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The Genome Modeling System installer
https://github.com/genome/gms/wiki
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"ClinSeq:Use gmt copy-number cn-view" crashes - missing annotation files. #87

Closed gatoravi closed 10 years ago

gatoravi commented 10 years ago

2014-01-23 23:46:03-0600 GGM: ERROR: One or more of the following annotation files is missing: 2014-01-23 23:46:03-0600 GGM: gtf_file = /opt/gms/GMS1/fs/gc12001/info/model_data/2772828715/build124434505/annotation_data/rna_annotation/106942997-all_sequences.gtf 2014-01-23 23:46:03-0600 GGM: ideogram_file = /gscmnt/sata132/techd/mgriffit/reference_annotations/hg19/ideogram/ChrBandIdeogram.tsv 2014-01-23 23:46:03-0600 GGM: ERROR: error processing inputs! 2014-01-23 23:46:03-0600 GGM: File (/opt/gms/AUIS907/fs/AUIS907/info/model_data/9139d1d4d0d6481db98962e328c724ee/buildcd3ac7397df94fb487cc7ba799d1ce2b/TST1/cnv/cnview/CNView_All/CNView_All_genes.tsv) does not exist at /opt/gms/AUIS907/sw/genome/lib/perl/Genome/Model/ClinSeq/Command/RunCnView.pm line 117

gatoravi commented 10 years ago

This path is hard-coded in GMT::CopyNumber::CnView

Check annotation build and clinseq annotations dir

my $clinseq_annotations_dir="/gscmnt/sata132/techd/mgriffit/reference_annotations/"; $ideogram_file ||= $clinseq_annotations_dir . "hg19/ideogram/ChrBandIdeogram.tsv";

obigriffith commented 10 years ago

This has been resolved by looking up cancer_annotation_db automatically and removing hard-coded paths. Missing ideogram files were also copied over into all branches of the cancer_annotation repos. See commits here: https://github.com/genome/gms-core/commit/c7ded243f8c4637f671d901e66748629c081259a and https://github.com/genome/gms-core/commit/194d48cc6bdd7b44124a4a4f662766282c2c7657