BD2KGenomics/cgl-docker-lib

Issues

• Update gdc-client to 1.4

  #290 opened 6 years ago by jvivian
  0

• Human_Homo_sapiens/hg38_GENCODE_v23_basic.bed.gz does not exist for BamQC

  #286 opened 6 years ago by akmorrow13
  2

• BamQC Makefile fails with unknown -f flag

  #287 opened 6 years ago by akmorrow13
  1

• Add BamQC

  #283 opened 6 years ago by jvivian
  0

• Update CutAdapt to 1.18

  #281 opened 6 years ago by jvivian
  0

• `gencode_hugo_mapping` fails on non-human genes

  #279 opened 6 years ago by jvivian
  0

• update samtools to 1.8

  #277 opened 7 years ago by tpesout
  0

• Flappy Jenkins test

  #276 opened 7 years ago by jvivian
  0

• Add GDC-Client

  #274 opened 7 years ago by jvivian
  0

• Open Source License

  #272 opened 7 years ago by Georgehe4
  0

• Update docker commands for Mango

  #271 opened 7 years ago by Georgehe4
  0

• Mango not available on https://quay.io/organization/ucsc_cgl

  #270 opened 7 years ago by akmorrow13
  4

• Fix bug in Hera's index build

  #267 opened 7 years ago by jvivian
  0

• Update DECA container to 0.1.0 release

  #265 opened 7 years ago by fnothaft
  0

• Bump to Apache Hadoop 2.7

  #256 opened 7 years ago by fnothaft
  0

• need rtg-tools container

  #263 opened 7 years ago by tpesout
  0

• Upgrade SNAP to 1.0dev.100

  #261 opened 7 years ago by fnothaft
  0

• Add retry to `docker push` in jenkins

  #260 opened 7 years ago by jvivian
  1

• Add python to Hera

  #258 opened 7 years ago by jvivian
  0

• Add Hera

  #252 opened 7 years ago by jvivian
  0

• Make CMAKE base image

  #254 opened 7 years ago by jvivian
  0

• Add DECA

  #250 opened 7 years ago by fnothaft
  0

• Misc upgrades for ADAM recompute

  #201 opened 7 years ago by fnothaft
  0

• latest does not exist

  #247 opened 7 years ago by antonkulaga
  1

• Add pizzly

  #248 opened 7 years ago by jvivian
  0

• Fix jenkins.py so that failing builds fail the build

  #211 opened 7 years ago by fnothaft
  0

• Update STAR to 2.5.3a

  #245 opened 8 years ago by jvivian
  0

• Refactor `spark-and-maven` on `apache-spark-common`

  #244 opened 8 years ago by fnothaft
  0

• Factor apt-get commands out

  #243 opened 8 years ago by fnothaft
  2

• command for dockerized rna-seq 3.2.1 - multiple samples using fastq for input

  #242 opened 8 years ago by hbeale
  0

• Make DESeq2 Container

  #240 opened 8 years ago by jvivian
  1

• Correct kallisto makefile so it pushes to quay

  #238 opened 8 years ago by jvivian
  0

• Update kallisto to 0.43.1

  #236 opened 8 years ago by jvivian
  0

• need upgraded bwakit image

  #232 opened 8 years ago by tpesout
  0

• picardtools needs to specify JAVA_OPTS when invoked

  #233 opened 8 years ago by tpesout
  0

• upgrade version of gatk

  #229 opened 8 years ago by tpesout
  0

• upgrade version of picardtools

  #228 opened 8 years ago by tpesout
  0

• Add an extension of the kallisto image for single cell work

  #226 opened 8 years ago by tpesout
  0

• Add gencode_hugo_mapping

  #219 opened 8 years ago by jvivian
  0

• need new kallisto version for rnaseq single cell

  #224 opened 8 years ago by tpesout
  0

• gencode_hugo_mapping docs

  #217 opened 8 years ago by cchng
  4

• Add rsem_postprocess

  #218 opened 8 years ago by jvivian
  0

• Update fastq-dump

  #220 opened 8 years ago by jvivian
  0

• Zero length bam files

  #215 opened 8 years ago by rcurrie
  10

• Update vg image to version v1.4.0-1744-gea8edfd

  #207 opened 8 years ago by cmarkello
  8

• Remove patch that added -M option to bwakit

  #205 opened 8 years ago by jpfeil
  0

• Add -M option to run-bwamem

  #203 opened 8 years ago by jpfeil
  0

• Spark containers don't seem to get pushed to quay

  #199 opened 8 years ago by fnothaft
  2

• Invoking tabix and bgzip

  #198 opened 8 years ago by adamnovak
  0

• Cross build spark versions

  #196 opened 8 years ago by fnothaft
  0