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Update container images for blast, bowtie, bowtie2, freebayes, etc. #359

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Feb 23, 2023
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Update container images for blast, bowtie, bowtie2, freebayes, etc. #359

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4 changes: 2 additions & 2 deletions core/src/main/scala/org/bdgenomics/cannoli/Blastn.scala
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Expand Up @@ -37,8 +37,8 @@ class BlastnArgs extends Args4jBase {
@Args4jOption(required = false, name = "-executable", usage = "Path to the blastn executable. Defaults to blastn.")
var executable: String = "blastn"

@Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/blast:2.12.0--hf3cf87c_4.")
var image: String = "quay.io/biocontainers/blast:2.12.0--hf3cf87c_4"
@Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/blast:2.13.0--hf3cf87c_0.")
var image: String = "quay.io/biocontainers/blast:2.13.0--hf3cf87c_0"

@Args4jOption(required = false, name = "-sudo", usage = "Run via sudo.")
var sudo: Boolean = false
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4 changes: 2 additions & 2 deletions core/src/main/scala/org/bdgenomics/cannoli/Bowtie.scala
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Expand Up @@ -35,8 +35,8 @@ class BowtieArgs extends Args4jBase {
@Args4jOption(required = false, name = "-executable", usage = "Path to the Bowtie executable. Defaults to bowtie.")
var executable: String = "bowtie"

@Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/bowtie:1.3.1--py38h29a62c4_1.")
var image: String = "quay.io/biocontainers/bowtie:1.3.1--py38h29a62c4_1"
@Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/bowtie:1.3.1--py310h4070885_4.")
var image: String = "quay.io/biocontainers/bowtie:1.3.1--py310h4070885_4"

@Args4jOption(required = false, name = "-sudo", usage = "Run via sudo.")
var sudo: Boolean = false
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4 changes: 2 additions & 2 deletions core/src/main/scala/org/bdgenomics/cannoli/Bowtie2.scala
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Expand Up @@ -36,8 +36,8 @@ class Bowtie2Args extends Args4jBase {
@Args4jOption(required = false, name = "-executable", usage = "Path to the Bowtie 2 executable. Defaults to bowtie2.")
var executable: String = "bowtie2"

@Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/bowtie2:2.5.0--py310h8d7afc0_0.")
var image: String = "quay.io/biocontainers/bowtie2:2.5.0--py310h8d7afc0_0"
@Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/bowtie2:2.5.1--py310h8d7afc0_0.")
var image: String = "quay.io/biocontainers/bowtie2:2.5.1--py310h8d7afc0_0"

@Args4jOption(required = false, name = "-sudo", usage = "Run via sudo.")
var sudo: Boolean = false
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4 changes: 2 additions & 2 deletions core/src/main/scala/org/bdgenomics/cannoli/Freebayes.scala
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Expand Up @@ -36,8 +36,8 @@ class FreebayesArgs extends Args4jBase {
@Args4jOption(required = false, name = "-executable", usage = "Path to the Freebayes executable. Defaults to freebayes.")
var executable: String = "freebayes"

@Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/freebayes:1.3.6--h346b5cb_1.")
var image: String = "quay.io/biocontainers/freebayes:1.3.6--h346b5cb_1"
@Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/freebayes:1.3.6--hbfe0e7f_2.")
var image: String = "quay.io/biocontainers/freebayes:1.3.6--hbfe0e7f_2"

@Args4jOption(required = false, name = "-sudo", usage = "Run via sudo.")
var sudo: Boolean = false
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4 changes: 2 additions & 2 deletions core/src/main/scala/org/bdgenomics/cannoli/MagicBlast.scala
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Expand Up @@ -37,8 +37,8 @@ class MagicBlastArgs extends Args4jBase {
@Args4jOption(required = false, name = "-executable", usage = "Path to the Magic-BLAST executable. Defaults to magicblast.")
var executable: String = "magicblast"

@Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/magicblast:1.6.0--hf1761c0_1.")
var image: String = "quay.io/biocontainers/magicblast:1.6.0--hf1761c0_1"
@Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/magicblast:1.7.0--hf1761c0_0.")
var image: String = "quay.io/biocontainers/magicblast:1.7.0--hf1761c0_0"

@Args4jOption(required = false, name = "-sudo", usage = "Run via sudo.")
var sudo: Boolean = false
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4 changes: 2 additions & 2 deletions core/src/main/scala/org/bdgenomics/cannoli/SnpEff.scala
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Expand Up @@ -39,8 +39,8 @@ class SnpEffArgs extends Args4jBase {
@Args4jOption(required = false, name = "-executable", usage = "Path to the SnpEff executable. Defaults to snpEff.")
var executable: String = "snpEff"

@Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/snpeff:5.1--hdfd78af_1.")
var image: String = "quay.io/biocontainers/snpeff:5.1--hdfd78af_1"
@Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/snpeff:5.1d--hdfd78af_0.")
var image: String = "quay.io/biocontainers/snpeff:5.1d--hdfd78af_0"

@Args4jOption(required = false, name = "-sudo", usage = "Run via sudo.")
var sudo: Boolean = false
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4 changes: 2 additions & 2 deletions core/src/main/scala/org/bdgenomics/cannoli/Star.scala
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Expand Up @@ -35,8 +35,8 @@ class StarArgs extends Args4jBase {
@Args4jOption(required = false, name = "-executable", usage = "Path to the STAR-Mapper executable. Defaults to STAR.")
var executable: String = "STAR"

@Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/star:2.7.10a--h9ee0642_0.")
var image: String = "quay.io/biocontainers/star:2.7.10a--h9ee0642_0"
@Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/star:2.7.10b--h9ee0642_0.")
var image: String = "quay.io/biocontainers/star:2.7.10b--h9ee0642_0"

@Args4jOption(required = false, name = "-sudo", usage = "Run via sudo.")
var sudo: Boolean = false
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4 changes: 2 additions & 2 deletions core/src/main/scala/org/bdgenomics/cannoli/Vep.scala
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Expand Up @@ -39,8 +39,8 @@ class VepArgs extends Args4jBase {
@Args4jOption(required = false, name = "-executable", usage = "Path to the Ensembl VEP executable. Defaults to vep.")
var executable: String = "vep"

@Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/ensembl-vep:106.0--pl5321h4a94de4_0.")
var image: String = "quay.io/biocontainers/ensembl-vep:106.0--pl5321h4a94de4_0"
@Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/ensembl-vep:108.2--pl5321h4a94de4_0.")
var image: String = "quay.io/biocontainers/ensembl-vep:108.2--pl5321h4a94de4_0"

@Args4jOption(required = false, name = "-sudo", usage = "Run via sudo.")
var sudo: Boolean = false
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4 changes: 2 additions & 2 deletions core/src/main/scala/org/bdgenomics/cannoli/VtNormalize.scala
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Expand Up @@ -39,8 +39,8 @@ class VtNormalizeArgs extends Args4jBase {
@Args4jOption(required = false, name = "-executable", usage = "Path to the vt executable. Defaults to vt.")
var executable: String = "vt"

@Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/vt:0.57721--h17a1952_6.")
var image: String = "quay.io/biocontainers/vt:0.57721--h17a1952_6"
@Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/vt:0.57721--h5eb663c_7.")
var image: String = "quay.io/biocontainers/vt:0.57721--h5eb663c_7"

@Args4jOption(required = false, name = "-sudo", usage = "Run via sudo.")
var sudo: Boolean = false
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