nellore/rail

Issues

• Stuck at Step 4/24: Align reads and segment them into readlets

  #85 opened 7 years ago by undiagnosed
  4

• Error align local mode_exit type 2

  #88 opened 6 years ago by gianmaz
  0

• release new rail to include update to fastq-dump version

  #87 opened 7 years ago by ChristopherWilks
  0

• Provide rse_gene and rse_exon tables in the rail output

  #83 opened 7 years ago by yevishere
  0

• Supress intermediary bw option

  #82 opened 7 years ago by yevishere
  0

• Allow --tag specification

  #81 opened 7 years ago by BenLangmead
  1

• Spurious error about existing bucket

  #75 opened 7 years ago by BenLangmead
  0

• Resolve error on NoSuchLifecycleConfiguration

  #59 opened 7 years ago by BenLangmead
  2

• Python subprocess OSError

  #69 opened 7 years ago by symbiologist
  0

• Bowtie Indices relative paths not supported

  #68 opened 7 years ago by imtherainman
  1

• Calculate AUC for each sample

  #47 opened 7 years ago by lcolladotor
  2

• Optionally skip "Copying Rail-RNA and bootstraps to S3..."

  #64 opened 7 years ago by BenLangmead
  1

• make it obvious which log file has the error when dooplicity fails on a step in local/parallel modes

  #43 opened 8 years ago by nellore
  1

• address make_temp_dir(common) in emr_simulator

  #49 opened 8 years ago by nellore
  0

• Normalize mean consistent with `recount`

  #48 opened 8 years ago by lcolladotor
  0

• error when specifying -r parameter...

  #46 opened 8 years ago by nickschurch
  5

• add precision/recall tests to line.py

  #45 opened 8 years ago by nellore
  0

• output_dir and mover not defined previously in stream_and_upload

  #44 opened 8 years ago by BenLangmead
  1

• Try harder to find pypy version number in pypy --version output

  #42 opened 8 years ago by BenLangmead
  1

• Unresolved ids in align_reads_delegate.py

  #41 opened 8 years ago by BenLangmead
  0

• make_it_rail requires verve@verve.webfactional.com's password

  #40 opened 8 years ago by BenLangmead
  2

• missing isofrags.tar.gz in parallel mode (v0.2.3b)

  #33 opened 8 years ago by jfear
  2

• Making this work with bioconda?

  #34 opened 8 years ago by DCGenomics
  1

• Unresolved reference in preprocess.py

  #35 opened 8 years ago by BenLangmead
  1

• Too few arguments for format string in preprocess.py

  #36 opened 8 years ago by BenLangmead
  1

• partition pipeline so high-utilization steps can use different instance type from low-utilization steps

  #32 opened 9 years ago by BenLangmead
  0

• improve load balance by indexing LZOs before first step

  #27 opened 9 years ago by nellore
  2

• add counters for debugging

  #9 opened 10 years ago by nellore
  1

• ideas for major feature additions in 0.3.0

  #28 opened 9 years ago by nellore
  0

• Local mode, manifest file (paired-end samples) throws errors

  #30 opened 9 years ago by lcolladotor
  1

• --no-dependencies install option errors out

  #29 opened 9 years ago by ChristopherWilks
  1

• explore rounding quality strings to a few (4-5) bins to further reduce redundancy

  #14 opened 9 years ago by nellore
  1

• add backup dependency urls to installer

  #22 opened 9 years ago by nellore
  1

• samtools stat in bam step?

  #23 opened 9 years ago by nellore
  1

• revisit how XS:i is done

  #25 opened 9 years ago by nellore
  1

• do something about 255'd mapqs

  #24 opened 9 years ago by nellore
  0

• optimize partitioner before realign_reads

  #19 opened 9 years ago by nellore
  1

• add job flow resume feature

  #20 opened 9 years ago by nellore
  1

• add uninstall

  #18 opened 10 years ago by nellore
  0

• use ncbi/ngs library to slurp in SRA reads

  #17 opened 10 years ago by BenLangmead
  1

• add task retries to emr_simulator

  #10 opened 10 years ago by nellore
  2

• explore using lz4 rather than gzip in parallel/local modes

  #16 opened 10 years ago by nellore
  0

• use latest gnu coreutils sort to increase speed in local/parallel mode; bundle with rail

  #15 opened 10 years ago by nellore
  0

• force "uploads" of all output (bams, bigwigs, preprocessed fastqs, etc.) in parallel mode to minimize network traffic

  #12 opened 10 years ago by nellore
  1

• upload index to slaves in parallel mode (optionally using torrent-based herd, if it's installed, to make this faster?) and use atexit to ensure that when engines receive SIGTERM, index in scratch dirs is deleted

  #8 opened 10 years ago by nellore
  1

• fix parallel mode by uploading rail to slaves so imports work when performing checks

  #7 opened 10 years ago by nellore
  1

• add dummy lines so all multiple output paths exist; not important now because data's big

  #6 opened 10 years ago by nellore
  1

• dynamically assign tasks in parallel-mode emr_simulator

  #13 opened 10 years ago by nellore
  1

• permit the following modes: annotation-only, annotation+data

  #4 opened 10 years ago by nellore
  1

• address consistency of mapqs; check unique.h of bt2 to figure this out

  #5 opened 10 years ago by nellore
  0