From f728f82b8ec2f29ad34d6ac27d30a6243a92f607 Mon Sep 17 00:00:00 2001 From: shane knapp Date: Mon, 30 Oct 2023 13:53:21 -0700 Subject: [PATCH 01/11] bumping mambaforge to something current --- deployments/biology/image/install-mambaforge.bash | 2 +- deployments/data8/image/install-mambaforge.bash | 2 +- deployments/datahub/images/default/install-mambaforge.bash | 2 +- deployments/ischool/image/install-mambaforge.bash | 2 +- deployments/shiny/image/install-mambaforge.bash | 2 +- 5 files changed, 5 insertions(+), 5 deletions(-) diff --git a/deployments/biology/image/install-mambaforge.bash b/deployments/biology/image/install-mambaforge.bash index 13f431411..0344ddcfa 100644 --- a/deployments/biology/image/install-mambaforge.bash +++ b/deployments/biology/image/install-mambaforge.bash @@ -3,7 +3,7 @@ set -ex cd $(dirname $0) -MAMBAFORGE_VERSION=4.10.3-7 +MAMBAFORGE_VERSION='23.3.1-1' URL="https://github.com/conda-forge/miniforge/releases/download/${MAMBAFORGE_VERSION}/Mambaforge-${MAMBAFORGE_VERSION}-Linux-x86_64.sh" INSTALLER_PATH=/tmp/mambaforge-installer.sh diff --git a/deployments/data8/image/install-mambaforge.bash b/deployments/data8/image/install-mambaforge.bash index 13f431411..0344ddcfa 100755 --- a/deployments/data8/image/install-mambaforge.bash +++ b/deployments/data8/image/install-mambaforge.bash @@ -3,7 +3,7 @@ set -ex cd $(dirname $0) -MAMBAFORGE_VERSION=4.10.3-7 +MAMBAFORGE_VERSION='23.3.1-1' URL="https://github.com/conda-forge/miniforge/releases/download/${MAMBAFORGE_VERSION}/Mambaforge-${MAMBAFORGE_VERSION}-Linux-x86_64.sh" INSTALLER_PATH=/tmp/mambaforge-installer.sh diff --git a/deployments/datahub/images/default/install-mambaforge.bash b/deployments/datahub/images/default/install-mambaforge.bash index 13f431411..0344ddcfa 100755 --- a/deployments/datahub/images/default/install-mambaforge.bash +++ b/deployments/datahub/images/default/install-mambaforge.bash @@ -3,7 +3,7 @@ set -ex cd $(dirname $0) -MAMBAFORGE_VERSION=4.10.3-7 +MAMBAFORGE_VERSION='23.3.1-1' URL="https://github.com/conda-forge/miniforge/releases/download/${MAMBAFORGE_VERSION}/Mambaforge-${MAMBAFORGE_VERSION}-Linux-x86_64.sh" INSTALLER_PATH=/tmp/mambaforge-installer.sh diff --git a/deployments/ischool/image/install-mambaforge.bash b/deployments/ischool/image/install-mambaforge.bash index 13f431411..0344ddcfa 100755 --- a/deployments/ischool/image/install-mambaforge.bash +++ b/deployments/ischool/image/install-mambaforge.bash @@ -3,7 +3,7 @@ set -ex cd $(dirname $0) -MAMBAFORGE_VERSION=4.10.3-7 +MAMBAFORGE_VERSION='23.3.1-1' URL="https://github.com/conda-forge/miniforge/releases/download/${MAMBAFORGE_VERSION}/Mambaforge-${MAMBAFORGE_VERSION}-Linux-x86_64.sh" INSTALLER_PATH=/tmp/mambaforge-installer.sh diff --git a/deployments/shiny/image/install-mambaforge.bash b/deployments/shiny/image/install-mambaforge.bash index 13f431411..0344ddcfa 100755 --- a/deployments/shiny/image/install-mambaforge.bash +++ b/deployments/shiny/image/install-mambaforge.bash @@ -3,7 +3,7 @@ set -ex cd $(dirname $0) -MAMBAFORGE_VERSION=4.10.3-7 +MAMBAFORGE_VERSION='23.3.1-1' URL="https://github.com/conda-forge/miniforge/releases/download/${MAMBAFORGE_VERSION}/Mambaforge-${MAMBAFORGE_VERSION}-Linux-x86_64.sh" INSTALLER_PATH=/tmp/mambaforge-installer.sh From 85deaa99eada8b9299c7fdde997c54f4fc7f88a5 Mon Sep 17 00:00:00 2001 From: shane knapp Date: Mon, 30 Oct 2023 14:07:11 -0700 Subject: [PATCH 02/11] bump python, begin dependency hell --- deployments/biology/image/environment.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/deployments/biology/image/environment.yml b/deployments/biology/image/environment.yml index b9a293752..13e41254d 100644 --- a/deployments/biology/image/environment.yml +++ b/deployments/biology/image/environment.yml @@ -2,7 +2,7 @@ channels: - bioconda - conda-forge dependencies: -- python=3.9.* +- python=3.10.13 - pip=22.2.* # Package to allow Jupyter Notebook or JupyterLab applications in one conda env to access other kernels (e.g. qiime2) From cdcfaef64fa89c227ed80405d29529a101d6e462 Mon Sep 17 00:00:00 2001 From: shane knapp Date: Mon, 30 Oct 2023 14:17:07 -0700 Subject: [PATCH 03/11] bump scipy --- deployments/biology/image/environment.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/deployments/biology/image/environment.yml b/deployments/biology/image/environment.yml index 13e41254d..41a9c23c7 100644 --- a/deployments/biology/image/environment.yml +++ b/deployments/biology/image/environment.yml @@ -46,7 +46,7 @@ dependencies: # pedagogy packages -- scipy=1.7.1 +- scipy=1.10.1 - pandas=1.3.2 - seaborn=0.11.2 From 4e875f9f884d350cdd84e1598cb8a4e681b302ee Mon Sep 17 00:00:00 2001 From: shane knapp Date: Mon, 30 Oct 2023 14:27:17 -0700 Subject: [PATCH 04/11] more dep hell as usual --- deployments/biology/image/environment.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/deployments/biology/image/environment.yml b/deployments/biology/image/environment.yml index 41a9c23c7..d6ea6e4c8 100644 --- a/deployments/biology/image/environment.yml +++ b/deployments/biology/image/environment.yml @@ -47,7 +47,7 @@ dependencies: # pedagogy packages - scipy=1.10.1 -- pandas=1.3.2 +- pandas=2.0.2 - seaborn=0.11.2 # compbio BioE c146, Fall 22 and into the future, issue 3785 From fd027f03397712d644aac14c5df4651a3dad8bba Mon Sep 17 00:00:00 2001 From: shane knapp Date: Mon, 30 Oct 2023 14:36:46 -0700 Subject: [PATCH 05/11] more dep hell as usual --- deployments/biology/image/environment.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/deployments/biology/image/environment.yml b/deployments/biology/image/environment.yml index d6ea6e4c8..e4608d931 100644 --- a/deployments/biology/image/environment.yml +++ b/deployments/biology/image/environment.yml @@ -30,7 +30,7 @@ dependencies: - syncthing==1.18.6 # Packages for IB120/201/CCB210 -- sympy=1.6.2 +- sympy=1.10.1 # Packages from bioconda for BioE-131, Fall 2020, Issue #1885 - bowtie2=2.4.2 From 62a8892466bc55c5cb22b5ff11b7bbd277312906 Mon Sep 17 00:00:00 2001 From: shane knapp Date: Mon, 30 Oct 2023 14:56:23 -0700 Subject: [PATCH 06/11] le sigh le bowtie --- deployments/biology/image/environment.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/deployments/biology/image/environment.yml b/deployments/biology/image/environment.yml index e4608d931..34d013756 100644 --- a/deployments/biology/image/environment.yml +++ b/deployments/biology/image/environment.yml @@ -2,7 +2,7 @@ channels: - bioconda - conda-forge dependencies: -- python=3.10.13 +- python=3.10.* - pip=22.2.* # Package to allow Jupyter Notebook or JupyterLab applications in one conda env to access other kernels (e.g. qiime2) @@ -33,7 +33,7 @@ dependencies: - sympy=1.10.1 # Packages from bioconda for BioE-131, Fall 2020, Issue #1885 -- bowtie2=2.4.2 +- bowtie2=2.5.2 - spades=3.14.1 # Packages for MCB280A, Spring 2022 From e99a899864529939b2fb5fc5ca3657f930998f71 Mon Sep 17 00:00:00 2001 From: shane knapp Date: Mon, 30 Oct 2023 17:42:38 -0700 Subject: [PATCH 07/11] last try today --- deployments/biology/image/environment.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/deployments/biology/image/environment.yml b/deployments/biology/image/environment.yml index 34d013756..2f9a031c0 100644 --- a/deployments/biology/image/environment.yml +++ b/deployments/biology/image/environment.yml @@ -9,11 +9,12 @@ dependencies: - nb_conda_kernels=2.3.1 # Packages from bioconda for IB134L +- biopython==1.81 - bwa=0.7.12 - samtools=1.3.1 - mafft=7.471 - emboss=6.6.0 -- augustus=3.3.3 +- augustus=3.5.0 - raxml-ng=1.0.1 - structure=2.3.4 - paml=4.9 From 7e2eb5b3dc59207eee00cdcfe62890a9cbdb6a03 Mon Sep 17 00:00:00 2001 From: shane knapp Date: Mon, 30 Oct 2023 17:55:49 -0700 Subject: [PATCH 08/11] maybe one more --- deployments/biology/image/environment.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/deployments/biology/image/environment.yml b/deployments/biology/image/environment.yml index 2f9a031c0..aa86f08e0 100644 --- a/deployments/biology/image/environment.yml +++ b/deployments/biology/image/environment.yml @@ -23,7 +23,7 @@ dependencies: - blast=2.12.0 - fastqc=0.11.9 - phyml=3.3.20200621 -- sra-tools=2.11 +- sra-tools=3.0.8 - hisat2=2.2.1 - subread=2.0.1 - plink=1.90b6.21 From b6da08d0d677dd872fed6bb5d984d438a725c9a0 Mon Sep 17 00:00:00 2001 From: shane knapp Date: Mon, 30 Oct 2023 18:04:08 -0700 Subject: [PATCH 09/11] blast! --- deployments/biology/image/environment.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/deployments/biology/image/environment.yml b/deployments/biology/image/environment.yml index aa86f08e0..6722cb6fc 100644 --- a/deployments/biology/image/environment.yml +++ b/deployments/biology/image/environment.yml @@ -20,7 +20,7 @@ dependencies: - paml=4.9 #- repeatmasker=4.0.9 - trimmomatic=0.39 -- blast=2.12.0 +- blast=2.14.1 - fastqc=0.11.9 - phyml=3.3.20200621 - sra-tools=3.0.8 From bed69fde75870deac30d5f4adfd95ca5b2725ed3 Mon Sep 17 00:00:00 2001 From: shane knapp Date: Mon, 30 Oct 2023 19:08:15 -0700 Subject: [PATCH 10/11] debump python --- deployments/biology/image/environment.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/deployments/biology/image/environment.yml b/deployments/biology/image/environment.yml index 6722cb6fc..467c63912 100644 --- a/deployments/biology/image/environment.yml +++ b/deployments/biology/image/environment.yml @@ -2,7 +2,7 @@ channels: - bioconda - conda-forge dependencies: -- python=3.10.* +- python=3.9.* - pip=22.2.* # Package to allow Jupyter Notebook or JupyterLab applications in one conda env to access other kernels (e.g. qiime2) From af166cb9b78a1fda680636ca769c4bc10a82fd4b Mon Sep 17 00:00:00 2001 From: shane knapp Date: Mon, 30 Oct 2023 19:27:30 -0700 Subject: [PATCH 11/11] oh my aching brain --- deployments/biology/image/environment.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/deployments/biology/image/environment.yml b/deployments/biology/image/environment.yml index 467c63912..43935f67b 100644 --- a/deployments/biology/image/environment.yml +++ b/deployments/biology/image/environment.yml @@ -14,7 +14,7 @@ dependencies: - samtools=1.3.1 - mafft=7.471 - emboss=6.6.0 -- augustus=3.5.0 +- augustus=3.3.3 - raxml-ng=1.0.1 - structure=2.3.4 - paml=4.9 @@ -34,7 +34,7 @@ dependencies: - sympy=1.10.1 # Packages from bioconda for BioE-131, Fall 2020, Issue #1885 -- bowtie2=2.5.2 +- bowtie2=2.4.2 - spades=3.14.1 # Packages for MCB280A, Spring 2022