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cancerit / BRASS

Breakpoints via assembly - Identifies breaks and attempts to assemble rearrangements in whole genome sequencing data.
GNU Affero General Public License v3.0
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conda installation issues #82

Closed alongalor closed 5 years ago

alongalor commented 5 years ago

I installed brass via conda in a new conda environment:

conda create --name brass python=2.7
conda activate brass
conda install -c bioconda brass

The installation finished successfully (full output included below). I opened a new terminal window and typed:

conda activate brass

I cd'ed to /home/my_user_name/anaconda3/envs/brass/ and tried to activate some of the brass-related packages without success. E.g.:

brass.pl
Can't locate PCAP/Cli.pm in @INC (you may need to install the PCAP::Cli module) (@INC contains: /home/ag457/anaconda3/envs/brass/bin/../lib/perl5/x86_64-linux-thread-multi /home/ag457/anaconda3/envs/brass/bin/../lib/perl5 /n/data1/hms/dbmi/park/alon/software/vcftools_0.1.13/perl /home/ag457/anaconda3/envs/brass/lib/site_perl/5.26.2/x86_64-linux-thread-multi /home/ag457/anaconda3/envs/brass/lib/site_perl/5.26.2 /home/ag457/anaconda3/envs/brass/lib/5.26.2/x86_64-linux-thread-multi /home/ag457/anaconda3/envs/brass/lib/5.26.2 .) at /home/ag457/anaconda3/envs/brass/bin/brass.pl line 50.
BEGIN failed--compilation aborted at /home/ag457/anaconda3/envs/brass/bin/brass.pl line 50.

I realize I could go ahead and install all the packages as prompted, but as far as I understand the point of conda is to avoid this type of thing! Any help would be greatly appreciated!

Thanks a lot,

Alon terminal_output.txt

keiranmraine commented 5 years ago

We do not support the conda packaging of this tool, I'd suggest you need to have the conda package for PCAP-core also.