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PapenfussLab / gridss

GRIDSS: the Genomic Rearrangement IDentification Software Suite
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conda gridss missing gridsstools from path? #541

Closed MjelleLab closed 2 years ago

MjelleLab commented 2 years ago

I have tried install grids both using conda and git clone https://github.com/PapenfussLab/gridss.git, however, grids stools file to be installed it seems. Any suggestions?

./virusbreakend --kraken2db virusbreakenddb_20210401 --output sample.virusbreakend.vcf --reference ref_genome_37.gz --jar gridss-2.12.2-gridss-jar-with-dependencies.jar CPCT02020337T_dedup.realigned.cram.unmapped.bam Fri Nov 5 13:19:42 MET 2021: Using working directory "." Fri Nov 5 13:19:42 MET 2021: Full log file is: ./sample.virusbreakend.vcf.virusbreakend.working/virusbreakend.20211105_131942.mh-ikom01.29865.log Fri Nov 5 13:19:42 MET 2021: Found /usr/bin/time Fri Nov 5 13:19:42 MET 2021: Using GRIDSS jar gridss-2.12.2-gridss-jar-with-dependencies.jar Fri Nov 5 13:19:42 MET 2021: Using reference genome "ref_genome_37.gz" Fri Nov 5 13:19:42 MET 2021: Using output VCF sample.virusbreakend.vcf Fri Nov 5 13:19:42 MET 2021: Using 8 worker threads. Fri Nov 5 13:19:42 MET 2021: Using input file CPCT02020337T_dedup.realigned.cram.unmapped.bam Fri Nov 5 13:19:42 MET 2021: Found /mnt/scratch/home/local/robinm/software/VIRUSBreakend/kraken2/kraken2 Fri Nov 5 13:19:42 MET 2021: Found /home/local/robinm/anaconda3/bin/gridss Fri Nov 5 13:19:42 MET 2021: Found /mnt/scratch/home/local/robinm/software/VIRUSBreakend/gridss/scripts/gridss_annotate_vcf_kraken2 Fri Nov 5 13:19:42 MET 2021: Found /mnt/scratch/home/local/robinm/software/VIRUSBreakend/gridss/scripts/gridss_annotate_vcf_repeatmasker Fri Nov 5 13:19:42 MET 2021: Found /home/local/robinm/anaconda3/bin/samtools Fri Nov 5 13:19:42 MET 2021: Found /home/local/robinm/anaconda3/bin/bcftools Fri Nov 5 13:19:43 MET 2021: Found /home/local/robinm/anaconda3/bin/java Fri Nov 5 13:19:43 MET 2021: Found /home/local/robinm/anaconda3/bin/bwa Fri Nov 5 13:19:43 MET 2021: Found /home/local/robinm/anaconda3/bin/Rscript Fri Nov 5 13:19:43 MET 2021: Found /home/local/robinm/anaconda3/bin/RepeatMasker Fri Nov 5 13:19:43 MET 2021: MISSING gridsstools. Fri Nov 5 13:19:43 MET 2021: Exit status 0 for exit $EX_CONFIG

See log file ./sample.virusbreakend.vcf.virusbreakend.working/virusbreakend.20211105_131942.mh-ikom01.29865.log for underlying error

MjelleLab commented 2 years ago

Solved by installing manually

d-cameron commented 2 years ago

Which conda gridss version was failing? gridsstools should be included as part of the conda install

d-cameron commented 2 years ago

Should be good in the new conda package