dib-lab/khmer-protocols

Issues

• khmer-protocols/mrnaseq/3-big-assembly.txt trinity installation

  #163 opened 8 years ago by taylorreiter
  2

• install applications using debian packages when available

  #48 opened 11 years ago by mr-c
  13

• [Acceptance] Installing khmer fails, setuptools doesn't exist, need to backport fix from Master

  #161 opened 10 years ago by bocajnotnef
  1

• 3-big-assembly.txt contains a newline that breaks scan (acceptance)

  #159 opened 10 years ago by bocajnotnef
  1

• Acceptance branch fails when calling Trinity; deprecated option

  #157 opened 10 years ago by bocajnotnef
  1

• 1-quality.txt breaks on clean systems

  #154 opened 10 years ago by bocajnotnef
  3

• Bring mrnaseq instructions up to date (under mrnaseq/)

  #151 opened 10 years ago by ctb
  3

• Switch layout of kp site over to simpler single-pane layout?

  #150 opened 10 years ago by ctb
  0

• Bring amazon instructions up to date

  #149 opened 10 years ago by ctb
  0

• Merge indicator needs removal

  #140 opened 10 years ago by mr-c
  1

• acceptance test failure in eel-pond/plot-expression.py

  #129 opened 10 years ago by mr-c
  5

• Missing directory while installing samtools (eelpond)

  #137 opened 10 years ago by GraceGanzel
  0

• AWS docs specify m1.large/chapter 2 specifies m1.xlarge

  #135 opened 10 years ago by GraceGanzel
  0

• Normalize by median pct

  #133 opened 10 years ago by tshori
  2

• Warning during normalize-by-median

  #131 opened 10 years ago by danbacastro
  5

• idba doesn't necessary produce scaffolds

  #127 opened 10 years ago by SherineAwad
  2

• Try out CONCOCT on metagenomes

  #126 opened 10 years ago by ctb
  0

• Add taxator-tk taxonomy to metagenome protocol

  #125 opened 10 years ago by ctb
  0

• Assemblies crash because of memory issues.

  #124 opened 10 years ago by SherineAwad
  0

• Develop checklist for protocols code review

  #118 opened 11 years ago by ctb
  8

• Develop checklist for protocols release

  #122 opened 11 years ago by ctb
  0

• Remove Run.txt and Readme.txt

  #109 opened 11 years ago by ctb
  1

• a link to khmer-protocols on khmer doc?

  #97 opened 11 years ago by qingpeng
  0

• testasm?

  #94 opened 11 years ago by SherineAwad
  0

• calc-best-assembly.py

  #87 opened 11 years ago by SherineAwad
  0

• Zlib dependency problem?

  #85 opened 11 years ago by znruss
  2

• -Q 33 may not be necessary in metagenomics quality trimming

  #86 opened 11 years ago by qingpeng
  0

• "Getting started with Amazon EC2" page lacks discussion about volume

  #79 opened 11 years ago by qingpeng
  0

• Add my graffle diagrams to docs

  #39 opened 11 years ago by ctb
  0

• Can we automatically figure out what adapters were used?

  #76 opened 11 years ago by ctb
  0

• make sequence annotation script look only at IDs, which are stable

  #40 opened 11 years ago by ctb
  0

• Add directions on tempdir for formatdb

  #75 opened 11 years ago by LSheneman
  0

• Update AWS screenshoots

  #72 opened 11 years ago by LSheneman
  0

• Document use of AWS snapshots

  #73 opened 11 years ago by LSheneman
  1

• Update protocols to use khmer 0.8

  #54 opened 11 years ago by ctb
  0

• Update khmer install instructions with pip

  #56 opened 11 years ago by ctb
  5

• Change QC protocol to indicate intermediate step appropriately

  #46 opened 11 years ago by ctb
  0

• Extract CD-HIT instructions from Likit or Eli

  #36 opened 11 years ago by ctb
  0

• Extract CEGMA instructions for @cswelcher or eli

  #37 opened 11 years ago by ctb
  1

• switch to using comma-delimited lists of files for input to Trinity

  #41 opened 11 years ago by ctb
  0

• Look into LAST instead of BLAST for annotation

  #45 opened 11 years ago by ctb
  0

• Condense software installs into one page

  #47 opened 11 years ago by LSheneman
  9

• Data sets to harvest for open marine transcriptome

  #50 opened 11 years ago by ctb
  2

• Add references to two test data sets

  #53 opened 11 years ago by ctb
  0

• Revise documentation to aid in learning

  #60 opened 11 years ago by LSheneman
  1

• Fix metadata so latest eel-pond shows up on google

  #71 opened 11 years ago by LSheneman
  2

• switch to pip based khmer installation

  #44 opened 11 years ago by mr-c
  4

• Update the AMI

  #38 opened 11 years ago by ctb
  6

• Jinja2 needed for blast server

  #59 opened 11 years ago by LSheneman
  0

• bigcount should be set to false by default on normalize-by-median.

  #43 opened 11 years ago by ctb
  1