dib-lab/elvers

Issues

• CreateCondaEnvironmentException: Could not create conda environment from /VirSorter2/virsorter/rules/../envs/vs2.yaml

  #163 opened 3 years ago by lifeifeifeifei
  0

• Hanging on setting up Trinity environment

  #162 opened 3 years ago by matthewabirk
  0

• stuck downloading packages when testing

  #160 opened 4 years ago by AntonioBaeza
  5

• Salmon Version Errors

  #158 opened 5 years ago by zdellaert
  0

• lastdb version 992 (dammit)

  #157 opened 5 years ago by zdellaert
  0

• use dammit annotations for DE (collapse "genes" based on annots)

  #131 opened 5 years ago by bluegenes
  5

• NameError: name 'pygments' is not defined

  #156 opened 5 years ago by olar785
  0

• Can't add rules for extra target multiqc

  #155 opened 5 years ago by olar785
  1

• Pandas was not already installed

  #151 opened 5 years ago by prvasquez
  0

• How to run DESeq2 with 3 treatments?

  #152 opened 5 years ago by matthewabirk
  3

• Error running dammit annotation

  #149 opened 5 years ago by prvasquez
  1

• another snakemake based toolkit

  #150 opened 5 years ago by ctb
  1

• deseq2 not running as standalone

  #146 opened 5 years ago by matthewabirk
  0

• --rerun-incomplete flag not working

  #147 opened 5 years ago by matthewabirk
  1

• suggestion, recorded tutorial

  #145 opened 5 years ago by johnsolk
  0

• collapse get_data and get_reference into one rule

  #144 opened 5 years ago by taylorreiter
  2

• Default trimmomatic setting for Phred score cutoff?

  #141 opened 5 years ago by matthewabirk
  1

• Default trimmomatic adapter files with broken path

  #139 opened 5 years ago by matthewabirk
  1

• Pinning version numbers in rule environment.yml files

  #135 opened 5 years ago by charlesreid1
  6

• modular versioning

  #138 opened 5 years ago by bluegenes
  0

• deseq parameter error

  #133 opened 5 years ago by prvasquez
  1

• confusing lack of an error error when gene_trans_map is missing?

  #98 opened 5 years ago by ctb
  0

• untab comments in .yml files

  #104 opened 5 years ago by ctb
  0

• allow downloading of assembly?

  #105 opened 5 years ago by ctb
  1

• do not require samples tsv for assembly-based workflows

  #82 opened 5 years ago by bluegenes
  1

• `assemblyinput` should be `transcriptome` or `reference`

  #106 opened 5 years ago by ctb
  0

• typo in rules/dammit/dammit-wrapper.py

  #125 opened 5 years ago by johnny3420
  1

• simplify config merge and check?

  #124 opened 5 years ago by bluegenes
  0

• can we trap snakemake Python tracebacks and output them to a file?

  #123 opened 5 years ago by ctb
  1

• meta issue for high-level error checking

  #110 opened 6 years ago by ctb
  2

• update conda envs

  #119 opened 5 years ago by bluegenes
  2

• add conda recipe

  #121 opened 5 years ago by bluegenes
  0

• update documentation on samples.tsv

  #111 opened 6 years ago by ctb
  1

• split tximport from deseq2

  #115 opened 5 years ago by bluegenes
  0

• single ended quantify/diffexp doesn't work.

  #109 opened 6 years ago by ctb
  8

• reference ARMOR

  #114 opened 6 years ago by ctb
  1

• binderizing eelpond

  #113 opened 6 years ago by ctb
  1

• provide "getting started" tutorials for assembly/annotation AND for diffexp AND for both

  #112 opened 6 years ago by ctb
  0

• unclear errors when config yaml file is badly formatted

  #107 opened 6 years ago by ctb
  1

• running diffexp on examples/nema.yaml doesn't do anything?

  #103 opened 6 years ago by ctb
  3

• Could not create conda environment from dammit-env.yaml and deseq2-env.yaml

  #89 opened 6 years ago by johnsolk
  7

• how should we generate the gene to transcript map?

  #79 opened 6 years ago by ctb
  6

• update deseq2 version

  #94 opened 6 years ago by bluegenes
  0

• Missing input files for rule deseq2_init_tx2gene

  #90 opened 6 years ago by johnsolk
  3

• dammit install issue from db_extra flag/update docs

  #87 opened 6 years ago by ACharbonneau
  0

• Explanation for my-samples.tsv headers?

  #81 opened 6 years ago by ACharbonneau
  1

• typo and broken links in readme

  #80 opened 6 years ago by mandyfrazier
  2

• read_table future warning

  #83 opened 6 years ago by ACharbonneau
  1

• busco pipebricks issue

  #88 opened 6 years ago by bluegenes
  0

• Trinity failing, empty log file

  #85 opened 6 years ago by mandyfrazier
  2