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JustinChu / JupiterPlot

A Circos-based tool to visualize genome assembly consistency or synteny between assemblies.
GNU General Public License v3.0
68 stars 11 forks source link

Change path for Samtools #22

Closed wlaw13 closed 4 years ago

wlaw13 commented 5 years ago

Is there a way to specify where Samtools is located? I'm using a server cluster and Samtools is installed in a common (unmovable) directory.

JustinChu commented 5 years ago

The makefile can be altered, but have you tried altering your PATH?

E.g. export PATH=/path/to/sam/bin:$PATH

wlaw13 commented 5 years ago

That seems to have worked? I'm at least getting a new error:

Can't locate Config/General.pm in @INC (@INC contains: /software/centos7/usr/share/autoconf /software/centos7/usr/share/automake-1.13 /software/centos7/usr/lib64/perl5/vendor_perl /software/centos7/usr/share/perl5/vendor_perl /software/centos7/usr/lib64/perl5 /software/centos7/usr/share/perl5 /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at /work-zfs/amccall2/WDL/Nanopore_Test_Data/JupiterPlot/JupiterPlot/circos-tools-0.22/tools/bundlelinks/bin/bundlelinks line 153. BEGIN failed--compilation aborted at /work-zfs/amccall2/WDL/Nanopore_Test_Data/JupiterPlot/JupiterPlot/circos-tools-0.22/tools/bundlelinks/bin/bundlelinks line 153. make: [Testing.rv.links.bundled] Error 2 make: Deleting file `Testing.rv.links.bundled'

Any suggestions?

JustinChu commented 5 years ago

This is a missing perl module issue. Make sure you have all the modules needed as mentioned in the readme.