simple installation of Perl on windows for Circos -- Strawberry Perl and Padre IDE
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Martin Krzywinski
Nov 26, 2015, 9:05:51 PM11/26/15
to circos-data-...@googlegroups.com
Installing Perl on Windows is made very easy by Padre Perl IDE.
I have just tested the following steps using a fresh Windows XP (Service Pack 3) install under VMWare Fusion.
1. Download Console2, a better command line terminal
2. Download and install 7-zip to unpack .tgz archives
2. Download and install Padre Perl IDE (Strawberry Perl)
3. Run Console2 and verify that perl is installed
C:\Program Files\Console2>perl -v
This is perl 5, version 14, subversion 2 (v5.14.2) built for MSWin32-x86-multi-thread
Copyright 1987-2011, Larry Wall
4. Install CPAN::minus
C:\circos>cpan App::cpanminus
CPAN: CPAN::SQLite loaded ok (v0.202)
Database was generated on Fri, 27 Nov 2015 01:36:50 GMT
CPAN: Module::CoreList loaded ok (v2.57)
App::cpanminus is up to date (1.7039).
5. Download and unpack Circos
Get the latest version of Circos from
e.g.
Unpack the archive using 7-zip to C:\circos. You should have something like this
C:\circos>dir
Volume in drive C has no label.
Volume Serial Number is 786F-5332
Directory of C:\circos
11/26/2015 05:43 PM <DIR> .
11/26/2015 05:43 PM <DIR> ..
07/10/2015 11:56 AM <DIR> bin
11/16/2015 04:40 PM 42,303 CHANGES
05/12/2014 08:20 AM 639 CITATION
11/26/2015 05:40 PM <DIR> data
03/17/2015 01:45 PM <DIR> error
07/15/2015 11:26 AM <DIR> etc
03/17/2015 11:59 AM <DIR> example
01/13/2015 03:16 PM <DIR> fonts
05/12/2014 08:20 AM 181,294 gddiag.png
05/12/2014 08:20 AM 666 INSTALL
11/16/2015 04:38 PM <DIR> lib
05/12/2014 08:20 AM 10,626 README
05/12/2014 08:20 AM 513 README.tools
05/12/2014 08:20 AM 3,521 README.tutorials
05/12/2014 08:20 AM 1,127 README.windows
05/12/2014 08:20 AM 61 SUPPORT
09/26/2014 10:35 AM <DIR> tiles
05/12/2014 08:20 AM 850 TODO
10 File(s) 241,600 bytes
10 Dir(s) 17,266,843,648 bytes free
6. Check which modules you are missing
C:\circos>perl bin\circos -modules
ok 1.23 Carp
ok 0.31 Clone
ok 2.60 Config::General
ok 3.36 Cwd
ok 2.131 Data::Dumper
ok 2.51 Digest::MD5
ok 2.82 File::Basename
ok 3.33 File::Spec::Functions
ok 0.22 File::Temp
ok 1.50 FindBin
ok 0.39 Font::TTF::Font
ok 2.46 GD
ok 0.2 GD::Polyline
ok 2.38 Getopt::Long
ok 1.15 IO::File
ok 0.33 List::MoreUtils
ok 1.23 List::Util
ok 0.01 Math::Bezier
ok 1.997 Math::BigFloat
ok 0.06 Math::Round
ok 0.08 Math::VecStat
ok 1.02 Memoize
ok 1.24 POSIX
ok 1.05 Params::Validate
ok 1.36 Pod::Usage
ok 1.03 Readonly
ok 2013031301 Regexp::Common
ok 2.50 SVG
ok 1.19 Set::IntSpan
ok 1.6611 Statistics::Basic
ok 2.30 Storable
ok 1.16 Sys::Hostname
ok 2.02 Text::Balanced
ok 0.59 Text::Format
ok 1.9724 Time::HiRes
For any modules that say "missing", install them using cpanm. For example, to install Config::General,
C:\circos>cpanm Config::General
Config::General is up to date. (2.60)
Importantly, Padre already comes with GD installed, which is the most vexing module to install due to its dependencies.
7. Create the example image
C:\circos\example>perl ..\bin\circos
debuggroup summary 0.26s welcome to circos v0.68-1 16 Nov 2015 on Perl 5.014002
debuggroup summary 0.26s current working directory C:/circos/example
debuggroup summary 0.26s command ..\bin\circos [no flags]
debuggroup summary 0.26s guessing configuration file
debuggroup summary 0.26s found conf file C:\circos\example\etc\circos.conf
debuggroup summary 0.67s debug will appear for these features: output,summary
debuggroup summary 0.67s bitmap output image ./.\circos.png
debuggroup summary 0.67s SVG output image ./.\circos.svg
debuggroup summary 0.67s parsing karyotype and organizing ideograms
debuggroup summary 0.87s karyotype has 66 chromosomes of total size 8,540,079,869
debuggroup summary 0.89s applying global and local scaling
debuggroup summary 0.98s allocating image, colors and brushes
...
debuggroup timer 41.46s report track_text_preprocess 0.459 s
debuggroup timer 41.46s report track_text_refine 0.004 s
debuggroup timer 41.46s report unitconvert 0.047 s
debuggroup timer 41.46s report unitconvert_decision 0.004 s
debuggroup timer 41.46s report unitconvert_delegate 0.012 s
debuggroup timer 41.46s report unitparse 0.143 s
debuggroup summary,timer 41.46s image took more than 30 s to generate. Component timings are shown above. To always show them, use -debug_group timer. To adjust the time cutoff, change debug_auto_timer_report in etc/housekeeping.conf.
Look at the output image C:\circos\example\circos.png -- screenshot attached.
8. Install the tutorials by downloading the tutorial archive and unpacking it into the C:\circos directory. This will create tutorials\ and add files to data\
Andrew Robins
Jun 24, 2020, 2:17:29 AM6/24/20
to Circos
How do I program in Perl on Windows 10? I don't have Windows XP. I have installed Strawberry. Do I need to download Padre? If so, where do I find Padre?
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