jcvi-cloud/cloudvigor

Build Scripts for creating a CloudVIGOR distribution image(s)

cloudvigor's Issues

Validation tests failing on Eucalyptus

1. I had to comment out the first test because there is a path in the
   related configuration file which is JCVI specific, so I'll have to work
   with Jeff on that. This causes the missing files in the diff.
2. For some reason, clustalw does not appear to be executing. This is causing the output to be different, although it may not be the only issue.

Fabric output for validate_tests task:

[172.17.31.103] run: diff -qr /usr/local/scratch/vigor-scratch/validate-test-data /usr/local/scratch/vigor-scratch/test-output
[172.17.31.103] out: Only in /usr/local/scratch/vigor-scratch/validate-test-data: 34615.aln
[172.17.31.103] out: Only in /usr/local/scratch/vigor-scratch/validate-test-data: 34615.cds
[172.17.31.103] out: Only in /usr/local/scratch/vigor-scratch/validate-test-data: 34615.fs
[172.17.31.103] out: Only in /usr/local/scratch/vigor-scratch/validate-test-data: 34615.pep
[172.17.31.103] out: Only in /usr/local/scratch/vigor-scratch/validate-test-data: 34615.stats
[172.17.31.103] out: Only in /usr/local/scratch/vigor-scratch/validate-test-data: 34615.tbl
[172.17.31.103] out: Files /usr/local/scratch/vigor-scratch/validate-test-data/FluB.aln and /usr/local/scratch/vigor-scratch/test-output/FluB.aln differ
[172.17.31.103] out: Files /usr/local/scratch/vigor-scratch/validate-test-data/FluB.cds and /usr/local/scratch/vigor-scratch/test-output/FluB.cds differ
[172.17.31.103] out: Files /usr/local/scratch/vigor-scratch/validate-test-data/FluB.pep and /usr/local/scratch/vigor-scratch/test-output/FluB.pep differ
[172.17.31.103] out: Files /usr/local/scratch/vigor-scratch/validate-test-data/FluB.stats and /usr/local/scratch/vigor-scratch/test-output/FluB.stats differ
[172.17.31.103] out: Files /usr/local/scratch/vigor-scratch/validate-test-data/FluB.tbl and /usr/local/scratch/vigor-scratch/test-output/FluB.tbl differ
[172.17.31.103] out: Files /usr/local/scratch/vigor-scratch/validate-test-data/GCV_32265.aln and /usr/local/scratch/vigor-scratch/test-output/GCV_32265.aln differ
[172.17.31.103] out: Files /usr/local/scratch/vigor-scratch/validate-test-data/GCV_32265.cds and /usr/local/scratch/vigor-scratch/test-output/GCV_32265.cds differ
[172.17.31.103] out: Files /usr/local/scratch/vigor-scratch/validate-test-data/GCV_32265.pep and /usr/local/scratch/vigor-scratch/test-output/GCV_32265.pep differ
[172.17.31.103] out: Files /usr/local/scratch/vigor-scratch/validate-test-data/GCV_32265.stats and /usr/local/scratch/vigor-scratch/test-output/GCV_32265.stats differ
[172.17.31.103] out: Files /usr/local/scratch/vigor-scratch/validate-test-data/GCV_32265.tbl and /usr/local/scratch/vigor-scratch/test-output/GCV_32265.tbl differ
[172.17.31.103] out: Files /usr/local/scratch/vigor-scratch/validate-test-data/GCV_32276.aln and /usr/local/scratch/vigor-scratch/test-output/GCV_32276.aln differ
[172.17.31.103] out: Files /usr/local/scratch/vigor-scratch/validate-test-data/GCV_32276.cds and /usr/local/scratch/vigor-scratch/test-output/GCV_32276.cds differ
[172.17.31.103] out: Files /usr/local/scratch/vigor-scratch/validate-test-data/GCV_32276.fs and /usr/local/scratch/vigor-scratch/test-output/GCV_32276.fs differ
[172.17.31.103] out: Files /usr/local/scratch/vigor-scratch/validate-test-data/GCV_32276.pep and /usr/local/scratch/vigor-scratch/test-output/GCV_32276.pep differ
[172.17.31.103] out: Files /usr/local/scratch/vigor-scratch/validate-test-data/GCV_32276.stats and /usr/local/scratch/vigor-scratch/test-output/GCV_32276.stats differ
[172.17.31.103] out: Files /usr/local/scratch/vigor-scratch/validate-test-data/GCV_32276.tbl and /usr/local/scratch/vigor-scratch/test-output/GCV_32276.tbl differ
[172.17.31.103] out: Files /usr/local/scratch/vigor-scratch/validate-test-data/GCV_35931.aln and /usr/local/scratch/vigor-scratch/test-output/GCV_35931.aln differ
[172.17.31.103] out: Files /usr/local/scratch/vigor-scratch/validate-test-data/GCV_35931.cds and /usr/local/scratch/vigor-scratch/test-output/GCV_35931.cds differ
[172.17.31.103] out: Files /usr/local/scratch/vigor-scratch/validate-test-data/GCV_35931.pep and /usr/local/scratch/vigor-scratch/test-output/GCV_35931.pep differ
[172.17.31.103] out: Files /usr/local/scratch/vigor-scratch/validate-test-data/GCV_35931.stats and /usr/local/scratch/vigor-scratch/test-output/GCV_35931.stats differ
[172.17.31.103] out: Files /usr/local/scratch/vigor-scratch/validate-test-data/GCV_35931.tbl and /usr/local/scratch/vigor-scratch/test-output/GCV_35931.tbl differ
[172.17.31.103] out: Files /usr/local/scratch/vigor-scratch/validate-test-data/Rhinovirus_genomes.aln and /usr/local/scratch/vigor-scratch/test-output/Rhinovirus_genomes.aln differ
[172.17.31.103] out: Files /usr/local/scratch/vigor-scratch/validate-test-data/Rhinovirus_genomes.cds and /usr/local/scratch/vigor-scratch/test-output/Rhinovirus_genomes.cds differ
[172.17.31.103] out: Files /usr/local/scratch/vigor-scratch/validate-test-data/Rhinovirus_genomes.pep and /usr/local/scratch/vigor-scratch/test-output/Rhinovirus_genomes.pep differ
[172.17.31.103] out: Files /usr/local/scratch/vigor-scratch/validate-test-data/Rhinovirus_genomes.stats and /usr/local/scratch/vigor-scratch/test-output/Rhinovirus_genomes.stats differ
[172.17.31.103] out: Files /usr/local/scratch/vigor-scratch/validate-test-data/Rhinovirus_genomes.tbl and /usr/local/scratch/vigor-scratch/test-output/Rhinovirus_genomes.tbl differ
[172.17.31.103] out: Files /usr/local/scratch/vigor-scratch/validate-test-data/rotaV_10_22_genome.aln and /usr/local/scratch/vigor-scratch/test-output/rotaV_10_22_genome.aln differ
[172.17.31.103] out: Files /usr/local/scratch/vigor-scratch/validate-test-data/rotaV_10_22_genome.cds and /usr/local/scratch/vigor-scratch/test-output/rotaV_10_22_genome.cds differ
[172.17.31.103] out: Files /usr/local/scratch/vigor-scratch/validate-test-data/rotaV_10_22_genome.pep and /usr/local/scratch/vigor-scratch/test-output/rotaV_10_22_genome.pep differ
[172.17.31.103] out: Files /usr/local/scratch/vigor-scratch/validate-test-data/rotaV_10_22_genome.stats and /usr/local/scratch/vigor-scratch/test-output/rotaV_10_22_genome.stats differ
[172.17.31.103] out: Files /usr/local/scratch/vigor-scratch/validate-test-data/rotaV_10_22_genome.tbl and /usr/local/scratch/vigor-scratch/test-output/rotaV_10_22_genome.tbl differ
[172.17.31.103] out: Only in /usr/local/scratch/vigor-scratch/validate-test-data: vigor-test-output.tgz
[172.17.31.103] out: Files /usr/local/scratch/vigor-scratch/validate-test-data/YFV_genome.aln and /usr/local/scratch/vigor-scratch/test-output/YFV_genome.aln differ
[172.17.31.103] out: Files /usr/local/scratch/vigor-scratch/validate-test-data/YFV_genome.cds and /usr/local/scratch/vigor-scratch/test-output/YFV_genome.cds differ
[172.17.31.103] out: Files /usr/local/scratch/vigor-scratch/validate-test-data/YFV_genome.pep and /usr/local/scratch/vigor-scratch/test-output/YFV_genome.pep differ
[172.17.31.103] out: Files /usr/local/scratch/vigor-scratch/validate-test-data/YFV_genome.stats and /usr/local/scratch/vigor-scratch/test-output/YFV_genome.stats differ
[172.17.31.103] out: Files /usr/local/scratch/vigor-scratch/validate-test-data/YFV_genome.tbl and /usr/local/scratch/vigor-scratch/test-output/YFV_genome.tbl differ
[172.17.31.103] out: 

Fatal error: run() encountered an error (return code 1) while executing 'diff -qr /usr/local/scratch/vigor-scratch/validate-test-data /usr/local/scratch/vigor-scratch/test-output'

Aborting.

clustalw package does not seem to be correct

1. The clustalw package does not execute. Either the clustalw package I retrieved is corrupted or I haven't installed it correctly.