Rail-RNA v0.2.4b

@nellore nellore released this Oct 12, 2016 · 194 commits to master since this release

Feature addition:

  • Rail-RNA now combines FASTQs from different lanes derived from a single TAR.

Rail-RNA v0.2.4a

@nellore nellore released this Oct 11, 2016 · 204 commits to master since this release

Bug fix:

  • Rail-RNA no longer exits with an error if the output bucket is not owned by the user.
  • Access to a bucket's lifecycle is no longer required to execute a job flow on EMR.

Rail-RNA v0.2.4

@nellore nellore released this Oct 7, 2016 · 209 commits to master since this release

Feature addition:

  • Rail-RNA now automatically unpacks sample FASTQs in TAR archives to accommodate TCGA raw data.

Bug fixes:

  • Rail-RNA no longer crashes for paired-end samples if it encounters a non-ATCG character an input sequence. All non-ATCGs are interpreted as Ns.
  • Some issues with writing to user-specified scratch directories have been resolved.

Rail-RNA v0.2.3b

@nellore nellore released this Feb 25, 2016 · 319 commits to master since this release

Bug fix:

  • On EMR, if connections to S3 had a high fail rate, the job flow would complete, but some output files would sometimes be missing. Now tasks are failed if this occurs.

Rail-RNA v0.2.3a

@nellore nellore released this Feb 22, 2016 · 320 commits to master since this release

Performance improvement:

  • Does not use LZO index in some steps on Elastic MapReduce because opening all the LZO indexes does not scale, can take a while, and thus can slow down an alignment job flow.

Rail-RNA v0.2.3

@nellore nellore released this Feb 21, 2016 · 321 commits to master since this release

Performance improvements:

  • Intermediate LZOs are now always indexed on Elastic MapReduce to improve load balance when a step is ingesting data from S3.
  • Hanging tasks during the first alignment step on Elastic MapReduce now use more processing cores so they finish faster.

Dependency updates:

  • Rail-RNA now runs on Bowtie v1.1.2 and Bowtie2 v2.2.7.

Rail-RNA v0.2.2d

@nellore nellore released this Feb 16, 2016 · 326 commits to master since this release

Bug fixes:

  • Reattempting preprocess tasks works again.
  • The task timeout on Elastic MapReduce has been increased from 10 minutes to 30 minutes so not every task attempt that's taking a while to reduce when writing bigWigs for large samples will fail.
  • Speculative execution on Elastic MapReduce is now by default. This eliminates the very unlikely scenario where a killed task attempt's incomplete output is preferred to that of a succeeded task attempt.

Rail-RNA v0.2.2c

@nellore nellore released this Feb 15, 2016 · 331 commits to master since this release

Bug fix:

  • Rail-RNA now correctly identifies reads with long poly-A tails and leaves them unmapped; this can greatly speed up the first alignment step when running on many samples. Previously, reads with long poly-A tails were not being recognized.

Rail-RNA v0.2.2b

@nellore nellore released this Feb 14, 2016 · 336 commits to master since this release

Bug fix:

  • Rail-RNA now indexes LZO'd preprocessed FASTQs so load imbalance doesn't break a job flow on Elastic MapReduce during the first alignment step.

Rail-RNA v0.2.2a

@nellore nellore released this Feb 11, 2016 · 341 commits to master since this release

Feature addition:

  • A new command line option --ignore-missing-sra-samples does not fail preprocess job flows if an SRA run accession number is not found by fastq-dump; instead, the sample is treated as missing.