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Commits on Feb 27, 2017

• Merge pull request #2 from UCSC-Treehouse/develop

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• Explicitly say if a file exists

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Commits on Feb 16, 2017

• Fix print for python3, don't force running bamqc

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Commits on Feb 6, 2017

• Run fusion inspector as part of fusion

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Commits on Jan 15, 2017

• Remove requirement that sample file name and id match as the core will not follow this, time to sort out the issue with RSEM having it in the top of the file, add check utility to verify all the fi…

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Commits on Jan 4, 2017

• Upgrade to fusion 0.0.2

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Commits on Dec 23, 2016

• Run docker ps as well as top for the top command

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Commits on Dec 20, 2016

• Handle r1 vs. R1, fix bug calling fusion pipeline

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Commits on Dec 15, 2016

• Merge pull request #1 from UCSC-Treehouse/develop

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Commits on Dec 12, 2016

• Open tsv file in universal line ending mode so files exported from Excel can be read

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Commits on Dec 9, 2016

• Backhaul the full bam rnaseq generates if not pruning, need to debug instances where its zero length before qc

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• Print error messages to console as well as errors file

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• Allow fab to run from a different directory (git call was failing), error if input files missing, don't create destination folder until we've verified we have files

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Commits on Dec 7, 2016

• Add prune option to process controlling whether to throw away various bams, add assertion that filename and submitter id match due to rnaseq rsem output embedding filename in output file which is u…

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Commits on Dec 5, 2016

• Add check that filename and sampleid match so MedBook importing RSEM keeps consistent

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• Promote reset_machine to external command, add few status prints

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Commits on Dec 2, 2016

• Add top to get top 5 processes by cpu usage on each machine, put return after error lines

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• Add fixup for openstack mnt issues to makefile, filter by docker-machines that are Running, log errors preventing running files to errors.txt, fix limit bug due to fabric parameters being strings, …

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Commits on Dec 1, 2016

• Detect whether on azure or openstack and pull reference files from closest blob store

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  dd0d10c

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• Fix bug where was hanging on qc prune because the file was write protected and it was waiting with a prompt for yes. Added -f to force

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• Change default output directory location to current directory

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Commits on Nov 30, 2016

• Revert test manifest to a single file

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• Prune some of the bams from the output of qc to reduce backhaul

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• Fix bug in qc only logic

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• Prune any bams from fusion output before backhauling

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• Switch to pulling references from azure blob store to reduce stress on firewall

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Commits on Nov 29, 2016

• Add git treeshop git commit hash to methods

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• Add limit parameter to process, start testing multi-machine processing

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• Verified working on clean machine, fixed issues with fabric put no honoring cd unless a relative destination is given

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• Added methods output, full run nominally works with backhaul to pstore

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Commits on Nov 28, 2016

• rnaseq and defuse running more or less fully automated

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Commits on Nov 26, 2016

• Try non-SSE defuse

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• defuse working after sorting out calling requirements, fastq cannot be gzipped etc...start of poor mans round robin parallel allocation and processing

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• Defuse sort of working along with copying of files, still messy and no consistency between azure and openstack

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Commits on Nov 24, 2016

• Start switching to timestamp for machine names so make and fab can be used interchangeably, start of azure support

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