Differences

This shows you the differences between two versions of the page.

--- circos-software [2014/07/31 09:48] – created aorth
+++ circos-software [2020/09/18 08:40] – aorth
@@ Line 4: / Line 4: @@
 ===== Information =====
-  * Version: 0.66
+  * Version: 0.69.9
   * Added: July, 2014
+  * Updated: April, 2020
   * Link: http://circos.ca/
 ===== Usage =====
-=== See versions of abyss which are available ===
+See versions of circos which are available:
-<code>module avail abyss</code>
+<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-0.66.tgz
+<code>$ wget http://circos.ca/distribution/circos-0.69-9.tgz
-tar zxf circos-0.66.tgz
+$ tar zxf circos-0.69-9.tgz
-cd circos-0.66</code>
+$ cd circos-0.69-9</code>
 ===== Check requirements =====
-Circos needs some perl modules, check which we satisfy already:
+Circos needs some Perl modules, check which we satisfy already:
-<code>cd bin
+<code>$ cd bin
-./test.modules</code>
+$ ./circos -modules</code>
-For missing modules, check and install from system package manager first:
+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</code>
+<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 other modules manually:
+Install any other missing modules manually using ''cpanm'':
-<code>Math::Round
+  * ''Math::Bezier''
-Math::VecStat</code>
+  * ''Math::VecStat''
+  * ''SVG''
+  * ''Set::IntSpan''
 ===== Install missing perl modules =====
 Create directories for perl modules:
-<code>sudo mkdir -p /export/apps/circos/0.66/{share,lib,lib64}/perl5
+<code>$ sudo mkdir -p /export/apps/circos/0.69-9/lib/perl5
-sudo chown -R aorth /export/apps/circos/0.66</code>
+$ sudo chown -R aorth /export/apps/circos/0.69-9
+$ cpanm -l /export/apps/circos/0.69-9/ Math::Bezier
-Prepare CPAN for installing into our prefix:
+...</code>
-<code>perl -e shell -MCPAN
-cpan[1]> o conf makepl_arg "INSTALLDIRS=site PREFIX=/export/apps/circos/0.66"
-cpan[2]> o conf mbuildpl_arg "--prefix /export/apps/circos/0.66"
-cpan[3]> o conf commit</code>
-Then install the missing modules one by one, ie:
-<code>install Math::Round</code>
 ===== Test again =====
-<code>PERL5LIB=$PERL5LIB:/export/apps/circos/0.66/lib64/perl5:/export/apps/circos/0.66/share/perl5 ./list.modules</code>
+<code>$ PERL5LIB=$PERL5LIB:/export/apps/circos/0.69-9/lib/perl5 ./circos -modules</code>
-Working!
 ===== Continue installation =====
-<code>cd ~/src/circos-0.66
+<code>$ cd /tmp/src/circos-0.69-9
-cp -r * /export/apps/circos/0.66</code>
+$ cp -r * /export/apps/circos/0.69-9</code>
 ===== Try to run =====
-Add install dir to PATH and PERL5LIBS and try to run it:
+Add install directory to PATH and PERL5LIB and try to run it:
-<code>PATH=$PATH:/export/apps/circos/0.66/bin PERL5LIB=$PERL5LIB:/export/apps/circos/0.66/lib64/perl5:/export/apps/circos/0.66/share/perl5 circos</code>
-It might complain about more missing modules, so install them also (with CPAN like above):
-<code>Math::Bezier
+<code>$ export PATH=$PATH:/export/apps/circos/0.69-9/bin
-Set::IntSpan</code>
+$ export PERL5LIB=$PERL5LIB:/export/apps/circos/0.69-9/lib/perl5
+$ circos -modules</code>
 ===== Fix permissions =====
-<code>sudo chown -R root:root /export/apps/circos/0.66</code>
+<code>$ sudo chown -R root:root /export/apps/circos/0.69-9</code>