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HenrikBengtsson / CBI-software

A Scientific Software Stack for HPC (CentOS oriented)
https://wynton.ucsf.edu/hpc/software/software-repositories.html
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sratoolkit: Fails on Wynton #7

Closed HenrikBengtsson closed 4 years ago

HenrikBengtsson commented 4 years ago

Issue

$ module load CBI sratoolkit

 2020-04-01 18:57:05 ⌚  qb3-dev3 in ~/repositories/UCSF-CBC/CBI-software/CBI/sratoolkit
± → fastq-dump --help
Can't locate JSON/PP.pm in @INC (@INC contains: /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 /wynton/home/cbi/shared/software/CBI/sratoolkit-2.10.0/bin/fastq-dump line 12.
BEGIN failed--compilation aborted at /wynton/home/cbi/shared/software/CBI/sratoolkit-2.10.0/bin/fastq-dump line 12.

Troubleshooting

The installation is in https://github.com/HenrikBengtsson/CBI-software/blob/develop/CBI/sratoolkit/

HenrikBengtsson commented 4 years ago

Installing 2.10.5 fixed the problem. It looks the above bug was specific to 2.10.0, cf. https://github.com/ncbi/sra-tools/issues/219