Differences

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--- circos-software [2020/04/07 13:36] – aorth
+++ circos-software [2020/09/18 10:14] – aorth
@@ Line 4: / Line 4: @@
 ===== Information =====
-  * Version: 0.69.9
+  * Version: 0.69-9
   * Added: July, 2014
-  * Updated: April, 2020
+  * Updated: September, 2020
   * Link: http://circos.ca/
@@ Line 21: / Line 21: @@
 Notes from the sysadmin during installation:
-<code>$ wget http://circos.ca/distribution/circos-0.69-9.tgz
+<code>$ cd /tmp
-$ tar zxf circos-0.69-9.tgz
+$ wget http://circos.ca/distribution/circos-0.69-9.tgz
-$ cd circos-0.66-9</code>
+$ tar zxf circos-0.69-9.tgz
+$ cd circos-0.69-9</code>
-===== Check requirements =====
+Circos needs some Perl modules, check which we satisfy already with our Perl 5.28.2 package:
-Circos needs some Perl modules, check which we satisfy already:
-<code>$ cd bin
+<code>$ module load perl/5.28.2
-$ ./circos -modules</code>
+$ ./bin/circos -modules</code>
-For missing modules, check and install from the system package manager first:
+Create directory for Perl modules and install missing modules with cpanm:
-<code>$ yum install perl-Clone.x86_64 perl-Config-General.noarch perl-Font-TTF.noarch perl-Readonly.noarch perl-Regexp-Common.noarch perl-Text-Format.noarch perl-Math-Round</code>
+<code>
+$ sudo mkdir -p /export/apps/circos/0.69-9/lib/perl5
+$ sudo chown -R aorth /export/apps/circos/0.69-9
+$ cpanm -l /export/apps/circos/0.69-9/ Clone Config::General Font::TTF::Font
+$ sudo yum install gd-devel
+$ cpanm -l /export/apps/circos/0.69-9/ GD GD::Polyline
+$ sudo yum remove gd-devel
+$ cpanm -l /export/apps/circos/0.69-9/ List::MoreUtils Math::Bezier Math::Round Math::VecStat
+$ cpanm -l /export/apps/circos/0.69-9/ Params::Validate Readonly Regexp::Common SVG Set::IntSpanStatistics::Basic Text::Format
+</code>
-Install any other missing modules manually using ''cpanm'':
+I don't install all the missing modules at once because sometimes they have errors and it's easier to track them down when you do less in one go.
-  * ''Math::Bezier''
-  * ''Math::VecStat''
-  * ''SVG''
-  * ''Set::IntSpan''
-===== Install missing perl modules =====
-Create directories for perl modules:
-<code>$ sudo mkdir -p /export/apps/circos/0.69-9/lib/perl5
-$ sudo chown -R aorth /export/apps/circos/0.69-9
-$ cpanm -l /export/apps/circos/0.69-9/ Math::Bezier
-...</code>
-===== Test again =====
+Test again:
 <code>$ PERL5LIB=$PERL5LIB:/export/apps/circos/0.69-9/lib/perl5 ./circos -modules</code>
-===== Continue installation =====
+When all module requirements are satisfied continue the installation:
 <code>$ cd /tmp/src/circos-0.69-9
 $ cp -r * /export/apps/circos/0.69-9</code>
-===== Try to run =====
 Add install directory to PATH and PERL5LIB and try to run it:
@@ Line 66: / Line 61: @@
 $ circos -modules</code>
-===== Fix permissions =====
+Fix permissions:
 <code>$ sudo chown -R root:root /export/apps/circos/0.69-9</code>