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Setting up mafft (7.123-1) ...
Setting up maq (0.7.1-5) ...
Setting up muscle (1:3.8.31-1) ...
Setting up perl-doc (5.18.2-2ubuntu1.7) ...
Setting up perl-tk (1:804.031-1build1) ...
Setting up phyml (2:20120412-2) ...
Setting up primer3 (2.3.6-1) ...
Setting up probalign (1.4-3) ...
Setting up probcons (1.12-9) ...
Setting up samtools (0.1.19-1) ...
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Setting up tigr-glimmer (3.02-3) ...
Setting up tm-align (20130511+dfsg-1) ...
Setting up bowtie (1.0.0-5) ...
Setting up hmmer (3.1b1-3) ...
Setting up libbsd-resource-perl (1.2907-1build1) ...
Setting up libgd-gd2-perl (1:2.46-3.1build1) ...
Setting up libset-scalar-perl (1.27-1) ...
Setting up lynx-cur (2.8.8pre4-1) ...
update-alternatives: using /usr/bin/lynx to provide /usr/bin/www-browser (www-browser) in auto mode
Setting up lynx (2.8.8pre4-1) ...
Setting up ruby (1:1.9.3.4) ...
Setting up ruby1.9.1 (1.9.3.484-2ubuntu1.14) ...
Setting up libruby1.9.1 (1.9.3.484-2ubuntu1.14) ...
Processing triggers for libc-bin (2.19-0ubuntu6.14) ...
Reading package lists...
Building dependency tree...
Reading state information...
The following NEW packages will be installed:
  libstatistics-distributions-perl
0 upgraded, 1 newly installed, 0 to remove and 50 not upgraded.
Need to get 9994 B of archives.
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Unpacking libstatistics-distributions-perl (1.02-1) ...
Processing triggers for man-db (2.6.7.1-1ubuntu1) ...
Setting up libstatistics-distributions-perl (1.02-1) ...
Reading package lists...
Building dependency tree...
Reading state information...
The following extra packages will be installed:
  libclass-methodmaker-perl libio-interactive-perl libsub-uplevel-perl
  libterm-progressbar-perl libterm-progressbar-quiet-perl libterm-readkey-perl
  libtest-exception-perl libtest-mockobject-perl libtest-warn-perl
  libuniversal-can-perl libuniversal-isa-perl
The following NEW packages will be installed:
  libclass-methodmaker-perl libio-interactive-perl libsub-uplevel-perl
  libterm-progressbar-perl libterm-progressbar-quiet-perl
  libterm-progressbar-simple-perl libterm-readkey-perl libtest-exception-perl
  libtest-mockobject-perl libtest-warn-perl libuniversal-can-perl
  libuniversal-isa-perl
0 upgraded, 12 newly installed, 0 to remove and 50 not upgraded.
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Get:2 http://archive.ubuntu.com/ubuntu/ trusty/universe libio-interactive-perl all 0.0.6-1 [10.6 kB]
Get:3 http://archive.ubuntu.com/ubuntu/ trusty/main libsub-uplevel-perl all 0.2400-1 [13.8 kB]
Get:4 http://archive.ubuntu.com/ubuntu/ trusty/main libterm-readkey-perl amd64 2.31-1 [27.4 kB]
Get:5 http://archive.ubuntu.com/ubuntu/ trusty/universe libterm-progressbar-perl all 2.14-1 [21.4 kB]
Get:6 http://archive.ubuntu.com/ubuntu/ trusty/main libtest-exception-perl all 0.32-1 [16.0 kB]
Get:7 http://archive.ubuntu.com/ubuntu/ trusty/main libtest-warn-perl all 0.24-1 [14.8 kB]
Get:8 http://archive.ubuntu.com/ubuntu/ trusty/universe libuniversal-isa-perl all 1.20120726-1 [8714 B]
Get:9 http://archive.ubuntu.com/ubuntu/ trusty/universe libuniversal-can-perl all 1.20140124-1 [11.8 kB]
Get:10 http://archive.ubuntu.com/ubuntu/ trusty/universe libtest-mockobject-perl all 1.20120301-1 [26.9 kB]
Get:11 http://archive.ubuntu.com/ubuntu/ trusty/universe libterm-progressbar-quiet-perl all 0.31-1 [4994 B]
Get:12 http://archive.ubuntu.com/ubuntu/ trusty/universe libterm-progressbar-simple-perl all 0.03-1 [7654 B]
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Selecting previously unselected package libio-interactive-perl.
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Preparing to unpack .../libsub-uplevel-perl_0.2400-1_all.deb ...
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Unpacking libterm-progressbar-quiet-perl (0.31-1) ...
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Unpacking libterm-progressbar-simple-perl (0.03-1) ...
Processing triggers for man-db (2.6.7.1-1ubuntu1) ...
Setting up libclass-methodmaker-perl (2.19-1) ...
Setting up libio-interactive-perl (0.0.6-1) ...
Setting up libsub-uplevel-perl (0.2400-1) ...
Setting up libterm-readkey-perl (2.31-1) ...
Setting up libterm-progressbar-perl (2.14-1) ...
Setting up libtest-exception-perl (0.32-1) ...
Setting up libtest-warn-perl (0.24-1) ...
Setting up libuniversal-isa-perl (1.20120726-1) ...
Setting up libuniversal-can-perl (1.20140124-1) ...
Setting up libtest-mockobject-perl (1.20120301-1) ...
Setting up libterm-progressbar-quiet-perl (0.31-1) ...
Setting up libterm-progressbar-simple-perl (0.03-1) ...
Reading package lists...
Building dependency tree...
Reading state information...
The following extra packages will be installed:
  libstaden-read1
The following NEW packages will be installed:
  libbio-scf-perl libstaden-read1
0 upgraded, 2 newly installed, 0 to remove and 50 not upgraded.
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Get:1 http://archive.ubuntu.com/ubuntu/ trusty/universe libstaden-read1 amd64 1.13.5-1.1 [182 kB]
Get:2 http://archive.ubuntu.com/ubuntu/ trusty/universe libbio-scf-perl amd64 1.03-1build4 [23.3 kB]
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Setting up libstaden-read1 (1.13.5-1.1) ...
Setting up libbio-scf-perl (1.03-1build4) ...
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Removing intermediate container 7adc9dbdb955
 ---> 1ca0a9d66656
Step 13/16 : RUN apt-get install -y curl &&     cpan install App::cpanminus
 ---> Running in aabe5835266c
Reading package lists...
Building dependency tree...
Reading state information...
The following extra packages will be installed:
  libcurl3
The following packages will be upgraded:
  curl libcurl3
2 upgraded, 0 newly installed, 0 to remove and 48 not upgraded.
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Get:2 http://archive.ubuntu.com/ubuntu/ trusty-updates/main libcurl3 amd64 7.35.0-1ubuntu2.20 [173 kB]
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(Reading database ... 44993 files and directories currently installed.)
Preparing to unpack .../curl_7.35.0-1ubuntu2.20_amd64.deb ...
Unpacking curl (7.35.0-1ubuntu2.20) over (7.35.0-1ubuntu2.17) ...
Preparing to unpack .../libcurl3_7.35.0-1ubuntu2.20_amd64.deb ...
Unpacking libcurl3:amd64 (7.35.0-1ubuntu2.20) over (7.35.0-1ubuntu2.17) ...
Processing triggers for man-db (2.6.7.1-1ubuntu1) ...
Setting up libcurl3:amd64 (7.35.0-1ubuntu2.20) ...
Setting up curl (7.35.0-1ubuntu2.20) ...
Processing triggers for libc-bin (2.19-0ubuntu6.14) ...

CPAN.pm requires configuration, but most of it can be done automatically.
If you answer 'no' below, you will enter an interactive dialog for each
configuration option instead.

Would you like to configure as much as possible automatically? [yes] yes

Would you like me to automatically choose some CPAN mirror
sites for you? (This means connecting to the Internet) [yes] yes
Fetching with LWP:
http://espejito.fder.edu.uy/cpan/authors/01mailrc.txt.gz
Reading '/root/.cpan/sources/authors/01mailrc.txt.gz'
............................................................................DONE
Fetching with LWP:
http://espejito.fder.edu.uy/cpan/modules/02packages.details.txt.gz
Reading '/root/.cpan/sources/modules/02packages.details.txt.gz'
  Database was generated on Sun, 24 May 2020 12:41:03 GMT
.............
  New CPAN.pm version (v2.27) available.
  [Currently running version is v2.00]
  You might want to try
    install CPAN
    reload cpan
  to both upgrade CPAN.pm and run the new version without leaving
  the current session.


...............................................................DONE
Fetching with LWP:
http://espejito.fder.edu.uy/cpan/modules/03modlist.data.gz
Reading '/root/.cpan/sources/modules/03modlist.data.gz'
DONE
Writing /root/.cpan/Metadata
Running install for module 'App::cpanminus'
Running make for M/MI/MIYAGAWA/App-cpanminus-1.7044.tar.gz
Fetching with LWP:
http://espejito.fder.edu.uy/cpan/authors/id/M/MI/MIYAGAWA/App-cpanminus-1.7044.tar.gz
Fetching with LWP:
http://espejito.fder.edu.uy/cpan/authors/id/M/MI/MIYAGAWA/CHECKSUMS
Checksum for /root/.cpan/sources/authors/id/M/MI/MIYAGAWA/App-cpanminus-1.7044.tar.gz ok

  CPAN.pm: Building M/MI/MIYAGAWA/App-cpanminus-1.7044.tar.gz

Checking if your kit is complete...
Looks good
Generating a Unix-style Makefile
Writing Makefile for App::cpanminus
Writing MYMETA.yml and MYMETA.json
cp lib/App/cpanminus.pm blib/lib/App/cpanminus.pm
cp lib/App/cpanminus/fatscript.pm blib/lib/App/cpanminus/fatscript.pm
cp bin/cpanm blib/script/cpanm
"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/cpanm
Manifying 1 pod document
Manifying 2 pod documents
  MIYAGAWA/App-cpanminus-1.7044.tar.gz
  /usr/bin/make -- OK
Running make test
PERL_DL_NONLAZY=1 "/usr/bin/perl" "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
# App::cpanminus/1.7044
t/happy_cpantesters.t .. ok
All tests successful.
Files=1, Tests=1,  1 wallclock secs ( 0.02 usr  0.01 sys +  0.08 cusr  0.01 csys =  0.12 CPU)
Result: PASS
  MIYAGAWA/App-cpanminus-1.7044.tar.gz
  /usr/bin/make test -- OK
Running make install
Manifying 1 pod document
Manifying 2 pod documents
Installing /usr/local/share/perl/5.18.2/App/cpanminus.pm
Installing /usr/local/share/perl/5.18.2/App/cpanminus/fatscript.pm
Installing /usr/local/man/man1/cpanm.1p
Installing /usr/local/man/man3/App::cpanminus.3pm
Installing /usr/local/man/man3/App::cpanminus::fatscript.3pm
Installing /usr/local/bin/cpanm
Appending installation info to /usr/lib/perl/5.18/perllocal.pod
  MIYAGAWA/App-cpanminus-1.7044.tar.gz
  /usr/bin/make install  -- OK
Removing intermediate container aabe5835266c
 ---> 2efe9777690b
Step 14/16 : RUN cpanm install File::chdir &&     cpanm install lib::abs &&     cpanm install File::Remove &&     cpanm install Spreadsheet::Read &&     cpanm install Statistics::ChiSquare &&     cpan install Text::CSV
 ---> Running in 89e48c724c49
--> Working on install
Fetching http://www.cpan.org/authors/id/D/DA/DAGOLDEN/install-0.01.tar.gz ... OK
Configuring install-0.01 ... OK
Building and testing install-0.01 ... OK
Successfully installed install-0.01
--> Working on File::chdir
Fetching http://www.cpan.org/authors/id/D/DA/DAGOLDEN/File-chdir-0.1010.tar.gz ... OK
Configuring File-chdir-0.1010 ... OK
Building and testing File-chdir-0.1010 ... OK
Successfully installed File-chdir-0.1010
2 distributions installed
install is up to date. (0.01)
--> Working on lib::abs
Fetching http://www.cpan.org/authors/id/M/MO/MONS/lib-abs-0.95.tar.gz ... OK
Configuring lib-abs-0.95 ... OK
Building and testing lib-abs-0.95 ... OK
Successfully installed lib-abs-0.95
1 distribution installed
install is up to date. (0.01)
--> Working on File::Remove
Fetching http://www.cpan.org/authors/id/S/SH/SHLOMIF/File-Remove-1.58.tar.gz ... OK
Configuring File-Remove-1.58 ... OK
Building and testing File-Remove-1.58 ... OK
Successfully installed File-Remove-1.58
1 distribution installed
install is up to date. (0.01)
--> Working on Spreadsheet::Read
Fetching http://www.cpan.org/authors/id/H/HM/HMBRAND/Spreadsheet-Read-0.81.tgz ... OK
Configuring Spreadsheet-Read-0.81 ... OK
Building and testing Spreadsheet-Read-0.81 ... OK
Successfully installed Spreadsheet-Read-0.81
1 distribution installed
install is up to date. (0.01)
--> Working on Statistics::ChiSquare
Fetching http://www.cpan.org/authors/id/D/DC/DCANTRELL/Statistics-ChiSquare-1.0000.tar.gz ... OK
Configuring Statistics-ChiSquare-1.0000 ... OK
Building and testing Statistics-ChiSquare-1.0000 ... OK
Successfully installed Statistics-ChiSquare-1.0000
1 distribution installed
Reading '/root/.cpan/Metadata'
  Database was generated on Sun, 24 May 2020 12:41:03 GMT
Running install for module 'Text::CSV'
Running make for I/IS/ISHIGAKI/Text-CSV-2.00.tar.gz
Fetching with LWP:
http://espejito.fder.edu.uy/cpan/authors/id/I/IS/ISHIGAKI/Text-CSV-2.00.tar.gz
Fetching with LWP:
http://espejito.fder.edu.uy/cpan/authors/id/I/IS/ISHIGAKI/CHECKSUMS
Checksum for /root/.cpan/sources/authors/id/I/IS/ISHIGAKI/Text-CSV-2.00.tar.gz ok

  CPAN.pm: Building I/IS/ISHIGAKI/Text-CSV-2.00.tar.gz

Welcome to Text::CSV (v.2.00)
=============================
If you install Text::CSV_XS v.1.02, it makes Text::CSV faster.

Checking if your kit is complete...
Looks good
Generating a Unix-style Makefile
Writing Makefile for Text::CSV
Writing MYMETA.yml and MYMETA.json
cp lib/Text/CSV_PP.pm blib/lib/Text/CSV_PP.pm
cp lib/Text/CSV.pm blib/lib/Text/CSV.pm
Manifying 2 pod documents
  ISHIGAKI/Text-CSV-2.00.tar.gz
  /usr/bin/make -- OK
Running make test
PERL_DL_NONLAZY=1 "/usr/bin/perl" "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
# PERL_TEXT_CSV: undef
t/00_pod.t ............... ok
t/01_is_pp.t ............. ok
t/10_base.t .............. ok
t/12_acc.t ............... ok
t/15_flags.t ............. ok
t/20_file.t .............. ok
t/21_lexicalio.t ......... ok
t/22_scalario.t .......... ok
t/30_types.t ............. ok
t/40_misc.t .............. ok
t/41_null.t .............. ok
t/45_eol.t ............... ok
t/46_eol_si.t ............ ok
t/50_utf8.t .............. ok
t/51_utf8.t .............. ok
t/55_combi.t ............. ok
t/60_samples.t ........... ok
t/65_allow.t ............. ok
t/66_formula.t ........... ok
t/70_rt.t ................ ok
t/71_pp.t ................ ok
t/75_hashref.t ........... ok
t/76_magic.t ............. ok
t/77_getall.t ............ ok
t/78_fragment.t .......... ok
t/79_callbacks.t ......... ok
t/80_diag.t .............. ok
t/81_subclass.t .......... ok
t/85_util.t .............. ok
t/90_csv.t ............... ok
t/91_csv_cb.t ............ ok
t/fields_containing_0.t .. ok
t/rt99774.t .............. ok
All tests successful.
Files=33, Tests=52231, 55 wallclock secs ( 6.84 usr  0.67 sys + 52.86 cusr  0.66 csys = 61.03 CPU)
Result: PASS
  ISHIGAKI/Text-CSV-2.00.tar.gz
  /usr/bin/make test -- OK
Running make install
Manifying 2 pod documents
Installing /usr/local/share/perl/5.18.2/Text/CSV_PP.pm
Installing /usr/local/share/perl/5.18.2/Text/CSV.pm
Installing /usr/local/man/man3/Text::CSV_PP.3pm
Installing /usr/local/man/man3/Text::CSV.3pm
Appending installation info to /usr/lib/perl/5.18/perllocal.pod
  ISHIGAKI/Text-CSV-2.00.tar.gz
  /usr/bin/make install  -- OK
Removing intermediate container 89e48c724c49
 ---> d2beb40936da
Step 15/16 : WORKDIR home/
 ---> Running in 1e23f559d32f
Removing intermediate container 1e23f559d32f
 ---> 7917546826a5
Step 16/16 : COPY autoConTAMPR home/autoConTAMPR
 ---> ddbd36883355
Successfully built ddbd36883355
Successfully tagged autocontampr:latest