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rerun ignores platform, when specified via run command #59

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sahilseth opened this issue Dec 2, 2015 · 1 comment
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rerun ignores platform, when specified via run command #59

sahilseth opened this issue Dec 2, 2015 · 1 comment
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@sahilseth
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For example if we run:

flowr run x=fastq_bam_bwa fqs1=$fqs1 fqs2=$fqs2 samplename=samp execute=TRUE platform=local rerun_wd=output/runs/fastq_bam_bwa-samp-20151201-18-07-17-aiJFUNjt start_from=aln1

This fails with the error:

-> Flow is being processed. Track it from cmd line using:
flowr status x=/Users/sahilseth/Dropbox2/Dropbox/public/flow-r/fastq_bam/output/runs/fastq_bam_bwa-samp-20151201-18-07-17-aiJFUNjt
OR from R using:
status(x='/Users/sahilseth/Dropbox2/Dropbox/public/flow-r/fastq_bam/output/runs/fastq_bam_bwa-samp-20151201-18-07-17-aiJFUNjt')
  |                                                                      |   0%sh: msub: command not found
Error in system(cmd, intern = TRUE) : error in running command
Error in x$value : $ operator is invalid for atomic vectors
@sahilseth sahilseth added this to the 1.0.0 milestone Dec 2, 2015
@sahilseth sahilseth changed the title rerun ignore platform, when specified VIA run command rerun ignores platform, when specified via run command Dec 2, 2015
@sahilseth sahilseth modified the milestones: 1.0.0, 0.9.10 Apr 14, 2016
@sahilseth
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This has been fixed

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