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Use BioContainers Docker images with version tags by default.
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@heuermh
heuermh committed Jan 24, 2018
1 parent a1eab2f commit 5d6342b
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Showing 8 changed files with 16 additions and 16 deletions.
4 changes: 2 additions & 2 deletions cli/src/main/scala/org/bdgenomics/cannoli/cli/Bcftools.scala
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Expand Up @@ -53,8 +53,8 @@ class BcftoolsArgs extends Args4jBase with ADAMSaveAnyArgs with ParquetArgs {
@Args4jOption(required = true, name = "-bcftools_reference", usage = "Reference sequence for analysis. An index file (.fai) will be created if none exists.")
var referencePath: String = null

@Args4jOption(required = false, name = "-docker_image", usage = "Docker image to use. Defaults to heuermh/bcftools.")
var dockerImage: String = "heuermh/bcftools"
@Args4jOption(required = false, name = "-docker_image", usage = "Docker image to use. Defaults to quay.io/biocontainers/bcftools:1.6--0.")
var dockerImage: String = "quay.io/biocontainers/bcftools:1.6--0"

@Args4jOption(required = false, name = "-use_docker", usage = "If true, uses Docker to launch BCFtools. If false, uses the BCFtools executable path.")
var useDocker: Boolean = false
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4 changes: 2 additions & 2 deletions cli/src/main/scala/org/bdgenomics/cannoli/cli/Bedtools.scala
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Expand Up @@ -57,8 +57,8 @@ class BedtoolsArgs extends Args4jBase with ADAMSaveAnyArgs with ParquetArgs {
@Args4jOption(required = false, name = "-bedtools_path", usage = "Path to the Bedtools executable. Defaults to bedtools.")
var bedtoolsPath: String = "bedtools"

@Args4jOption(required = false, name = "-docker_image", usage = "Docker image to use. Defaults to heuermh/bedtools.")
var dockerImage: String = "heuermh/bedtools"
@Args4jOption(required = false, name = "-docker_image", usage = "Docker image to use. Defaults to quay.io/biocontainers/bedtools:2.27.1--0.")
var dockerImage: String = "quay.io/biocontainers/bedtools:2.27.1--0"

@Args4jOption(required = false, name = "-use_docker", usage = "If true, uses Docker to launch Bedtools. If false, uses the Bedtools executable path.")
var useDocker: Boolean = false
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4 changes: 2 additions & 2 deletions cli/src/main/scala/org/bdgenomics/cannoli/cli/Bowtie.scala
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Expand Up @@ -47,8 +47,8 @@ class BowtieArgs extends Args4jBase with ADAMSaveAnyArgs with ParquetArgs {
@Args4jOption(required = false, name = "-bowtie_path", usage = "Path to the Bowtie executable. Defaults to bowtie.")
var bowtiePath: String = "bowtie"

@Args4jOption(required = false, name = "-docker_image", usage = "Docker image to use. Defaults to quay.io/biocontainers/bowtie.")
var dockerImage: String = "quay.io/biocontainers/bowtie"
@Args4jOption(required = false, name = "-docker_image", usage = "Docker image to use. Defaults to quay.io/biocontainers/bowtie:1.2.1.1--py27pl5.22.0_0.")
var dockerImage: String = "quay.io/biocontainers/bowtie:1.2.1.1--py27pl5.22.0_0"

@Args4jOption(required = false, name = "-use_docker", usage = "If true, uses Docker to launch Bowtie. If false, uses the Bowtie executable path.")
var useDocker: Boolean = false
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4 changes: 2 additions & 2 deletions cli/src/main/scala/org/bdgenomics/cannoli/cli/Bowtie2.scala
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Expand Up @@ -47,8 +47,8 @@ class Bowtie2Args extends Args4jBase with ADAMSaveAnyArgs with ParquetArgs {
@Args4jOption(required = false, name = "-bowtie2_path", usage = "Path to the Bowtie 2 executable. Defaults to bowtie2.")
var bowtie2Path: String = "bowtie2"

@Args4jOption(required = false, name = "-docker_image", usage = "Docker image to use. Defaults to quay.io/biocontainers/bowtie2.")
var dockerImage: String = "quay.io/biocontainers/bowtie2"
@Args4jOption(required = false, name = "-docker_image", usage = "Docker image to use. Defaults to quay.io/biocontainers/bowtie2:2.3.4--py27pl5.22.0_0.")
var dockerImage: String = "quay.io/biocontainers/bowtie2:2.3.4--py27pl5.22.0_0"

@Args4jOption(required = false, name = "-use_docker", usage = "If true, uses Docker to launch Bowtie 2. If false, uses the Bowtie 2 executable path.")
var useDocker: Boolean = false
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4 changes: 2 additions & 2 deletions cli/src/main/scala/org/bdgenomics/cannoli/cli/Bwa.scala
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Expand Up @@ -73,8 +73,8 @@ class BwaArgs extends Args4jBase with ADAMSaveAnyArgs with ParquetArgs {
@Args4jOption(required = false, name = "-sequence_dictionary", usage = "Path to the sequence dictionary.")
var sequenceDictionary: String = _

@Args4jOption(required = false, name = "-docker_image", usage = "Docker image to use. Defaults to quay.io/ucsc_cgl/bwa:0.7.12--256539928ea162949d8a65ca5c79a72ef557ce7c.")
var dockerImage: String = "quay.io/ucsc_cgl/bwa:0.7.12--256539928ea162949d8a65ca5c79a72ef557ce7c"
@Args4jOption(required = false, name = "-docker_image", usage = "Docker image to use. Defaults to quay.io/biocontainers/bwa:0.7.17--pl5.22.0_0.")
var dockerImage: String = "quay.io/biocontainers/bwa:0.7.17--pl5.22.0_0"

@Args4jOption(required = false, name = "-use_docker", usage = "If true, uses Docker to launch BWA. If false, uses the BWA executable path.")
var useDocker: Boolean = false
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4 changes: 2 additions & 2 deletions cli/src/main/scala/org/bdgenomics/cannoli/cli/Freebayes.scala
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Expand Up @@ -50,8 +50,8 @@ class FreebayesArgs extends Args4jBase with ADAMSaveAnyArgs with ParquetArgs {
@Args4jOption(required = true, name = "-freebayes_reference", usage = "Reference sequence for analysis. An index file (.fai) will be created if none exists.")
var referencePath: String = null

@Args4jOption(required = false, name = "-docker_image", usage = "Docker image to use. Defaults to heuermh/freebayes.")
var dockerImage: String = "heuermh/freebayes"
@Args4jOption(required = false, name = "-docker_image", usage = "Docker image to use. Defaults to quay.io/biocontainers/freebayes:1.1.0.46--htslib1.6_2.")
var dockerImage: String = "quay.io/biocontainers/freebayes:1.1.0.46--htslib1.6_2"

@Args4jOption(required = false, name = "-use_docker", usage = "If true, uses Docker to launch Freebayes. If false, uses the Freebayes executable path.")
var useDocker: Boolean = false
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4 changes: 2 additions & 2 deletions cli/src/main/scala/org/bdgenomics/cannoli/cli/Samtools.scala
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Expand Up @@ -50,8 +50,8 @@ class SamtoolsArgs extends Args4jBase with ADAMSaveAnyArgs with ParquetArgs {
@Args4jOption(required = true, name = "-samtools_reference", usage = "Reference sequence for analysis. An index file (.fai) will be created if none exists.")
var referencePath: String = null

@Args4jOption(required = false, name = "-docker_image", usage = "Docker image to use. Defaults to heuermh/samtools.")
var dockerImage: String = "heuermh/samtools"
@Args4jOption(required = false, name = "-docker_image", usage = "Docker image to use. Defaults to quay.io/biocontainers/samtools:1.6--0.")
var dockerImage: String = "quay.io/biocontainers/samtools:1.6--0"

@Args4jOption(required = false, name = "-use_docker", usage = "If true, uses Docker to launch samtools. If false, uses the samtools executable path.")
var useDocker: Boolean = false
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4 changes: 2 additions & 2 deletions cli/src/main/scala/org/bdgenomics/cannoli/cli/SnpEff.scala
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Expand Up @@ -53,8 +53,8 @@ class SnpEffArgs extends Args4jBase with ADAMSaveAnyArgs with ParquetArgs {
@Args4jOption(required = false, name = "-snpeff_path", usage = "Path to the SnpEff executable. Defaults to snpEff.")
var snpEffPath: String = "snpEff"

@Args4jOption(required = false, name = "-docker_image", usage = "Docker image to use. Defaults to heuermh/snpeff.")
var dockerImage: String = "heuermh/snpeff"
@Args4jOption(required = false, name = "-docker_image", usage = "Docker image to use. Defaults to quay.io/biocontainers/snpeff:4.3.1t--0.")
var dockerImage: String = "quay.io/biocontainers/snpeff:4.3.1t--0"

@Args4jOption(required = false, name = "-use_docker", usage = "If true, uses Docker to launch SnpEff. If false, uses the SnpEff executable path.")
var useDocker: Boolean = false
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