From a53b175ccda4052f4a0d98ed5543b1b90b0a9937 Mon Sep 17 00:00:00 2001 From: Michael L Heuer Date: Fri, 28 Apr 2023 10:43:28 -0500 Subject: [PATCH 1/5] Update minimap2 container image to 2.25--h7132678_0. --- core/src/main/scala/org/bdgenomics/cannoli/Minimap2.scala | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/core/src/main/scala/org/bdgenomics/cannoli/Minimap2.scala b/core/src/main/scala/org/bdgenomics/cannoli/Minimap2.scala index 4f82226..3c04a2c 100644 --- a/core/src/main/scala/org/bdgenomics/cannoli/Minimap2.scala +++ b/core/src/main/scala/org/bdgenomics/cannoli/Minimap2.scala @@ -36,8 +36,8 @@ class Minimap2Args extends ReadGroupArgs { @Args4jOption(required = false, name = "-executable", usage = "Path to the Minimap2 executable. Defaults to minimap2.") var executable: String = "minimap2" - @Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/minimap2:2.24--h7132678_1.") - var image: String = "quay.io/biocontainers/minimap2:2.24--h7132678_1" + @Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/minimap2:2.25--h7132678_0.") + var image: String = "quay.io/biocontainers/minimap2:2.25--h7132678_0" @Args4jOption(required = false, name = "-sudo", usage = "Run via sudo.") var sudo: Boolean = false From b80ad023ab2cf6246d7d34742e475910721b86cd Mon Sep 17 00:00:00 2001 From: Michael L Heuer Date: Fri, 28 Apr 2023 10:44:18 -0500 Subject: [PATCH 2/5] Update blast container image to 2.13.0--hf3cf87c_1. --- core/src/main/scala/org/bdgenomics/cannoli/Blastn.scala | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/core/src/main/scala/org/bdgenomics/cannoli/Blastn.scala b/core/src/main/scala/org/bdgenomics/cannoli/Blastn.scala index 492faa7..fcf1a26 100644 --- a/core/src/main/scala/org/bdgenomics/cannoli/Blastn.scala +++ b/core/src/main/scala/org/bdgenomics/cannoli/Blastn.scala @@ -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:2.13.0--hf3cf87c_0.") - var image: String = "quay.io/biocontainers/blast:2.13.0--hf3cf87c_0" + @Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/blast:2.13.0--hf3cf87c_1.") + var image: String = "quay.io/biocontainers/blast:2.13.0--hf3cf87c_1" @Args4jOption(required = false, name = "-sudo", usage = "Run via sudo.") var sudo: Boolean = false From 7c5772b0ddc831e0451742eec9f9687ed2acda96 Mon Sep 17 00:00:00 2001 From: Michael L Heuer Date: Mon, 16 Oct 2023 11:37:57 -0500 Subject: [PATCH 3/5] Update bowtie2 container to 2.5.2--py39h6fed5c7_0. --- core/src/main/scala/org/bdgenomics/cannoli/Bowtie2.scala | 4 ++-- .../main/scala/org/bdgenomics/cannoli/SingleEndBowtie2.scala | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/core/src/main/scala/org/bdgenomics/cannoli/Bowtie2.scala b/core/src/main/scala/org/bdgenomics/cannoli/Bowtie2.scala index 89aad75..71e24c9 100644 --- a/core/src/main/scala/org/bdgenomics/cannoli/Bowtie2.scala +++ b/core/src/main/scala/org/bdgenomics/cannoli/Bowtie2.scala @@ -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/bowtie2:2.5.1--py310h8d7afc0_0.") - var image: String = "quay.io/biocontainers/bowtie2:2.5.1--py310h8d7afc0_0" + @Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/bowtie2:2.5.2--py39h6fed5c7_0.") + var image: String = "quay.io/biocontainers/bowtie2:2.5.2--py39h6fed5c7_0" @Args4jOption(required = false, name = "-sudo", usage = "Run via sudo.") var sudo: Boolean = false diff --git a/core/src/main/scala/org/bdgenomics/cannoli/SingleEndBowtie2.scala b/core/src/main/scala/org/bdgenomics/cannoli/SingleEndBowtie2.scala index 184ed0c..15b6b20 100644 --- a/core/src/main/scala/org/bdgenomics/cannoli/SingleEndBowtie2.scala +++ b/core/src/main/scala/org/bdgenomics/cannoli/SingleEndBowtie2.scala @@ -39,8 +39,8 @@ class SingleEndBowtie2Args 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/bowtie2:2.5.2--py39h6fed5c7_0.") + var image: String = "quay.io/biocontainers/bowtie2:2.5.2--py39h6fed5c7_0" @Args4jOption(required = false, name = "-sudo", usage = "Run via sudo.") var sudo: Boolean = false From e8957ce1198a94ab0df01b2a27e0da495146d625 Mon Sep 17 00:00:00 2001 From: Michael L Heuer Date: Thu, 9 Nov 2023 22:21:13 -0600 Subject: [PATCH 4/5] Update bedtools container to 2.31.1--hf5e1c6e_0. --- .../main/scala/org/bdgenomics/cannoli/BedtoolsIntersect.scala | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/core/src/main/scala/org/bdgenomics/cannoli/BedtoolsIntersect.scala b/core/src/main/scala/org/bdgenomics/cannoli/BedtoolsIntersect.scala index cbbda02..e3a6dc4 100644 --- a/core/src/main/scala/org/bdgenomics/cannoli/BedtoolsIntersect.scala +++ b/core/src/main/scala/org/bdgenomics/cannoli/BedtoolsIntersect.scala @@ -47,8 +47,8 @@ class BedtoolsIntersectArgs extends Args4jBase { @Args4jOption(required = false, name = "-executable", usage = "Path to the Bedtools executable. Defaults to bedtools.") var executable: String = "bedtools" - @Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/bedtools:2.30.0--h468198e_3.") - var image: String = "quay.io/biocontainers/bedtools:2.30.0--h468198e_3" + @Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/bedtools:2.31.1--hf5e1c6e_0.") + var image: String = "quay.io/biocontainers/bedtools:2.31.1--hf5e1c6e_0" @Args4jOption(required = false, name = "-sudo", usage = "Run via sudo.") var sudo: Boolean = false From b6904d31fb9a0d8d6dc20cfe36c62beddcce42a5 Mon Sep 17 00:00:00 2001 From: Michael L Heuer Date: Thu, 9 Nov 2023 22:22:50 -0600 Subject: [PATCH 5/5] Update blast container image to 2.15.0--pl5321h6f7f691_0. --- core/src/main/scala/org/bdgenomics/cannoli/Blastn.scala | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/core/src/main/scala/org/bdgenomics/cannoli/Blastn.scala b/core/src/main/scala/org/bdgenomics/cannoli/Blastn.scala index fcf1a26..c3afb60 100644 --- a/core/src/main/scala/org/bdgenomics/cannoli/Blastn.scala +++ b/core/src/main/scala/org/bdgenomics/cannoli/Blastn.scala @@ -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:2.13.0--hf3cf87c_1.") - var image: String = "quay.io/biocontainers/blast:2.13.0--hf3cf87c_1" + @Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/blast:2.15.0--pl5321h6f7f691_0.") + var image: String = "quay.io/biocontainers/blast:2.15.0--pl5321h6f7f691_0" @Args4jOption(required = false, name = "-sudo", usage = "Run via sudo.") var sudo: Boolean = false