Differences

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--- circos-software [2020/04/07 13:28] – aorth
+++ circos-software [2022/11/28 08:10] (current) – aorth
@@ Line 4: / Line 4: @@
 ===== Information =====
-  * Version: 0.67
+  * Version: 0.69-9
   * Added: July, 2014
-  * Updated: August, 2015
+  * Updated: November, 2022
   * Link: http://circos.ca/
 ===== Usage =====
-=== See versions of circos which are available ===
+See versions which are available:
 <code>$ module avail circos</code>
+Load one version into your environment and run it:
+<code>$ module load circos/0.69-9
+$ circos</code>
 ===== Installation ======
 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:
-<code>$ cd bin
-$ ./circos -modules</code>
-For missing modules, check and install from the system package manager first:
-<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>
-Install any other missing modules manually using ''cpanm'':
+Circos needs some Perl modules, check which we satisfy already with our system Perl:
-  * ''Math::Bezier''
+<code>$ ./bin/circos -modules</code>
-  * ''Math::VecStat''
-  * ''SVG''
-  * ''Set::IntSpan''
-===== Install missing perl modules =====
+Create a directory for custom Perl modules and install missing modules with cpanm:
-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
+$ cpanm -l /export/apps/circos/0.69-9 Math::Bezier Math::VecStat SVG Set::IntSpan</code>
-...</code>
-===== Test again =====
+Test again:
-<code>$ PERL5LIB=$PERL5LIB:/export/apps/circos/0.69-9/lib/perl5 ./circos -modules</code>
+<code>$ PERL5LIB=$PERL5LIB:/export/apps/circos/0.69-9/lib/perl5 ./bin/circos -modules</code>
-===== Continue installation =====
+When all module requirements are satisfied continue the installation:
-<code>$ cd /tmp/src/circos-0.69-9
+<code>$ cd /tmp/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 62: / Line 51: @@
 $ circos -modules</code>
-===== Fix permissions =====
+Fix permissions:
 <code>$ sudo chown -R root:root /export/apps/circos/0.69-9</code>