Compiling failed after installing prerequisite.

[carolinie36]

Hello,
I am currently trying to use PCAP-core for cgpPindel. Before installing PCAP-core, I installed cgpBigWig, version 0.4.3. However, when I tried to compile PCAP-core, the system said that "ERROR: Please see README.md and install cgpBigWig."

I checked that cgpBigWig was installed properly. Could you give me a comment about this? Thanks in advance!

[shinox]

Hi,
I am not a developer but my observation is:
is cgpBigWig in the PATH and PERL5LIB? also I found You need to point PCAP to the folder where cgp is installed i.e. ./setup.sh //
For me it fails on Bio-HTS but this is test problem cause perl scripts always reference /usr/bin/perl instead where actual version of perl is on the cluster (HPC has many perl locations) and there are threaded and non threaded builds of perl too.
If someone could point me where I can edit the discovery so the test scripts are created with version of perl I want I would be very grateful,

Thank You

[keiranmraine]

Unless you need the legacy ICGC PanCancer version of this I recommend you switch to the ongoing supported version:

https://github.com/cancerit/PCAP-core