lsof failed to start - Githubissues

cancerit / cgpPindel

Cancer Genome Project Insertion/Deletion detection pipeline based around Pindel

http://cancerit.github.io/cgpPindel/

GNU Affero General Public License v3.0

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Closed jb-adams closed 7 years ago

jb-adams commented 7 years ago

Hello,

I am attempting to run cgpPindel. However, when I run the pindel.pl command with all required parameters, I receive the following error message:

"lsof" failed to start: "No such file or directory" at (eval 32) line 12. at /u/jadams/my_software/PCAP-core/lib/PCAP/Threaded.pm line 308

Any idea how to go about fixing this?

Thanks

keiranmraine commented 7 years ago

You need a system tool called lsof installing. On Ubuntu this is installed as:

apt-get install -yq --no-install-recommends lsof