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cancerit / ascatNgs

Somatic copy number analysis using WGS paired end wholegenome sequencing
http://cancerit.github.io/ascatNgs/
GNU Affero General Public License v3.0
68 stars 17 forks source link

Error during Installation via source code. #104

Closed as7a5 closed 3 years ago

as7a5 commented 3 years ago

Hi I get the following error as I compile it from source code.:

./setup.sh /gpfs/share/apps/ascatngs/4.5.0 /gpfs/share/apps/cgpvcf/2.0.4/lib/perl5:/gpfs/share/apps/allelecount/4.2.1/lib/perl5:/gpfs/share/apps/pcap-core/5.4.0/lib/perl5

. . .

PERL_DL_NONLAZY=1 "/gpfs/share/apps/perl/5.28.0/bin/perl" "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
t/1_pm_compile.t .. 1/? 
#   Failed test 'use Sanger::CGP::Ascat::Implement;'
#   at t/1_pm_compile.t line 56.
#     Tried to use 'Sanger::CGP::Ascat::Implement'.
#     Error:  Can't locate PCAP/Threaded.pm in @INC (you may need to install the PCAP::Threaded module) (@INC contains: /gpfs/share/apps/ascatngs/4.5.0/raw/ascatNgs/perl/blib/lib /gpfs/share/apps/ascatngs/4.5.0/raw/ascatNgs/perl/blib/arch /gpfs/share/apps/ascatngs/4.5.0/lib/perl5/x86_64-linux-thread /gpfs/share/apps/ascatngs/4.5.0/lib/perl5/x86_64-linux-thread /gpfs/share/apps/ascatngs/4.5.0/lib/perl5 /gpfs/share/apps/cgpvcf/2.0.4/lib/perl5/x86_64-linux-thread /gpfs/share/apps/cgpvcf/2.0.4/lib/perl5/x86_64-linux-thread /gpfs/share/apps/cgpvcf/2.0.4/lib/perl5 /gpfs/share/apps/allelecount/4.2.1/lib/perl5/x86_64-linux-thread /gpfs/share/apps/allelecount/4.2.1/lib/perl5/x86_64-linux-thread /gpfs/share/apps/allelecount/4.2.1/lib/perl5 /gpfs/share/apps/pcap-core/5.4.0/lib/perl5 /gpfs/share/apps/ascatngs/4.5.0/lib/perl5/x86_64-linux-thread /gpfs/share/apps/ascatngs/4.5.0/lib/perl5 /gpfs/share/apps/ascatngs/4.5.0/lib/perl5/x86_64-linux-thread /gpfs/share/apps/ascatngs/4.5.0/lib/perl5 /gpfs/share/apps/cgpvcf/2.0.4/lib/perl5/x86_64-linux-thread /gpfs/share/apps/cgpvcf/2.0.4/lib/perl5 /gpfs/share/apps/allelecount/4.2.1/lib/perl5/x86_64-linux-thread /gpfs/share/apps/allelecount/4.2.1/lib/perl5 /gpfs/share/apps/pcap-core/5.4.0/lib/perl5 /gpfs/share/apps/perl/5.28.0/lib/site_perl/5.28.0/x86_64-linux /gpfs/share/apps/perl/5.28.0/lib/site_perl/5.28.0 /gpfs/share/apps/perl/5.28.0/lib/5.28.0/x86_64-linux /gpfs/share/apps/perl/5.28.0/lib/5.28.0 .) at /gpfs/share/apps/ascatngs/4.5.0/raw/ascatNgs/perl/blib/lib/Sanger/CGP/Ascat/Implement.pm line 43.
# BEGIN failed--compilation aborted at /gpfs/share/apps/ascatngs/4.5.0/raw/ascatNgs/perl/blib/lib/Sanger/CGP/Ascat/Implement.pm line 43.
# Compilation failed in require at t/1_pm_compile.t line 56.
# BEGIN failed--compilation aborted at t/1_pm_compile.t line 56.
Bailout called.  Further testing stopped:  Unable to 'use' module Sanger::CGP::Ascat::Implement
FAILED--Further testing stopped: Unable to 'use' module Sanger::CGP::Ascat::Implement
make: *** [test_dynamic] Error 255

Can you help please?

keiranmraine commented 3 years ago

As per the readme, you need to install all dependencies first: https://github.com/cancerit/ascatNgs#dependenciesinstall

If you are able, I highly recommend you use either the docker container or a singularity image (built from the docker image):

docker pull docker pull quay.io/wtsicgp/ascatngs:4.5.0
# or
singularity pull docker://quay.io/wtsicgp/ascatngs:4.5.0