linux-libc-dev make manpages manpages-dev + pinentry-curses xz-utils +Suggested packages: + binutils-doc bzip2-doc cpp-doc gcc-9-locales dbus-user-session + libpam-systemd pinentry-gnome3 tor debian-keyring g++-multilib + g++-9-multilib gcc-9-doc gcc-multilib autoconf automake libtool flex bison + gdb gcc-doc gcc-9-multilib parcimonie xloadimage scdaemon glibc-doc bzr + libstdc++-9-doc make-doc man-browser pinentry-doc +The following NEW packages will be installed: + binutils binutils-common binutils-x86-64-linux-gnu build-essential bzip2 cpp + cpp-9 dirmngr dpkg-dev fakeroot g++ g++-9 gcc gcc-9 gcc-9-base gnupg + gnupg-l10n gnupg-utils gpg gpg-agent gpg-wks-client gpg-wks-server gpgconf + gpgsm libalgorithm-diff-perl libalgorithm-diff-xs-perl + libalgorithm-merge-perl libasan5 libassuan0 libatomic1 libbinutils + libc-dev-bin libc6-dev libcc1-0 libcrypt-dev libctf-nobfd0 libctf0 + libdpkg-perl libfakeroot libfile-fcntllock-perl libgcc-9-dev libgomp1 + libisl22 libitm1 libksba8 liblocale-gettext-perl liblsan0 libmpc3 libnpth0 + libquadmath0 libstdc++-9-dev libtsan0 libubsan1 linux-libc-dev make manpages + manpages-dev pinentry-curses wget xz-utils +The following packages will be upgraded: + gpgv +1 upgraded, 60 newly installed, 0 to remove and 20 not upgraded. +Need to get 49.9 MB of archives. +After this operation, 213 MB of additional disk space will be used. +Get:1 http://archive.ubuntu.com/ubuntu focal/main amd64 liblocale-gettext-perl amd64 1.07-4 [17.1 kB] +Get:2 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 gpgv amd64 2.2.19-3ubuntu2.2 [200 kB] +Get:3 http://archive.ubuntu.com/ubuntu focal/main amd64 bzip2 amd64 1.0.8-2 [34.1 kB] +Get:4 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 xz-utils amd64 5.2.4-1ubuntu1.1 [82.6 kB] +Get:5 http://archive.ubuntu.com/ubuntu focal/main amd64 manpages all 5.05-1 [1,314 kB] +Get:6 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 wget amd64 1.20.3-1ubuntu2 [348 kB] +Get:7 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 binutils-common amd64 2.34-6ubuntu1.3 [207 kB] +Get:8 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libbinutils amd64 2.34-6ubuntu1.3 [474 kB] +Get:9 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libctf-nobfd0 amd64 2.34-6ubuntu1.3 [47.4 kB] +Get:10 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libctf0 amd64 2.34-6ubuntu1.3 [46.6 kB] +Get:11 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 binutils-x86-64-linux-gnu amd64 2.34-6ubuntu1.3 [1,613 kB] +Get:12 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 binutils amd64 2.34-6ubuntu1.3 [3,380 B] +Get:13 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libc-dev-bin amd64 2.31-0ubuntu9.9 [71.8 kB] +Get:14 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 linux-libc-dev amd64 5.4.0-126.142 [1,118 kB] +Get:15 http://archive.ubuntu.com/ubuntu focal/main amd64 libcrypt-dev amd64 1:4.4.10-10ubuntu4 [104 kB] +Get:16 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libc6-dev amd64 2.31-0ubuntu9.9 [2,519 kB] +Get:17 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 gcc-9-base amd64 9.4.0-1ubuntu1~20.04.1 [19.4 kB] +Get:18 http://archive.ubuntu.com/ubuntu focal/main amd64 libisl22 amd64 0.22.1-1 [592 kB] +Get:19 http://archive.ubuntu.com/ubuntu focal/main amd64 libmpc3 amd64 1.1.0-1 [40.8 kB] +Get:20 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 cpp-9 amd64 9.4.0-1ubuntu1~20.04.1 [7,500 kB] +Get:21 http://archive.ubuntu.com/ubuntu focal/main amd64 cpp amd64 4:9.3.0-1ubuntu2 [27.6 kB] +Get:22 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libcc1-0 amd64 10.3.0-1ubuntu1~20.04 [48.8 kB] +Get:23 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libgomp1 amd64 10.3.0-1ubuntu1~20.04 [102 kB] +Get:24 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libitm1 amd64 10.3.0-1ubuntu1~20.04 [26.2 kB] +Get:25 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libatomic1 amd64 10.3.0-1ubuntu1~20.04 [9,284 B] +Get:26 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libasan5 amd64 9.4.0-1ubuntu1~20.04.1 [2,751 kB] +Get:27 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 liblsan0 amd64 10.3.0-1ubuntu1~20.04 [835 kB] +Get:28 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libtsan0 amd64 10.3.0-1ubuntu1~20.04 [2,009 kB] +Get:29 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libubsan1 amd64 10.3.0-1ubuntu1~20.04 [784 kB] +Get:30 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libquadmath0 amd64 10.3.0-1ubuntu1~20.04 [146 kB] +Get:31 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libgcc-9-dev amd64 9.4.0-1ubuntu1~20.04.1 [2,359 kB] +Get:32 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 gcc-9 amd64 9.4.0-1ubuntu1~20.04.1 [8,274 kB] +Get:33 http://archive.ubuntu.com/ubuntu focal/main amd64 gcc amd64 4:9.3.0-1ubuntu2 [5,208 B] +Get:34 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libstdc++-9-dev amd64 9.4.0-1ubuntu1~20.04.1 [1,722 kB] +Get:35 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 g++-9 amd64 9.4.0-1ubuntu1~20.04.1 [8,420 kB] +Get:36 http://archive.ubuntu.com/ubuntu focal/main amd64 g++ amd64 4:9.3.0-1ubuntu2 [1,604 B] +Get:37 http://archive.ubuntu.com/ubuntu focal/main amd64 make amd64 4.2.1-1.2 [162 kB] +Get:38 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libdpkg-perl all 1.19.7ubuntu3.2 [231 kB] +Get:39 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 dpkg-dev all 1.19.7ubuntu3.2 [679 kB] +Get:40 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 build-essential amd64 12.8ubuntu1.1 [4,664 B] +Get:41 http://archive.ubuntu.com/ubuntu focal/main amd64 libassuan0 amd64 2.5.3-7ubuntu2 [35.7 kB] +Get:42 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 gpgconf amd64 2.2.19-3ubuntu2.2 [124 kB] +Get:43 http://archive.ubuntu.com/ubuntu focal/main amd64 libksba8 amd64 1.3.5-2 [92.6 kB] +Get:44 http://archive.ubuntu.com/ubuntu focal/main amd64 libnpth0 amd64 1.6-1 [7,736 B] +Get:45 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 dirmngr amd64 2.2.19-3ubuntu2.2 [330 kB] +Get:46 http://archive.ubuntu.com/ubuntu focal/main amd64 libfakeroot amd64 1.24-1 [25.7 kB] +Get:47 http://archive.ubuntu.com/ubuntu focal/main amd64 fakeroot amd64 1.24-1 [62.6 kB] +Get:48 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 gnupg-l10n all 2.2.19-3ubuntu2.2 [51.7 kB] +Get:49 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 gnupg-utils amd64 2.2.19-3ubuntu2.2 [481 kB] +Get:50 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 gpg amd64 2.2.19-3ubuntu2.2 [482 kB] +Get:51 http://archive.ubuntu.com/ubuntu focal/main amd64 pinentry-curses amd64 1.1.0-3build1 [36.3 kB] +Get:52 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 gpg-agent amd64 2.2.19-3ubuntu2.2 [232 kB] +Get:53 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 gpg-wks-client amd64 2.2.19-3ubuntu2.2 [97.4 kB] +Get:54 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 gpg-wks-server amd64 2.2.19-3ubuntu2.2 [90.2 kB] +Get:55 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 gpgsm amd64 2.2.19-3ubuntu2.2 [217 kB] +Get:56 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 gnupg all 2.2.19-3ubuntu2.2 [259 kB] +Get:57 http://archive.ubuntu.com/ubuntu focal/main amd64 libalgorithm-diff-perl all 1.19.03-2 [46.6 kB] +Get:58 http://archive.ubuntu.com/ubuntu focal/main amd64 libalgorithm-diff-xs-perl amd64 0.04-6 [11.3 kB] +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) +Selecting previously unselected package liblocale-gettext-perl. +(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 ... 15774 files and directories currently installed.) +Preparing to unpack .../liblocale-gettext-perl_1.07-4_amd64.deb ... +Unpacking liblocale-gettext-perl (1.07-4) ... +Preparing to unpack .../gpgv_2.2.19-3ubuntu2.2_amd64.deb ... +Unpacking gpgv (2.2.19-3ubuntu2.2) over (2.2.19-3ubuntu2.1) ... +Setting up gpgv (2.2.19-3ubuntu2.2) ... +Selecting previously unselected package bzip2. +(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 ... 15788 files and directories currently installed.) +Preparing to unpack .../00-bzip2_1.0.8-2_amd64.deb ... +Unpacking bzip2 (1.0.8-2) ... +Selecting previously unselected package xz-utils. +Preparing to unpack .../01-xz-utils_5.2.4-1ubuntu1.1_amd64.deb ... +Unpacking xz-utils (5.2.4-1ubuntu1.1) ... +Selecting previously unselected package manpages. +Preparing to unpack .../02-manpages_5.05-1_all.deb ... +Unpacking manpages (5.05-1) ... +Selecting previously unselected package wget. +Preparing to unpack .../03-wget_1.20.3-1ubuntu2_amd64.deb ... +Unpacking wget (1.20.3-1ubuntu2) ... +Selecting previously unselected package binutils-common:amd64. +Preparing to unpack .../04-binutils-common_2.34-6ubuntu1.3_amd64.deb ... +Unpacking binutils-common:amd64 (2.34-6ubuntu1.3) ... +Selecting previously unselected package libbinutils:amd64. +Preparing to unpack .../05-libbinutils_2.34-6ubuntu1.3_amd64.deb ... +Unpacking libbinutils:amd64 (2.34-6ubuntu1.3) ... +Selecting previously unselected package libctf-nobfd0:amd64. +Preparing to unpack .../06-libctf-nobfd0_2.34-6ubuntu1.3_amd64.deb ... +Unpacking libctf-nobfd0:amd64 (2.34-6ubuntu1.3) ... +Selecting previously unselected package libctf0:amd64. +Preparing to unpack .../07-libctf0_2.34-6ubuntu1.3_amd64.deb ... +Unpacking libctf0:amd64 (2.34-6ubuntu1.3) ... +Selecting previously unselected package binutils-x86-64-linux-gnu. +Preparing to unpack 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(2.31-0ubuntu9.9) ... +Selecting previously unselected package gcc-9-base:amd64. +Preparing to unpack .../14-gcc-9-base_9.4.0-1ubuntu1~20.04.1_amd64.deb ... +Unpacking gcc-9-base:amd64 (9.4.0-1ubuntu1~20.04.1) ... +Selecting previously unselected package libisl22:amd64. +Preparing to unpack .../15-libisl22_0.22.1-1_amd64.deb ... +Unpacking libisl22:amd64 (0.22.1-1) ... +Selecting previously unselected package libmpc3:amd64. +Preparing to unpack .../16-libmpc3_1.1.0-1_amd64.deb ... +Unpacking libmpc3:amd64 (1.1.0-1) ... +Selecting previously unselected package cpp-9. +Preparing to unpack .../17-cpp-9_9.4.0-1ubuntu1~20.04.1_amd64.deb ... +Unpacking cpp-9 (9.4.0-1ubuntu1~20.04.1) ... +Selecting previously unselected package cpp. +Preparing to unpack .../18-cpp_4%3a9.3.0-1ubuntu2_amd64.deb ... +Unpacking cpp (4:9.3.0-1ubuntu2) ... +Selecting previously unselected package libcc1-0:amd64. +Preparing to unpack .../19-libcc1-0_10.3.0-1ubuntu1~20.04_amd64.deb ... +Unpacking libcc1-0:amd64 (10.3.0-1ubuntu1~20.04) ... +Selecting previously unselected package libgomp1:amd64. +Preparing to unpack .../20-libgomp1_10.3.0-1ubuntu1~20.04_amd64.deb ... +Unpacking libgomp1:amd64 (10.3.0-1ubuntu1~20.04) ... +Selecting previously unselected package libitm1:amd64. +Preparing to unpack .../21-libitm1_10.3.0-1ubuntu1~20.04_amd64.deb ... +Unpacking libitm1:amd64 (10.3.0-1ubuntu1~20.04) ... +Selecting previously unselected package libatomic1:amd64. +Preparing to unpack .../22-libatomic1_10.3.0-1ubuntu1~20.04_amd64.deb ... +Unpacking libatomic1:amd64 (10.3.0-1ubuntu1~20.04) ... +Selecting previously unselected package libasan5:amd64. +Preparing to unpack .../23-libasan5_9.4.0-1ubuntu1~20.04.1_amd64.deb ... +Unpacking libasan5:amd64 (9.4.0-1ubuntu1~20.04.1) ... +Selecting previously unselected package liblsan0:amd64. +Preparing to unpack .../24-liblsan0_10.3.0-1ubuntu1~20.04_amd64.deb ... +Unpacking liblsan0:amd64 (10.3.0-1ubuntu1~20.04) ... +Selecting previously unselected package libtsan0:amd64. +Preparing to unpack .../25-libtsan0_10.3.0-1ubuntu1~20.04_amd64.deb ... +Unpacking libtsan0:amd64 (10.3.0-1ubuntu1~20.04) ... +Selecting previously unselected package libubsan1:amd64. +Preparing to unpack .../26-libubsan1_10.3.0-1ubuntu1~20.04_amd64.deb ... +Unpacking libubsan1:amd64 (10.3.0-1ubuntu1~20.04) ... +Selecting previously unselected package libquadmath0:amd64. +Preparing to unpack .../27-libquadmath0_10.3.0-1ubuntu1~20.04_amd64.deb ... +Unpacking libquadmath0:amd64 (10.3.0-1ubuntu1~20.04) ... +Selecting previously unselected package libgcc-9-dev:amd64. +Preparing to unpack .../28-libgcc-9-dev_9.4.0-1ubuntu1~20.04.1_amd64.deb ... +Unpacking libgcc-9-dev:amd64 (9.4.0-1ubuntu1~20.04.1) ... +Selecting previously unselected package gcc-9. +Preparing to unpack .../29-gcc-9_9.4.0-1ubuntu1~20.04.1_amd64.deb ... +Unpacking gcc-9 (9.4.0-1ubuntu1~20.04.1) ... +Selecting previously unselected package gcc. +Preparing to unpack .../30-gcc_4%3a9.3.0-1ubuntu2_amd64.deb ... 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(1.19.7ubuntu3.2) ... +Selecting previously unselected package build-essential. +Preparing to unpack .../37-build-essential_12.8ubuntu1.1_amd64.deb ... +Unpacking build-essential (12.8ubuntu1.1) ... +Selecting previously unselected package libassuan0:amd64. +Preparing to unpack .../38-libassuan0_2.5.3-7ubuntu2_amd64.deb ... +Unpacking libassuan0:amd64 (2.5.3-7ubuntu2) ... +Selecting previously unselected package gpgconf. +Preparing to unpack .../39-gpgconf_2.2.19-3ubuntu2.2_amd64.deb ... +Unpacking gpgconf (2.2.19-3ubuntu2.2) ... +Selecting previously unselected package libksba8:amd64. +Preparing to unpack .../40-libksba8_1.3.5-2_amd64.deb ... +Unpacking libksba8:amd64 (1.3.5-2) ... +Selecting previously unselected package libnpth0:amd64. +Preparing to unpack .../41-libnpth0_1.6-1_amd64.deb ... +Unpacking libnpth0:amd64 (1.6-1) ... +Selecting previously unselected package dirmngr. +Preparing to unpack .../42-dirmngr_2.2.19-3ubuntu2.2_amd64.deb ... +Unpacking dirmngr (2.2.19-3ubuntu2.2) ... +Selecting previously unselected package libfakeroot:amd64. +Preparing to unpack .../43-libfakeroot_1.24-1_amd64.deb ... +Unpacking libfakeroot:amd64 (1.24-1) ... +Selecting previously unselected package fakeroot. +Preparing to unpack .../44-fakeroot_1.24-1_amd64.deb ... +Unpacking fakeroot (1.24-1) ... +Selecting previously unselected package gnupg-l10n. +Preparing to unpack .../45-gnupg-l10n_2.2.19-3ubuntu2.2_all.deb ... +Unpacking gnupg-l10n (2.2.19-3ubuntu2.2) ... +Selecting previously unselected package gnupg-utils. +Preparing to unpack .../46-gnupg-utils_2.2.19-3ubuntu2.2_amd64.deb ... +Unpacking gnupg-utils (2.2.19-3ubuntu2.2) ... +Selecting previously unselected package gpg. +Preparing to unpack .../47-gpg_2.2.19-3ubuntu2.2_amd64.deb ... +Unpacking gpg (2.2.19-3ubuntu2.2) ... +Selecting previously unselected package pinentry-curses. +Preparing to unpack .../48-pinentry-curses_1.1.0-3build1_amd64.deb ... +Unpacking pinentry-curses (1.1.0-3build1) ... +Selecting previously unselected package gpg-agent. +Preparing to unpack .../49-gpg-agent_2.2.19-3ubuntu2.2_amd64.deb ... +Unpacking gpg-agent (2.2.19-3ubuntu2.2) ... +Selecting previously unselected package gpg-wks-client. +Preparing to unpack .../50-gpg-wks-client_2.2.19-3ubuntu2.2_amd64.deb ... +Unpacking gpg-wks-client (2.2.19-3ubuntu2.2) ... +Selecting previously unselected package gpg-wks-server. +Preparing to unpack .../51-gpg-wks-server_2.2.19-3ubuntu2.2_amd64.deb ... +Unpacking gpg-wks-server (2.2.19-3ubuntu2.2) ... +Selecting previously unselected package gpgsm. +Preparing to unpack .../52-gpgsm_2.2.19-3ubuntu2.2_amd64.deb ... +Unpacking gpgsm (2.2.19-3ubuntu2.2) ... +Selecting previously unselected package gnupg. +Preparing to unpack .../53-gnupg_2.2.19-3ubuntu2.2_all.deb ... +Unpacking gnupg (2.2.19-3ubuntu2.2) ... +Selecting previously unselected package libalgorithm-diff-perl. +Preparing to unpack .../54-libalgorithm-diff-perl_1.19.03-2_all.deb ... +Unpacking libalgorithm-diff-perl (1.19.03-2) 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... +Setting up linux-libc-dev:amd64 (5.4.0-126.142) ... +Setting up libctf-nobfd0:amd64 (2.34-6ubuntu1.3) ... +Setting up libnpth0:amd64 (1.6-1) ... +Setting up libassuan0:amd64 (2.5.3-7ubuntu2) ... +Setting up libgomp1:amd64 (10.3.0-1ubuntu1~20.04) ... +Setting up bzip2 (1.0.8-2) ... +Setting up libfakeroot:amd64 (1.24-1) ... +Setting up fakeroot (1.24-1) ... +update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode +update-alternatives: warning: skip creation of /usr/share/man/man1/fakeroot.1.gz because associated file /usr/share/man/man1/fakeroot-sysv.1.gz (of link group fakeroot) doesn't exist +update-alternatives: warning: skip creation of /usr/share/man/man1/faked.1.gz because associated file /usr/share/man/man1/faked-sysv.1.gz (of link group fakeroot) doesn't exist +update-alternatives: warning: skip creation of /usr/share/man/es/man1/fakeroot.1.gz because associated file /usr/share/man/es/man1/fakeroot-sysv.1.gz (of link group fakeroot) doesn't exist +update-alternatives: warning: skip creation of /usr/share/man/es/man1/faked.1.gz because associated file /usr/share/man/es/man1/faked-sysv.1.gz (of link group fakeroot) doesn't exist +update-alternatives: warning: skip creation of /usr/share/man/fr/man1/fakeroot.1.gz because associated file /usr/share/man/fr/man1/fakeroot-sysv.1.gz (of link group fakeroot) doesn't exist +update-alternatives: warning: skip creation of /usr/share/man/fr/man1/faked.1.gz because associated file /usr/share/man/fr/man1/faked-sysv.1.gz (of link group fakeroot) doesn't exist +update-alternatives: warning: skip creation of /usr/share/man/sv/man1/fakeroot.1.gz because associated file /usr/share/man/sv/man1/fakeroot-sysv.1.gz (of link group fakeroot) doesn't exist +update-alternatives: warning: skip creation of /usr/share/man/sv/man1/faked.1.gz because associated file /usr/share/man/sv/man1/faked-sysv.1.gz (of link group fakeroot) doesn't exist +Setting up make (4.2.1-1.2) ... +Setting up gnupg-l10n (2.2.19-3ubuntu2.2) ... +Setting up xz-utils (5.2.4-1ubuntu1.1) ... +update-alternatives: using /usr/bin/xz to provide /usr/bin/lzma (lzma) in auto mode +update-alternatives: warning: skip creation of /usr/share/man/man1/lzma.1.gz because associated file /usr/share/man/man1/xz.1.gz (of link group lzma) doesn't exist +update-alternatives: warning: skip creation of /usr/share/man/man1/unlzma.1.gz because associated file /usr/share/man/man1/unxz.1.gz (of link group lzma) doesn't exist +update-alternatives: warning: skip creation of /usr/share/man/man1/lzcat.1.gz because associated file /usr/share/man/man1/xzcat.1.gz (of link group lzma) doesn't exist +update-alternatives: warning: skip creation of /usr/share/man/man1/lzmore.1.gz because associated file /usr/share/man/man1/xzmore.1.gz (of link group lzma) doesn't exist +update-alternatives: warning: skip creation of /usr/share/man/man1/lzless.1.gz because associated file /usr/share/man/man1/xzless.1.gz (of link group lzma) doesn't exist +update-alternatives: warning: skip creation of /usr/share/man/man1/lzdiff.1.gz because associated file /usr/share/man/man1/xzdiff.1.gz (of link group lzma) doesn't exist +update-alternatives: warning: skip creation of /usr/share/man/man1/lzcmp.1.gz because associated file /usr/share/man/man1/xzcmp.1.gz (of link group lzma) doesn't exist +update-alternatives: warning: skip creation of /usr/share/man/man1/lzgrep.1.gz because associated file /usr/share/man/man1/xzgrep.1.gz (of link group lzma) doesn't exist +update-alternatives: warning: skip creation of /usr/share/man/man1/lzegrep.1.gz because associated file /usr/share/man/man1/xzegrep.1.gz (of link group lzma) doesn't exist +update-alternatives: warning: skip creation of /usr/share/man/man1/lzfgrep.1.gz because associated file /usr/share/man/man1/xzfgrep.1.gz (of link group lzma) doesn't exist +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 libdpkg-perl (1.19.7ubuntu3.2) ... +Setting up libubsan1:amd64 (10.3.0-1ubuntu1~20.04) ... +Setting up libcrypt-dev:amd64 (1:4.4.10-10ubuntu4) ... +Setting up gpgconf (2.2.19-3ubuntu2.2) ... +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 libalgorithm-diff-xs-perl (0.04-6) ... +Setting up libcc1-0:amd64 (10.3.0-1ubuntu1~20.04) ... +Setting up liblocale-gettext-perl (1.07-4) ... +Setting up gpg (2.2.19-3ubuntu2.2) ... +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 libalgorithm-merge-perl (0.08-3) ... +Setting up gnupg-utils (2.2.19-3ubuntu2.2) ... +Setting up libtsan0:amd64 (10.3.0-1ubuntu1~20.04) ... +Setting up libctf0:amd64 (2.34-6ubuntu1.3) ... +Setting up pinentry-curses (1.1.0-3build1) ... +Setting up manpages-dev (5.05-1) ... +Setting up gpg-agent (2.2.19-3ubuntu2.2) ... +Setting up gpgsm (2.2.19-3ubuntu2.2) ... +Setting up dirmngr (2.2.19-3ubuntu2.2) ... +Setting up libasan5:amd64 (9.4.0-1ubuntu1~20.04.1) ... +Setting up gpg-wks-server (2.2.19-3ubuntu2.2) ... +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 gpg-wks-client (2.2.19-3ubuntu2.2) ... +Setting up binutils (2.34-6ubuntu1.3) ... +Setting up dpkg-dev (1.19.7ubuntu3.2) ... +Setting up libgcc-9-dev:amd64 (9.4.0-1ubuntu1~20.04.1) ... +Setting up cpp (4:9.3.0-1ubuntu2) ... +Setting up gnupg (2.2.19-3ubuntu2.2) ... +Setting up gcc-9 (9.4.0-1ubuntu1~20.04.1) ... +Setting up libstdc++-9-dev:amd64 (9.4.0-1ubuntu1~20.04.1) ... +Setting up gcc (4:9.3.0-1ubuntu2) ... +Setting up g++-9 (9.4.0-1ubuntu1~20.04.1) ... +Setting up g++ (4:9.3.0-1ubuntu2) ... +update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode +update-alternatives: warning: skip creation of /usr/share/man/man1/c++.1.gz because associated file /usr/share/man/man1/g++.1.gz (of link group c++) doesn't exist +Setting up build-essential (12.8ubuntu1.1) ... +Processing triggers for libc-bin (2.31-0ubuntu9.7) ... + + + + +================ +\slivar install + +================ + + + + +Reading package lists... +Building dependency tree... +Reading state information... +0 upgraded, 0 newly installed, 0 to remove and 20 not upgraded. + + + + +================ + +apt-get clean + +================ + + + + + + + + +================ + +rm + +================ + + + + + + + + +================ + +installed packages + +================ + + + + +locales: + Installed: 2.31-0ubuntu9.9 + Candidate: 2.31-0ubuntu9.9 + Version table: + *** 2.31-0ubuntu9.9 100 + 100 /var/lib/dpkg/status +locales-all: + Installed: 2.31-0ubuntu9.9 + Candidate: 2.31-0ubuntu9.9 + Version table: + *** 2.31-0ubuntu9.9 100 + 100 /var/lib/dpkg/status +wget: + Installed: 1.20.3-1ubuntu2 + Candidate: 1.20.3-1ubuntu2 + Version table: + *** 1.20.3-1ubuntu2 100 + 100 /var/lib/dpkg/status +build-essential: + Installed: 12.8ubuntu1.1 + Candidate: 12.8ubuntu1.1 + 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